texts:
I heard a prof. saying that when people are getting older that there aren't only fat cells getting between and around muscle cells, so that humans gets weaker and weaker, but also that fat cells can get into muscle cells.

Is this true, and how is this done?


texts: Theoretically, is domestication of (virtually) any animal possible?

texts:
Looking at ones that manage well alongside us human animals, such as dogs and cats, we see that this is possible for evolved, distant animals to have heritable, preferable traits around people. However, when especially looking at lions and the like, it doesn't seem to work out as well.

Some people have tigers as pets, but in general it is believed that they are more "wild" and not as tame and domesticated as other animals (such as dogs and cats).

Is it possible to selectively breed and enable any animal to be more like dogs and cats? Even sharks? Tigers? Alligators?

If domestication worked so well with dogs and cats, such as them living (for the most part) peacefully and well with people, wouldn't the process be beneficial for other animals so we could all live better side-by-side?

In short, can you theoretically get any animal to have heritable traits?


texts: What happens when lightning strikes us? How is it fatal?

texts: How does a person die due to lightning? Is the cause of death similar to that due to electric shock? Why do minor shocks don't show similar effects in small magnitude (like paralysis in that part)?


texts: Problems understanding membrane potential

texts:
I understand that membrane potential is the difference of the extracellular and intracellular ionic charges, due to their concentrations. We say that the extracellular space has a charge of 0 and then take the membrane potential with respect to the extracellular space. The intracellular space is normally around -60mV due to more negative charges being in the cell than the extracellular space.

This is how I understand membrane potential.

From this understanding, it is hard for me to see why I can't get this right:

We work with a regular cell with potassium 120mM inside and 4.5mM outside.

Say that we increase the intracellular concentration of potassium by 10 mM, a +1 valence ion which contributes to POSITIVE membrane potential.

What I envision is that as we put more positive ions in the cell, the cell is now more positive in regard to the extracellular matrix. However the Nernst equation states that the membrane potential actually gets MORE NEGATIVE!!
http://www.physiologyweb.com/calculators/nernst_potential_calculator.html

What is it that I am misunderstanding? Thank you.


texts: The selective pressure of contraceptives

texts:
Is it possible that the use of contraceptives will produce evolution humans? Contraceptives can reduce reproductive success, so shouldn't selection favour resistance to them?

In this case it might be useful to think of evolution as a "black box", an information processing mechanism  where only input and output is relevant. From this point of view, we would expect the box to produce an output comparable to the resistance that evolution will produce in a population experiencing a poisoning effect which seriously damages its reproduction mechanism.

The evolutionary "output" from such poisoning  has been studied in great detail. Are there any lessons relevant to future human evolution in these studies?


texts: How to mark an ant with the least disturbance to the ant and the nest

texts: How would one go about marking one or more ants in a nest so as to least disturb the ant and the nest? The goal is to be able to know which ant you marked months, or many years up to a lifespan later, while at the same time have the least influence of the markings on the behavior of the ant and the interaction between the marked and not-marked ants.


texts: How could be the concentration of airborne pathogens in a specific indoor space be measured?

texts: I wonder if it is possible to measure the concentration of airborne pathogens in a specific indoor space in order to extract a percentage value. This value would be helpful to determine specific infection control strategies that would decrease this percentage and improve the indoor air quality.


texts: Are recessive, deleterious alleles less common on the X chromosome than the autosomes in humans?

texts: As there is a potential for them to be more readily purged in hemizygous males (and in cell lineages in females with the deleterious-allele-bearing chromosome activated), I would expect the frequency of deleterious alleles to be lower on this chromosome than in autosomes. Is this information known?


texts: What is the role of the tissue surrounding neurons in decision making and taking control of impulses?

texts: How does the fatty tissue surrounding neurons supports and enhances the speed of electrical impulses? How does it stabilize connections that take control of impulses and decision-making? The cells surrounding the neurons in this case being either glial cells (neuroglia) which provide support and protection for neurons in the central nervous system and peripheral nervous system, or myelin an insulating sheath around many of the nerve fibers consisting of proteins and phospholipids.


texts: I'm looking for an inducer that strongly activates the androgen receptor, but not the glucocorticoid receptor that is not DEA regulated. I know that SARMS (Selective Androgen Receptor Modulators) are something of a hot topic in some corners of some fields, but I'm having some trouble in my laboratory finding one. My research necessitates the independent induction of AR (Androgen Receptor). Does anyone know how to go about this search or know of some chemical?


texts: Protein structure prediction using PSSM? Or not?

texts:
I have been studying protein structure prediction algorithms. A lot of recent work uses something called the PSSM, the position-specific scoring matrix.

I think that what a PSSM does is to build a 2-D matrix of all possible residue pairs in a protein, then scores how likely it is that the two residues mutate in tandem. Co-evolution of two positions which are far from each other in the primary sequence are an indication that they are in contact. When one residue in a contact pair changes, that generally destabilizes the protein, and the other residue in the pair is under selective pressure to compensate. Knowing this gives you a good start on building the protein contact map.

Do I have that right?

If that is correct, then this technique of protein structure prediction depends on having many examples of proteins in a homologous family. You need nature to do a lot of sampling for you. And you need to dredge up massive numbers of homologs from genomics projects. I've read that creating the multiple sequence alignments for PSSM work is computationally intensive. If I understand the process correctly, I can see why.

My main question is: what can protein structure prediction models built using PSSM do, when there isn't a PSSM?

For example, the Top7 protein is a fully-novel protein fold that does not have any homologs in nature. It was created in 2003 using RosettaDesign software. Rosetta's protein structure prediction algorithms predate PSSM as far as I know. Sixteen years later, there are exactly six variants of Top7, all of which have been made in the laboratory. That hardly sounds like enough data for a statistically-valid PSSM, and in any case, the variants were not naturally selected.

If you don't have a PSSM, is it even possible to enter your sequence into a model that expects one?

Thanks for your input.


texts: Minor differences in morphology of a snake: Why designate it a different species?

texts:
I was motivated to ask based on an answer to another question that I read on SE-Biology:

  You can differentiate this species [Ashok's Bronzeback (Dendrelaphis
  ashoki)] from closely related D. girii based on it having a longer
  "postocular" black line than D. ashoki -- in D. ashoki it stops
  shortly caudal to the eye...

When the differences are so minor (e.g. "longer "postocular" black line") what's the reason for designating them as two different species?

Is there a objective reason when to call them different species? Would those two not interbreed?

Note: I'm not just asking "If they interbreed why is it a different species?"

I'm more in the vein of asking: "If two species so similar are still different species why are they different? Is there an objective metric to draw the line at which point we differentiate as different species."

Edit:

I've asked a related question over here:

Can Eskimos be regarded a distinct species from Kalahari Bushmen based on morphological differences & geographic isolation?


texts: Why Doesn’t Hypercalcemia Cause Muscle Spasms?

texts: If you have more calcium in the cell, wouldn’t more attach to troponin and initiate muscle contraction? Why does hypercalcemia cause muscle weakness instead of spasms?


texts: What forms this pad on the side of the face?

texts:
I've been trying to figure out this for the best portion of this morning, but what structures are responsible for the pad highlighted in red? (sorry for low quality of picture, was just watching the show at the time)

It's from my understanding that the zygomatic (in green) runs to the edge of the ear in a relative straight line and most muscles have their origins or insertions bellow it. I know there are some fat pads (such as the nasolabial fold in purple) on top of everything on the face, but are these all fat pads that just allign? I've seen this pad on both man and women often, although it seems more proeminent in women.


texts: How does reversibility of lactic acid fermentation work?

texts:
For the production of lactic acid we need pyruvate from glycolysis.
This process is known as lactic acid fermentation. One of the features of this process is reversibility. How does this reversibility work?


texts: Why does the proportion of transposable elements vary so much across species?

texts:
Intuitively, transposable elements (TEs) are harmful as they may cause genome instability. However, some people argue that TEs are also sources of variations, especially regulatory sequences[1].

If TEs are harmful, then their proportions may be low in most species. And if they are beneficial, then their proportions should be high. Either case leads to the conclusion that their proportions should stay close to each other. However, the fact is that the proportion varies greatly across different species:

Maize: 85% [2]
Human: 45% [3]
Arabidopsis: 10% [4]
Plasmodium: absent [5]

Why is that? Is there other factors that influences the proportion of TE, such as evolutionary pressure?

Reference

[1] Rita R, et al. 2012. Transposable elements: an abundunt and natural source of regulatory sequences for host genes. Annu. Rev. Genet 46:21-42
[2] Schnable PS, et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112-15
[3] International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921
[4] Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
[5] Biemont C, Vieira C. 2006. Genetics: junk DNA as an evolutionary force. Nature 443:521-24


texts: Can other animals see black differently?

texts:
I am not sure if this is the right place for this question, but this is a debate that has been going on between two colleagues for days and I need a resolution because it's driving me crazy. So any help would be appreciated.

It is a common philosophical argument that it is impossible for one person to know if another person is at the same place on the colour wheel (e.g. how I see blue and how you see blue could be different, and we will never know). By that reasoning, it is possible that some species see colours differently to us. However, black and white are not the colour wheel because they are not colours. So essentially, the question is, could another species that "sees" by sensing light with their eyes as humans do ever see an "absence of light" as a colour OTHER than black.

I am not quite sure what these two imbeciles are debating, but I believe they are arguing as follows:

Party 1: Black and white are shades not colours, and therefore, even if another species saw colours differently, they would always see black as black, white as white, and all shades of grey relative as usual to the colours they see.
Party 2: Black is only inserted into our vision by our brain to resolve the "problem" of not receiving any light. So, therefore, it is equally possible that another species could deal with this problem" differently, and they will see something other than black.


texts: Difference between bacteria and bacteroids?

texts: During nodule formation Rhizobium is converted to bacteroids. What's the difference between them?


texts: What evolutionary explanations are there for death?

texts:
I know death and cancer doesn't hurt humans' reproductive success. It's not helping either.

Why do we die? Why dying humans (all of us) are common? What's the point of dying?


texts: Ribosomes producing proteins, but need proteins to be produced?

texts:
So according to my textbook:

  RNA is used to create ribosomal RNA (known as rRNA) which is then combined with proteins to form the ribomsomes necessary for protein synthesis.

