texts: Why are so many species reproducing late this year?

texts:
Hope this question is OK for this site, couldn't see where else to ask it.
We've spent a few days out in the countryside recently, and have been very surprised at how many species appear to have very young offspring so late in the season. I was always under the impression that the vast majority of animals and fish produced young in the spring (March/April).
For example, we saw tadpoles, fluffy (ie obviously very young) coots and weeny minnows. I would have expected that all of these would have been born/laid a good 3 or 4 months ago, and so would be more mature by now.
Caveat: We didn't do a scientific study, this is just a strong impression we got from days out in north west England.


texts: How to model species interactions on population size dynamic?

texts:
Here are two classical discrete time models of population size dynamic. The exponential growth model

$$N_{t+1} = r\cdot N_t \qquad\qquad(1)$$

and the logistic growth model

$$N_{t+1} = r\cdot N_t \left(1 - \frac{N_t}{K}\right) \qquad\qquad(2)$$

, where $r$ is the growth rate, $N_t$ is the population size at time $t$ and $K$ is the carrying capacity.

I am wondering how are species interaction generally modelled into this framework. Let's consider three interacting species called "a", "b" and "c" with populations sizes at time $t$, $Na_t$, $Nb_t$, $Nc_t$, respecitively. The effect of these three species on the focal species are $\alpha_a$, $\alpha_b$ and $\alpha_c$.

How do we typically compute, for both a logistic and an exponential discrete time model, the recursive equation of the focal species' population size?

For the exponential model, is it

$$N_{t+1} = r\cdot N_t \cdot (Na_t \alpha_a + Nb_t \alpha_b + Nc_t \alpha_c) \qquad\qquad(3)$$

or

$$N_{t+1} = r\cdot N_t + Na_t \alpha_a + Nb_t \alpha_b + Nc_t \alpha_c \qquad\qquad(4)$$

or something else? And for the logistic model, is it

$$N_{t+1} = r\cdot N_t \left(1 - \frac{N_t}{K}\right) \cdot (Na_t \alpha_a + Nb_t \alpha_b + Nc_t \alpha_c) \qquad\qquad(5)$$

or

$$N_{t+1} = r\cdot N_t \left(1 - \frac{N_t \cdot (Na_t \alpha_a + Nb_t \alpha_b + Nc_t \alpha_c)}{K}\right) \qquad\qquad(6)$$

or something else?

It is possible that we typically define more parameters that just the $\alpha$ values I define above to describe a species interaction even in the simplest models. Ideally, I would love an answer that draws from a source (a textbook in theoretical ecology, a peer-reviewed article or whatever).


texts: What is the name of this plant, from Bangladesh?

texts: This is a small plant from my backyard. I have found the flower closes in the evening.


texts:
According to Genomes

PCR is

  A technique that results in exponential amplification of a selected region of a DNA molecule [in test tube].

DNA cloning is

  Insertion of a fragment of DNA into a cloning vector, and subsequent propagation of the recombinant DNA molecule in a host organism.

While, Molecular Biology of the Cell, Sixth Edition says in a summary:

  DNA cloning (through the use of either cloning vectors or the polymerase chain reaction) in which portion of a genome (often an individual gene) is purified away from the remainder of the genome by repeatedly copying to generate many billions of identical molecules.

Here DNA cloning has been used to mean DNA replication in general.

Question: Which author's view is correct, or at least provides the most accepted definitions?


texts: What are some examples of small-scale physical phenomena that snakes fear?

texts:
What are some ways to use technology to repel snakes?

One idea I was researching is low-frequency sound, which I read snakes could "feel" even though they are naturally deaf. Would this be a viable option? What sound ranges would need to be used?

What are some other ways? Could targeted light be another option?


texts: What is the function of dreaming? Does a particular hormone secretion interfere with dreaming? Why do some people dream more?

texts: I'm really interested to know when we are sleeping how a series of stories come to our mind that we called this process dreaming. If you know a useful article on this topic, please tell me thanks.


texts: Does the modern synthesis theory of evolution deny that acquired characteristics can be inherited?

texts:
The following is an wikipedia article on Lamarckism.
https://en.wikipedia.org/wiki/Lamarckism

According to Ernst Mayr, any Lamarckian theory involving the inheritance of acquired characters has been refuted as "DNA does not directly participate in the making of the phenotype and that the phenotype, in turn, does not control the composition of the DNA."[75] Peter J. Bowler has written that although many early scientists took Lamarckism seriously, it was discredited by genetics in the early twentieth century.
The evolutionary biologist T. Ryan Gregory contends that epigenetic inheritance should not be considered Lamarckian.

It seems to me that the assertion that acquired characteristics can be inherited was denied by the modern synthesis theory of evolution.
Is this true?
If yes, what is the reason of the denial?


texts:
I understand that each half of the human brain handles different parts of our thinking. Left brain, right brain, that whole topic.

But in pictures, the brain is always depicted as having symmetrical structure. I'm curious about that. I realize that it might be silly to expect such a complex tool to be truly symmetrical, so my question is:

Is the brain functionally symmetrical or not? By functionally, I'm referring to whether the specialized groups within the brain all exists on both sides or rather each side contains different components.


texts: What is the difference between ferritin and hemoglobin?

texts:
I have been reading that ferritin is the store of iron but hemoglobin is actually the amount of this in blood.

Does hemoglobin get sourced from ferritin? Is it possible for a person to be low on ferritin but normal on hemoglobin? Will he feel any symptoms of anaemia, if so?


texts: Why are women more susceptible to radiation?

texts:
The answer to this question on the Space.SE indicates women are more susceptible to radiation in space than men.

Why is this the case? Is it merely that women have less muscle mass (which being more dense than fat) and therefore may receive a greater dose when exposed?


texts: Species Identification : What insect is this?

texts:
I noticed this insect in the end of last December on the window of my room in Pune, India. There are at least 15 such insects on this window and 12 on another. None of these have moved even a millimeter since I first noticed them. They don't move even when the window is lightly banged. They are almost 1 to 1.5 cm in length and their tails have two ends. They are almost transparent.
Imgs:


texts:
I have a set of scaffolds from a genome assembly, and I want to align a collection of proteins from various species to it. I can do this using BLAST in two ways:

Create a BLAST database of the scaffolds, and run tblastn on it with
the proteins as the query.
Create a BLAST database of the proteins, and run blastx on it with
the scaffolds as the query.

Should both of these produce the exact same hits? Will there be any significant difference in running time between them?


texts: Could alternatives to Photosynthesis be possible?

texts:
I'm working on a world for stories and games, and I'm trying to figure out some more diverse plantlife. There are areas of the world that won't get enough sunlight for Photosynthesis, so I'm thinking about alternatives.

We can use Piezoelectric components to charge batteries, so could Piezosynthesis be possible in plants, if there was enough air movement to, say, move a sail-like fin back and forth enough to generate a similar "power" to photosynthesis?


texts: Radiation mutation breeding in plant seeds: practical aspects

texts:
I did read some seed irradiation papers and they all use Gy as unit of measure, however I have never seen seed weights reported.

How did they calculate that, since Gy is J/kg?

Differencies aside between using gamma and X-rays, is there any equivalent dose I can apply using an X-ray tube fitted with a dose area product meter?

I am not sure if I can assume that spreading seeds in an area and then irradiating up to a certain dose area product would mean that each of those seeds was exposed to a certain amount of radiation.

Suggestions welcome, thank you.


texts: What is the definition of Mitotic Index?

texts:
Sometimes I find Mitotic Index defined as (i) the number of dividing cells over the number of non-dividing cells, other times as the (ii) the number of dividing cells over the total number of cells...

When reading a paper, which definition is more likely to be correct?


texts: Are efflux pumps mutations or are they originally present in N. gonorrhoea?

texts:
I'll start by saying that I am no biologist. I am a math major trying to create a mathematical model for gonorrhea strain competition. My assignment is to create a model similar to a model that was already was already created, see page 9 of Evolution of within-host Antibiotic Resistance in Gonorrhea.

I wanted to try to incorporate the efflux pump into a mathematical model. Before I do that, I would first like to see whether efflux is gained through mutations. If it is, my model will be pointless since mutations are already covered in the original model from the research paper.

Feel free to add better tags. I thought mine was appropriate.


texts: How far does your center of mass move from stance to stance?

texts:
When the human body is perfectly centered, the center of mass is on the centerline around the belly button.  However, the human body is not always in this rigid posture.  We have many postures that we use.  How much does the center of mass shift, left to right, if we look at different stances.  I'm not so much interested in dynamic motions like walking, but rather static positions like:

At attention (obviously the center of mass will be very centered)
Weight shifted to one leg
A S-Curve, like from the traditional Greek statues

Obviously the center of mass will shift with respect to the ground, staying between the feet, but what I'm interested in is how it shifts with respect to the torso's centerline.


texts: Immunoprecipitation compared to western blotting

texts:
Immunoprecipitation and western blotting are both used to locate a specific protein within a sample and to isolate it.  In immunoprecipitation, a specific antibody and agarose beads ( or other insoluble beads) are used to precipitate the protein. In western blotting, SDS-PAGE is carried out and primary and secondary antibodies are used to locate and isolate the proteins on the nylon membrane.

My question is: which technique should be used when? what is the difference between the two? is one of them "better" / does one of them have advantages over the other?


texts: I am combing through my 23 & me raw data and I am a little confused on SNP terminology. I am using NCBI's genome browser and SNP database. As an example we can all follow here is a link to a CYP1A1 SNP https://www.ncbi.nlm.nih.gov/snp/rs28399430. When you open this link you will see alleles listed as G>C. Which one of these is the reference genome and which is the pathogenic allele? Is the relationship always constant (like in x>y, x is always the reference and y is the substitution). If you scroll down to the genome browser view, there also doesn't appear to be any way to tell + vs - sense strand (ie making it difficult to tell G for C mutations or vice versa). I would just assume its the top strand? The ultimate goal here is for me to look through 23&me and compare my SNP genotype to the reference genome and see if my genotype exhibits pathogenic SNPs in certain genes.


texts: Online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology

texts:
Where can I find an online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology?

