texts: Why is hunting big animals more dangerous for the species?

texts:
I've heard in a lecture about protection of primates that one reason the classical population dynamics doesn't work is that the aboriginal hunters tend to hunt the big, strong and healthy individuals that have the best chance of becoming a successful parent.

Is this effect really so significant that it outweighs the fact that the hunters don't have to hunt so many of them in order to get the same amount of meat?

[Additional explanation]:

This question asks about the best strategy in protecting rare wild animal species against excessive hunting. We don't have to intervene when lions hunt zebras because less zebras means less food for lions - so the ratio of zebras and lions doesn't change much so there's no danger of any species getting extinct. Unlike the natural predators and prey, it has been found that the amount of meet hunted by people in forests isn't anyhow dependant on the number of animals living in the nature because humans use tools which give them a huge advantage over the "prey". Also, number of people living in a forest isn't  dependent on the sources in the wild, due to the rise of agriculture.

There was a research how much is the size of an animal connected to the probability a hunter will hunt specifically this animal and it has been found that the hunters tend to pick the physically biggest, strongest and healthiest individuals. This phenomenon has been marked as dangerous for the future preservation of wild species because (that's my guess) the most healthy and strong are the most likely to rear healthy offspring. I said to myself that from what I've learned about evolution, the difference between the physical fitness of an individual feed by a less strong parent (compared to the rest of the population) and an individual feed by a stronger parent can't be so big that it overweighs the fact that when a hunter hunts smaller animals, he's more likely to hunt more of them (That's something that has been studied) so the overall number of hunted animals is actually bigger. So my question is, wheter I'm correct or wheter the factor of the bigger number of animals you hunt when you hunt small animals actually isn't as important as the fact that healthy and strong parents will rear healthy and strong offspring.


texts: Mechanisms and Assumptions of the Species-Area Realtionship

texts:
I would like to choose a model to use to describe a species area relationship based on plant species richness data that I have collected.  Rather than choosing the power model a priori, I am considering all options (eg. exponential, untransformed, etc).

Does anyone know of any good recent synthesis work on how to choose the best model?  Of particular interest are the assumptions behind each model, and the ecological mechanisms that each model might imply.


texts: Has an ape ever drawn/painted something?

texts: I know there are plenty of examples of apes making paintings and drawings, but has there ever been a recorded case of one representing something in their art?


texts:
So, some people and I encountered an adventure game where you have a bee in a jar and need to move it from place to place before it suffocates, and someone tried to find out how long a bee would actually survive in the jar. We've found three relevant papers:

Oxygen consumption in the foraging honeybee depends on the reward rate at the food source [1]
Oxygen consumption and body temperature of active and resting
honeybees [2]
Physiological Correlates of Foraging Efforts in Honey-Bees: Oxygen
Consumption and Nectar
Load [3]

which has given us what we think is a good high-end guess of 40µl of oxygen per minute consumed.

However, we don't know at what point the oxygen level would get too low for the bee, or if carbon dioxide poisoning  would occur. Does anyone have a source for the minimum oxygen levels a bee needs to survive, or the point at which CO₂ toxicity becomes a problem?


texts: How did hydrophilic plants become established on an isolated island with an arid coastal zone?

texts:
I find unconvincing the existing explanation of how several hydrophilic endemic plants became established at St Helena. This is one of the most isolated islands in the world, has an arid semi-desert coastline and moist and humid highlands where endemic hydrophilic plants grow. It has been suggested that plants originally arrived either as driftwood from the beaches or arrived inland because occasional birds accidentally blown to the island had seeds on their foliage or claws. However, not only would the brushwood of these hydrophilic plants be unlikely to propagate or survive the arid conditions of the coastal region, these plants normally propagate by root, not by seed.

Has the following third mechanism ever been suggested for the establishment of plants on an isolated island? I wonder whether brushwood fortuitously arrived at the point where streams were discharging into the sea. Despite the arid conditions at all other coastal regions, some plants could take root at these wet beach areas and then spread along the streams growing in the damp alluvial soil into the interior heights of the island. I know the migration of plants along the length of a stream or river (riparian zones) have been studied but I can find no reference to the idea that this can also explain the presence of hydrophilic plants in damp highland regions of an island with a surrounding arid coastal region.


texts: What is the diet preference of American cockroaches?

texts:
I found a research article1 on the diet preference of German cockroaches. It reveals that those cockroaches prefer to eat bananas most. I wonder if it is the same for American cockroaches. And also, can American cockroaches survive on wood and water alone?
 1. El-Sharabasy, H.M., Mahmoud, M.F., El-Bahrawy, A.F., El-Badry, Y.S. and El-Kady, G.A., 2014. Food preference of the German cockroach, Blattella germanica (L.)(Dictyoptera: Blattellidae). Cercetări Agronomice în Moldova, 2(158), pp.81-88.


texts: Why doesn't the spinal cord get thicker the further up we go?

texts:
The cervical and lumbar enlargements exist on the spinal cord as a result of the increased nerve input/output required for the arms and legs respectively.

However, I don't understand how the enlargements could exist by themselves without the rest of the spinal cord getting thicker.

The following is an exaggerated view of what I think a spinal cord should look like. The cervical region needs to be thicker as it has to accommodate the original nerves from the legs (blue) AND the new nerves from the arm (red). There are now ~2x as many nerves needed to go to the brain - thus the spinal cord above the cervical area should be twice as big. It is not - it just enlarges around the cervical area and returns to normal.

Why does the spinal cord not get thicker the further up we go? Doesn't it need to accommodate more nerve fibers and thus be thicker?


texts: What happens between making a DNA library and screening by nucleic acid hybridization?

texts: I understand how a plasmid library is made and how each clone is put on the nitrocellulose membrane and nucleic acid hybridization is done. What I don't understand is how each clone is "identified" and separately put on the membrane?


texts: Questions to ask to a panel of people that will be sequenced

texts:
Some genes have been shown to be associated with left-handedness.

Working with some clinicians, I've recommend them to ask their patients (whose genome will be sequenced) if they are "right or left-handed".
It's a simple phenotype (without any ethical issue) that will be later fun/interesting to analyze through the sequencing data outside of the main study.

Do you know any other such kind of simple phenotype that we could ask to our patients ? :-)


texts: What is the proper pronounciation of the scientific name of the ground elder / Aegopodium podagraria?

texts: A audio sample would be great. As a kind of bonus: I would appreciate a kind of database, which contains a lot of botanical plant names.


texts: Im assuming 'cicada' with this insect but which one ? Small size- c1c-2 cm -


texts: glossary of biotechnological engineering

texts:
Similar to A good book for history of biology/biotechnology for lay people

but not for lay people.

Can anyone recommend an advanced dictionary of biotechnological engineering concepts in English (contemporary, not historical)?

There doesn't seem to be anything adequate at my research institution nor even country.  I have been looking for PDF's and e-books since they can be previewed more easily than ISBN #'s, but any suggestions are welcome.


texts:
So i'm looking into the ebola crisis and it seems the death toll is really getting crazy.  I understand that it's a cytomegalovirus and that it basically overwhelms the immune system due to it's size and virulence but why is it so bad now?  What has changed about it?

The folks at the Dallas hospital were said to have 'broken protocol' but to me it seems the virus may be more infectious this time around.  Has it changed?  Mutated?


texts: Why does it matter to predict protein structure?

texts:
And how do you predict it ? What is your input data (sequence of amino acids, temperature, pH, ...) ? Is there a "standardized" input that scientists agree on ?

Moreover, I've read that knowing the structure of a protein helps predicting its function, but is the prediction [Structure -> Function] reliable ? Should't we predict directly the function if that's our interest (I don't mean we should not take into account predicted structure, but I don't understand why the structure IS the purpose instead of the function)
I also read the structure helps predicting affinities with other proteins and how it will bind : same question here, is this prediction [Structure -> Affinity] reliable and why don't we predict directly affinities.