I'm a bit confused with this statement, as ribosomes are needed to synthesise proteins, but in order to create ribosomes proteins are needed in the first place. How does this work, does the proteins needed for the creation of rRNA come from a different source? Or by synthesising proteins via ribosomes produce more proteins than required to create the ribosomes in the first place?

Also, where are the proteins synthesised? On cytoplasmic ribosomes, or on ribosomes bound to the RER?

Thanks!


texts: What is this insect seen in Northern Italy?

texts:
I am from Northern Italy, close to the border with Slovenia.

I saw this thing today on the window, and was sure it was a piece of a dry rosmarine branch carried there by the wind - until it started to move.

It looks like a cocoon of some kind, on the top of it there is an opening from which a head of something like a caterpillar comes out, sometimes together with some portion of its body with two (?) tiny legs on each of its body "segments". But I imagined cocoons as something attached to a branch, not moving.. While this thing moved from one point of the window to another, always attached to the window (not using what I think are the caterpillar's legs). (I must admit I am reluctant to open the window and examine it from a closer range :) ; the photograph is taken from inside the house).

What can this insect be? (the length is around 4-5 cm)


texts: What is this red liquid produced by a fungal colony?

texts:
In a jar, where I had some orchid plants, a fungi start growing few days ago. I removed the plants and let the fungi to expand and grow more.  After some days, red drops started to appear on the surface of the fungal body (images below).

Does anyone know what this probably can be or recognize the fungi? Is it an antibiotic or something else?


texts: Why is blood pressure higher the more distal an artery is?

texts: Why is blood pressure generally higher in more distal arteries?


texts:
There are many poisonous fungi in nature. For example Amanita Phalloides.
What reasons could a fungus need poison for? Some species, like venomous snakes, use poison to kill other species as prey. But what about fungi? I can't think of any purpose for poison in fungi. If poison has no real function in fungi shouldn't evolution get rid of it?


texts: Optimizing Gel Electrophoresis: Ampere, Volts and Buffer concentrations

texts:
I am a master student in biochemistry, and I have used gel electrophoresis many times before. What I want to know is how one should adjust the mA (mAmpere) compared to the voltage and the buffer one uses.

Normally I used 1xTAE buffer (run at 90V) or 1x sodium borate buffer (run at 110V). I know that if I adjust the voltage up, the buffer heats up faster, the samples travel faster, but the "picture" of the gel becomes more blurry. This is however all I know about adjust the parameter.

So my questions can be summarized as the following:

How should I adjust the ampere, is there a range I should be in
compared to the buffer or sample I am running?
Does the ampere effect the travel speed if adjusted up or down?
Can I adjust the concentration of the buffer to run sample at a
higher voltage, what effects will this have (to increase or decrease
concentration)?
Is there a relationship between the ampere and the voltage which I
can manipulate, in this case: how and why?


texts: There are reactions with large Delta G negative values. Why these reactions are irreversible? As in: out of 10 steps of Glycolysis, 3 are irreversible steps. I need an explanation for why they are irreversible.


texts: Is it possible to have undamaged healthy cell, that is dead?

texts:
I am trying to clarify my understanding of how unicellular organisms are alive, given my existing background (computational modelling, unrelated to biology). During my thoughts on subject I have came to a conclusion that any unicellular organism, given it's undamaged, and has enough resources (so it does not undergo autolysis), must be always alive.

Is my conclusion true? In other words, is it possible to have completely undamaged cell that appears healthy, but yet is dead? And by "dead cell" I mean a cell that does not move, does not consume any resources, does not respond to any external stimulus an alive cell would respond to, does not divide, etc.


texts: How many abdominal sclerites would be there in a cockroach?

texts:
Every tegmina of a cockroach has sclerites which are analogous to the bones of humans.

Every abdominal segment of cockroach consists of two lateral sclerite plates called pleura along with a dorsal terga and a ventral sterna. But what will be the case with the last body segment where 10th sternum is absent?

I mean will, there be any pleuron in the tenth segment because, following our textbook, pleura serve for articulation among sterna and terga and also spiracles are present in the first eight abdominal segments but the 10th sternum is absent in Periplaneta americana.

Actually there is no evidence of the presence of any pleurons in the last segment in our text book.

Moreover, there are no abdominal spiracles in the 9th and 10th segments so there is no particular reason to say that pleura are present in the 9th and 10th segments as well.


texts: Can someone help me to identify what kind of pear is this?

texts:
I went to my local groceries supermarket (in Lima, Peru) and found this cheerful looking pear named locally as "pera canela". But I found it weird as the only variety which I'm aware of is Packham's pears. I tried to do some research on different cultivars and species known of pears. So far the only ones which I found were in this wikipedia's entry but it didn't help me much.

Below is a set of pictures I took of the pear referred to as "pera canela"

Figure 1. Picture of packed Pera canela, the printed label shows its local name.

Figure 2. Picture of Pera canela's as they are on a basket in groceries stand. Seen in the background.

Figure 3. Picture of Pera canela seen closer for identification.

I've tasted it and it is a little bit more sweeter than the Packham's variety, on the juicier factor I would say that it is pretty much the same as Packham's

So far by comparing it with different entries on Wikipedia. I'm not very sure if it's a local name given to either Abate fetel or perhaps to Bosc
 varieties, or could it be a D'Anjou?

Since I'm not good at identifying plants, can somebody help me identify which kind of pear it is? It would also greatly help me if the answer could include its scientific name so I could do more research into it.


texts: Is there variation of AT/CG ratio along species?

texts:
Chargaff's rules say that the number of Adenine of the number of Thymine in a genome are equal (nA=nT) and similarly nC=nG. This makes obvious sense knowing that C binds to G and A to T.

But what about the ratio $\frac{nA+nT}{nC+nG}$?

Is there variation along species of this ratio that is higher than expected by random processes? If yes, what causes this variation?


texts: What is the difference between effective and efficient selection?

texts:
I always thought of the efficiency of natural selection in the context of molecular evolution. I.e. that linked selection and smaller population size cause less efficient selection. It took me a while before I even noticed that people also say the efficacy of selection.
When researching the answer myself, I found that older papers talk more often about efficacy (like this one). I also found that besides the natural-selection context, it seems efficiency of selection is also used in the context of breeding (like here). However, you can certainly find cases when used in the context of natural selection. Finally, there are about 4x more papers that contain the words "efficiency" and "natural selection" compared to "efficacy" and "natural selection".
So, is effective and efficient natural selection the same thing? Is "efficacy of selection" and "efficiency of selection" be used interchangeably?
-- EDIT --
I am interested in the use of these two words in the context of natural selection only. Unlike in other contexts, in natural selection dictionary definitions of the two words do not make much sense.


texts: Aside from Homo Sapiens, do the males of any other species care for the offspring of those unrelated to them?

texts: Elsewhere I heard that male Long-tailed Tits will care the offspring of their brother if they're unable to have their own. However, I'd like to know if there is a case of such behavior where the two are unrelated to one another.


texts: semantic similarity measurement for cell line ontologies

texts:
I have a set of cell line pairs and I want to know to what extent the pairs are similar based on their ontologies.
The problem I have is that I have found a Python library called Fastsemsim, but it has many similarity measurements. Or to be exact, there are actually many ontology similarity measurements. And I want to know which similarity measurement is best suited for my case (cell line ontologies similarities). There might be a couple of good ones that are good for cells ontologies.
These are a set of similarity measurements that are available in Fastsemsim.

Semantic Similarity

SemSim.TermSemSim
SemSim.ObjSemSim
SemSim.ObjSetSemSim
SemSim.SetSemSim
Specific Semantic Similarity measures
SemSim.MixSemSim
SemSim.avgSemSim
SemSim.maxSemSim
SemSim.BMASemSim
SemSim.SemSimUtils

Source:
https://fastsemsim.readthedocs.io/en/latest/library.html


texts:
Some yeast cells have very low mitochondria copy number (see number of mitochondria in non budding cell, you can count mtDNA). This makes them susceptible to fluctuations, and one can conceive that some yeast cells might arise entirely without mitochondria. Would they survive? Could they reproduce?

Please, assume they have all the nutrients required, in particular excess glucose to ferment, so mitochondrial energy output is dispensable.

If you could point me to some references that would be awesome.


texts: Have there been carbon fixation pathways of, in particular, oxygen-producing bacteria, that have been replicated in the lab or at least the enzymes for the pathways have been successfully produced in the lab?


texts:
Hinz et al. 2008 found that COX-2 may be inhibited by paracetamol, and this is attributed to it's analgesic and antipyretic properties. However, there are other more recent claims from Andersson et al., 2011 that a toxic intermediate metabolite, NAPQI, may be acting on TRPA1-receptors in the spinal cord. Whilst I'm vaguely aware that the end goal is to affect prostaglandins, to me at least it remains unclear how that translates to painkilling.

There are also other theories I would imagine.

This exceedingly common drug seems shrouded in mystery. I know very little about pharmacology (evidently!), so some expert insight into the popular theories, and why they're popular, would be greatly appreciated.

What are the most popular theories in a nutshell?

Why are they a popular theory?
Which protein is targeted?
How does that inhibition introduce the analgesic and antipyretic properties?

Is it possible multiple theories are correct?
Why is so little known about paracetamol? Is it exceptionally difficult, or the norm in pharmaceutical research of relatively old effective drugs? If it ain't broken, why fix it!


texts: Genetic variation and sensitivity of wild cabbage

texts:
1: Is it true that the genetic variation of kale plants is smaller
  than wild cabbage?

I think so, because of human selection of the kale plants.

  2: Are broccoli and cauliflower more sensitive to changing
  environmental conditions than wild cabbage?

I think so, because domesticated crops have a lower genetic diversity than wild varieties. Genetic diversity is useful for adaptation

  3: Is it a good recommendation to grow new Sprout plants from the
  seed of wild cabbage plants?