I have tried the following:

Batch tool for GSFS: PROBLEM: It says that my input yeast genes are not human genes (which probably means that the tool will work only with Human genes).
http://bioinformatics.clemson.edu/G-SESAME/Program/geneCompareTwo1.php : PROBLEM: provides score for every gene pair input. I have ~3600 genes. Impossible to do it for eveyr pair.
DAVID batch viewer gives a 1xN matrix (functional similarity score of one gene to a set of N genes, when I want all possible pairs of similarities which will give an NxN matrix)
GO funsimmat- I am unable to get this to work, so I'm not sure if it will give me the desied results.
GO FastSemSim- same as 4.


texts: I was wondering how I can go about gaining permission for reuse of a figure in this post. I was hoping to reuse the image that is exemplifying the cross section of the retina. If anyone know please let me know I appreciate the help!


texts: How hard would it be to create a protein "by chance"?

texts:
I just read an article about David Gelernter, who was arguing against Darwin's theory of Natural Selection. He said one particular thing which stood out to me:

"...how hard it would be to create just one new protein by chance — the odds are so astronomical that there are fewer atoms in the entire universe in comparison: “The odds bury you. It can’t be done.”

I'm wondering how one could back up this idea. My back of the envelope (not being a biologist...) would go something like this:

Protiens are made of amino acids. Amino acids are essentially made up of four things, C, H, O, and N. In order to "make" amino acids, I just gotta give these things the right energy so they can strip some electrons and hook up to each other. If want to make all amino acids with say 20 molecules, I get four choices for each of twenty things, or $4^{20}\sim 10^{12}$ possible amino acids. Wikipedia tells me "most proteins are built from up to 20 different amino acids", so how many proteins are there made up to 20 amino acids?

$$(10^{12})^{20}\sim 10^{240}$$

So ignoring overcounting and how stupid this estimate is, that's a big number. And indeed, that's bigger then the number of atoms in the universe (like $10^{80}$ by some estimates).

Can someone confirm that's how he arrived at that estimate?

NOTE: Careful, I am not trying to get into an argument about Darwin - I only want to know how people who use this argument, make this argument.


texts: How would circular dominance of alleles be determined on the genetic level?

texts:
The distinction between dominant and recessive alleles seems to be due to loss or gain of function in the proteins they code for. Alleles have been observed exhibiting incomplete and hierarchical dominance.

Another type is "circular dominance," which is modeled in some computer programs but it isn't clear whether this occurs in nature. In this case, the dominance of alleles works similarly to rock-paper-scissors.

Would circular dominance exist in nature? How would alleles determine circular dominance?


texts: What's the mixture of carbon and haemoglobin called

texts: I know of oxyhaemogloblin , the mixture of oxygen and haemoglobin  , but carbon and haemoglobin combination is what's confusing


texts: Is there a database providing information about optimum temperature and inactive temperature of enzymes?

texts:
I want to know optimum and inactive temperature of some enzyme, but I can't find these information in NCBI, wiki or UniProt. So I want to know if there are some database which provide these information?
Thanks for help.


texts:
According to the textbook Alberts Molecular Biology of the Cell (5th ed., p. 902), negative feedback loops cause oscillations when they are long delayed. I just can't figure out why.

Except for that, in case of short delayed feedback, the inhibition doesn't seem to be full and to go down only mid-way, according to the attached plot. Why?


texts: Trying to identify a baby bird seen in Palermo, Sicily

texts:
I'm trying to identify a baby bird that i saw in a pond in Palermo, Sicily, Italy. Unfortunately i did not see any parents!
Any help is appreciated.
Thanks,
Robert


texts:
How correlated are the lengths of tendons in different part of a human body?

E.g., if the we consider two humans, A, and B. Human A has a patellar tendon of length 2 cm, and human B has a patellar tendon of length 1 cm, i.e. twice shorter. Should we expect all tendons in human A to be approximately twice larger than in human B?


texts:
So I read that our brain produces 700 new neurons in the hippocampus every day and that if we perform cognitive demanding tasks, eat omega-3 or exercise (other things?) it can produce even more neurons.

What happens with this new neurons? Say I'm learning some new skills, what role do those new neurons play in the process? Is it possible to learn without neurogenesis?

Edit: I'm interested in this topic (eg: brain, hippocampus, learning). Where can I learn about this from the basics? What classes teach this in college?


texts:
My gels look significantly different in MES (2-(N-morpholino)ethanesulfonic acid) and MOPS (3-(N-morpholino)propanesulfonic acid). That is to be expected. What I don't understand is why the simple presence of the counter-ion significantly changes the velocity of certain proteins.

Is this due to the different pH (MES is usually run at pH 8.0, MOPS is usually run at pH 7.0) or is the charge distribution on the counter-ion responsible for everything?


texts: What is this black and white worm in a white case?

texts:
The case is very small and it's an off white color.

The thing living inside can come out of either end. It's a black and white looking worm. It will poke its head out and move everywhere!

They are all over my back porch and some are even coming in my house!


texts: Elevated transaminases after blood transfusion?

texts:
This sparks HCV immediately in my mind.
However, there may be other possibilities too.

What can you deduce from elevated transaminases if you only know that the healthy adult patient received blood transfusion in Africa?


texts: Does N1-methyl-pseudouridine occur naturally in any RNA?

texts:
Pseudouridine occurs naturally in some RNAs. But what about the methylated variant of it, N1-methyl-pseudouridine? The latter is a key ingredient in both the Pfizer and Moderna Covid-19 vaccines, probably due to its relative "potency" in evading immunogenicity to exogenous mRNA itself and its ability to apparently put ribosomes in a sort of "overdrive". (It's use in mRNA therapeutics has been patented by Moderna in 2012 or so.)
Does N1-methyl-pseudouridine occur naturally, in particular, does it occur in RNA?


texts: What is difference between the malaria (cross) types?

texts:
When the doctor does the diagnose she says "you have malaria. 2 crosses". Now, I've heard those crosses go from 1 to 5, and historically I've had from 1 to 4, but I wonder: what is the difference between them?

Also there's this popular thing of people saying that an odd number is more dangerous than an even number. Is this scientific or something?

Cheers


texts: Estimates of historical human population size

texts:
What are the estimates of minimum historical human population size, and how are they obtained from the current human genetic diversity?
I seem to recall a Scientific American article from over 30 years ago claiming a figure of 500-1000, but I can’t find any estimate now.


texts: Does eating nonsalty food with MSG make you thirsty?

texts:
Assume that you're thirsty after eating food  that didn't taste salty while you were eating it.
Quora posts and https://msgdish.com/msg-problems-and-answers/ still impute the thirst to salt:

The Problem with MSG Problems - MSGdish
“Chinese food makes me so thirsty—it’s the MSG.” — Well, chances are, if you’re thirsty after eating Chinese food (or any food), you’ve probably consumed a good dose of sodium in the food or you’ve not had enough liquids recently. And, while MSG does contain sodium, it has only 1/3 the sodium of table salt. Chinese food contains a lot of high-sodium ingredients, including soy sauce, broths and other sauces. In fact, there are lots of foods (snack crackers and flavored chips, condiments, soups and sauces, commercially-prepared entrees) we eat all the time that typically contain much more salt than MSG. It’s time to stop blaming Chinese food (and MSG) for your thirst. Many Americans are chronically under-hydrated, and a salty meal of any ethnicity can send us all racing for water afterward.

But Hungry Onion

But since the food didn’t feel overly salty at the time, the only reason I can think of for the thirst is MSG.

and Wired.com impute the thirst to the MSG respectively:

The exact flavor MSG confers is difficult to describe, and many just say it increases the "taste intensity" of food. One thing is certain: It makes people thirsty, encouraging them to eat and drink more. Americans consume about 28,000 tons of MSG per year, according to one estimate reported in the June 1995 Journal of Environmental Health.


texts: CO2 availability to phytoplankton in oceans and climate change impacts

texts:
I learned through research that increasing levels of atmospheric CO2 was increasing the acidity level of ocean waters. I then was looking into how this was affecting the phytoplankton and read that warmer water was actually decreasing the amount of CO2 in the water for the phytoplankton to use.

I am now confused as to why many sources claim that greater atmospheric CO2 is making ocean waters more acidic but at the same time CO2 is decreasing in availability to phytoplankton. How does all of this relate to climate change? Would you be able to explain to me what is happening or direct me to sources that explain it?

One of my students in my Environmental Science class asked me this question, and it seemed very much worthwhile to post the Q&A to Bio.SE!  [Note: the student never got back to me with her sources of information, so unfortunately I cannot include them here].


texts: Is Norway spruce (Picea abies (L.) Karst.) isohydric or anisohydric species?

texts:
Question from a thesis defense list ask me this. But I can't find the exact answer on the internet or in books. In my thesis, I described isohydric plants, for example maize, lupin, pea, poplar. This plants response to a decrease in soil water in same way. How Norway spruce response to decrease in soil water? As a isohydric plant or anisohydric?

Thank you for your time and help.


texts: Do neural axons extend around connections like this?

texts:
I was wondering if axons sometimes connect like this:

Note that I'm not referring to situations where the path of that network is curved and the 3rd / 4th neuron is just as close to the 1st neuron as the 2nd is, I'm talking about situations where the 3rd / 4th neuron is physically 2-3x as far from the first than the second neuron, or more. This is relevant to neural simulation.


texts: Does testosterone increase female sexual behavior?

texts:
According to my lecture notes testosterone generally increases sexual behavior.
Given that it's generally thought to be the male hormone I'm not quite sure whether they mean that it also increases sexual behavior in females.

What is the effect of testosterone on female sexual behavior?


texts: Do any fish have to hold their urine in deep water?

texts:
I know this is going to sound really weird! But I was confronted with this claim and the person strongly had faith in it! I said faith since he couldn't provide any evidence.

Is there any kind of fish that is forced to hold his urine when in deep water ?
If yes, is there any relationship between the case with fish's scale ?
Does that make the fish's meat not proper (poisonous) to eat ?