To sum up a bit, I have the impression that the structure in itself is not important to know except that it is a good predictor of other protein properties (like function of affinity) and that the structure is kind of an 'intermediate' ? What am I missing ?


texts:
Suppose we have an alignment. When a phylogeny tool (PhyML in this case) is used on this alignment, a tree consisting of 5 clades is returned.

The thing is: suppose we have this alignment on a web site, and some user uploads a new sequence to add to this alignment. After realign with the new sequence, phylogeny inference is applied, and then, a tree visualizer.

I'd like to know which one of the 5 clades contains the new sequence (if any), without the need of looking at the tree.

How should I approach this issue? I think that first of all, I should define my clades (how to?), and then, measure distances from my new sequence, to all clades, and keep the one with the shortest distance...But I'm not sure if this is a good strategy (not to say I'm not sure how to accomplish this..)

This is maybe more of a concept question...

I'm working with biopython.


texts: Book for molecular biology comparative to major taxonomic groups

texts:
Want recommendation of books on molecular biology (or molecular cell biology), that elaborately compares the  structures and phenomena in the major taxonomic groups.

For say, whenever studying about a phenomenon ( may it be a structure like ribosome or nuclear DNA or plasmid or small RNA or nuclease enzymes, or may be phenomena like central dogma (replication, transcription, translation) or recombination or cell-division and its regulation, or may be protein folding or protein degradation, or biosignaling pathways)... I could get the analyses about in detail the similarities and the differences of the processes in different taxonomic groups.  Such as, How does that process happen in prokaryotes (both archaea and eubacteria) and eukaryotes? Or if further zoom-in; how the process varies in major group of archaea, bacteria(Gram-positive and Gram negative), protists, animals (invertebrates and vertebrates),  plants(bryophytes, pteridophytes, gymnosperms, angiosperms), or fungi (glomeromycetes,ascomycetes, basidiomycetes etc)? or how the processes takes place in the mitochondrial and plastidial genomes of the different groups of organisms?

Best if the book could provide ample amount of data tables.

There are books and articles specific to a few certain taxonomic groups; but I'm looking for the big picture or the bird's eye view.

Thanks in advance.


texts: How can I make sure my UV-purificator kills bacteria?

texts: I'm going to show a UV-purificator for water on science fair. How can I easily check if purificator kills most of the bacteria? I need a quick and possibly easy method.


texts:
Does Budding Yeast Sacchromyces cerevisiae produces significant amount of carotenoids?
Have anybody estimated the ratio of flux going in branches 1. Cholesterol synthesis(via squalene)
2. Coenzyme Q6 and 3. Dolichols Glycoprotein and others from the branch point of Farnesyl diphosphate.

Here is the kegg pathway

http://www.genome.jp/kegg-bin/show_pathway?map00900
I also have pathway formatted but couldn't upload.


texts: How to calculate the number of sterile insects that must be released in SIT?

texts:
The sterile insect technique (SIT) is used to control insect pests through overwhelming the population in sterile males. The increase in sterile males released into an environment causes the increase in infertile matings. This, in theory, would reduce the population.

However, how would you calculate the number of sterile flies needed to be released in order to be effective? It would be dependent on the reproduction rate of the insect, initial density, and sex ratio in the young, but is there an equation to express this? Or is there simply a generic ratio of the target population that is used?

I'm looking at the example of the New World Screwworm fly, and the eradication in Central America.


texts: Is the "Great Pacific Garbage Patch" beneficial for marine wildlife?

texts:
A study was just released by researchers at Scripps Institute of Oceanography revealing a drastic increase in the amount of plastic adrift in the Pacific Ocean. According to the paper, the amount of plastic in the North Pacific Subtropical Convergence Zone has increased 100-fold over the last 40 years.

But most of the news stories coming out about this discovery are thin on facts about the dangers of plastic. And the research even suggests marine wildlife may be benefiting from the artificial flotsam.

Clearly this increase in trash can't be good. Can it?


texts:
I photographed this flower on the street in Los Angeles.
It looks like a lilac, but I am not sure.


texts: What are the "stars" we see after a bump on the head?

texts:
Sorry  if this might appear funny. When I close my eyes for a longer time, and suddenly open  it, I see some twinkling white small circles, and when i concentrate on anyone of them it disappears, as if the image is falling on the blind spot.

This also happens when I am struck on my head sometimes accidentally. I would see thousands of tiny objects floating. What are these and why they appear shiny ?


texts: What is neutral genetic differentiation? Presumably it's a measure of the distance between organisms in terms of their genetics, but what does 'neutral' refer to?


texts: How to search for organisms by criteria such as growth substrate and overflow metabolites?

texts:
I'm looking for a database or a systematic way to search for organisms which meet certain criteria. My criteria descending importance are:

growth substrate
chemolithoautotrophy (on which substrate)
overflow metabolite
methanogen
Nitrogen-fixation

Is there a database / some other means to find this information other than manual digging?

I tried NCBI taxonomy, LINNAEUS, uBio, KEGG, organism-tagger and others, but these don't appear to be capable of this kind of query. They all seem to require the organism name to begin with. But maybe I'm missing something?

thanks for any hints.

Ingvar


texts: Why do we have to move in the cold for higher chance of survival?

texts:
To survive in the cold temperatures, a person should move as much as possible so that they do not freeze to death. But constantly moving also leads to the body becoming more and more exhausted.
Why doesn't the human body "know" that it is better to invest energy directly in heat rather than in movement and the resulting heat?
After all, the body already optimizes blood circulation, protecting the inner organs better than limbs like hands and feet.


texts: What genes in a plant determine whether a stem is erect or climbing?

texts:
I was randomly reading this Wiki article on Jasmine and this question crossed my mind after reading the following lines:

  Jasmine can be either deciduous (leaves falling in autumn) or evergreen (green all year round), and can be erect, spreading, or climbing shrubs and vines.

How can a plant be both erect and climbing at the same time?

I have looked for genetic mechanisms related to this, correlating environmental or other stimulus with this phenomenon, but have not found a satisfactory explanation.

So how does this occur?


texts: Multiple transcripts matching same gene in de novo assembled RNA-seq data, but FPKM values vary?

texts:
I have a data set of de novo assembled RNA-seq datasets across different sample types.

When BLASTing, many of the matches of the individual transcripts match to the same gene on the reference genome. However, each individual transcript has its own unique FPKM value.

I'm confused, firstly, as to how you can have multiple sequences from the same gene with different FPKM values — and of course, I'm also wondering what would be a suitable approach for the subsequent analysis. Should I just add the FPKM values together for the sequences with the same matches?


texts: Why do we have more sweat glands in our palms?

texts: Why is it that we have more sweat glands in areas such as the palms of our hands and the soles of our feet? I just learned that there are more there but I am curious as to why that is.


texts: Why are watermelons sweeter in the center?

texts:
Today I had a slice of watermelon and when I reached the outer parts of the pulp I wondered why those are less sweet.

Whether or not the sugar occurs in crystalline form in watermelons is still an open question, but a quick search on the internet did not yield acceptably thorough answers.

The options I found are as follows (in descending order of personal preference):

Watermelons ripen from the center outwards.

If this is the case, then watermelons wouldn't grow during the ripening, right? So they would need to achieve their final size before the ripening sets in. Or maybe it's the other way around: They ripen as they grow, and as such the center has the highest concentration of sugar.
The sugar is needed by the new seedlings to grow. (Although I think this hypothesis has been disproven with apples.)

Has any of this been proven, has there been research done on this matter?


texts: Book on current state of knowledge on the genetics of intelligence

texts:
I'm looking for a book that gives a good summation of the current state of knowledge on the genetics underlying intelligence.