I don't think this is the best idea, because genetically engineered Sprout plants could be much better.


texts: Is there benefit of use of red light over dim white light when interacting with rodents in the dark phase?

texts: I've come across some "percieved wisdom" that rats and mice do not "see" red visible light and so use of this wavelength will allow humans to interact with rats in their active nocturnal phase without affecting their circadian rhythms.  Having gone to read the evidence for myself of this I can see evidence that red visible light does indeed impact rodent circadian rhythm (Dauchy et al J Am Assoc Lab Anim Sci. 2015 Jan; 54(1): 40–50) so is not a "fix" to allow us to see without the rodent being impacted.  What I cannot see is if there is any "benefit" to use of red vs white light if it has to be used or whether it just has the same impact and the only negative is the human can see less!!!!  Can anyone help ?


texts: What is the ratio of head to waist and waist to floor of the human anatomy?

texts:
I'm trying to find the ratio of upper body to lower body. That is, the ratio of the length of the waist to the head over the length of the waist to the floor.

It's been harder to track down a readable outline of the ratios of the human body than I expected.


texts: Is a female spider, well-fed by sexual cannibalism, less likely to mate again?

texts:
The Wikipedia page on sexual cannibalism (e.g. female spiders eating their mates) currently has a statement that sounds wrong to me, but I don't feel expert enough to edit it out:

  An additional benefit to cannibalization is the idea that a well-fed female is less likely to mate again.

I can't see why that would be the case. Why not continue to seek a second, better, mate? Unless perhaps being well-fed makes you a slower, larger target for predators, so hiding for a while is a better tactic.

The reference given is to

  Female hunger can explain variation in cannibalistic behavior despite male sacrifice in redback spiders. 9, 33–42 (1988)

A bit of searching suggests the author meant to include Behaviour Ecology as the journal name. I've only read the abstract, but it does not seem to support the statement. It suggests a well-fed female is less likely to consume her mate, which seems intuitive.

Am I right that this Wikipedia sentence is incorrect? If I am wrong, is there an explanation for the effect that I am missing?


texts: What is the difference between hsa-miR-33a and hsa-miR-33b?

texts:
Does anyone know what is the difference between two miRNAs like hsa-miR-33a and hsa-miR-33b? The last letter in them shows what?

Also, if we know that hsa-miR-33a targets gene A, can we say that hsa-miR-33b targets gene A, too? or can we say that it is much probable that hsa-miR-33b targets gene A since hsa-miR-33a targets A?


texts: Questions about scientific method in neuroscience

texts: In what ways does intuition from subjective experience guide topic choice in neuroscience? How important is it to frame research questions quantitatively? Can our own beliefs about how we think bias what topics are studied in neuroscience?


texts:
If I represent DNA as binary values, what is the best way of computing distance between them.

So :
A = 00,
T = 11,
G = 01 and
C = 10

Hamming Distance between ATGC and TAAC is 3, however their binary representations give a different answer:

Hamming Distance of 00110110 and 11000010 = 5.

Whats the best way of distance computation if the DNA bases are represented in this way?


texts:
Fish are often plagued by external parasites, which are presumably difficult for them to remove.

There are well known cases where large fish come to coral reefs and allow smaller fish to pick off their parasites. See below a moray eel being "cleaned" by a shrimp.

Some fish, like sunfish, even get cleaned up by birds: https://www.youtube.com/watch?v=U60obmWODLQ

But on land, we have many social animals that solve this problem more directly by grooming each other. How come the fish never seem to do this? Many of them are already social, and I imagine they wouldn't have much trouble digesting the external parasites. Why don't they groom each other?


texts:
Why are sponges not considered to have tissue level organization?
Quite a few places seem to say that sponges do not have 'true tissue' and only have specialized cells.

Unlike Protozoans, the Poriferans are multicellular. However, unlike higher metazoans, the cells that make up a sponge are not organized into tissues. Therefore, sponges lack true tissues and organs;

The Wikipedia page on sponges says -

Sponges are similar to other animals in that they are multicellular, heterotrophic, lack cell walls and produce sperm cells. Unlike other animals, they lack true tissues and organs.

I have not been able to find what defines true tissue, so I would like to understand what characteristics a group of cells must have for it to be considered proper tissue.


texts: Is it possible to trace of the ancestry of a person by only using his/her genetic information?

texts: Is it possible to trace the descent of a person only using his/her genome sequence?


texts: How to biologically interpret path weight summation in weighted and directed gene regulation network?

texts:
I've considered asking this question on Bioinformatics SE, Mathematics SE, and Stats SE, however I've judged that my question belongs on Biology SE because I am interested in a biological (domain-specific) interpretation rather than a further development of the mathematics or software.

My question pertains to applying graph theory to biology, so first I will describe the graph in its mathematical properties and how they reflect biological properties.

The graph

Let's consider a weighted and directed graph whose nodes represent genes and whose edges represent the binary relation gene A regulates gene B. The directionality of the edges is imposed in order to reflect that gene A regulates gene B does not imply that gene B regulates gene A. The magnitudes of the weights are to represent some measure of how "strongly"  one gene is regulating another, and the signs of the weights are to represent whether the regulation is upregulation (positive) or downregulation (negative). For this graph, edges with a weight of zero are considered equivalent to 'no regulation' and should be excluded from the graph.

Path Analysis

Restricting ourselves to paths that do not visit the same node twice, what is the biological interpretation of the sum of the weights (of the edges) of a path between two nodes in the aforementioned graph?

I have conflicting intuitions. For example, why would these weights be additive? I'm not imposing that such weights have to be correlation coefficients, for example, but they are commonly used weights in networks that are not additive so it warrants some consideration in the more general case. If they're not additive, then their summation is not necessarily meaningful. Conditioned on being meaningful in the first place, my other inuition is that the meaning of such a summation would reflect the strength of 'indirect' regulation


texts: How do burrowing animals get enough oxygen?

texts:
Tree borers make a small hole in a tree. At the end of it, they chew on wood to elongate the tunnel. They digest food and grow. All this takes oxygen.
The entrance to the tunnel is generally small. Some borers plug the entrance. Even without that, air circulation must be non-existent. How do they breathe?
It just seems off hand that tree borers might be an extreme case. But I have the same question about all kinds of burrows. How do worms do it? Rodents? Ants?
Do burrowers have any special behaviors or adaptations to help them cope?

Thank you all for your answers and comments. But I suspect there is more to it than that. I doubt enough oxygen diffuses down the length of the burrow to keep an insect alive under bark.
A tree died in my yard recently. The bark now comes off easily. When a tree is stressed or diseased, insect often attack. They finish off the tree if the original problem doesn't. Clearly that has happened here. They have eaten almost the entire layer under the bark. No wonder the bark is peeling off. There is almost nothing left of the wood it was attached to.

Most of the burrows are long and narrow. The insects carefully leave a small strip of wood between adjacent tunnels.
Here is a close up of two burrows from the bottom of the previous picture. It was taken before I pulled off all the bark. You can see they started at the bottom, and grew as they climbed.

Here is the bark that covered the burrows. When insects chew the wood, the wood does not disappear. At the bottom you can see a portion of the sawdust that packed the burrow. Most of it fell out when I peeled off the bark. I have seen other pieces of bark where it clearly filled the entire burrow.
At the top, you can see the holes where they dug out.

Now that the tree is dead, the bark is falling off. But it wasn't when they started. Trees do not make it easy for insects to eat them. I expect the bark was well attached. I doubt it was porous enough for air to penetrate. I doubt there was damage, such as the long crack you can see along one burrow.
Sometimes wood can be surprisingly porous. You can literally blow smoke lengthwise through a plank of red oak. But that is cut and dried wood. Live wood is full of sap.
I expect that insects do not make holes in the tunnel. They make it hard for predators to get it.
And yet enough oxygen does get in.

A year later, I still think about this off and on. While having a small mass reduces oxygen needs, oxygen is needed to chew a tunnel in wood and grow. I cannot believe that enough oxygen diffuses down a long narrow tunnel packed solid with sawdust.
Here is a photo from when I burned a log from the tree. You can see the surface is covered with burrows. There are also holes into the interior.

Here I have split the log. You can see the holes continue deep into the tree and lead to chambers. These burrows are almost entirely free of sawdust.

Here is a detail view.

I expect they are kept clear because insects need to crawl down them. One reason would be they need air.
Yet the surface burrows are packed. It seems likely an insect that can chew tunnels in wood can poke holes in bark. Does anyone know if they do this?
One last thought. I heat my home with wood. When I carry firewood home, I store it under this tree. People tell me you can transport insects in firewood...


texts: What's the purpose of Cdk activity having more than one method of becoming inactive?

texts:
Cdk becomes partially active once its bound to cyclin and then gets phosphorylated and fully active once a Cdk-activating kinase (CAK) phosphorylates the partially active Cdk. This fully activated Cdk complex can be inactivated through a Wee1 kinase which phosphorylated the Cdk at a different site or through the binding of a Cdk Inhibitor protein (CKI).

Why would the cell need more than one way to inactivated this complex? Are there two methods in case one of them should "fail?" (i.e. the kinase not phosphorylate the Cdk complex in the proper spot) or is there some alternative reason?


texts: What is the difference between transport proteins and effector proteins in gram-negative bacteria?

texts: When considering pathogenic gram-negative bacteria, is there any difference between the function of  transport proteins and effector proteins? Or are they of the same functionality? Any reference would be very helpful.


texts: Molarity of phosphate in intracellular phosphate buffer system

texts: Phosphate buffer system keeps intracellular pH near the pKa of the $\ce{H2PO4^- <=> HPO4^2-}$ equilibrium, pH 7.2. Most intracellular phosphate is bound up in larger molecules like phospholipids, nucleic acid, ATP, neither of which have a pKa suitable for buffering. How much free phosphate is left to actually buffer in the cell (in moles per litre)?


texts: Does dormant poison ivy contain urushiol in the above-ground portion of the plant?

texts:
I recently had a run-in with poison ivy (late spring; Canadian shield).

The poison ivy plants had not yet leafed-out so I failed to identify them as a hazard.

I think I must have either trampled and broken the stems of the plants, or dug up and broke the roots (or both), and therefore was exposed to the poisonous sap.
While the plants had not leafed-out, they were also not truly dormant (it wasn't the middle of winter).

Question:

I'm wondering if there is a time of year when the above-ground portion of poison ivy plants would not contain urushiol.

In other words, in the dead of winter, when the plants are dormant, do poison ivy twigs contain the poisonous sap?


texts: What is a Archival Tumor Tissue ? For What Purpose is it collected?

texts:
Over the course of Conducting trials various tissue and tumor samples are collected  from the patients.