I don't know what depth would be proper to define here but I guess the matter to be rare and not so important to define.


texts: How does the closure of M-type potassium channels by muscarinic receptors result in increased excitation of the target neuron?


texts: Were early human beings (about 100 - 200 K years ago) far more promiscuous than we are now?

texts:
I found that many friends of mine are quite easy in sexual relationship. Ex, I knew a lot of girls went to the night club & met a stranger & brought home to sleep  with him even she had never known his name. The next morning, the guy left her & she starts to do the same way to get another guy maybe in 3 days or so.

So that triggered my thought. I wonder "Are early human beings (about 100 - 200 K years ago) far more promiscuous than we are now?"

My hypothesis is "Yes", that is "Early human beings are far more promiscuous than we are now". So how i came up this? Cos Human came from Chimpanzee right?, so if we want to know early human, then we could study Chimpanzee. The early human & Chimpanzee could have some similarities.

There is a research saying that "Chimpanzees are far more promiscuous than humans" http://www.nature.com/news/specials/chimpgenome/interactive/chimp_interactive_graphic_pf.html

So, that proved my hypothesis.

Also, when human evolved, they started to realized that promiscuousness wss not healthy & not good for society so they started to develop some regional/society (ex,  monogamous relationship) codes to prevent that.

Do you approve my hypothesis?


texts:
How many loci in the human genome are heterozygous? How about other species?

EDIT:
I was wondering, considering for example the whole world population, how many of the human genes actually have two or more different alleles, or, vice versa, which genes everybody shares because there are no different versions of them. Since this seems not to be clear, I don't consider a mutation in a single individual an allele, maybe take 1% occurrence amongst all individuals as a start? I'm no biologist though...

By loci I mean whatever you think makes sense. Again, I don't mean single bases, preferably something like the classic idea of a gene. But I'm happy for whatever you can tell me.


texts: How long does it take for a hard clam (Mercenaria mercenaria) to reach sexual maturity?

texts: How long does it take for a wild hard clam (Mercenaria mercenaria) to reach an age where they are reproductive? How does fecundity depend on age and size? I've looked at several hard clam life cycles and none of them have this information. They tend to agree that hard clams are long lived and take multiple years to reach a size suitable for harvest. While I am more interested in wild hard clam, please do also share information on farmed hard clam if you have it?


texts:
Location: Austria, Vienna Ottakringer Wald
Date: Feb 8

I found something beneath a tree with epiphyta , which I thought to be Viscum album but is vividly yellow instead of white and I found no leaves.

My search of subspecies of Viscum album initially revealed:

  Viscum album subsp. austriacum (Wiesb.) Vollmann. Fruit yellow; leaves 2–4 centimetres (0.79–1.57 in). Central Europe. On Larix, Pinus, Picea.

But then I began to think it shouldn’t be V. album. In illustrations of V. album there aren't the thin stalks between berries and branches as in my specimen.

Perhaps Loranthus europaeus?


texts:
I was reading this page: Equilibrium Potentials when I found the following example at the end of the page: "If the K+ equilibrium potential is –90 mV and the membrane potential is –70 mV, in what direction will K+ move through open K+ channels?".

The site gives the answer, and it turns out that K+ moves out of the cell. I'm not entirely sure if I understand why this is the case.

(1) Because the equilibrium potential for K+ is –90mV, this means that the intracellular region must be negatively charged, at –90mV, to have zero net flux of K+ across the membrane. Therefore K+ would leave the cell, making the interior more negative from –70mV to –90mV.

(2) But the resting membrane potential is still –70mV. Will this membrane potential be established by other ions? If not the case, K+ will be pulled inside the cell again, then we wouldn't be able to tell that K+ goes out.

(3) I find the starting conditions somewhat confusing. "K+" goes out means that there needs to be a potential difference. Is the question assuming we have, as starting conditions, the same concentration of K+ at both sides? Otherwise it is not clear why K+ should stop leaving the cell at any moment (even when it is at the state of equilibrium).

(4) Can we conclude, as a general rule, that if MRP is the membrane resting potential and EP is the X+ equilibrium potential, then X+ leaves the cell if EPMRP. Would the roles be reversed for X–?


texts: Could a cavity in a human tooth "heal over" or possibly fill back in?


texts:
It is approx 1.5 inch (3 cm to 4.5 cm) long

The insect's back and wings.

Insect from its forward side

Just few hours ago (around night 10 to 10.30 pm local time), this insect entered into our home, flying in high-speed and hitting to wall, objects, and to us. To keep it calm we turned the room-light off. Then it became steady on my father's shirt even after the light again turned on, and it was a beautiful moth-like insect. After taking photo it gently freed out of the room.

Here in India, it is rainy season (after summer).

P.S. I've very very little-experience in practical-zoology, however after few hours google search it seems to match with those moths tagged as "hawk-moths", and another notable feature when it was flying it looked like a hummingbird or a small bird, that was written in the description of some "hawk-moths" in different sites. Initially we're taking time to decide whether it is an insect or a bird.


texts: microscopic slide cleaning and maintenance

texts: we do lot of gram staining and some spore staining. we normally wash our slides with detergent then rinse in D/w, dry it and store it. But on reusing this slide we have to flame it and also clean it with alcohol number of times to make it grease free. also these reused slides have some sort of deposit which does not go with cleaning and evend oes not hamper our staining too.  can anyone please suggest the best simple way to clean microscopic slide and to make it grease free and how to store it.


texts: Determining the percentage of the query of an alignment from a BLAST output

texts:
Given this BLAST output, how can I determine the percentage of the query sequence in the alignment? I know that it's also referred to as 'query cover' but I can't seem to find anything online that tells me how to calculate this.

I have given it a go and valued it as 145/147, but I'm not too sure on this. Can anybody clarify whether or not this is correct? Any help is highly appreciated


texts: What is a selectively neutral genotypic change?

texts:
I am reading the paper "Neutral evolution of mutational robustness". Because I am new to neutral evolution, I have a few questions.

Firstly, from my understanding, genotypic neutrality means the genotype is not responsible for an increase in fitness. What else can we say about genotypic neutrality? Does it have something to do with the population being randomly selected?
Secondly, how to understand a neutral network exactly? Another article says "by linking every pair of genotypes that are mutually accessible through mutations, genotypes organize themselves into neutral networks", so what means "mutually accessible through mutations"?
Thirdly, the neutral network is like an assumed black box we know nothing about, is it right? That is why in the original article with title "neutral evolution of mutational robustness", the authors mentioned that "one can infer important structural information about neutral networks from data on evolving populations."


texts: How long can human tissue last without blood?

texts:
I've heard it said various times that the body's tissues will begin to necrotize after being cut off from the blood supply for only a few minutes, but that can't be true.

A few years ago, I woke up one morning and apparently I'd been sleeping just right so that the main artery to my left arm was totally pinched closed, because it was completely numb.  Not just "arm's fallen asleep", either; I had no mental control over the entire arm and no feeling in it.  I could lift it up with my right hand, and it would fall back down immediately when I let go of it, and I didn't feel anything when it landed on the mattress.  It kind of freaked me out at first, but in just a few minutes I felt the "pins and needles" feeling of circulation returning, and it was 100% back to normal within less than an hour.

Given that I had presumably been sleeping on it like that for several hours, and yet I somehow didn't end up with a dead, useless arm that needed to be amputated, I know from personal experience that tissue doesn't die within a few minutes.  So how long does it really take?


texts: What are the biological and nutritional benefits of having numerous smaller meals a day?

texts:
I have heard here and there that instead of consuming 3 largish meals (the traditional 3 meals a day), that consuming several smaller meals throughout the day is beneficial for health (and weight loss).

How true is this statement?  What are the biological advantages, if any, of such a diet?


texts: How do plants get their O₂ for respiration during the night?

texts:
If I am not mistaken the stomata are closed during the night. As a result I have a hard time to imagine how the plant can get the O2 it needs for respiration during the night. I thought the plant could produce the O2 internally through some chemical reaction. Such reaction might include splitting H2O absorbed through the roots in two. Or maybe the O2 diffuses well enough through the plant tissues.

How do plants get their O2 for respiration during the night?


texts: Deionized water - can it be beneficial for metabolic acidosis?

texts:
I ran into an interesting question today that examined the science around alkaline water and its advertised 'generalized health benefits' assumed to be (but incorrectly) stemming from a rise in blood pH. Logic behind the misassumption itself stemming from a rise in urine pH.

What I'm trying to figure out, is would deionized water (slightly acidic water) actually improve short term metabolic blood acidosis and ironically raise pH levels? Proposed ideas are 1) an acidic water stimulated elevation in bicarbonate secretion (kidneys and exocrine pancreas ) and  reabsorption (to circulation), 2) elevated mineral resorption or 'leaching' from cells. These don't sound all that great in themselves, but regarding a short-term net effect on pH (either on urine or a hypothetical blood ph), could not deionized water have a net alkaline effect due to bicarbonate regulation and cellular reabsorption of minerals being inherently 'slower' than the near instantaneous acid-base reaction?

Alkaline metabolic products of an acidic source that may be included in water (ie lemon) do not count as justifications to an answer. Only looking at water.

If anyone has any relevant studies, feel free to share them, I can't seem to find anything outside of fish.


texts: Earliest ancestor of humans who could integrate into modern society

texts:
Assuming the current model of human evolution to be correct, approximately when did the earliest ancestor of humans live, who was intelligent enough, that if raised from a young enough age, could learn the necessary skills to live in today's society:

learn a modern language
learn to read and write
learn to use most common tools and household items
learn to drive a car, use a telephone, a computer, have an average job.


texts: What are the statistical tools for distinguishing molecular analogy from homology?

texts:
Scientists have developed statistical tools that distinguish "distant" homologies from coincidental molecular homoplasy in extremely divergent sequences.
What are these tools?How are they used ?

I have very less knowledge about statistics.


texts:
I've been reading through 'The Selfish Gene' by Dawkins. At a few places in the book he states that incest is damaging because it would give a very high chance of lethal recessive genes becoming active due to the high probability of both children having the gene compared to one child and one stranger from the same species.

However, this leaves me with the question why lethal genes would evolve in the first place. The only reason I can think of is that these genes have some secondary purpose and survive natural selection because of that.