I have read textbooks on human population genetics but I'm looking for something more specific.

I'd be happy for pointers to any books on neuroscience, developmental psychology, genetics that give some coverage to this topic.

I am not really looking for a popular science book.


texts: What is the Attributable Risk of birth defects in Zika infected pregnancies?

texts:
Vital Signs: Update on Zika Virus–Associated Birth Defects and Evaluation of All U.S. Infants with Congenital Zika Virus Exposure — U.S. Zika Pregnancy Registry, 2016

A recent CDC report shows that 10% of laboratory confirmed Zika pregnancies in the US had "birth defect reported."  However, I cannot seem to find an attempt to compare this to a base rate in the US of a similar population.  Is there existing information or a way to determine the Attributable Risk (difference in rate of a condition between an exposed population and an unexposed population).

10% sounds scary, but without a base rate, it's not very meaningful in the context of determining how dangerous the Zika virus is.

EDIT (for clarification):

I'm primarily concerned with the method in which birth defects were collected. 'Clinical experts reviewed reported information to ensure that each fetus or infant with birth defects met the criteria of the USZPR case definition.', but this seems to have been done only with the Zika-positive groups and not with a Zika-negative group. They compare it to a pre-Zika baseline, in which inclusion to the surveillance was different and determination/clinical review of each case was different. Did they (or another research group) perform clinical evaluation of birth defects during the surveillance period on Zika-nagative pregnancies using the same methodology?


texts: Is it possible to give a person an allergic reaction in a very specific place?

texts:
Can I give a person an allergic reaction at a very specific spot in a tissue?
And if so, how accurate can i get?


texts: What accounts for the apparent lack of biodiversity in "bamboo forests"?

texts:
While hiking on the Hawaiian island of Maui, I passed from a forest with normal variety in trees and other flora, to a "bamboo forest" area in which the only plants that I could see were bamboo.

This was surprising to me! Why does only bamboo (appear to) grow in this area?

The assumption I'm making is that bamboo forests happen elsewhere in the world, not just in Maui.


texts: What is the scientific and common name of this bug?

texts:
Captured this under my stereo microscope. Much more beautiful than appearing on my camera sensor.
Can someone help me identify it and explore more?
Also is it having a compound eye ?
Location: New Delhi.


texts: Does anyone know of a protein/molecule that can be attached to one end of the DNAs temporarily ? eg. i would like to only to allow one strand of DNA be ligated to another DNA molecule to either it's 3' or 5' but not both. thanks


texts: Are there baby drinks closer to breast-milk?

texts: Many women cannot or will not feed their children with breast-milk. It is my understanding breast-milk has many advantages over formula. Some psychological like oxytocin and some physiological like advanced antibodies. Have there been any attempts to create a formula with better psychological and physiological properties? Is it even possible to include antibodies in formula or milk?


texts:
RT is capable of synthesizing a complementary dna strand ( as in HIV life cycle.) Then why is
DNA pol used when cDNA (synthesizing the second strand of it ) has to be synthesized from mRNA ( For eg.to construct a cDNA library) ?


texts:
I hold no strong opinions towards homosexuality one way or the other; I'll personally refrain, but don't apply my personal tastes to the rest of the world.

I remember seeing some articles a while back, and in some online debates, that there's been evidence in favour of a genetic component of homosexuality. I ignored it back then (before it became legalised), since it didn't affect me. However, after deep thinking, I started to seriously doubt those stories.

My gripe is this, based on my extremely limited understanding of Evolutionary Biology, organisms with genes which boost survivability, will tend to become more abundant. Genes that made organisms more fertile and reproduce more, will tend to become more abundant.

So, if say a particular gene, reduced effective fertility of organisms, that gene may be expected to be absent after a while. Fewer organisms with that gene would reproduce each successive new filial generation. There will be a diminishing marginal increase in the population of these gene bearers, before there eventually starts to become negative growth. I expect that population, may eventually find themselves in extinction, or on the brink of it.

In the few 100,000 years that Homo Sapiens have walked this planet, I guess there's been sufficient time for a population of genetically predisposed homosexuals to become extinct, or reach its brink. Certainly not the 5% - 10% estimated population we have today.

As such, I am unable to understand how homosexuality might be determined by genes in spite of natural selection.

My understanding of Evolutionary Biology may be severely lacking; especially as my teachers in the subject believed it was blatantly false, and were not really interested in making their students understand it. Some even going to the extent of making it seem as ridiculous as possible (I live in a country, where more than 90% of the population are genuinely religous (as in they truly believe in the existence of God) in one form or the other). I would appreciate answers to my question.

Of course, whether or not treatment of homosexuals should change, is another separate matter. It certainly does not follow from any conclusion of this inquiry; the answer to this question, is irrelevant as far as LGBT rights are concerned.


texts: How is the site of administration of a vaccine decided?

texts:
Vaccines can either be given intramuscular or subcutaneous or intradermal. I know the technique used is specific for each organism. What decides this?
I understand the reason for oral vaccines in polio but, why should a vaccine that is given s/c not be given im?

If there is a logic to this (which I am sure there is), it would be a lot easier to remember the same.


texts:
This morning I saw a bird that I have never seen before. Since it was quite big, I'm very interested in knowing its name.

The bird was quite big, at least 2-3 times of a common blackbird. The wings were completely black but the whole back strip was quite yellow. Also the tail was yellow. The tail widens towards the end.

The bird flew very strange... it trundled towards the ground and then flew back up some meters before trundling down again. I observed the bird in Zurich, Switzerland at the outer border of the city. A big forest is quite near and there are some huge trees very close to the bird.

Then one last thing to add: I'm not really sure about that, but it could be that the bird had a nest on top of a big tree.

Any ideas which bird that could be?


texts:
What is the distribution/probability density function (PDF) of recessivity/dominance of new mutations?

I very welcome any partial answer that does not give the whole PDF but just some information about the expected value or the variance of this distribution.

Here is a related question


texts: Which predators only eat some parts of their prey? (Warning — graphic content)

texts: In an small city in middle-east somewhere near a desert, an unknown predator attacks sheeps, goats and chickens. These attacks began a few weeks ago and until now more than 150 sheeps have been attacked. It causes panic and rumors among people and despite official investigations no result has been achieved yet.


texts: Can I use multiple bicistronic RBS sequences in a synthetic biological circuit?

texts:
The bicistroninc RBS sequences (BCDs) developed by Mutalik et al. [1] aim to remove context sensitivity from translation and therefore ensure more predictable gene expression. However, I have been told that having multiple transcriptional units, each using BCDs, can make cells sick. The explanation that I was given was that the toxicity is from small peptides that are produced from transcription from the first RBS sequence.
Has anyone demonstrated toxicity from multiple BCDs or is it apocryphal? If it has been demonstrated, is the mechanism of toxicity known and is there a way to use multiple BCDs while maintaining healthy cells?
[1] V. K. Mutalik et al., “Precise and reliable gene expression via standard transcription and translation initiation elements,” Nat. Methods, vol. 10, no. 4, pp. 354–360, Apr. 2013.


texts: Can anyone identify what is the name of this plant?

texts:
I found this plant on the side of the street in Melbourne, Australia. Looked like someone just removed it and threw it from their garden. So I took it home and planted it.