One such sample is the Archival Tumor Tissue.
Could someone kindly clarify what is the meaning of the term archival tumor?, and what data is gleaned from it.


texts: Parasite? or a possible home infestation?

texts:
I found this bug on my bed tonight.  It's smaller than a sesame seed. 6 legs and 2 antenna.

Is this causing my dog and I to itch? Should I be concerned?


texts: What are the consequences of inbreeding?

texts: Inbreeding increases the risk of getting two identical recessive genes, alleles, that cause a disease which wouldn't have been activated with mixed genes. That's how I understand it anyway. But I sometimes read and hear that inbreeding among humans also causes decreased intelligence, especially emotional and social intelligence. Is there any support for such claims, and if so how does that work?


texts:
There are several answers and articles about how the brain stores data, but none specifically cover whether a human's brain stores duplicate data.

I was reading in this article that a human brain can have a capacity of 1 terabyte to 2.5 petabytes. But for example, if you read a book a dozen of times, will it be stored as data several times?

Let me put it this way. When we read a book a couple of times, we remember it better. Is that because it's stored in several synapses and then retrieved better while trying to remember, or is it because reading it over and over makes the missing parts be stored?

We do recognize a familiar phrase when reading a book, which means the brain can differentiate the unknown from known. What matters is that does it decide to store it again or not? Just like a computer who refuses to save a file if the file already exists.


texts: Does Krebs cycle occur in fast glycolytic muscle fibres?

texts:
They have mitochondria. So they can have aerobic respiration. (?)
Does Krebs cycle occur in their mitochondria?


texts:
I'm trying to couple the following terms:
cytoplasmic determinants, induction, positional information, hox genes, pattern information, morphogenisis, determination and differentiation.

I hope someone can explain me the connection between these terms,

thankyou,


texts: Phosphorylation alters structure: Specific Example?

texts:
Why does phosphorylation activate an enzyme?

A common answer to this question is that the introduced phosphate group "alters the structure" of the enzyme.

Can somebody point out a specific example of such an alteration? I.e. like a "before/after" illustration?

Or is the whole mechanism of activation still largely uncharacterized?


texts: Why do the vines change their spinning direction?

texts:
Look at the vines holding onto the lattice. The "vine springs" change their spinning direction in the middle. Why? And how do they achieve this?

(By the way, what's the name for this plant? Is is correct to call these "springs" vines?)

Edit: I notice that some vines fail to get in touch with the lattice, in such case they still change direction.


texts: Is cancer a defect of the immune system?

texts: Is cancer due to a defect in the immune system?


texts:
A high school class has analyzed plasmids by the help of restriction enzymes and electrophoresis.

The class got delivered two different plasmids, pBR 322 and pC 508. These two plasmids were going to be clipped by EcoR I and Hind III.

Figure 1 shows the two plasmids with specification of the two cutting points for EcoR I and Hind III.

Furthermore, the cutting points are also shown for the enzyme Pst I.

In figure 2 you can see the result of the restriction analysis.

Questions:

1) Analyze and explain the results in figure 2

2)  What DNA-pieces would be formed if you had clipped with Pst I ?

1) You can see that the figure is showing the result of the restriction-analyzis. As for the plasmid pBR 322, you see that the result of the cutting of Hind III and EcoR I, is that both enzymes have the same size. Figure one shows that Hind III cuts over 0 bases and EcoR I cuts at 0 bases.

In pC508 you see that both enzymes have cut two times. EcoR I have cut at 1200 and 5800 bases, which you can see on figure 1. You can see the result of this in figure 2 (the gel electrophoresis). Hind III cuts at 6400 and 1200 bases, which again is an explanation as why the DNA-molecyles (figure 2) have different size.

2) If Pst I was used instead on the plasmid pBR 322, you would get the same size as Eco and Hind, because they all cut one place. If you had cut in pC508 you would get the bases 4800 and 6700 (as figure 1 shows)

Are these questions correctly answered?


texts:
I liked the question about F' and R plasmids.

What is a good resource that describes what is known about the functions and diversity of plasmids in the wild? Prokaryotes or eukaryotes?

Wikipedia points to five kinds of plasmids (fertility (F), resistance (R), col plasmids (offensive genes that let a bacteria kill other bacteria), degradative function plasmids, and virulence plasmids). There is a brief section on yeast/euk plasmids too. It seems like plasmids could actually convey nearly any gene. Restriction enzymes are found mostly on plasmids and they would seem to be defensive - maybe those are degradative.

Are there references that are more detailed and nuanced?


texts: At what point do scientists consider something sentient vs random and/or genetic?

texts:
When I was thinking about sentience from a scientific point of view, I was confused about the bio-electric mental difference between a paramecium, dog, human, and supercomputer.

At what point does electricity go from being random and genetic to creating logic gates for perceived "sentience" / intelligence?


texts: What is the big plant with white flowers on the photo?

texts:
What is the 3m tall plant with white flower? It is from Central Europe and there is a creek near to it. I have a guess, but I want to know for sure...

Is the small one the same species?

More high res photos here:

https://ibb.co/cAaUMU
https://ibb.co/ih4Zo9
https://ibb.co/eJSyFp
https://ibb.co/gstS89
https://ibb.co/kQ2OWU


texts: How do we know that dinosaurs were related to lizards and/or birds?

texts: Do we clearly know what the living closest relative of the dinosaurs are? And connected to the first question, in scientific manner how do we know these relationship between extinct species and living ones?


texts: How do I identify the different stages of meiosis under microscope?

texts:
This is a question I'm troubled with as my exams are knocking at the door. I need help so I decided to post this here.

Here's what I know and understand about meiotic stages:

Specimen: Grasshopper (Gesonula punctifrons) testis whose 2n= 23

Note: The character in bold and italics is the identifying feature of the concerned stage.

Prophase:

Leptotene

The uncondensed chromosomes are visible as a cloud of thin threads.
Each chromosome consist of two chromatids which are not visible.
The single darkly stained X chromosome is found at the periphery of the nucleus.
Late in this stage the chromosomes attach themselves by telomeres to the inner membrane of the nuclear envelope forming a bouquet.
Nuceolus and nuclear membrane are present.(not visible under compound
microscope)

Zygotene

The uncondensed chromosomes are visible as a cloud of threads.
Homologous chromosomes undergo synapsis  forming bivalent.
The single darkly stained X chromosome is present slightly off the periphery of the nucleus.
Nucleolus and nuclear membrane are present.(not visible)

Pachytene

The chromosomes show some degree of condensation.
The sister chromatids separate to form tetrad a structure with four chromatids.
Crossing over between non sister chromatids of homologous chromosomes occur leading to formation of X shaped chiasmata.
Nucleolus and nuclear membrane are present.(not visible)

Diplotene

The chromosomes are thick and darkly stained.
The chromosomes are wooly in appearance.
The paired chromosomes separate from each other except for the chiasmata.
Nucleolus and nuclear membrane begin to diappear.(can't be detected)

Diakinesis

The chromosomes are thick and darkly stained.
Terminalisation of chiasmata initiates.
The bivalents appear rod, diamond or oval shaped.
The nucleus and nuclear membrane disappear completely.

Metaphase-I

The chromosomes are thick and darkly stained.
Presence of twelve chromosomal elements (11 tetrad + X chromosome).
The chromosomes are aligned at the equitorial plate.
Terminalisation of chiasmata completes.

Anaphase-I

Two groups of chromosome are in the act of separation.
One group is with 11 autosomes and the other group with 11 autosomes and a X chromosome.
The chromosomes are T or V shaped.
Each chromosome is in dyad state.
The centromere is undivided.

Metaphase-II

There is 11-12 dyads present.
The chromosomes are thick and darkly stained.
The dyads are arranged in circle or flower like fashion.
The chromosomes are rod like

Anaphase-II

The sister chromatids of a dyad separate due to splitting of centromere.
Two groups of chromosome are in the act of separation.
One group is with 11 autosomes and the other group with 11 autosomes and a X chromosome.
The chromosomes are rod like

Here's an image which has nearly all the stages except telophase.Can someone label the stages?

Here's what I feel about them:

Finally am I correct? How do I identify them correctly? Could you site some authentic references?


texts: Plants without bacteria? is it theoretically possible?

texts:
I know from school, that all live on the Earth need bacteria as low-level "machines" that break down/extract/convert/produce chemical elements and combinations, other high-level organisms needed. But it is a natural way.

But is it possible to have a world with plants (without mammals or microorganisms and without bacteria) that could exist in the long term. Saying the atmosphere of these world has already enough nitrogen, oxygen and CO2, and of course there is water.

What could break this artificially created world with such conditions (say the world created not from low-level living structures)?
Could bacteria emerge in the world?


texts:
As far as I know, DNA is the construction protocol of all organisms on Earth.

Does it change when influenced by time and environment (physical laws)?

As parents with schizophrenia are more likely to have children with schizophrenia and an individual with no genetic predisposition for schizophrenia can suffer from such a condition because of drug abuse or environmental influence, does this prove that human DNA is changing during our lifespan?


texts: Is 7-nitroindazole neuroprotective against meth because it oxidizes peroxynitrate?

texts:
So 7-nitroindazole (7-NI) prevents methamphetamine (METH) induced neurotoxicity AND completely prevents meth induced dopamine depletion, but doesn't prevent meth induced hyperthermia. Strangely, a different study said that its possibly because of 7-NID's ability to prevent hyperthermia, (however it is important to note that this study did not test body temperature), yet all the other studies say the opposite, that 7-NI doesn't prevent meth induced hyperthermia.

Keep in mind that colder enviromental tempratures significantly attenuated METH-induced neurotoxicity

Could the reason as to why 7-NI prevents METH induced neurotoxicity and dopamine depletion simply be because it oxidizes dopamine oxidizer peroxynitrite noting that non-meth induced hyperthermia also cause neurotoxicity and produces peroxynitrite while showing the same neurotoxicity markers as METH induced neurotoxicity such as nitrotyrosine?


texts: Can anyone tell me what tree does this leaf belong to?

texts: I found a lovely tree in my friends yard and we do not have a clue what tree is it. The leaf texture is a but like the ginko biloba, but the shape is different. Can anyone identify it? (It's in Romania, Eastern Europe, but I suspect it's not a local tree)


texts: Isotretinoin and retinoid receptors in brain confusion?

texts:
I am considering starting a treatment with Accutane(Isotretinoin), however I am not sure about what the effects on the brain are. Here are two studies that contradict each other:

http://www.ncbi.nlm.nih.gov/pubmed/11696672
The first one states that using an antagonist, they increased the rats' working memory. So logically, using the agonist (isotretinoin), it would cause a loss of working memory?