Is this simply the entire story or are there things that I'm missing? It seems to me that the having possibility of getting healthy offspring from incest is beneficial to a species, if only because finding a mate would be easier, so those secondary effects would have to be pretty good.

Also I'd be curious if any research has been done which has found examples of side effects of these lethal genes that would make them preferable.


texts: Are polyploidal organisms parasatized by selfish genes? And if not, why not?

texts:
Certain prokaryotes are polyploids. For example, Thermus thermophilus has about five copies of its genome (http://jb.asm.org/content/192/20/5499.full). One extreme polyploid, Epulopiscium fishelsoni, has tens of thousands of copies of its genome (http://www.pnas.org/content/105/18/6730.full). (Some eukaryotes are polyploid as well.)

As each copy replicates separately it would seem likely that spontaneous mutations would arise and over time, and such an organism would become a hybrid of many distinct genomes coexisting in a single cell.  This seems like an ideal place for selfish copies to arise (though perhaps no more so than any other organism - I think I've read that even prokaryotes are prone to plasmid parasites).

So, does this happen?  If not, why not? Is there some copy-checking mechanism (some extremeophiles seem to have a DNA-repair mechanism) or some mechanism that inhibits reproduction by genomes that are (somehow) determined to not be contributing to the overall metabolism of the cell?


texts: Which cells will pass cancer to offspring?

texts:
Each of these types below contains a DNA mutation. Which type(s) will affect the children of the individual whose cell it is.

Red blood cell
T cell
Skin (epithelial) cell
Neuron from the brain
Sperm cell
Cell from lining of the uterus
Placenta cell
Stem cell

My attempt: I think it's only a sperm cell, because that is the only cell to get passed on.  Is this right?


texts:
Can somebody please identify this bird for me?

I spotted this in July 2012 while birding in Ranganthittu Bird Sanctuary.


texts: Does the given pedigree show a Y-linked dominant trait?

texts: I think that since every generation has males affected only, the trait must be Y-linked. Also, since every generation expresses the trait, I think it should be dominant. However, the answer key says that the answer is autosomal dominant. Could someone please clarify this and give a tip on how to recognise the difference?


texts: How long does it take for a cricket to die at subzero temperatures?

texts:
I am on a number of reptile groups and I often hear freezing recommended as a humane way to get rid of surplus feeder insects.

However, they can also revive if you don't leave them in there long enough.

If I had a bag of crickets and put them in the freezer, how long would it take for them to die in this way?


texts: How did the molecular machinery for recombination originate?

texts:
I'm wondering about the origins of genetic recombination. During crossover new chromosomes are created. They have different allele combinations from the original two chromosomes. This process allows the combinatorial explosion needed for biological diversity. I am puzzled by the accuracy of this very complicated process of generating new genetic information.

Starting from single cell, When did the first genetic recombination appear? How did it come to existence? In my understanding, it could not have been the result of evolutionary process since genetic recombination must be done right at the first attempt.


texts: What is the recommended PPM when foliar feeding L-amino acids

texts:
It is said that L-amino acids such as histidine, methionine, aspartic acid, glutamic acid, asparagine and glutamine can revert plant stomata closure, increase quality of fruits and assist maturity. It is also said that the best way to apply is through foliar feeding.

I would like to start experimenting with different amino acid foliar feeds but would first like to know if there is a recommended maximum/minimum/recomended Parts per million(PPM) , for foliar feeding of these compounds.


texts:
I am a student, and I have written a paper (in drug discovery) which I want to publish. While searching for possible journals I came across Webmedcentral.

Is Webmedcentral a reputable scientific publisher?
What is the impact factor for this journal?


texts: Where do I purchase a fly with the collagen tagged?

texts: Where can I purchase a fly with tagged collagen?  My senior undergraduate research paper is observing the collagen in larvae with normal diet compared to larvae with an experimental diet.  I need flies that have the protein tagged so I can observe the collagen under a fluorescent microscope.  Instead of using an expensive antibody (my budget is $300) to tag the protein, my advisor suggested purchasing stock flies that already have the tagged protein.


texts: Do non-human primates have mental disorders like humans?

texts: I was at the zoo today and watched a gorilla pick at a scab on its finger, compulsively, until it started bleeding. Is this OCD or is it just a nervous thing that non-human primates do at the zoo? Do gorillas share any of the same mental disorders that humans have?


texts: Why is Benzylpenicillin better in Bacterial Meningitis than Amoxicillin?

texts:
Both are beta lactams.
However, benzylpenicillin, which is also called penicillin G i.e. narrow group antibiotic.
I have now in both the following as a mechanism of action

  Binds to PBP in bacterial cell wall, causing deficit in the cell wall and causing cell death.

where I would like to differentiate clearly benzylpenicillin from amocillin.

How is benzylpenicillin better in bacterial meningitis than amoxicillin?


texts: Effects of antibiotics on bacterial growth

texts:
I will do an experiment on effects of antibiotics on antibacterial growth and I will use three antibiotics: ampicilin, chloramphenicol and streptomycin. To make a hypothesis I must have a guess on which antibiotic will have the most severe effect on bacteria. So, do you know any source to find this information out or I would appreciate if you explain the reasoning behind a comparison of how severe these antibiotics.

Edit: Bacteria that will be used is E.coli.


texts:
For a science experiment for school, I have set up 15 Winogradsky columns, and will be looking at the microbial growth inside the columns over a period of 25 days.
I have read that, due to gas produced by the microbes, it is good to leave the cap loosely closed to prevent an explosion from gas buildup. However, I have also read that sulfate-reducing bacteria that grow in the column can produce toxic hydrogen sulfide gas. Wouldn’t the hydrogen sulfide also escape in small amounts and pose a health risk? What would be the correct protocol to follow here?


texts: Is gas produced by bacteria always mainly methane? Or, are there bacteria out there that produce some biogas composed mainly of hydrogen, natural gas, propane, butane?


texts: Emergence of novel protein interactions by mutation of amino acids

texts: Are there any examples of proteins that, without coming from a recent duplication event, underwent a mutation(s) that caused it to have a novel interaction with a new ligand, substrate, other protein or molecule? By novel I imply that it doesn’t revert to an ancestral interaction or develop an interaction that is already performed by a close relative. I imagine that such mutations would be extremely rare, and that duplication is almost always necessary to have them fixed in a lineage.


texts: Spatial distribution of axons connecting distant groups of neurons

texts:
It would help me to shape my picture of the brain, if I knew the following:

Consider two specified groups of neurons A and B in the brain that are well-located but quite distant from each other (e.g. two roughly spherical nuclei, or two Brodman areas corresponding across hemispheres), and which are (more or less) directly connected synaptically, i.e. axons of the first group build synapses with dendrites of the second, the distance being mainly bridged by the axons. I assume there are lots of examples on different scales.

My question is: Is there a preferred way how the axons are organized, i.e. spatially distributed in the brain? Do they run  mostly parallel to each other in bundles, or are there (maybe exceptional) cases, where the axons (or small subsets of axons) take individual routes, possibly quite far from each other?

I am aware that with intermediate groups of neurons, there are different and non-parallel pathways of one group of neurons to the other. So my question is explicitly about directly connected groups.

(Are there too many simplifying assumptions in my question that make it vacuous?)


texts: I have a very basic biology question. I am reading the description of gene FAM166A here, and I have no idea what "sequence similarity 166" means. What does 166 stand for, what is this gene's sequence "similar to"? And what does member A mean?


texts: How to evaluate broad-sense heritability of microbiome associated plant genotypes in R

texts: I have a data containing 196 accessions of A. thaliana from which I studied leaf bacterial and fungal community and, therefore, sequenced and found several OTUs. Now, I want to evaluate broad-sense heritability of microbes across accessions of A. thaliana in R. Kindly reply and if needed, I'll provide the data table.


texts: Giving a sign to Pressure Potential, Osmotic Potential And Other Similar Quantities

texts:
When these quantities are mentioned with what reference do we give signs to them?
Why is Osmotic Pressure positive, but Osmotic Potential, negative?
What about Turgor Pressure (Pressure exerted by the protoplasmic fluid on the cell wall) and the Wall Pressure (Pressure exerted by the Wall as a reaction to the Turgor Pressure), what signs do we assign to them?
What I understand is that it's based on the tendency of water to enter or exit the system being studied, but I lack clarity on how signs are being assigned to these different quantities. When we talk about soil having a low, does low mean more negative or does it mean a lower magnitude osmotic potential, for example?


texts: Techniques of molecular medicine/biology for aesthetic medicine?

texts:
Are there scientifically valid methods (possibly in the developmental stage) that can be used for aesthetic medicine. Usually surgical of physical therapies are used for aesthetic medicine, but actually all the problems of aesthetic appearance should be traceable to the genetic/epigenetic causes and that is why the molecular treatment at that level should be possible and optimal.

My question is can be considered also as a veterinary medicine question (aesthetics of pets) and that is why it is really a biology question.

https://journals.sagepub.com/doi/full/10.1177/2470289718787086 is the only more or less relevant article that I have managed to find.

Also CRISPR can be quite promising tool, but I have not managed to find scientific studies for aesthetic medicine of it.


texts: Which are the most extreme artificial environments that lifeforms/ecosystems have adapted to?

texts:
I have heard of 'extremophiles', lifeforms that naturally thrive in all sorts of extreme environments.

Is there any evidence to suggest that lifeforms are adapting to the extreme environments (such as in mining waste, nuclear waste etc) that result from human activity?


texts: Are there any online resources for finding the signaling pathways that two proteins both belong to?

texts:
I am studying the proteins GSK3 and AMPK and I am trying to identify the signaling pathways that both of these proteins belong to. From reading journal papers I have found out that both of these proteins belong to the mTOR signaling pathway. I know on KEGG if you type the name of a gene involved in a signaling pathway (e.g. GSK3B) in the search bar on the page showing a signaling pathway (e.g. the mTOR pathway), you can find more information about that gene. However, I was wondering if there are any resources online where you can type the names of multiple genes and you can find out the signaling pathways that all of the genes are in?
Any insights are appreciated.


texts: How much energy takes C4 photosyntesis to make glucose?

texts:
Wikipedia has a kind of contradiction that I would like to understand:

According to this link

  The C3 pathway requires 18 ATP for the synthesis of one molecule of glucose while the C4 pathway requires 20 ATP. [...]