The plant had damaged leaves which I removed. (https://i.stack.imgur.com/htnbK.jpg)


texts: How to determine which is the nucleotide sequence of a gene?

texts: I have came across a few  genes that show different nucleotide sequence in different databases. I then found out that the sequences are actually reverse complement of each other. How do i determine which is the actual nucleotide sequence of a gene,and not the reverse complement version of it?


texts: Is it possible that there are unknown vitamins?

texts: Is it possible that there are vitamins or other essential nutrients about which we still do not know?


texts: What sort of biofiltration is best for a small, portable, biofiltration unit?

texts:
I've been exploring the idea of a system to allow re-use (drinking) of RV greywater, or at least the freedom to dump in storm drains (I think the requirements are looser about this, but it still has to be somewhat purified)

Greywater is wastewater that does not contain feces. The primary contaminants would be food waste, various soaps (probably only biodegradable or non-antibacterial), and used shower water. I would also probably add urine, after sterilization to remove pathogens.

I was thinking of pre-filtration to remove larger fragments and detritus. Probably with the highest grade of this

-Processing rate would have to be 10 liters per day absolute minimum. 2x to 3x that would be best.

-Weight and volume are both at premium


texts: Data on Recombination rate and Gene Positions in Humans

texts:
I am looking for estimates of per base pair recombination rate in humans and indication on gene positions. The goal is to be a able to plot recombination rate in the y-axis and position (in bp) along all chromosomes in x-axis. Then add the genes on the graph.

I have never had to search for this kind of data. Can you give me some hints of where I could find these data into a simple format like the simple table presented below?

> Gene Positions
from       to
1145146    1147112
1568742    1570012
...

> Recombination rate
from   to       r
1      156787   1.2*1e-9
156788 256888   2*1e-8
....


texts: How do I get the current "camera position" in PyMol so I can reuse it in scripts?

texts:
I have a few protein models I want to take pictures of with various ligands bound.  It would be nice if I could do it from the same "position", but the only way I can figure out to repeat the same view is with zoom resi. 64, 152, 150 or the like, which isn't framed that well.

How can I manually position the viewport, capture it's parameters, and repeat it in the script?

I have found get_view, e.g.

PyMOL>get_view
### cut below here and paste into script ###
set_view (\
     0.590180993,    0.670941532,    0.448923886,\
    -0.507570565,    0.740831316,   -0.439937204,\
    -0.627747774,    0.031782545,    0.777776182,\
     0.000000000,    0.000000000, -417.497009277,\
     0.741809845,    7.078243256,   16.473480225,\
   329.157806396,  505.836212158,  -20.000000000 )
### cut above here and paste into script ###

but this doesn't work in a .py script, where I need to modify it to cmd.set_view(...), as it complains it wants just (or up to 5) arguments, not 18.  The wiki is vague about it, it just says

  PYMOL API

cmd.set_view(string-or-sequence view)


texts: What happens when someone is stung by a jellyfish?

texts:
What happens in the human body when someone is stung by a jellyfish; namely a box jelly. Judging by what I have heard about the stings I'm guessing that they involve a neurotoxin.

But what is actually happening? What are the symptoms and what happens after the sting (treatments and survivability)?


texts: I heard about this supplement that lengthens telameres, slowing down aging. Does it cause cancer? I can't seem to find any definitive proof either way... https://www.tasciences.com


texts: RNA vaccination and Autoimmune Reactions

texts:
To my knowledge we do not have any robust experience with RNA vaccination. Most likely this will change in the near future as RNA vaccines against COVID are in the pipeline. The rationale behind this method: Viral mRNA is injected (I guess in a muscle), the mRNA is translated (in muscle cells, for instance), the protein is exposed on the cell surface to cause a response of the immune system. As we know proteins tend to interact and build complexes. I speculate that this could easily lead to an immune response against cellular protein structures.
Is there any knowledge or speculation concerning an autoimmune disease in succession of RNA vaccination?


texts:
It is approx 2cm long and was discovered in house after a bush walk & BBQ at Riverside Garden Reserve in Mandurah, Western Australia. It has 6 legs.

Thanks! :-)


texts: Why would you plate cells at different densities in a colormetric assay?

texts: The aim of my experiment is to see if a kinase inhibitor reduces cancer cell viability. I am using 2 different cell densities 50,000 cells/well and 100,000 cells/well and different doses of the kinase inhibitor.


texts: Ribosomal Turing Machines, DNA/RNA computation

texts:
I'm a computer science guy, recently crossing over to do some research in computational biology on RNA secondary structure prediction. While looking through the materials I got a crazy idea, what if you could design a synthetic ribosome that acts as a Turing Machine on strings of RNA? (you could do similar things with DNA enzymes)

The immediate applications could be stuff like correcting mutations in RNA to cure genetic diseases, which is a relatively simple computation:

Check if a string is bad.
If so, fix bad letter.

Another could be "shredding" DNA/RNA of viruses:

Check if a string is a virus.
If so, shred it.

I'm not sure the status of the literature on this is, or synthetic biology's ability to create something like that. Do you think it is a good idea to pursue this idea or not?

I realize this is a soft question. Perhaps a better one would be, is this possible?


texts: How can green algae be both multicellular and unicellular? What are the cases in which it can be both uni and multi cellular?


texts: Is there a correlation between muscle fibers and body types?

texts:
I have been told the number of muscle fibers a particular muscle has varies from person to person. Unfortunately, the person who told me this did not know much more than this. Initial searching on the web did not reveal much detail on this; some random sources suggested there was a correlation but they weren't referenced.

Is there a general correlation between the number of muscle fibers and body type (mesomorph, endomorph, ectomorph)?

What about a correlation between muscle fiber type (Type I/Type IIa/Type IIx/Type IIb) and body type?


texts: How cotranscription events affect splicing?

texts: I want to know how and how often does cootranscription takes place? Can transcription regulators influence splicing during cotranscription?


texts: Is this a spider caught on video floating its web between trees?

texts:
I live in the US and have trail cameras on my property to capture wildlife, visitors, stray animals, etc.  Several are equipped with infrared and I have watched hundreds of hours of video. Many videos feature a large amount of insects flying so I know what a bug looks like on infrared.

What I captured yesterday is completely different. It is a perfectly round sphere floating from one side of my driveway to the other and back again. It appears to me to be on convection currents passing between the trees that line my driveway.

I uploaded this video to Youtube and would be very grateful if you could take a look and tell me if you think it is indeed a spider floating its web between trees. Additionally, are you aware if this phenomenon has ever been captured on video before?  I searched the web looking for other videos but am unable to find any.

The 'orb' appears at 10 seconds into this video.


texts: Terrestrial locomotion of bats and pterosaurs

texts: Bats and pterosaurs have skin attached to their forelimbs that aid them in flying and when they are on land, they use all four of their limbs to walk in a quadrupedal posture. Can these organisms be considered as true quadrupeds? Is there a different term used for this type of locomotion?


texts: Is there a formal definition of `nature` in Biology?

texts:
I've been discussing with a friend about Earth Day and at a certain point came out the question

  What do you call "nature"?

He said that he considers "nature" basically all matter, including plastics and all kind of man-made materials.

I said that as far as I understand, "nature" is the ensemble of all Earth's ecosystems, thus if something is not part of an ecosystem, it is not "nature".

Is there an official definition of what is considered to be "nature"?
If yes, what is it? If no, is there a reason?


texts: Relationship between membrane current and voltage in neurons

texts:
Depolarization of neurons leads currents of different magnitudes flow in or out of the cell, and the Sodium and Potassium currents can be separately plotted (Purves):

Caption: Relationship between current amplitude and membrane potential,
taken from experiments such as the one shown in Figure 3.2. Whereas the late outward
current increases steeply with increasing depolarization, the early inward current
first increases in magnitude, but then decreases and reverses to outward current
at about +55 mV (the sodium equilibrium potential). (After Hodgkin et al.,
1952.)

Here we see the dependency of the currents (early: Sodium, late: Potassium) on membrane potential.