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360864/
Here they state that not only did isotretinoin not have negative effects, but it actually had positive effects.

I am more inclined to believe that it has negative effects, because most anecdotal evidence says that it makes patients feel "foggy" and "forgetful". Can anyone please enlighten me? What exacly does this stuff do to the brain and is it irreversible?


texts: Any examples of an organism's life cycle where the reproductive stage occur before the 'adult' stage?

texts:
Most life cycles we knew of consist of a juvenile stage (e.g. larval for insects, sporozoite for some intracellular parasites), a reproductive stage and an adult stage. Usually the reproductive stage occur when the organism reached the adult stage.

But are their examples of organisms where its natural life cycle involve reproduction at an early stage, and then the parent then went through more distinctive stages after the reproductive stage and then dies off? For example:

The closest thing I can think of is the life cycle of mayflies, which dies a short period after the mating stage. But mayflies has only one adult stage thus it is does not really answer the question


texts: Why aren't mitochondria and plastids considered symbiotes of eukaryotic cells?

texts: Mitochondria and plastids have their own DNA, their own membranes, and their reproduction is not tied to the reproductive cycle of the host cell. However, they are considered to be organelles rather than a separate species in symbiosis with eukaryotes. Granted, mitochondria and plastids are incapable of living outside their parent cells, and likewise eukaryotes are incapable of surviving without the help of mitochondria and plastids. But this is also true of many other symbiotic pairs in Eukarya. So where does the distinction lie? What makes mitochondria and plastids organelles rather than separate organisms?


texts: What is the structure and function of chromosomes during interphase?

texts:
Ok, it seems to be easy but I have probably ignored something by accident.

Interphase is the phase where things are growing and the preparation for cell division happens. Its stages G1, S and G2. DNA replication in S stage. So the DNA in some chromosomes must have the pieces of information about how to do the DNA replication. - I am not sure  about thing.

I would say to the part: structure that chromosomes are diploid at the given stage. - It does not feel right anyway.

What would you answer to the main question?


texts: To what extent does the cooking time impact the nutritional content when boiling potatoes?

texts:
I wonder to what extent the cooking time impacts the nutritional content when boiling unpeeled potatoes with unsalted water.

http://www.livestrong.com/article/340060-does-boiling-potatoes-reduce-their-vitamins/ says:

  Boiling potatoes whole in their skins minimizes the amount of vitamin C that is lost. According to the Food
  and Agriculture Organization of the United Nations, boiling unpeeled potatoes results in losses of up to 30
  percent of vitamin C, but boiling peeled potatoes can cause losses of up to 40 percent. About 2 percent of the
  vitamin B-6 is lost due to boiling potatoes, as well as about 23 percent of the thiamine. A 3.5-ounce serving of
  potato boiled in the skin provides 22 percent of the daily value for vitamin C, but boiled peeled potatoes
  provide only 12 percent. Peeling potatoes before boiling can also increase vitamin B-6 losses, with unpeeled
  boiled potatoes containing 15 percent of the DV per 3.5-ounce serving and peeled boiled potatoes containing
  only 13 percent of the DV. There is no difference in thiamine content between peeled and unpeeled boiled
  potatoes.

  [...]

  The higher the temperature and the longer the cooking time, the more of the vitamins will be lost

However, it does not mention how the loss curve looks like.


texts:
I have been having difficulties with low transduction efficiencies of my retrovirus production. I expand my plasmid of interest (on MiG-GFP plasmid) in DH5α E Coli for ~24 hours, purify with Qiagen midi prep kits, then put on ~90% confluent 293FT cells with either retronectin or polybrene for 24 hours. I then change media and harvest supernatant at 48 and 72 hours of incubation with the 293FT cells. I then expose 3T3 cells to varying volumes of the virus containing 293FT media and am able to transduce about 10% of the 3T3 cells, which is really low. That being said, here and there I am able to get very high transduction efficiencies on the 3T3 cells, but for unknown reasons. I have tried concentrating the virus but transduction efficiencies don't increase all that much. And I have tried growing up the plasmid in Stbl3 cells, which if anything gives me worse virus.

Anything here jump out as being responsible for low transduction efficiencies. Or is there another way somebody does this that works really well?


texts: What is the advantage of not having cytokinesis after karyokinesis?

texts: In nature most of the cells are mononucleated, but in some cases like osteoclasts, umbrella cells of transitional epithelium, tapetal cells of another etc. are multinucleated. Wikipedia article about tapetum says that it is a strategy to increase the production of proteins. Why don't cells just up-regulate their genes for more production? What is the benefit of not having cytokinesis?


texts: Why does my anti-ubiquitin antibody visualization not work on my PAGE gel?

texts:
I am using 2D gel electrophoresis to visualize polyubiquitinated proteins. However, while I can see actin and heat shock protein using when appropriate antibodies, I cannot visualize them using anti-ubiquitin antibody. Could it be degradation problem?

I run isoelectric focusing at 200 V overnight (at least 18 hours) and 700 V the last 30 minutes. I am worried that I am applying more volts than needed, because the standard protocol is 200 V for 20 minutes, 450 V for 15 minutes, 750 V for 15 minutes, 2000 V for 30 minutes, but due to problems with the power unit I cannot do this.

I am sure I have polyubiquitination because I use a drug that triggers polyubiquitinated protein accumulation inside the cells.

I would like to add also that cells are collected by scraping in cold PBS and then they are placed in ice and the pellet is also collected at 4 degrees to prevent protein degradation.


texts: What is this cloud of red pond creatures?

texts:
Today I came across a pond in the Netherlands where I noticed a cloud, for lack of a better word, of small red creatures swirling around near the surface of the water, as can be seen in this video:

https://youtu.be/ZQMox-bbJ9s

And here is a picture:

The surface was unfortunately quite reflective, but the motion is visible. The creatures were too small for me to see any structure to them with the naked eye. Some tadpoles can be seen in the video, which are much larger. They would swim straight through the cloud now and then, so perhaps the tadpoles consider the red stuff food. The entire cloud consisted of various dense clusters connected with less dense or thinner parts, as can be seen to some extent in the video, and its total size was perhaps 2 meters or so.

What was I looking at?


texts: Dendritic cells have a larger surface area due to extended dendrites (membrane folding into itself). Do other mammalian cells (with functions other than immunological) present these membrane folds?


texts: What determines the thickness of Cornea?

texts:
In eye-operations such as Lasik and Femto, the thickness of cornea is key decision factor whether the operation is feasible. A normal thickness is between 500-600 µm. Cornea consists of a very special tissue having no blood supply and no vessels so it gets nutrients through diffusion of tear fluid and oxygen directly from air (hence in a way, it has its own respiration system not dependent on lungs).
Now I started to think the following questions:

I. What determines the thickness of cornea?

Helper questions

II. Is the thickness of cornea determined genetically so twins have the same cornea thickness?
III. Is the thickness determined by the environment and psychological things? Eg. how does diving affect cornea? Look it cannot get oxygen anymore through the air with the mask. What about drying? Does cornea gets too much nutrients all of a sudden from eye fluids?
IV. Does Homo Sapiens have more this kind of independent tissues? What about other animials? What determines the thickness of Cornea there?


texts: Is the amount of cholesterol the body produces affected by how much cholesterol you take in with food?

texts:
In the past I've been told multiple times that if you don't eat foods containing cholesterol, your body will increase its production of cholesterol to balance out the lack of nutritional cholesterol. On the other hand, if you eat sufficiently much cholesterol, the body will adapt its production of cholesterol in the other direction.

What evidence is there to support this statement?


texts: How does air-liquid interface (ALI) culture work?

texts:
For studying diseases, such as chronic obstructive pulmonary disease (COPD), cells are often grown in air liquid interface.

I understand that the common way of establishing this these days is to grow cells in culture well inserts with a permeable bottom, then put medium only in the well and not the insert.

Here is an image from Stemcell Technologies:

The last images implies that the level of the medium is just high enough to cover only the basal side of cells. Is this realistic? Given that the monolayer is a few microns thick, is it really just a matter of carefully pipetting just enough medium? It seems like the error of a pipette is too high for this.

In practice, I am getting the impression that the level of liquid is actually higher than the apical surface of the cells, but it is somehow prevented from seeping out of the well and into the insert. If so, how? The bottom of the insert is permeable; even if you grow cells to confluence, surely there will be a small hole or two somewhere which causes a leak?


texts:
The missus was bitten/stung in the palm by this (we think) in NE Scotland this morning. Pain was immediate, described as like getting a pin stuck in her hand. Apparently her first attempt to flick it away failed, and it took her second attempt to remove it. Afterwards, a short black stinger appear to remain embedded and had to be removed with tweezers.

She got fairly immediate swelling (white circle around the site, and red swelling further out). Even 20 minutes later, the swelling and pain remain.

This may or may not be the entirety of the insect.

Location: NE Scotland (indoors)

Time of Year: Early October
Size: Very small. Few mm long at most


texts: Sensitivity vs. Limit of Detection of rapid antigen tests

texts:
I'm comparing a bunch of SARS-CoV2 rapid antigen tests:

Source
Columns 4 and 6 list the values for sensitivity and limit of detection (LOD). How come that a test with a several times lower limit of detection can have a worse sensitivity?
As an example, consider tests #2 and #4:
#2 - Sensitivity: 97.7% - Limit of detection: 2.0*10^2.4 = 502 TCID50/ml
#4 - Sensitivity: 91.4% - Limit of detection: 2.5*10^1.8 = 158 TCID50/ml
Shouldn't these values correlate, i.e. the more sensitive a test is the smaller the amount it is still able to detect?


texts: Relaxing Eyes when using Virtual-Reality-Glasses?

texts:
Accommodation is the process by which the vertebrate eye changes optical power to maintain a clear image or focus on an object as its distance varies (eye focusing). For distant vision, the ciliary muscle must relax and the eye’s crystalline lens is stretched out.