According to this other link:

  [...]. The C3 pathway requires 18 molecules of ATP for the synthesis of one molecule of glucose, whereas the C4 pathway requires 30 molecules of ATP.[...]

Also, I don't understand much of this, I was just curious. I found this link (not sure if reduction also means generate glucose):

  However, the C4 pathway of CO2 reduction expends more energy (5 ATP and 2 NADPH) than C3 pathway (3 ATP and 2 NADPH) (Hopkins 1999).

And this link:

  ATP consumed in C4 plants
  C4 cycle ( which involves regeneration of PEP from C3 acid) - requires 2 ATP per CO2 fixed.
  C3 cycle ( which is common in C2,C3,C4 cycle)- requires 3 ATP per CO2 fixed.
  Total - 5 ATP per CO2 fixed.
  Thus to form a hexose or to fix 6 CO2 6*5= 30 ATP

All emphasis mine.

So... Does C4 requires 20 or 30 ATP per molecule of glucose? I think I found more evidence over 30 than 20, is that correct?


texts: Why are plants referred to by their Latin species names, and not by their popular names?

texts:
Often the names of herbal ingredients in certain cosmetics products are given by their scientific names like Anthemis nobilis instead of chamomile or Lavandula angustifolia instead of lavender.

Is there any reason why this practice is followed? Wouldn't those who have allergies to certain plant materials be better off reading "coriander leaf extract" instead of scratching their heads over what "Coriandrum sativum leaf extract" is? Why put something more complex when something simpler would be more beneficial to the consumer?


texts:
So I know that memory cells "remember" the most efficient way to kill a pathogen should it show up again... but what is the mechanism by which memory cells become activated by the second contact with a pathogen? How do they interact with the other immune cells to enhance immunity?

For example: phagocytes engulf pathogens and plasma cells release antibodies, but what do the memory cells actively do?


texts: Large coalitions of lions taking over multiple prides?

texts:
I have noticed while watching lion documentaries that coalitions with more than 3 males tend to take over multiple prides and have 1 large pride in their territory while coalitions with 3 lions or less tend to take over just 1 pride.

As a very good example the Mapogo brothers(6 lions) take over multiple prides and they even split the territory between a coalition of 4 and a coalition of 2.

On the other side of the spectrum Tau and Banda are just 2 lions in a coalition. They take over just 1 pride with 3 lionesses in heat and no cubs. Tau does it by instinct and Banda is strategic.

Why is there so much of a difference between the small coalitions that take over just 1 pride and the large coalitions that take over multiple prides? Do large coalitions do better when they take over multiple prides from less aggression? Do small coalitions do better when they take over just 1 pride from more and closer defenses against other male lions?


texts: Can someone please tell me which animal does this spine belong to? I found it today on the beach..


texts: If our eye lens and cornea were flat would we still receive the world upside down?

texts:
Usually the effect of a pinhole (or camera obscura) and the lens of our eyes are creating the world upside down on our retina.

Now imagine the lens and cornea would be flat is the pinhole effect still capable of creating a reversed image or would our vision be total blurred because (parts of) objects  shining straight in the middle into our eye would not be reversed while parts above or beneath the middle would be reversed?


texts: How does the helicase enzyme break the hydrogen bonds between the strands of DNA?

texts:
I know helicase breaks the hydrogen bonds between the strands of a DNA, but how is this done?

Does it put an ion between the strands of the nucleic acid so that the bond breaks apart itself or is there some other mechanism?


texts: Mathematical models of lineage selection

texts:
I'm interested in the concept of lineage selection (Aboitiz, 1991) as an explanation for why traits would be selected for that enhance the rate at which evolution can occur, rather than directly enhancing an individual's fitness. (Such traits could include gene duplication; body plans that can easily be adapted to new niches; learning (which enhances evolution due to the Baldwin effect) and so on. Questions about the evolution of such traits are collectively termed "evolution of evolvability.") The term "lineage selection" does not refer to group selection or kin selection, but simply to selection between distinct genetic lineages in a mixed population.

What I would like to know is whether a mathematical theory has been developed along the lines of the Price equation that can capture the concept of lineage selection and make predictions about it. Lineage selection does not appear to be modelled by the Price equation itself, at least not in a straightforward and obvious way, because on the face of it the Price equation only directly accounts for the relation between a trait and the number of offspring in the next generation, rather than the number of surviving descendants several generations later, which is what is required for lineage selection.

The reason I'm looking for a mathematical model is that there are a number of intuitions that many people seem to share about lineage selection and I'd like to understand what assumptions are needed in order for them to be true. In particular, it seems clear that large populations are needed for lineage selection to be effective, and I'd like to understand precisely the relationship between population size and the effectiveness of lineage selection. (My intuition is that with a population size of around a million, lineage selection can select for traits that have a beneficial effect around 20 generations later, since $1,000,000\approx 2^{20}$, but this intuition lacks a formal basis.)

A literature search did not turn up anything along the lines of what I'm looking for, but this is not my main field and I may simply not know the most appropriate search terms to use.


texts: carbohydrates and lipids as a source of energy? why?

texts: Why carbohydrates and lipids basically used as a sources of energy? Why only proteins are used as building blocks of all the creations? Yes there are some parts of cells like cell walls in which carbohydrates are used but 98% portion of cell is made up of proteins? Why it so?


texts: Do men have significant hormonal cycles?

texts:
I know there's a similar question here. But that discussion dissolved into lunar cycle and a correlation with it.  I want to find more towards the original question of is there a periodic hormone cycle in men.
The links i have read suggest that there's probably a daily one for sure. But few hint at monthly ones too.
 That link seems to have very shaky science, but my biology is too weak for me to find the actual studies. Anyone else with more informed opinions? Any studies tracking purely hormone levels in men over a period of couple of months/years?

[EDIT]
   I understand it's clear there are cycles within the day or around the 24-hr mark now. I still am looking for studies focusing on longer term cycles like week,months etc.


texts: Binomial nomenclature: Why am I seeing different genera with the same species name?

texts:
I have looked online but still do not understand how two organisms can have the the same species names but be in different genera?

Do all genera share common species names?

Also which would be more closely related, two organisms with the same genus name but different species name or two organisms with different genus names but the same species name?

According to a textbook, the two with the same genus are more closely related, but I do not understand why?


texts: What would happen if nerves didn't have refractory period? And, what part of his nervous system or neurons are not needed?


texts: Protein - one polypeptide molecule or a collection of molecules?

texts: I'm struggling a bit in Bio 111 with confusing terminology between the terms "chain" and "molecule". I understand the primary structure of a protein is a chain of amino acids connected by peptide (covalent) bonds - easily a molecule. And the secondary helix structure could be a single molecule/polypeptide chain. Up to this point, chain = molecule. But a beta-pleated secondary structure would have to be two or more chains (molecules) connected by hydrogen bonds. No? Or is a beta-pleated sheet considered one molecule? One chain?


texts: I read somewhere that according to a research, I don't remember what the date was, that our cells stop synthesising DNA around noon and restart it around the sunset. The research told that it was actually a survival benefit for cells when ozone was not formed so that the DNA does not get damaged. Would somebody like to guess how our cells know when to do so and if it is a protection against present ozone depletion due to CFCs?


texts:
I would like to know how many appendages the arthropod Phronima sedentaria has, and how they are arranged. It's not hard to find picture references, but Phronima's transparency makes it difficult to tell from live photos, while what drawn diagrams and text descriptions I've been able to find diverge wildly.

From what I've been able to determine, it has a bulbous head which may or may not have antennae, near to which are two to four pairs of limbs. There is a small gap, then a much longer pair of limbs ending in claws, followed potentially by a second longer pair, and then two to four shorter pairs of limbs. The tail is lined by three pairs of swimmerets, possibly tipped with paddles or bristles.

The best possible answer for this would be a picture like this one, with the assurance that it does indeed represent Phronima sedentaria accurately, though I would be happy with a confirmation of appendage count. Additionally, while I would prefer information about Phronima sedentaria specifically, I can make do with such information about any member of the genus so long as it is specific.


texts: Effect of Aging on SA node's sympathetic fibers

texts:
I am trying to understand the effect of aging on the sympathetic fibers of SA node.
I know that aging shifts the vagal curve to left in frequency due to aging.
However, I am interested if aging has similar effect on sympathetic fibers.

In young heart, heart's intrinsic functions can work with simultaneous parasympathetic and sympathetic processes.
If there is no change in the sympathetic function, then those processes have to happen at different times.
I am having this kind of schematic picture in my mind:

where intrinsic functions occur in 100-110 BPM normally.
However, aging shifts V1 to V2, no intersection anymore between V2 and S1.

What is the effect of aging on the sympathetic fibers of SA node?


texts:
If person A is infected (COVID-19) and person B is not, could the following work as a vaccination?  Person A exhales (coughs?) into a a transparent bag.  The bag is radiated for a long time with a strong ultraviolet (UV) light as is found in some residential well-water systems.  Person B inhales the contents of the bag.

I am curious mostly about how virus particles are damaged at the molecular level by UV light and how this relates to how vaccines are manufactured today.


texts: Is it feasible to grow edible crops for lawns?

texts: Is it possible to grow some type of plant that functions well as a lawn (e.g. is somewhat grass like), but that is humanly edible?  Would anything that currently exists fit this role?  For example possibly spinach or lettuce might work somewhat, but probably wouldn't be ideal.  If not, could we bioengineer something to fit that role?  I am thinking if we can, this could solve world hunger!


texts: Does the testicle's temperature increases with the body temperature during a high fever?

texts: The testes is the male sexual organ. It is positioned outside the abdomen along with the scrotum. I would like to know if its temperature is independent from the body temperature due to its location.


texts: Reason for specific location of a gnat swarm?

texts:
While checking on my yard trees, I noticed a tiny swarm of gnats above one small maple that has a metal cup holder stake used to help train the trunk straighter. Approximate swarm size of 20 - 30 gnats and they hovered about 6 inches above the top of the cup holder.