What I was wondering was this: It looks like the dependency of the Sodium current on the membrane potential is very non-linear.
However, experiments which assess the amplitude of injected current on excitatory postsynaptic potentials (EPSP) state that the amplitude of EPSPs are proportional to the injected current. How is this consistent with the non-linear current/permeability changes of Sodium? Is the Sodium current linearly dependent on voltage (and vice versa) before the action potential threshold is reached?


texts: Is this a simple Hardy-Weinberg problem?

texts:
Phenylketonuria is a severe developmental disability due to a rare autosomal recessive allele. Approximately 1 in every 10,000 newborns suffer from this disease. Calculate the frequency of the allele causing this disease and the frequency of heterozygous "carrier" individuals.

What I've come up with is that this is a Hardy-Weinberg problem. Is this true?
My answers:
frequency of allele causing disease = 0.01
frequency of heterozygous "carrier" individuals = 0.0198


texts: Which C. elegans would be appropriate for general study?

texts: Would wild type N2 be best or Dyp-11? I know they're different, but I just want to observe the worms to see life stages, movement, etc. Dyp-11 seems like it would be easy to see but N2 is the wild type so I need help making an appropriate decision.


texts: Condition for a genetically modified group of cell to remain and to spread?

texts:
I was wondering: when a treatment modifies a group of gene (like in gene therapy), what makes a group of cell remains?

I mean, when a cell divide itself to create new ones, if a cell was initially genetically modified, it will lead to two modified one, right? But, I assume that we have a finite number of cells in our body, so if the process was going on like that, we would just have to modify one cell of our body. But, besides this, the other cells divide themselves too, so there might be something that makes a group of cell dominant (like the proportion, the number of neighbors of one cell...).

So, my question (cut in three) is:

What are the conditions for a group of modified cells to remain?
In what extend the modification can spread?
If it can't spread, why?

(I'm not a biologist student (I studied it in high school, so I may be able to understand the basics), but I'm interested in making a mathematical model of such a process. So if there is an answer, could you make it understandable for someone who has only the basis?)


texts: Ecological specialization and relative abundance

texts:
I am reading Evolution in Changing Environments by R. Levin but have a hard time.

Claim

At page 25, Levin says as a conclusion

  The more efficient a caste at meeting the contingency for which it is specialized, the lower its abundance. This is seen in Figure 2.5b

Here is figure 2.5b It is actually a reprodcution I did in R but ressemble closely the original

W1 is the fitness in environment 1 and W2 is the fitness in environment 2. The figures comes with the following legend:

  The optimal population consists of two castes in the proportions of the line segments by the Adaptive Function (dotted line). Thus castes C1 and C2 are more or less equally common, but a population of C1 and the more specialized C3 will be mostly C1.

The terms "Adaptive Function" is not really defined in the book but it basically mean the overall fitness given the fitness components W1 and W2. The terms "castes" and "contingencies" aren't accurately defined either. In his model, the population experiences only these two environments, where $p$ is the probability to be found in one specific environment. As I understand little from this book, it is hard to know what kind of a prior information I could/should give you.

Question

Can you help me to understand the above statement and why it makes sense?


texts: Genes-of-interest analysis between organisms

texts:
I am interested in identifying the differential expression between several genes-of-interest of different organisms.

I am trying to assess the benefits of RNA sequencing over microarrays. Both techniques are a means to an end. With both of these two methods one can "count" the differences between two conditions, e.g. cell types, time points etc. They do use different technology to achieve it, but they both give a certain number 't' in the end, which can be looked at as the strength of the expression of a specific gene under a certain cellular condition. One can than compare the two (or more) conditions to get a picture of what is different in the cell due to the changes.

As I am new to this field, can someone tell me what the advantages are of RNA sequencing over micro arrays? Alternatively, information on comparisons between microarrays and RNA sequencing methods are welcome.


texts: I'm just curious as to whether crocodiles and if you require specifics, saltwater crocodiles, could eat bread as infants. I was watching Lake Placid and I was curious as to whether infant saltwater crocodiles could even digest bread.


texts:
Location: Johannesburg, South Africa

Colour: Brown/Grey

Legs: 6 or 7 pairs

Size: ~10mm

I've been finding these guys in my bath tub the past two mornings. I've caught and released them. I'd like to know what they are so that I can decide whether pest-control measures are needed.


texts:
I have found in a wooden house, in the mountains of central Spain this very curious insect:

I was wondering if that was its skin or whether it's decomposition or sand or saw-dust.  That particular region of Spain does have stink-bugs ... but this one doesn't look like anything I've seen before.  A google image search returns mostly arachnids ... but it seems to have only 6 legs.


texts: Nerves, Neurons, Axons and Dendrites by Example

texts:
Here is a simple diagram of a neuron:

A few (very closely related) questions:

Where are receptors located (for pain, pressure, temperature, etc.): in the axon terminals or the dendrite tree?
Please confirm: for sensory nerves, signals travel from axon terminal to dendrite tree, yes?
According to Wikipedia, axons communicate with each other across synapses, and nerves are chained bundles of axons (basically forming a cable with each other). However, if sensory signals travel from axon to dendrite, then how can axons be chained together? In other words, if axons are a "male" recepticle, and dendrites are a "female" recepticle, then how can you have a chain of all-male recepticles?
Please confirm: a nerve is just the cabling that houses bundles of long, individual strands of neurons, yes?


texts: Why do our bodies maintain blood pressure but not the flow rate?

texts:
This might be a silly question but i'm not not clear

I'm always told that blood pressure is homeostatic parameter and can't not be changed but isn't what important is the flow rate to the organs? why not maintain flow rate

Doesn't having enough blood flow to the organ already satisfy our bodies to function properly or do pressure play any role? what happens if blood flow is constant but blood pressure drop below normal

there's some case when one have blood lost , pressure drop and our bodies respond by constricting artery and that results in decreased cardiac output.Isn't that worst? decrease cardiac output just to maintain blood pressure

Forgive my little understanding out this I know my thought is kind of logically wrong but please help me understand. thank you


texts: Transcranial Magnetic Stimulation on science fair

texts: My friends and I would love to make a TMS machine and apply it to make famous "god helmet". We know that magnetic stimulation may cause visions of angels, gods etc. My question is: what are the dangers?


texts: How does this small brown crescent-headed land planarian(?) "look around" and sense its envirnoment?

texts:
This 2-3 cm long, thin brown worm with a wide "anchor" or hammer or crescent shaped head was seen in northern Taiwan slowly moving along a damp tile outdoor surface. It moved by contraction/extension and regularly lifted its head appearing to explore its environment, as if to say "where should I go next"?
Comments suggest that this is a land planarian.
Question: Is it possible to confirm that this is a land planarian and to understand what sensory organs it has on its head in order to "look around" and decide where to go next?


texts: Does THC excretion increase if urine volume increases?

texts: In regards to the body metabolizing and excreting THC: if urination is increased as a result of drinking lots of fluids, does that mean that more THC is leaving the body? To rephrase the question, is metabolism required for urination? Or can you simply urinate as a body process without metabolizing toxins from your body?


texts: I'm going to engage into making florariums (a garden in the bottle). I've heard, that violets die in closed space. Do anyone have an idea, what is the reason for that? Lack of oxygen or CO2 or moisture control issues?


texts: Why do human ears have a lower boundary for the lowest energy perceivable signal than eyes?

texts:
I am currently hearing a lecture about human machine interaction. The lecturer is not a biologist (neither am I, we are both computer scientists), but he makes some statements about biology which I think are questionable.

One statement was that the energy of the lowest perceivable signal for eyes is  and the energy of the lowest perceivable signal for ears is . He cites those values from the following (German) source:

  Schmidtke, H. et al. Handbuch der Ergonomie mit ergonomischen
  Konstruktionsrichtlinien und Methoden. Koblenz: Bundesamt für
  Wehrtechnik und Beschaffung (BWB)

  HdE (2002): 2.4.1, Abb. 2

  [KIT-Bibliothek: 2007 E 1808-1(2) (Präsenzexemplar)]

It is clear that those values vary from person to person. Assuming they don't vary too much, it is interesting to know why the human ear can detect signals with lower energy than the human eye.