When using a Virtual Reality Device (Occulus Rift, Samsung VR, Sony VR, Google Cardboard etc.) the eye has to focus on the screen that is only a few centimeters away from the eyes. I am aware of the Vergence-Accommodation Conflict. Yet I ask myself,

Is the ciliary muscle relaxed or contracted when looking at a (virtually) far distant object projected on the LCD of the VR-Device?


texts: Why does hypergranulation prevent the epithelialization of a wound?

texts:
I recently read about how does a wound heals. I read that when the granulation tissue protrudes out of the wound bed (proud flesh), the epithelialization cannot occur because the protruding proud flesh is in the way.

But I don't really understand why. Keratinocytes migrate on the surface of the granulation tissue. Even if it bulges out they should follow the geometry of it, shouldn't they? Otherwise I think none of our wounds would heal...


texts:
With respect to the the Wnt pathway in KEGG, the KGML file of this pathway has description of each interaction between a pair of genes. These interactions are designated in the form:

  entry1="46" entry2="41" type="PPrel"
  subtype name="inhibition" value="--|"/
  subtype name="phosphorylation" value="+p"/

In some entries, the reaction "subtype" entries are 2 in number while in some, it is one, as for the above-mentioned interaction. Another entry is as follows:

   entry1="47" entry2="46" type="PPrel"
      subtype name="phosphorylation"
    value="+p"/   relation

Why do some of the entries have 2 interaction types while some have one? What does this signify biologically?

There is an interaction type called "compound". What does a compound interaction signify biologically?

  <relation entry1="17" entry2="16" type="PPrel">
    <subtype name="compound" value="4"/>
    </relation>


texts: Why a particular species of bacteria give rise to particular type of colony?

texts:
Bacterial colony varies in form, elevation, margin, opacity, chromogenesis etc. What gives definite character to a colony and what is the source of all the diversity? Is the reason similar to that of structure of salt crystal (i.e basic elements connect in a very definite way with each other)?

UPDATE (clarification)

On this page, it is observed that colonies can take various shapes, as if they have some internal structure, so that for example, form, elevation and margin differ and can even be described as having a particular shape.

Assuming that bacteria do not have any form of social organization or specification, what factors cause their colonies to have a particular shape, and that shape is well-defined for each species?

Also, for example, this picture on this website clearly shows a bacteria colony that is like ice crystals. If bacteria colony has no inner structure, what makes the bacteria to follow such a crystal-like pattern? Why not a shapeless goo, as one would imagine?


texts: How much electrical energy is required for intracellular stimulation of a neuron?

texts:
How much electrical energy is required for intracellular stimulation (firing) of a human neuron? Electrical energy is measured in joules, and equal to voltage multiplied by current. If you don't know energy,  you may specify voltage applied and current. Just for example, to capture heart, a pacemaker must discharge 0.1 microjoule of electrical energy.

There might be more parameters involved like pulse width,  phase etc.  Energy combines all the parameters in one single value. In case you don't know energy level,  please specify the defining parameters as well.


texts: Is there a difference in how Gas is produced which determines if it becomes a burp or flatulence?

texts:
I know that some gases are heavier than air and in the case of a gas leak it's best to escape to higher ground, while some gases are lighter than air such as Helium. However unlike Helium I haven't seen a burp burst into flames while I have had the unfortunate pleasure of being present at a party where flatulence was lit on fire.

So I am wondering if there is a difference in how the gas is produced which determines if it's becomes a burp or flatulence.


texts:
The point of my question is not to talk about events that are uncontrolled by living organisms. My question is about controlled randomness, or I'd like to say adaptive random process. Process that are random because it was selected in order to be random.

The first thing that pop in my mind when thinking of "adaptive random process" in biology is Fair Meiosis. Do you have other examples of "adaptive random process"? An individual might display a random behaviour in order to avoid that others to predict its future behaviour. Is there any evidence for such things? Do you know any other evidence on what I called "adaptive random process"?


texts: Where can I find pdb files for macromolecules like receptors?

texts: I have tried going to the RCSB website and quite frankly it was useless since when I looked up receptors like say the metabotropic glutamate receptor 2 (mGluR2) I got no helpful results.


texts: Immunological factors for the cause of headaches following SAR-CoV-2/COVID vaccination

texts:
It is generally-accepted that headaches are a common side effect from receiving the COVID vaccine.

Vaccine recipients with pre-existing immunity experience systemic side effects with a significantly higher frequency than antibody naïve vaccines (e.g., fatigue, headache, chills, fever, muscle or join pains, in order of decreasing frequency, P < 0.001 for all listed symptoms, Fisher’s exact test, two-sided).

— Florian Krammer et al.: "Robust spike antibody responses and increased reactogenicity in seropositive individuals after a single dose of SARS-CoV-2 mRNA vaccine" doi: https://doi.org/10.1101/2021.01.29.21250653
I am trying to understand why. What theories or known biological, immunological or otherwise physiological mechanisms would cause recipients of the vaccine to report headaches as a common side effect?


texts: Is brewer's yeast a good source of protein for humans?

texts:
I read that brewer's yeast protein is not a "real protein" and is not usable by non-ruminants. Is that true?

If yes, how can I know what kind of protein is good for humans (especially athletes)


texts: Non-cavitating ultrasound for denaturation of short strands of DNA (~20 bp)?

texts:
I know that there is existing research on ultrasound-induced transient cavitation bubbles that mechanically denature DNA by generating violent shock waves locally in solution.

I would like to know if it is possible for non-cavitating ultrasound to denature short strands of DNA, ~20 base pairs in length (please cite sources, if possible). The mechanism should be mechanical, without involving thermal or cavitation effects of ultrasound. The ultrasound acts as a pressure wave, of the order of 10 MPa, and the DNA helices require a force of ~15 pN to initiate unzipping. I just need proof that this has been successfully demonstrated.

Thank you in advance.


texts: Does the humeroradial joint move medially/laterally?

texts:
The humeroradial joint is a ball-and-socket joint that, if unrestricted, would allow for movement around all possible axes. However (as succinctly stated from Wikipedia):

  the annular ligament, by which the head of the radius is bound to the radial notch of the ulna...prevents any separation of the two bones laterally.

As a result of the annular ligament, the proximal radioulnar joint and -- quite honestly -- the humeroulnar joint, the humeroradial joint is considered to be "limited." In other words, the humeroradial joint is typically considered only to be capable of taking part in flexion/extension of the elbow and lateral/medial rotation of the forearm.

However, although no internet/textbook search I've conducted mentions it, I'm wondering does the humeroradial joint allow any movements at all in the frontal plane (i.e., adduction/abduction)?

Here's a visual:

It seems unlikely, but at least a slight "jittering" seems possible.

Although just barely related, the knee (a hinge joint) comes to mind because of its somewhat unexpected (based on classification, not structure) ability to "slightly rotate" when unlocking.


texts: What is the medical definition of death? And how do medical examiners determine whether a person has really deceased, as opposed to for example a condition like brain death?


texts:
This question got me thinking about something. LUCA is the last universal common ancestor of all current living organisms, which is a very different definition from the first-ever living organism. Is there any evidence that LUCA had evolved and diverged from a now-extinct, more primitive lifeform?

To rephrase, is there any evidence to suggest that at some point, the first-ever living organism(s) had diverged into two phylogenetic groups, one being now-extinct and the other describing all current life?


texts: Can an infectious diseases come from a plant?

texts: Coronavirus, HIV, 1918 Flu, etc. They all come from animals. Do any infectious diseases (in humans) come from plants? More specifically, are there viruses that infect plants that can mutate to infect humans?


texts: Why can blood group O be given to all blood groups?

texts: The blood of persons of blood group O contains antibodies against antigens A and B. The red blood cells of persons of blood group A have A antigen on their surface. If someone with blood group A receives blood from a donor of group O, then anti-A antibodies in the donor blood should attack the A antigens on the recipient's red cells. Shouldn’t this be a problem?


texts:
I was wondering about the physics of color, and now am interested in finding out if there are any resources (databases, text files, html tables, or pdf listings) of species and their associated colors or (ideally) color wavelength spectrum.

For example, a rose bush might have a pink (flower) color spectrum and a green (leaf) and brown (stem) color spectrum. A worm might have a brown and pink color spectrum. A lion might have a yellow and brown and gold color spectrum. Wondering (a) if any of this information is captured in any form on the web (such as 1 journal article per species), and (b) if it is aggregated into a database, text file, table, or other sort of list which includes lots of species (animals, plants, fungi, rocks, etc.), so it would say the wavelength of visible light that it emits, or some ranges of it, or even a hex color range.


texts: What's the simplest set-up to demonstrate soiless plant growth to middle school students?

texts: I'm looking for a simple, inexpensive way to demonstrate that soil is not needed for plant growth to middle school students.  I plan to germinate bean seeds in cotton, but where do I take it from there?


texts:
This is a moth that we found on a curtain inside the house a couple of days ago. Unfortunately, these pictures did not come out as well as I thought before I realized it outside. But I was struck my the silver-white eyeglass-shaped spots on the wings. It also had an interestingly shaped head, but that didn't come out well. The closest I have come to identifying it is that it looks similar to a Dot Moth, but those don't seem to be native to Southern California (Los Angeles).

It was about an inch long, maybe less. It vibrated its wings after I disturbed it.


texts: What is a good review book/source for microbiological diagnosis?

texts:
I am trying to find the diagnosis figure for different bacteria where phases are illustrated.

I am using at the moment: 1) First Aid for the USMLE Step 1 2013 and 2) Medical Microbiology by Murray et al, 7e.

What is a good review source for basic microbiological diagnosis?


texts: Why do pandas have a high probability of giving birth to twins?

texts:
According to the BBC documentary "Wild About Pandas", about half of panda birth result in twins.  Why do they have such a high probability compared to other mammals?  What factor(s) control that fraction in general for mammals?