I know there's studies on the phenomena of swarm behavior, and out of curiosity as to what they would do I put my hand a couple inches above the cup holder. The little swarm repeatedly moved straight upwards 3-4 inches then returned to the original spot as soon as I removed my hand. When I raised my hand up towards the swarm they would move higher and higher and also follow my hand back down as I lowered it. No matter how high I raised my hands if I removed it quickly they returned immediately to the original location. I checked back a half hour later and they are still there and acted the same way.

What might be the reason for that specific preferred location of the swarm? I has been cloudy and humid all morning and I wonder if the metal of the cup holder is changing the air temperature or some other quality that far above itself? I did also notice a stronger sweet smell of the clover in that location but do have clover all over the yard. My other trees, including a very similar sized young maple but without any support next to it, have no swarms so the metal cup holder perhaps is a correlating factor?

I tried adding a picture for reference but can't get it to upload.


texts:
In my mulch bed today I came across a tiny red worm, between $\frac{1}{4}$ and $\frac{1}{2}$ an inch long. It moved across the ground by sitting upright on one end, waving the other end back and forth (presumably for some momentum), and then flipping over and standing on the other end. It did this motion flipping end-over-end, kind of like a slinky. Observed in the Chesapeake Bay region.
I haven't been able to find anything on this little creature through searches. An article about leaping nematodes is the only thing remotely in the neighborhood of what I saw but the motion described is different and these sound far too small to be the same creature. Any ideas what this is?


texts: Is there an evolutionary advantage associated with migraine?

texts:
I have read Wikipedia article on Genetics of migraine headaches and I don't buy it

  Because genetics influence susceptibility to migraine, it can be
  shaped by evolution. Fitness-impairing disorders, including severe
  headache, tend to disappear as a result of natural selection, and
  their frequency decreases to near the rate of spontaneous
  mutation. However, migraine has not
  diminished over millions of years of evolution. Its prevalence has at
  least been maintained at a high level, and has even been shown to be
  increasing.
  This phenomenon suggests that a central nervous system (CNS)
  susceptible to severe, intermittent headache has been linked to an
  important survival or reproductive advantage.

the argument in wiki is equivalent to since we know that evolution is correct - it means that headaches must benefit us somehow otherwise we wouldn't have it so let's think of some reasons - which is in my opinion is a fallacy.

I could believe that this is a bad side effect of some more efficient to survival trait like being smart, (which is partially covered in same article)

  Finally, migraine may be a component of imperfect central nervous
  system design. Evidence has suggested a dysfunction of pain-inhibitory
  pathways in migraine and discordant interaction between the ancient
  brain stem design and the more evolved neocortex.

EDIT:

I have read the meta post and answer from WYSIWYG, and I agree that they do partially answer my question in regard that a mild 'badness' can get past. I would argue that my question is different in a way that I am referring to specific point The trait might have a tradeoff which essentially makes no change to the overall fitness
The way I understand it is that one gets some 'perk' that is beneficial in some situations and disadvantageous in others and they cancel each-other out. (I just don't see how without some huge benefit migraines would get past). What I am asking is what so advantageous we must have gotten - that such horrible thing like migraines got through.

Are there any studies done - that incapacitating migraines are coupled with an evolutionary trait?


texts: Do we have fundamental conflict in biology?

texts:
As saying "fundamental conflict", I mean something like two (or more) widely accepted results from different areas (or scales) can not exist logically together. In physics, there have been three conflicts1. I wonder if in biology, do we have such conflicts? And how biologists resolved that?

1  One of them is the conflict between Einstein's general relativism and quantum mechanics. String theory, if it is proved to be true, will reconcile this (read more). But it can also be like the controversy of the property of light. Some said it was particle, some said it was wave. Modern physics says it is both.


texts: Can a phosphodiester bond form between RNA and DNA?

texts:
In the initiation of DNA synthesis:

  the RNA segments are first synthesized by primase and then elongated
  by DNA polymerase (Wikipedia).

What does 'elongated' mean in this context? Is it possible for RNA and DNA to form a phosphodiester bond to make a single strand which is part RNA and then part DNA?


texts: Why do animals only eat some parts of their food?

texts:
For example monkeys/apes only eat part of a fruit and then throw the rest. Cats (big and small species) only eat some parts of their prey and then they abandon it.
Humans on the contrary leave as few leftover as possible.

What do we know about the parts that animals eat ? and how do we know it ?


texts: Why squirrel behaviour varies greatly throughout India?

texts:
Common squirrels seen in India, probably Indian palm squirrels; seem to have drastic different behaviour. And all squirrels of a definite locality, behave in a very consistently same whay. That seems like  My drastic experiences at 3 localities were as follows.

On West Bengal (Howrah, Hooghly and Burdwan District): Squirrels seem to be incredibly timid. They always maintain a safe distance from human being. They sometimes consume human food leftover, or respond to cater; but the feeder person needs to be go away from the spot. They are also quite a bit picky eater, among human remains they mainly depend on paddy, some of them don't even touch grounnuts.
On Uttarpradesh Tourist spots, particularly Agra and Delhi, squirrels come too close to the tourists. Sometimes they take food directly from human hand. Some of them even follow the tourist population for foods. Some of these squirrels are very aggressive, however they are somewhat vulnerable because people easily touch them. They aren't very picky eaters, rather they are sort of gluttony... eats whatever the tourists feed them.
On Uttarakhand state, on many places (including the non-tourist) the squirrels come very closer to human being.  Not always for food, but they just come too close to human being. They aren't aggressive. They aren't very picky eaters. Though some are little bit timid; some are super easy to touch. They are super vulnerable.

I'm really surprised how the behaviour of these 3-striped squirrels vary throughout India and is consistent with locality. Learnt behaviour from parent/ peer squirrels? Epigenetic imprints? Genetic variability? Scarcity of foods? Its super surprising.


texts: Species richness corrected for area -- should area be log-transformed?

texts:
I am doing a study to compare plant species richness (total number of species per site) to a bunch of environmental factors of sites at which these plants were surveyed. Because these sites are different in size, I have converted species richness to a species density measurement by dividing by the log of site area (species density = species richness/log[area]).

I log-transformed area, because the relationship between species richness and area at my sites is linear on a semi-log scale. Now that I have calculated species density in this way, I am having a hard time convincing myself that calculating density with log(area) was the correct approach. Does anyone have some insight on this? My community ecology background is not strong and I am getting bogged down in the literature.

Thanks!


texts:
I need to get haplotype data for HapMap or 1000 Genomes for CEU, MKK, TSI, CHB and JPT for ± 1 Mb at LCT gene. I'm quite new in the area. Actually I don't know the meaning of "± 1 Mb". From which sites and how do I get the data? Do I need a program?

As far as I understand, LCT gene is on Chromosome 2. That's why I used following code:
wget -r --reject="index.html*" http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
Now I have a vcf file.

I also obtained a vcf file from Data Slicer ( http://grch37.ensembl.org/Homo_sapiens/Tools/DataSlicer ). I chosed populations and wrote 2:135,787,840-135,837,200 for region lookup. What does this file contain? How can I see the file content? What else do I have to do to get haplotypes? I will try to cluster and visualize haplotypes accorgind to populations. If you can guide me, I am very happy.

Thanks!


texts: How potent is the venom from the Australian platypus?

texts:
The Australian platypus, is a marsupial with a unique feature - in that the males of the species have venom sacs around their hind-claws.

My understanding is that this venom is not lethal to humans, however, how potent is this venom to other animals?

Also, how does the platypus 'manufacture' this venom?


texts: Why do we use an autoclave at 121°C (250F)? (Origin)

texts:
Let me start by saying I know why, but I am inquiring more about the origin.
My question is more related to literature that I cannot seem to find.
I've found some helpful papers and information on the origin of the using 121°C for sterilizing equipment, and killing bacteria but I wanted to ask the question anyways and see if anyone knew something more about it.
So to restate my question, I want to see data as to why 121°C and not 120°C?
Originally I though it is because the experiments might've been conducted in F and the inter-conversion from F to C yielded 121°C which is an odd number.
From what I could gather it started in the food industry with a company that made canned products and their canned products were exploding. This company approached MIT and after some research they found that at 121°C (250F) for 60 min in retort would kill the spores surviving the previous processing. (further exp. reduced the time to 10 min, for canned clams)
This is detailed in the paper which was published in 1897
https://www.jstor.org/stable/1623441?seq=1#metadata_info_tab_contents
The autoclave was invented in 1879 (18 years prior to the publication).
At the end of the publication it says:

Detailed descriptions of the organisms and of many more experiments will be given in our full paper on this subject to appear in a forthcoming number of the Technology Quarterly

I have not been able to find this specific issue of Technology Quarterly
The authors (S. C. Prescott and W. Lyman Underwood) also say:

As we have shown in our previous paper, in order to insure
sterilization in practice, it is necessary to obtain and maintain a
temperature in excess of 121°C (212F) throughout the contents of the
can. Intermittent sterilization may be employed, but is less efficient
and is not practicable upon a large or commercial scale. We have found
by experiment that sixty minutes at 121°C (250F) is sufficient time for
sterilizing corn, and it seems probable that this can be shortened
somewhat or the temperature reduced.