According to my lecturer, the reason is because we can hear in all directions, but see only in one direction. He argues that hearing is much more important for this reason to detect predators, even if they are silent.

However, this argumentation seems very weak to me. I would rather think that there is a range in which "interesting" signals occur. If the interesting signals have lower energy for sound than for visual signals the ear adapted to this range.

I guess if the hypothesis of my lecturer is correct, then animals which can see in all directions would (always / very often) have much worse ears. If my hypothesis is correct, then there would be no significant difference in animals with "panorama-vision" and animals without in terms of lowest perceivable energy for ears and eyes (assuming fair comparisions; unfair would be comparing fish with land animals as the medium might play a big role).

Is there any source (written by somebody from biology, not form computer science) which makes a claim about this question?


texts: How is ATP involved in muscle contraction?

texts:
The sliding filament mechanism as explained by my text does not elaborate on how ATP is involved in the cross bridge binding and contraction process. How does muscle contraction utilize ATP?

In my text explains this is the procedure for a contraction:

Ach released by motor neuron cross cleft and binds to motor end
plate
AP generated in response to binding of Ach gated channels and propagates down T tuble
T tuble triggers Ca2+ from sarcoplasmic reticulum
Ca2+ binds onto tropinin on actin filament and removes tropomyosin
This opens up sites for myosin to attach to actin using protein heads
Actin filament is pulled toward the center of sarcomere, causing contraction

I see that the action potential definitely needs ATP in order to be generated, aside from that I am surprised that the actual contraction via cross bridge binding does not seem to need ATP.


texts: How is the electrical potential difference distributed between two stimulating electrodes?

texts:
Suppose I set the voltage value of an isolated stimulator with a floating ground. I place one electrode above the spinal cord (positive) and the other placed subcutaneously far away from the spinal cord (negative). The circuitry within the stimulator will operate in such a way that the electrical potential difference between these two electrodes is the value I specify.

The stimulator can fix the electrical potential difference between the two electrodes in multiple ways:

Hold the positive electrode's potential constant while changing the negative electrode's potential.
Hold the negative electrode's potential constant while changing the positive electrode's potential.
Adjusting both electrode potentials using a rule.

Although each of these ways can fix the voltage between the electrodes, they do not have equal effects on the biological environment that the electrodes are placed in. Going back to my example, if the stimulator obeys 1, I would expect a larger effect to be induced local to the spinal cord, in contrast to 2, which would would have a greater effect in the subcutaneous area. This is because there is an initial heterogenous charge distribution.

How should I assume my stimulator is fixing the potential difference between my electrodes?


texts: How do the antibodies in colostrum survive the infant’s digestive system?

texts: What happens when the antibodies in colostrum reach the infant's stomach? Why aren’t they destroyed by digestive enzymes?


texts: What is the difference between intracardiac and extracardiac reflexes in cardiac regulation?

texts:
The primary parameters of heart pumping are

strength of contractility (inotropic positive; Frank-Starling relationship)
rate of relaxation (lusitropic positive)
heart rate (chronotropic positive)

which change the secondary parameters according to the marginals

Heart rate
Stroke volume

Contractility
Starling relationship

Which of these paramecers are controlled intracardiacally and which extracardiacally?


texts: What causes the preliminary changes in resting membrane potential in neurons?

texts:
Background: The neuron's membrane resting potential is maintained at a certain voltage. The neuron has a lipid bilayer with certain protein channels which allow the movement of ions in both directions (in and out). Some of these protein channels are gated by:

1) mechanical changes (stretching, pressure, etc)

2) voltage changes- regulated by electrical signals (transport of Na+, K+ through protein channels)

3) Ligands (neurotransmitters, etc)

(Guyton and Hall, Textbook of Medical Physiology, 2016)

Question: If action potentials are brought about by voltage-gated channels which are activated by the change in voltage, what brings about this change in voltage which activates voltage-gated channels?

It sounds a bit convoluted. Here's a quote from Wikipedia's Membrane Potential page:

  Because voltage-gated ion channels are controlled by the membrane potential, while the membrane potential itself is influenced by these same ion channels, feedback loops that allow for complex temporal dynamics arise, including oscillations and regenerative events such as action potentials.

Hopefully this quote will help to communicate my confusion.


texts: Well, I was watching a video about chameleons and I saw that their cells can change color. Can someone explain me how is this possible?


texts: Where can I find clinical trial data published in JAMA?

texts:
Data in the paper:

http://jama.jamanetwork.com/article.aspx?articleid=336799

is cited in the statistical analysis in the book Clinical Trial Data Analysis using R. Can anyone help me find it?


texts: Can an importin without any cargo pass through the NPC?

texts: Can an importin (nuclear import receptor) without any cargo pass through the Nuclear Pore Complex (NPC)? If it can, wouldn't it be a waste of energy to have the 'unloaded' importin enter the nucleus and then binding to GTP?


texts: I was walking around outside my house when I found this little guy clinging to the outer wall of my house. The house in question is located in Indiana, United States. What is interesting to note is that the skin that is normally covered up by the frog's hind legs is yellow, but the rest of its belly is not, and this can only be seen when the frog is spreading its hind legs. You can see some of the yellow skin poking out from behind the left hind leg in the picture. This was at night, and the frog couldn't have been longer than an average person's index finger.


texts: Should I consider [H+] as substrate in MCT transport equation?

texts:
I'm trying to model the transport of lactate in cells (in both direction via Monocarboxylate transporters):

[Lactate]intra + [H+] <----> [Lactate]extra + [H+]

I found some data on kinetics of Lactate itself (Km and Vmax) but I don't find anything on [H+].

My initial thought was to consider [H+] as a substrate, and model the transport as a sequential ordered Bi-Bi reversible reaction (from this paper: Poole & Halestrap (1993). Transport of lactate and other monocarboxylates across mammalian plasma membranes. doi:10.1152/ajpcell.1993.264.4.c761)

But it require a lot of parameters (Ki, Km, Vmax) for each substrate involved (especially H+).

So my question is: Should I consider [H+] as a substrate or just as an external parameter that impact the direction of the flux ?

Thanks everyone

(first question on Stackexchange)


texts: What do trans-fats do when in human body?

texts:
Trans fats cause health problems, especially to the heart.  https://en.wikipedia.org/wiki/Trans_fat#Health_risks

My guess is that all effects happen because trans-fats are inherently toxic as the body never evolved to process them. But then L-glucose has no harmful effects, even if it cannot be digested.

So how are trans-fats processed in the body differently, and where does all the harm happen?


texts: How C. Elegans is used for siliencing genes

texts: The experiment that is using C. Elegans to silence the Genes. I have a question about Why and how C. Elegans can use the DNA plasmid that is generated with the gene of interest in the bacteria by being fed the bacteria?


texts: How Much DNA do Siblings whose Parents are First Cousins Share?

texts: On average, two siblings generally share 50% of their genome. How much does this increase if the siblings' parents are first cousins?


texts: Is it possible to transplant a brain and would it keep the memory? If not, what would be the prerequisite to transplant one?


texts:
If you ask Wikidata "Does the species lion (Q140) have a parent taxon line up to the Osteichthyes (Q27207, bony fishes)?", it answers yes:

SELECT ?item1
 WHERE {
  wd:Q140 wdt:P171* ?item1.
  ?item1 wdt:P171 wd:Q27207.
 }

Here's a direct link.

Now, I assume that this must be wrong at some level (I'm no biologist, so please correct me if I'm wrong), so I tried to find the error.