Additional question about the allometry formula:

I am a little surprised that it is not the ratio between the neonatal mass and the adult body mass that enters the formula, but just the neonatal mass.  Any ideas on that?


texts:
There is a bird's nest on my balcony in the wall above the door with birds who breed. They have fledglings who already hatched. (I assume this because I sometimes hear quiet sweet chirping.) I sit on my balcony often for breakfast and sometimes for lunch almost every day. When I do this, the birds stop feeding their fledglings (because they are afraid of me or because it is some natural instinct to not reveal their nest).
A friend of mine (who installed a birdhouse on her balcony) told me that the fledglings die if they are not fed constantly. She told me that she doesn't use her balcony anymore (or at least not longer than 5-10 minutes) because of this.
So my question is: Do fledglings die if they are not fed constantly? How long can they survive without food? (like 30 minutes or so)
I would like to use my balcony because I really enjoy having my meals on it but I also don't want the fledglings to starve.


texts: Problem with bacterial transformation with electroporation

texts:
I have a problem with a bacterial transformation of a yeast gene that I can not solve.

I isolated yeast DNA and did a PCR to get my product. I am using pCGCUm vector with a GFP construct. I digest both my plasmid and my product with SmaI and ClaI for 4h each. After that I purify the product from a gel and perform a ligation with high efficiency T4 ligase for 30 minutes at 22°C. Then I transform my electrocompetent cells with electroporation (2000V, 5ms), recover it in 0.5ml LB for 2h and plate it on LB-A plates.

First time I only did:

insert1
insert2
Empty vector

and it did not work (empty plates for insert and confluent growth (after 18h) of some weird colonies on EV).

I did the same ligation again and this time I included controls

This is what I did:

insert1
insert2
Empty vector
negative control (EK cells + electroporation)
positive control (EK cells + undigested vector)

Now I got:

insert1 (no colonies)
insert2 (big colonies a lot of them)
Empty vector (big colonies a lot of them)
negative control (EK cells + electroporation) (no colonies)
positive control (EK cells + undigested vector) (big colonies a lot
of them)

The negative control suggests that my competent cells are ok, at least they are not resistant to AMP.

What confuses me is that even with positive control I get some weird big colonies - if I got nice transformants here I would assume that either digestion of ligation was not successful, but now I doubt that).

Another thing that is weird is that now I got that colonies also on my insert2 plate.

The scan image of big colonies looks like that:

I have a question if anyone has had that kind of colonies? I was thinking of maybe having contaminated cuvettes for electroporation but I had them in 100% EtOH for 3 days and then dried in fume hood for 3 hours before electroporation.


texts: Is forced cell growth related to apoptosis?

texts: Could an instance of forced cellular growth cause some cells to have their self-destruct mechanisms to malfunction or 'turn off'thus preventing apoptosis?


texts: How does proximal centriole of human sperm function?

texts: I've read that the human's unfertilized oocyte ( stuck at metaphase 2 of meiosis ) lacks centrioles and that it completes meiosis 2 after fertilization as sperm gives its proximal centriole. Then what about the centrioles required for mitosis of zygote?? How does proximal centriole function?


texts: Insect making continuous sound in summers

texts:
In deciduous to tropical-deciduous forests and residential places with such vegetation I have found this insect to make continuous sounds all through the day (even in nights sometimes) during the summers. Average summer temperature > 30 C around noon and ~ 28-29 around nights with high humidity.

I want to know what is the reason they make this sound ?

Recently, I found several of them dead near light poles etc..., and some sit very close to windows of air-conditioned rooms. I think they want some cool environment.


texts: (Rough) Model for DNA evolution in E. coli genes

texts:
I need a model of in-gene DNA drift. I'm not interested in bacterial phylogenies alone.

Here is what I understand:

Sequences corresponding to genes have both exons and introns, but in bacteria the proportion of introns is low.
Because I'm talking about genes, sequence changes are not very neutral but subject to selection.

I have checked a few papers linked in Wikipedia about this subject, but I notice that they are tuned for entire sequences, and many of them almost predate the genomic era.

What are some current, canonical sources in this area?


texts: Tumour resistance: single-cell or population effect?

texts: Drug resistance can arise through a number of mechanisms. For instance, EGFR mutation when treating with EGFR inhibitors, or compensatory activation of alternative survival pathways. But does it occur at the level of a single cell, or would it be a population effect? In other words, would cells exposed to e.g. targeted kinase inhibitors slowly compensate with other pathways (and that would happen in every such cell) or would there be a sub-population of cells that is sensitive to inhibitors and another subpopulation inherently resistant and predisposed towards amplifying other pathways.


texts: What are the (evolutionary) advantages of secondary transport?

texts:
Secondary active transport uses electrochemical gradients as a source of energy for the uphill transport of substrates (coupled to downhill transport of the ion).

However except for in a few cases (e.g. Electron transport chains) the electrochemical gradient is formed by ATPase pumps which use energy from ATP to pump the ions.

So why not just use ATP in the first place (and not have to set up the gradient). (I do understand that the gradients are useful for signalling, action potentials etc. but that is a seperate issue.) i.e. What is the advantage of secondary transport.

My (complete) speculation:
Is secondary transport perhaps used because it allows a sort of inherent regulation. Stop the gradient forming pump and you immediately stop all the secondary transport using that particular gradient? If that is the case are secondary transport proteins in groups with similar functions/pathways utilising the same gradient?


texts: This plant is hardly 40/50 days old and given to me in seed form claiming to be hibiscus plant seed.I m not sure that it s hibiscus plant.. Please identify.


texts: Metrics or operations on genome sequences in human genomic research?

texts:
Edit distance may be an important metric for measuring the similarity of two genome sequences.  For example, if A = GCAATT and B= CGAATA, then the edit distance of A and B is 3. Such a metric is intuitive and may be useful in comparing the similarity of two sequences.

I wonder is there any more complex or advanced metrics used in human genomic research?


texts: How did a plant evolve to know there were animals alive that would eat it's fruit when it decided to produce this fruit?

texts: How did plants come to "know" there were animals alive that would eat it's fruit when it first produced this fruit?


texts: Is ebola non-contagious until symptoms appear? Why?

texts: There's been a lot of talk lately about the man who recently came down with ebola in Dallas, Texas. While I live elsewhere, I keep hearing quotes from CDC and state officials that ebola is not contagious until a person shows symptoms. This is generally used in the context of "Don't worry too much; we have the situation under control." Is this true in all cases? Why?


texts:
How many different smells can a human recognize?

If the space of smells is not discrete, how many dimensions it has (for example, the space of colors is three-dimensional).


texts:
I'm confused over the two terms vascular cambium and intrafascicular cambium.

Is vascular cambium the same as intrafascicular cambium?


texts: What is the principle behind Microagglutination test (MAT)?

texts: Could some one please help me understand the principle behind the MAT. Also, is it only used to detect leptospira or can it be used to detect other pathogens as well? Kindly share links to papers if possible. Thanks!


texts:
How is movement of proteins and lipids between different domains of cell membrane prevented?

Why is the noncytosolic layer not able to do lateral movements between domains but cytosolic layer is able to do so?


texts: Are cells guaranteed to get at least one mitochondrion when they divide?

texts: If mitochondria exist at random within a cell, isn't there a possibility that cell division will result in a daughter cell with no mitochondria?  If not, what is the process for guaranteeing at least one is present in each daughter cell?  If so, what happens to that cell?


texts: Locomotion of Hydra: Why Somersaulting is better than Loop locomotion when moving to a larger distance?

texts: In my text I read about different types of locomotion of Hydra where I learnt that generally Hydra moves by somersaulting and it is faster than 'Loop locomotion' which Hydra uses for moving to a large distance. At the end of the chapter the question is "Why somersaulting is better for going to a larger distance?" I cannot find a good answer to it.


texts: Evolution after the development of sexual reproduction

texts:
My understanding of evolution is that genetic mutation occurs in individual members of a species, and they become a new species.

Isn't a definition of species a group of genetically similar organisms that are pretty much exclusive in breeding ability?

Wouldn't there have to be a male and female with the same genetic divergence at the same time to make a new species?  What is the popularly accepted mechanism for the splitting into a new species in organisms that require sexual reproduction?


texts: What is the difference between taxonomical aids Flora, Manual and Catalogue?

texts: The three type of books mentioned above are taxonomical aids that offer information about species found in an area. However, the exact difference between them is not clear to me. Please explain.


texts: Differential gene expression analysis between species

texts:
I have RNA Seq data from mouse and human skin ( 2 replicates each) and want to compare the expression of the orthologous genes to find any which are differentially expressed.
I have quantile normalized the gene expression matrix across all 4 samples (2 mouse + 2 human). I eventually want to calculate the log fold change in expression of all orthologous genes between the 2 species. However before I do this, I should control for gene length, right? Will this be enough to give me an idea of the differentially expressed genes or should I be employing more sophisticated methods?
Any comments would be helpful. Thanks a lot.


texts:
We say cell wall is dead but nobody says cell membrane is dead.

Is cell membrane living or dead ? If it is not dead then why is it not included in protoplasm :

  Protoplasm is the living contents of a cell that is surrounded by a
  plasma membrane.

(Source : Wikipedia)


texts:
I am new to the world of neuroscience and I would like to understand how come every paper in neuroscience that I read uses a Poisson process to model neural firing. Do I just have a biased sample of the papers I chose to read, or is it a biological fact that neural firing must follow a Poisson process? Why can't it follow, say, binomial, since it either spikes or it doesn't in a given time period. Also, where can I read more about how such a biological phenomena was discovered?

A small correction: I do appreciate the explanation on the difference between the two distributions but I am a statistician who is trying to understand my neuroscience colleagues and communication is key in statistics. I am just trying to comprehend why everyone in the field is using Poisson as opposed to using Binomial even when the bin size you decided on is sufficiently small. In other words, why would you not use Binomial, the bin size is so small that your data is only 0's and 1's (i.e. the spike happened or did not happen within this bin). Is it because Poisson counts discrete occurrences in a continuous domain? What discipline-specific papers would you recommend to read that justify/discuss/explain the continuous domain on neural spiking?


texts: In what sense is the "histone code" a code?

texts:
Since I started learning about molecular cell biology, I have witnessed an increasing amount of attention to this thing called a "histone code." However, unlike the central dogma of molecular cell biology (i.e. DNA RNA Protein), I still feel very confused about what exactly constitutes the histone code. Is this term code being used rigorously like it is for the central dogma? That is,  is there an actual code? If so, what is its alphabet (e.g. GTAC for DNA, GUAC for RNA, the amino acids for  proteins)? What kind of words does it encode (e.g. codons for RNA to protein)?