They are using °C, but since it's 1890's retorts (autoclaves) used in food industry might be F and the authors probably converted retort eqipment readings to °C for scientific community.
Also, this was what pioneered thermal death study and if you look at the temperature that they used for the study they are kind of sporadic. Probably because they wanted to see what temperature + time would reach the center of the can. The length of heating, or processing, and the pressure which is given vary somewhat in different factories and that might’ve been what led them to the 121°C and not 120°C.
Further research was done in this field:
In 1956 and 1958  F. H. Deindoerfer & A. E. Humhrey found that 250F (121C) is the optimal temperature to avoid damage nutrient media. They also discussed analytical methods for heat sterilization times.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1057515/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1057690/
What I've been specifically looking for is the first thermal death study with D&Z values that led to the widespread usage of 121°C. Andy why the time and psi required for sterilizing biological samples. I know and found papers on what is used to validate Autoclaves.
Geobacillus sterothermophilus (known as Bacillus sterothermophilus also) is used for validating autoclaves and that is due to it being very heat resistant, making a good biological indicator of microbial life post sterilization. The one paper I found which had some graphical data about its thermal death rate uses °C instead of F. I cannot seem find any information on the bacterial Log reduction at 120°C comparing it to 121°C. This answer might as well as be a mathematical equation leading to the that temperature, but that is only venue I haven't explored
Paper on Geobacillus sterothermophilus: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1057891/
If anyone can find that Technology Quarterly paper I mentioned at the start that'd be great.


texts: What do the column labels in this table mean?

texts:
This table shows the effect of sound (song and tones) on female birds. However, I'm not sure what the labels (F1 22, P and η2) mean. I've seen the labels on other tables too.

(from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3508516/)

If anyone could help I'd be very grateful :)

thanks!


texts: In humans either for biological or cultural reasons there are life expectancy differences by sex. But how about non human mammals? Are there known life expectancy differences in non human mammals by sex?


texts: Almost philosophical question about controlling a pest/plague

texts:
Once in a math congress someone presented a paper on a mathematical model used to predict the impact of certain measures that could be taken in order to control some pest/plague. A guy in the audience interrupted the speaker and asked why not to "kill them all"(referring to the specimens of the pest/plague) and put a stop to the problem. The speaker observed that we were thinking that kind of things because almost all of us were mathematicians and so we were not aware that it would be a big problem to do that.

From my point of view, he was suggesting that "the right way to control a plague is not to kill them all" is a standard, uncontroversial fact that all biologists would agree. My question is about this last point.

Is that a scientific thesis or an ideological one? I mean, do biologists have theories that allow them to know that the "right" way to control a plague is not to kill every specimen of the species?

Why is it the case that we can assure that exterminating a species is necessarily going to affect, directly or not, humankind?

Is it a matter of chance and, as we are not completely certain of what may happen after exterminating the species, then we don't want to take a risk?

Thanks! And feel free to edit tags :)


texts: Difference between KEGG Pathway and Module (from KO mapping)

texts: At the KEGG otholog mapping query page I can map pathways and modules. I can't seem to find an extremely low level description of the difference between the two. I think I understand what a pathway is. I can't seem to find any definition or description of what a module is.


texts: Are there studies that investigate the heritability of "believing in supernatural" (or related concepts)?


texts: Does the renal vein have a greater glucose concentration than the renal artery?

texts: My IGCSE markscheme says that the renal vein has a lower concentration of glucose? I would expect the renal artery to have lower glucose concentration as water is lost from the kidneys. Why is it so?


texts: Earth overshoot day: is it a sound concept?

texts:
Today, August 8th, is Earth Overshoot Day (EOD) for 2016, the day when humanity supposedly has consumed the natural resources available from the planet for the year 2016; we're now running a deficit, somehow. At least if your believe the calculations of the Global Footprint Network (GFN), the think tank behind this concept. EOD is well reported by media every year, and perhaps it does some good as an ecology awareness thing. But is the idea scientifically sound?

EOD is based on the ecological footprint concept. The ecological footprint of a person (measured in hectares) is the area of the earth required to extract the natural resources needed to sustain that person: to grow crops, keep farm animals, obtain natural resources for consumables, etc. It's a very complex thing to calculate, and of course people argue about what the correct formula should be. One article by Willis Eschenbach (2010) goes into some depth and argues that the formula used by GFN vastly overestimates the footprint. I don't know who is right, but it does seem like the footprint is very difficult to estimate, so we should probably be careful with drawing strong conclusions.

But I have a more fundamental problem with EOD. Regardless of how it's calculated, the claim that we have today "overshot" our yearly earth-budget, at 8 months out of 12, means that we are consuming about 1.5 of the available food and natural resources available; or that the footprint of humanity is 1.5 Earths. This is not some kind of parable: GFN really claims that we have exhausted our natural resources, by a wide margin, and that this has been going on since the 1970's.

My question is, what are we all living on then?

As of today there should be no more food around, or any other natural-derived product for that matter. If GFNs estimate is correct, shouldn't humanity be long dead? Shouldn't we expect 1/3 of the earth's "surplus" population to die off pretty quickly? Doesn't the fact that we're not dead prove that EOD is wrong? Isn't it physically impossible for our total footprint to exceed 1 Earth?

EDIT: Nice to see that this question stirred a lot of debate! :) I think several answers bring up one key point that resolves the problem: GFN defines the footprint not as the actual area required for production at present (which must be < 1 Earth), but the area required for sustainable production (which is larger). Exactly how the sustainable area is defined is still mysterious to me, but I guess it is at least theoretically possible.


texts:
I have been trying to confirm the Km of a substrate (which is 34 +/- 4 mM). This value was obtained in 50 mM MOPS, pH 6.3. I conducted my kinetics assay in a buffer of pH 7 and obtained a Km value in the 21.5. According to this paper, Fig. 2C, the normalized specific activity of the enzyme is about 70% at pH 6.3 and about 47% at pH 7. If I divide 34 mM at pH 6.3 by 0.7 (which should get me the optimum Km at the optimum pH of 5.5) and then multiply by 0.48, then I get 23 mM. However, the paper says Km is between 30 - 38 mM, so if I divide 30 and 38 separately by 0.7 and multiply by 0.47, I get 20 and 25.6 mM respectively. Because my value falls within this range, this then must mean that I have the right enzyme and the same result as the paper.

So my questions are:

When the paper says Km is "34 +/- 4 mM", can I assume that means the Km can be anywhere between 30 - 38 mM? I'm surprised to see how wide the range is. I assumed Km is usually just one value with a deviation of at most 0.1.
Do pH change Km values? I understand that pH changes the shape(s) of the enzyme and/or substrate. Therefore that must affect how much it wants to bind to the substrate. If the enzyme's desire to bind to a substrate decreases due to increase in pH, for example, that would mean more substrates are needed to surround the enzyme, thus increasing Km.
If pH does change Km, is this how I determine the Km value of a different pH value if the Km value at another pH is already known? I know that specific activity and Michaelis constant are different, but how much product can be converted per minute depends on how much the enzyme likes to bind to a substrate, which is represented by the Michaelis constant. Did my reasoning and calculation arrive at the right conclusion? If not, how is the calculation done?


texts: I had surgery when woke up I felt like I only had 20% energy & felt extremely tired. Is this a common sensation? Why do people feel so tired after surgery?


texts: What is the structure of DNA polymerase III?

texts:
According to Snustard and Simmons the structure of DNA polymerase III is the following, where the clamp loader( γ -δ complex ) is present on one side:

But according to Lehninger the clamp loader is centrally located:

Which one is right? Besides where can I find a correct diagrammatic representation of DNA polymerase III?

I recently found this paper which supports the second mentioned structure of DNA pol III.


texts:
I had a discussion with a high school student about the effect and production of nicotine. He mentioned that nicotine is naturally produced in our brain so when the person takes to smoking, the brain stops producing its own nicotine and starts craving it from an external source. According to him, this is how nicotine addiction develops. How true is this?

The students also claimed that nicotine in cigarettes is harmless. I have already seen the answer about how toxic it is to humans, but I would love to know:

What's the lethal dose for nicotine via ingestion (not inhaling)?
How does nicotine compare to other toxic substances - for example, cyanide or any other known poison? Is it more toxic or less toxic?

THANK YOU


texts: I am a science fiction fan, and when I watch movies with aliens, I get annoyed at the fact that they're all humanoid. I think, "What are the chances that it will look that similar to humans?" But I wondered recently "What if there is an ideal shape for an organism in a specific environment?" An example is that all mammals have 4 limbs, and all fish have gills and fins (except for some, but I will get to that). What if that is because that is the perfect form for an organism in that kind of environment? Along with that, some fish have evolved to do certain, unique things, whether to camouflage, attack, or develop a symbiotic relationship (am I correct on that?), which brings up the question, how much does the mindset and disposition of an organism affect its end body shape, and how much more random does it make the process of evolution? What I mean to say is, say biologists were able to create organisms and watch them evolve quickly. If you took two single celled organisms that had no similarities, and put them in the exact same environment, would they evolve to look similar? Or would they develop their own, unique ways of surviving in their environment?


texts: Additive genetic variance with $n$ alleles

texts:
The genetic variance of a quantitative trait (the quantitative trait in question is fitness) can be express as the sum of two components, the dominance and additive variance:

$$\sigma_D^2 + \sigma_A^2  = \sigma^2$$

, where $\sigma$ is the genetic variance, $\sigma_D^2$ is the dominance variance and $\sigma_A^2$ is the additive variance. $\sigma_D^2$  and $\sigma_A^2$ are given by

$$\sigma_D^2 = x^2(1-x)^2(2\cdot W_{12} - W_{11} - W_{22})^2$$

$$\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$$

, where $W_{11}$, $W_{12}$ and $W_{22}$ are the fitness of the three possible genotypes and $x$ and $1-x$ give the allele frequencies.

Question

The above definition makes sense for one bi-allelic locus.

How are $\sigma_D^2$, $\sigma_A^2$ and $\sigma^2$ defined for a locus that have $n$ alleles?

Here is a related question


texts: Can you use images taken at different exposure times in western blot image analysis?

texts:
I am doing Western blot data analysis where I have images from a number of experiments (where the samples in the experiments are biological/technical replicates). For each experiment, I labelled the membrane with antibodies against the same proteins of interest.
I want to combine the data from these experiments so that they are all displayed on the same graph.
I took my images at a variety of exposure times (e.g. 5 sec, 30 sec, 1 min, etc). For one protein X, I have found that the images taken at 30 seconds exposure are the best for analysis, as the bands are saturated at higher exposure times.
However, for one experiment, for the protein X labelling, I cannot use the 30 second exposure image for my analysis as there are ghost bands. I have an image taken at 5 seconds exposure which I can use instead.
I was wondering when combining data from western blot images from different experiments, for a specific protein of interest (e.g. protein X), do all the images have to be taken at the same exposure time? All the protein X images I will be using were taken at 30 seconds exposure except for one which is taken at 5 seconds exposure.
Any insights are appreciated.


texts: If the human atlanto-axial joint is pivotal only, what accounts for the craniums additional degrees of freedom?

texts:
The atlanto-axial joint is supposedly a pivot joint. I assumed it would be considered a ball-and-socket joint, based on a) the physical shape of the dens, and b) the degrees of motion of the cranium relative to the spinal column.