This query displays that path more explicitly, starting with mammals:

Mammals (Q7377) have Tetrapoda (Q19159) as a parent taxon.
Tetrapoda (Q19159) have Tetrapodomorph (Q1209254) as a parent taxon.
Tetrapodomorph (Q1209254) have Rhipidistia (Q150598) as a parent taxon.
Rhipidistia (Q150598) have Sarcopterygii (Q160830) as a parent taxon.
Sarcopterygii (Q160830) have Osteichthyes (Q27207) as a parent taxon.

The third point seems strange, because Rhipidistia are described as a taxon of fish, which would mean that all mammals are fish.

Maybe this comes from the fact that tetrapods (and therefore mammals) evolved from Sarcopterygii 390 million years ago, as described here.

Is "having evolved from" considered a parent taxon in biology? If not, which of the five statements above is wrong?


texts: How many genes are needed for a living organism?

texts:
I am interested in this question as I'm doing research into early life on earth which is believed to have been single-celled. Therefore, by extension, it seems only logical that the first life would be as genetically simple as is possible, therefore I present the above question.

How many genes / pairs of AA would be the bare minimum for something to be considered alive and function as an organism.


texts: For all those who keep in touch with advancements in field of biology iPSCs ought not to be a foreign term. iPSCs are now being used to make organ models to be able to study diseases and how drugs will affect them without needing any living host. I expect this organ modelling to become more and more advanced in future and soon all complete organs to be made using this technology. However should making a complete living brain ever be allowed for studying diseases as we are mostly our brain, so maybe while using such living brains we are making conscious systems on which we are experimenting?


texts:
Within a species there may be subspecies that are named using trinomial nomenclautre. For example the Grizzly Bear, Ursus arctos horribilis is a subspecies of the Brown Bear Ursus arctos.

The dictionary definitions of subspecies seldom expand beyond this:

  A taxonomic category that ranks below species, usually a fairly permanent geographically isolated race.

I'm assuming redefining species into subspecies is not a completely arbitrary process as the definitions would imply, but is based on biology. What are the biological criteria for a group within a species to be "upgraded" to a subspecies?


texts: Understand and reproduce withdrawn publication method - Blastp - covid19

texts:
I try to reproduce the method of this withdrawn paper. I know this paper has been debunked and withdrawn. I am curious to understand the details of the method used on it. I am a programmer and I don't work on the field of Biology.

I have some questions about "The identified amino acid and nucleotide sequence" with
MultAlign software:

I have trouble to understand how those supposed "inserts" were selected:

"Insert 1": The selection is where there are dashes and dots on the second and third lines because the sequence is not present in SARS-GZ02
"Insert 2": The beginning of the "insert" start with these dash and dots but why is it stopped at 155 ?
"Insert 3": The end at 261 is at a dash for the second line but why does it starts at 256?
"Insert 4": why these start and end of selection?

Later on the paper they used these selected regions with Blast and on the "motif alignement" column these letters are used which are a little different:

"Insert 1": TNGTKR (first letter "G" removed)
"Insert 2": HKNNKS ("YY" removed)
"Insert 3": RSYL-TPGDSSSG (4 letters at 250 added)
"Insert 4": QTNS-PRRA

Why are some different from the selection ?

Even for the first "insert", I can't find those alignement with Blast using for example GTNGTKR or TNGTKR. If someone could indicate me the good parameters in Blast to find these alignements it would be awesome.

Sorry if it sounds too ingenuous, thank you for your time reading all this.


texts:
What flying insect is this?
Found in Russia. Approx. 7 cm.


texts: Can we measure the rate of mutation in (say) E. coli without gel electrophoresis or genome sequencing?

texts: If so, how? And, what are the pros and cons?


texts: Have we ever observed fertile offspring with a different number of chromosomes than the parents?

texts:
Chimpanzees are supposedly the closest relative of humans from a DNA perspective, they are both diploid, and they both undergo meiosis. However, chimpanzees have 24 chromosome pairs while humans have 23.

Have we ever observed a situation where the offspring of meiosis has a different number of chromosome pairs than the parents, the offspring lived, and the offspring was not sterile? How does evolution explain the shifting of chromosome pair counts?


texts: Why does our eyes got wet when we feel emotional or whenever we are hurt?

texts: I was thinking like whenever when we feel emotional or whenever we got hurt we got tears from our eyes but why is that happen ? Why our eyes got wet ?


texts: Do nerves work as I think they work and what does that mean for our senses?

texts:
Let me start off with a couple of metaphors.

In the third Lord of the Rings film, a signal for help is sent from Minas Tirith to Gondor, using a chain of beacons. When the keepers of one of these beacons sees that the one next to his lit, his orders are to light his own thus passing on the chain reaction. When the last one within sight of Gondor is lit, the message that Minas Tirith wants help is received.
There is nothing conveyed in the fire itself, no information within the flames, the beacons are either on or off. The only reason the beacons convey a message is that the citizens of Gondor know why that beacon would be lit.

Imagine a simple pressure sensor inside a building that is connected by a wire to an electric light on a control panel in a security room. When someone steps on the sensor it completes the circuit which sends electricity straight to the light turning it on. A label on the light says what it's connected to and where it is. So that when the light comes on, the person at the control panel knows someone is in that sector of the building.
But to be more precise, he knows someone has activated that particular pressure sensor, if it wasn't labelled he would have no idea what the message meant.

My understanding of the human nervous system is that it works in the same way. Based on information I learned from children's educational programs as a child and a few bits I picked up since.

Our ears have sensors designed to respond to sound. Each and every one has a direct connection to the brain via a chain of nerve cells. When one of the sensors is sufficiently stimulated, it zaps the neuron it's connected to, this in turn causes the neuron to zap the next one and so on all the way up to the brain.

The impulses/spikes themselves contain no actual information, they are just pure electricity, every spike contains the same amount of voltage. The only reason the brain is able to interpret them is because it knows exactly where each and every chain is connected to. When the impulse reaches the brain it knows it comes from a sensor in the ear that is responsible for a particular level of sound, the brain takes these signals and translates them into the sounds we hear. Nerve cells work something like binary, they are either on or off with nothing in between. The frequency of the spikes going along the chain indicates how intense the sound is. If the brain didn't know where that chain was connected to then the signal could mean absolutely anything.

This is supported by the condition known as synaesthesia where, because "wires are corssed" in the brain there are people who hear colour or taste music.

My questions are, is my reasoning correct? Is this exactly how nerves and perception work? Has this been scientifically proven beyond a doubt? Is there something within the impulses that contains additional information? Are the workings of the nervous system debated in scientific circles? I've been told we've never been able to plug an eyeball or any other kind of human sensory device into a computer so we've never been able to examine it as it's working, is this true?

But most of all, does this mean there are things our senses cannot detect?
I already know there are things beyond our range of vision and hearing and the brain blurrs then together. What I mean is this...

I know that we have different senses in our ears that are designed to respond to higher or lower sounds. Say we have a sensor that responds to a level 1 sound (I don't know the unit of measurement for sound) and next to it is a sensor that responds to a level 2 sound. What happens if we try to hear a 1.5 sound? Is it not detected by the ear because we don't have sensors in that range?

Can we only sense something if we have a sensor for it and are those sensors only built to sense one ultra specific thing?


texts: what books do you recommend to undstand horvath clock?

texts:
I’ve read about horvath clock, and the new theory of aging. One that describes DNA methylation as the upstream root for all age related symptoms.
I want to read more, and understand this at a much deeper level.
I don’t mind if it takes me six months or a year to understand it.
Where should i start? What are the book(s) to read?


texts: Butterfly/Moth identification: Puppa is half green, half brown, and 1,5cm long, found in Upper Austria

texts:
Question: What butterfly is going to evolve out of the puppa illustrated in the attached picture?