If these things are not known, how do we know it's actually a code then?

Thanks!


texts:
This is pretty specific question maybe. Anybody have an estimate? For Toll Like Receptors there are something like 10...

http://www.jbc.org/content/276/4/2551.long

I'm only finding NOD1 and NOD2 => only 2?


texts: Do individual mammal hairs absorb water?

texts: In my look into the world of shaving I've seen claims that it is better to shave after a shower because the hairs will absorb water and soften, making the shave easier. Likewise, I've seen it claimed that natural hair brushes (i.e. boar and badger hair brushes) should be soaked before use. My question is: do the hair fibers actually absorb water, presumably thickening in the process, or does the water just adsorb onto the surface (maybe lifting the scales in the cuticle) meaning you can wet hair in aggregate, but it doesn't soften when soaked? Especially, is there a side-by-side comparison of a single hair under a microscope before and after soaking showing what happens?


texts: Expected reproduction rate of a dandelion and/or fern

texts:
I am working a basic mathematical/computer simulation of an ecosystem, and I need to know the birth rate of each organism in my simulation. However, I could not find any data for how often a small, asexually-reproducing plant, like a fern or dandelion, reproduces. Does anybody know either a) the time to reach sexual maturity and the expected offspring of one dandelion or fern OR b) when starting with one plant, the expected living dandelion or fern plants after a year?

In other words, if I plant one dandelion or fern in a closed system (providing it with requisite water, food, sunlight, etc), how many can I expect to find at the end of the year?

These values don't have to be exact, I can adjust them later, but I need something to use as a baseline.


texts: Textbooks commonly state that red blood cells are removed by the liver and spleen. Do those organs destroy the red blood cells within capillaries that course through those organs or are they transported into the liver/spleen cells to be broken down into their constituents? What causes them to be destroyed/removed from the circulation?


texts: Why is dopamine or a dopamine-receptor agonist not pumped into the brain of Parkinson patients?

texts: I am aware that dopamine cannot cross the blood-brain barrier, but can't it be pumped inside the cerebrospinal fluid via some permanent tube implant? Wouldn't Parkinson patients chose that over succumbing to the disease? Why hasn't it even been ever tried?


texts: Why don't chilli peppers taste as hot in space?

texts:
The following commentator writes:

  Chili peppers don’t taste as hot in space as they do on Earth. Nobody knows why.

We know that the 'hot' feeling of chilli peppers is caused by Capsaicin. We read:

  Capsaicin inside the pepper activates a protein in people’s cells called TRPV1. This protein’s job is to sense heat

There appears to be some question about the cause of the 'spicy' taste of chilli peppers.

My question is: What is the reason that chilli peppers don't taste as hot in space?


texts: Could being exposed to excess UV in the arctic lead to a human eye color change? If so, what is the mechanism?

texts:
The CBS News article Expedition Antarctica: A father and son's journey to save the planet says (in part):

  Thirty-two years ago, Robert Swan made history as the first person to walk to both poles. Even as a young man, these grueling expeditions took a harsh toll on his body. Passing directly beneath the hole in the ozone layer, Swan's face became badly burned and his eyes even changed color. But the Arctic explorer now says that all of that physical duress pales in comparison to the agony of watching his son go through the same experience 32 years later. (emphasis added)

Skin color change can happen after exposure to UV light. From Wikipedia:

  Melanin is a natural pigment produced by cells called melanocytes in a process called melanogenesis.

Question: Can the human eye really change color due to excess UV light from the Sun, in this case through a polar "hole" in the ozone layer? If so, what is the mechanism?

above: "This winter, Barney and Robert Swan became the first explorers to ever trek to the South Pole surviving exclusively off of renewable energy." Robert (the elder) is on the right. From here. Credit: SHELL-Technical Partners


texts:
The white bird in this picture, swimming between the ducks, was seen in Beijing, China, in januari 2017. It was cold: the water seen in the picture is liquid, but not far from this, the water was frozen. We also saw it standing on the ice.

It has an orange beak with what seems to be a small black spot at its end. It also has black as the top of its head. We did not find a similar bird when searching ducks, goose or even swans. What species is this?


texts:
What is the minimum eye which confers some evolutionary advantage?

By minimum I mean anything less than this has no advantage whatsoever and therefore is not favored by natural selection.

By eye, I mean not just a light sensor but also infrastructure which converts the light stimulus into an advantageous response.

Ideally would like a clear unambiguous before/after case especially on the infrastructure between the mutated protein and the cell's response mechanism which translates this into a survival advantage.

(I assume Opsin proteins floating around the cytoplasm by themselves confers no advantage without some kind of other infrastructure)

please also provide an estimate of the number of coordinated DNA base pairs which needed to change to confer this advantage so that a proper probability estimate can be done.


texts: How might one determine if bacteria are nitrogen fixing or not?

texts: If you had an isolate bacteria sample how would you determine if they were nitrogen fixing?


texts: Do different microscopes and attached cameras differ in crop factor between each other?

texts:
I analyzed a bunch of microphotographs recently and used "% of image area" to describe the area of structures (chorionic villi, had to show their density in placenta). However my professor suggested I should have used mm2. There is no problem in conversion, but I suspect different microscopes may have different areas of field of view for the same scale. Thus the conversion will make the results just more difficult to interpret.

So does the absolute area of microphotographs of the same scale and size differ between microscopes/cameras? Or is it somehow standartized?


texts: If it were possible to live forever, would our brains grow infinitely with the number of memories that we store? Or would we remove old memories as we create new ones?


texts: How to protect my mounted insect specimens from ... insects?

texts:
I have a modest collection of insect specimens that I caught, prepared, mounted, and dried myself. I'm entirely an amateur collector, so my procedure may be causing me this trouble now, but here's how I preserved them.

Killed in the freezer
Placed in a sealed container on a dry platform, with a 50% isopropyl alcohol solution under it. This lets the specimen thaw and remain moist, while the alcohol prevents rotting.
Kept in container for two to three days.
Stretched over foam and held in place with paper and pins.
Kept on stretching board for three weeks.
Placed in a consumer grade display box.
Stored in a dark, dry closet.

It's been a while since I worked on this hobby, but I do like to pull the collection out from time to time and admire it. Today, I was surprised and disappointed to find that some of my best specimens have been turned to dust by a small caterpillar type bug. There are live bugs in my display case, eating my bugs!

I've had these for years without issue, and now I find this. What can I do about it? How can I keep this from happening again? Should my preservation procedure include some other step? How are they even surviving? There's no moisture in there at all!

I'd rather not put something toxic in my display case, as I like to take them out and examine them without the glass in the way. I don't want to be exposed to toxic things every time I look at them. I hope there's some effective, cheap, and safe thing I can do. I've become rather proud of my collection, but it's disheartening to have worms eating them before they've even eaten me.

Here's some pictures of the devastation:

That stain on the right used to be a specimen.

The big pile of dust there on the left used to be a praying mantis. I don't even know what the pile on the right use to be.

This beetle's entire insides have been eaten.

This horsefly looks like it was mounted a hundred years ago.

Apparently moths and butterflies don't taste very good.

The culprit! This little guy and his pals are responsible. You can see exoskeleton sheddings all throughout the other pictures.


texts: Understanding the meaning of $s$ and $t$ in a population genetics equation

texts:
Sewall Wright in this article (1937) at the end of page 313 gives the equation:

$$\Delta q = (s+tq)q(1-q) \space\space\space\space\space\space\space\space\space(1)$$

This equation is an approximation who holds only when $t$ and $s$ are small. $q$ is the frequency of allele A. $s$ and $t$ define the fitness of the three possible genotypes AA, AB and BB. I am not sure which genotype has fitness equal to 1 and I don't how $t$ and $s$ define the genotype fitnesses.

Let's assume for example that the genotype BB has fitness of 1. Then, the fitness of the genotypes AB and AA might be given by $1-t$ and $1-s$ respectively or $1-s$ and $1-t$ respectively or eventually by $1-t$ and $1-(s+t)$ (or variants) or even $s$ and $t$ (and opposite) or $st$ and $s$ (and variants). The genotypes fitness might as well be given by $1-st$ and $1-s$ but it would not be make much sense given the assumptions used for the approximation.

My question is: do you know how is the fitness of the three genotypes defined in equation (1)?


texts: How to know if a woman is fertile without actually making her pregnant?

texts: How to know if a human female is fertile (can give birth to child in future) without making her pregnant? Any signs, tests?


texts: How can I determine the mRNA sequence from a given template DNA strand?

texts:
Can I determine the sequence of nucleotides of the mRNA strand transcribed from a template DNA strand that goes from (5' to 3')?
I know that RNA-Polymerase enzyme cannot work but on the (3' to 5') direction of the template DNA strand. So, for instance, if the question was to:
Determine sequence of nucleotides in the transcribed mRNA from the DNA strand
5'...A-T-T-C-G-T-T-A-C....3'
Which direction should I start with?


texts: Does a bigger breast give creamier milk?

texts:
It is fairly common for a woman to have one breast larger than the other.  I have also heard that, for a breastfeeding mother it is common for one of the breasts to yield a creamier milk whilst the other is more watery and has less nutritional value.
Is there any correlation between the larger of the two breasts and the one which yields the fattier milk?


texts:
Location: Asansol-Durgapur region, West Bengal, India
Question:
Do they belong to the same species?
Note:

I presume the bird in Pic-1 is a male  Purple-rumped sunbird (Leptocoma zeylonica).
I think the birds in Pictures : 2-5 could be non breeding male Purple sunbird (Nectarinia asiatica) because they match very much with the Wikipedia description though the bird in Pic-2 has a short tail.
Pic-4 and Pic-5 capture the same bird.


texts: Is it possible to genetically alter human beings to see parts of the infrared?

texts: Most electron transitions take place in the infrared region,The ability to see this part of the electromagnetic spectrum without reliance on sophisticated technology would have tremendous advantages. Is it possible to manipulate human genes to see this part of the spectrum?