A pivot joint is distinct from a typical ball-and-socket joint because it only allows for a single degree of freedom; yaw - to rotate about it's own axis or diameter, like a spindle. A typical ball-and-socket joint allows at least one additional plane of limited movement.

I can think of (or observe) at least three degrees of freedom of the cranium, relative to the spinal column; pitch & roll. Pitch allows you to direct your gaze from the ceiling, to the floor. Roll allows lateral movement in a similar manner, so you can point your left ear to the ground, and then your right.


texts:
I have bought a hobbyist kit which involves growing E. coli. The steps said to grow the E. coli on an LB agar Petri dish overnight. No incubation devices were included in the kit.

I let the E. coli grow overnight at room temperature (65-75°F), but there's pretty minimal growth, if any. I found this question which seems to imply that it's hard to grow E. coli without having temperatures near 37°C, which is much warmer than I can reasonably make my house.

Is it possible for me to do this experiment without purchasing an incubator of some sort? If so, does the lack of growth indicate that I've made a mistake somewhere?


texts: Virus plaque assay, pfu/ml calculation on plates with too little plaques formed

texts:
I am a student, so I hope it is okay to put this question here. I've done the virus plaque assay in a practical recently and have a few questions regarding the plaque count for pfu calculation.

In the plates corresponding to times 0 and 10 mins, a few plaques formed (less than 5 plaques in every plate where plaques could be seen) Should I still calculate pfu with those results, or should I leave it as 0 pfu, and use only plaque counts that are at least more than 10?


texts: Why would a mammalian vector plasmid require an antibacterial resistance gene?

texts:
I have been trying to understand the composition of plasmids used in recombinant DNA cloning, such as this: https://www.genecopoeia.com/wp-content/uploads/2020/02/pReceiver-M35-051818.pdf
and I am wondering what purpose the ampicillin resistance gene has when transfected into a mammalian cell host (as it says it is for).
I understand that ampicillin resistance is used for selection in bacterial cells so that only transformed bacteria are grown as well as ampicillin being needed to prevent bacterial contamination among a mammalian cell culture, but I don't see why mammalian cells require a resistance gene to an antibiotic.

Thanks


texts:
It is known that many plants typically die when exposed to temperatures of 40 to 50°C (I believe, these figures relate to exposure times of ~1–2 hours). When a plant is heated, what is the mode of action at the cellular level that results in the death of the plant? What are the main mechanisms involved?

P.S. I have read that at high temperatures plants synthesize heat-shock proteins, so I am not sure if this plays a role in the death of the plant. Another obvious effect following heating is the damage/denaturation of some chlorophylls (but a plant should be able to survive the loss of some photosynthesis; e.g. detaching leaves will not kill a plant).

Any explanation is greatly appreciated.


texts: How does a tiny spider interpret/cope with gravity?

texts:
The Question:

Does a tiny spider know that it is walking on a wall or a ceiling as opposed to the (horizontal) ground? Does gravity play a role in this knowledge?

Further thoughts:

I am interested in how other organisms sense gravity, and how they are affected by it. I have read how gravity played an important role in the physical evolution of all animals, but am interested in how the animals perceive gravity, and to what extent they are aware of/affected by it.

Can you point me to any research in this area?

The following is an excerpt from work of the German Aerospace Center, showing how the orientation of a fish is guided via a mixture of gravity and light:


texts:
It seems we only found bacteria that hate oxygen. Are there any bacteria that love oxygen and would thrive in high oxygen environment?

If it slowed down or stop multiplying in low (as in normal earth atmosphere) oxygen content it would be the best.


texts: How to obtain normalised ECG given ECG readings across lead 1, 2, and 3?

texts:
I saw this youtube video on ECG readings and cardiac dipole vector locus of the heart across the three leads. Posting screenshots from it:

My question is how to obtain the graph (2nd image) from the 3 graphs in the first image? Should I simply add them or is there something more to it?

link: https://www.youtube.com/watch?v=H8jVRhQkRjg


texts: Does human eye lens have a magnification of its own?

texts:
I have always wondered if the lens in our eyes have any sort of magnification by default. And if yes, if we're actually seeing everything around us bigger/smaller than what they actually are!

Has any research been done on this?


texts: What is the status of the "Free Energy Principle" as a theory of living organisms?

texts:
The free energy principle states that biological organisms maintain their order by minimizing a function called variational free energy (VFE).
While it is the case that the minimum to VFE also minimizes Helmholtz free energy under certain assumptions, VFE is distinct from Gibbs free energy or Helmholtz free energy and is borrowed from statistics (variational Bayesian inference). It measures the degree to which the approximate posterior deviates from the exact posterior.
It has been argued that the free energy principle explains many facts about brain function. However, I would like to learn about biologists' views on the broader claims as a principle that seeks to explain all aspects of the function of living organisms. I would be grateful for direct answers and for any references that discuss this issue.


texts: bacterial cell wall degradation in humans

texts: can human degrade the D-amino acid present in bacterial cell wall, I'm confused about it i have read somewhere that human can do so.If yes than why we need antibiotic to kill bacteria???If it is not so than why??


texts: How does allele dominance work in polyploid organisms?

texts:
You know how there are tables to demonstrate allele dominance in diploids, such as the table found in this question?

Well, I was wondering how this works with tetraploids, hexaploids, octoploids, etc.

One might assume that you would need a four-dimensional table for tetraploids, a six-dimensional table for hexaploids, and an eight-dimensional table for octoploids.

One might assume that if you have an octoploid with a gene that has one dominant allele and seven recessive ones that the dominant trait would be expressed.

One might conclude that recessive traits would be expressed a lot less often in octoploids than in diploids in a population that commonly has both kinds of alleles.

Are all three of these assumptions correct? If not, what is the truth?


texts:
Is there any actual difference between inoculation and vaccination or are these terms interchangeable?

In case the difference exists, would it be correct to say that inoculation is purposefully infecting a person with a pathogen in a controlled way, even when the person is already infected, to induce immunity while vaccination is administering dead or weakened pathogens to a healthy person as a preventive measure to check future infections?

Also, would it be correct to say that vaccination is an advanced form of inoculation?


texts: What natural defence mechanism does the human body have against lead poisoning?

texts:
It is known that lead ion takes place of necessary ions, like calcium, in the body, but does not perform their task, hence wrecking the system. So how does the body eventually recognise this threat and get rid of the lead deposit in the body? And if such a natural defence mechanism exists, why is it not effective enough?

For example, is the process in which lead gets stored in the bones one of the safety mechanism of the body, so that it stays away from other delicate organs?


texts: Which poses the greater threat to ecology Global Ocean Acidification or Warming?


texts: How does the ideal free distribution work?

texts:
I have recently completed a study on Brent Goose. I found that Brent Geese occupy high quality habitat first then once this is full of geese, they fill up low quality habitat. However, there were always fewer geese in the low quality habitat.

This pattern therefore seems like a good match for the ideal free distribution…but is it?

Under the ideal free distribution, do birds fill up high quality first, then low quality habitat second?

Or do birds fill up both high and low quality habitats simultaneously, but fill up high quality at a faster rate?

Or does the ideal free distribution not make explicit the order/rate at which birds fill up high and low quality habitats?


texts: Is there an equivalent to a refresh rate for the brain and consciousness?

texts:
Computers have a clock rate that synchronizes their processors. In spite of tempting analogies, the brain is clearly not simply an organic computer. It is constantly changing, rewiring and pruning its pathways, awash in changing nutrients, hormones and other chemicals in a manner that dwarfs any computer ever built.

But is there a biological equivalent to a refresh or clock rate in the brain that organizes perception, cognition and reaction? Is there a timing signal that creates the fleeting now of our consciousness? Or are the various sensory inputs, internal processing, memory storage and accessing, cognition, and signal output only loosely coordinated?


texts: Why do doctors do chemo or transplantation for cancers that don't respond well to these treatments?

texts:
From the UpToDate article on multiple myeloma:

  In most people, chemotherapy partially controls multiple myeloma;
  rarely, chemotherapy leads to complete remission.

Also:

  Transplantation, when successful, prolongs survival, leads to a
  remission, and, infrequently, cures multiple myeloma. However,
  transplantation has several limitations. The high-dose chemotherapy
  given before transplantation usually fails to kill all of the plasma
  cells, allowing the condition to relapse after transplantation. Such
  treatment also puts the patient at risk for serious infections and
  bleeding, which can be fatal.

UpToDate is used by 700,000+ physicians worldwide; it's not alternative medicine. Thus, if even mainstream medicine recognizes the relative ineffectiveness of chemo and transplantation for multiple myeloma, why do they do it?


texts:
I had the following question on an exam of mine and I got the points for the question, but I am wondering if someone could please explain why it is correct, or rather, if it is correct at all:

  As living organisms grow, they increase in complexity and decrease in entropy. How does this relate to the second law of thermodynamics?

  (A) Living organisms, like everything else in the universe, spontaneously decrease in entropy over time.

  (B) The increase in entropy of the universe exactly balances out the decrease in entropy as the organism grows.

  (C) Energy cannot be created or destroyed, so the energy used for growth is later used to increase entropy.

  (D) The resulting increase in entropy of the universe is greater than the decrease in entropy associated with the growth.

I answered D, as it seemed like the most likely answer out of all of them, and I got the points.

According to the 2nd Law of Thermodynamics, the entropy of the universe will increase with time.

Please correct me if I am wrong, but from my understanding this only applies to closed systems--so how exactly would it apply to organisms (which are open systems)? Is it because organisms release heat through chemical reactions and thus add to the entropy of the universe while decreasing their own entropy?

Thank you!

-Aleksandr