Characteristics: Puppa is half green, half brown, and 1,5cm long
Further details: I don't know if this is relevant we found it on our mint plant, presumably it has eaten its leaves along with the lice on it.


texts:
In embryological development, undifferentiated cells developed into specific types.  As far as I understand, a key differentiating factor is the regulation of gene expression via transcription factors.

However, if all cells have identical genomes and, therefore, identical transcription factors, what is the source of difference in their morphogenesis? Does it rely on some element of randomness in external factors?


texts: Problem: What is this pattern of inheritance?

texts:
The following question was on a pretest of mine, and I'm trying to figure out the answer using what we've learned about Mendelian and non-Mendelian patterns of inheritance. I'm struggling quite a lot with this question; I'm not sure if that's because of me or if the question itself is poor/confusing.

I don't know what the answer actually is, as there was no answer key to go along with the exam. My best guess is that the pattern of inheritance is Incomplete Dominance based on the Red x Yellow cross and the fact that neither allele was dominant over the other in the resulting progeny. But is it even possible to state this with full confidence? What about the other crosses?

  In a plant species, plants may produce red, yellow, or orange flowers. The table below shows the results of crosses between the plants that produce each flower color.

  Based on this information, which pattern of inheritance controls flower color in this plant species?

  (A) Codominance

  (B) Complete dominance

  (C) Incomplete dominance

  (D) Multiple alleles


texts: Why do people feel shame when exposed nakedly?

texts:
Why do people feel shame? Meaning the kind of shame specifically related to exposing 'private parts'.

Where does it come from (i.e. social factors due to upbringing, inherent in our genes etc.)?
What is its evolutionary purpose?


texts: What is the film that covers the tongue?

texts: What is the film that covers the tongue in the mornings, even after brushing the teeth and tongue the night before and why does it have color variations?  Do the different colors mean anything?


texts: Relation between OD with different microbial growth

texts: Equal volumes of cell suspensions of Escherichia coli, Saccharomyces cerevisiae, Streptococcus lactis and Mycoplasma pneumoniae, all have the same OD600nm = 0.50. Which cell suspension would have the minimum and maximum number of cells, respectively?


texts: I'm looking for a reference that gives some information quantifying sources of mutations that occur within cells. These can be general, but I'm interested in some percentage of mutations caused by external vs internal sources (like mutagens vs replication errors).


texts: What percent of your blood can you lose before you need a transfusion

texts: Losing a little blood is okay. If your a normal healthy person, and got into an accident, how do they know if you need a transfusion or if you'll be okay? This is hypothetical.


texts: Why we shiver/tremble/shake while performing some work which requires high accuracy?

texts:
Shivering when nervous or anxious is a common thing.

But, shivering or trembling sometimes also occurs when we are performing a work which requires high accuracy. In such case, our whole body doesn't shivers but a part (usually hand) which is involved with that work shivers. The most common example is threading a needle. It requires great accuracy and you might have noticed that when you are doing so, your hands are continuously shaking which prevents you from accomplishing that task flawlessly. Even when we aren't in a state of nervousness, our hands tremble. It's un-resistable.

Yet another quick example - Try to stretch your one arm and try to keep it straight (have it loose, don't try to force it straight), you might notice that your arm is actually shaking a little bit. You can't hold it exactly straight without moving even a little bit.

It's also noticeable when we try to pin-point a small spot with our hand(finger) without actually touching it. (that finger and the hand as a whole starts trembling)

So, what's the reason? It isn't anxiousness as we shiver even when we are calm.
Perhaps, it's gravity which is pulling our hand down and we are trying to lift it continuously which creates a imbalance? But, then we should shiver always?


texts: What's the difference between inflammation and fever? And why is fever called an inflammatory response? Does the word inflammation have both a general and a specific meaning?


texts: What is the fundamental reason for death from too high or low internal temperature?

texts:
I have read something about why we die from over/underheat, but always found too general reasons. Such that the liver fails. But why does the liver fail? I would like to know the most fundamental reason why not having the right internal temperature can make us die. Ignoring the very extremes where it is I think obviuos, like temperatures below 0°C and above 100°C when the water freezes and vaporizes.

So, a little bit of what I thought could be the reasons. If anything here is wrong, please correct my thinking.

As far as I understood, as the temperature changes, the speed of chemical reactions changes as well. Temprerature goes up, the reactions happen faster and if the temperature decreases, the reactions slow down. So if our body temperature changes, the speed of everything in our body should change as well. So with higher internal temperature we should just be more active, speedy and so, and with low temperature we should become slower. But that does not fit into the fact that we die from too high internal temperature. So, is it that the speed of different reactions changes in different rates, so the organism is not kept "in sync" and dies for that reason?

Or - as temperature changes, the volume of all materials changes as well. I think that's called thermal expansion. But different materials have different rates of that process. So as our temperature changes, something inside us just literally breaks or deforms too much and we die?

So why do we (and other organisms) die from not having the right temperature? Am I on the right track or am I completely wrong? Thanks for any answer.

Jakub


texts: Herd immunity without vaccines? (corona question)

texts:
Obviously there is herd immunity against many viruses such as measles because of vaccines.

Can we say that there is herd immunity against any particular virus even though people are not getting vaccinated, and what virus would that be?

Do you typically get herd immunity without vaccines against viruses without vaccines or do the viruses just linger around and infect fewer people because many have already become immune after catching the virus and developing anti-bodies?

What is "normal" virus behaviour?


texts: I live in Brisbane, Australia and these creatures arrived a few weeks ago for a day or so and then they disappeared. There were thousands of them. I would love to know what they are.


texts: What obstacle(s) would be most prevalent in an attempt to use virotherapy to inject Cas into cells to target a cancerous mutation?

texts:
Let's say a human cell mutates cancerously, we identify the mutated gene sequence and use CRISPR to mutate the patient's cells to include some variation of the cas genes and spacer sequences matching the mutated cancerous sequence.
Then design a virus to "infect" cells (cancerous and healthy) with this cas gene sequence and spacer sequences.
The infected cells would then produce a specific cas9-like protein targeting the mutated cancerous gene sequence in the patient. As the modified protein producing cells multiplied to replace the old ones, the custom cas9-like protein would detect and remove the targeted cancerous sequence.
More elaborately the approach could be used to inject a large library of known cancerous sequences as cas spacers in reproductive cells to start developing a species-wide defense against a significant range of cancerous mutations.
What primary obstacles would be in the way? I suspect research has been done on this.
My knowledge so far:

Basic understanding of virotherapy - I'd like to clarify my question is asking about something beyond research I've seen on anti-cancer oncolytic viruses which target cancer cells. My question is about repairing the cells rather than killing them.
A big picture of how CRISPR functions and how it can be modified to achieve specific gene editing functions. Spacer DNA sequences matching targeted gene sequences (usually threats such as bacteriophages) are used by the cas genes to produce proteins called cas9 (or some variation) which couple with crRNA and tracrRNA to match and slice targeted DNA sequences.
a closer look at the specifics of cas9 and its behavior.

Potential problems I considered but couldn't find specific studies on:

Whether the viral delivery of the modified dna would be prevented by the immune system before all the cancer cells could be "infected".

Whether human DNA's size (roughly 1000x the size of some bacteria DNA) might be too "large of a search space" for the cas9 or cas9-like proteins to "find" the targeted sequence.

Whether customization of cas9 into some more specialized / effective variant would overcome any obstacles to this approach.


texts: Genotype frequencies and fitness values in haploid population with clonal growth

texts:
I found a small problem, and I am not sure at all about my answers. If someone could correct it, that would be awesome.

  Consider a heterogeneous population with the following genotype frequencies and fitness values (attention: haploid individuals with clonal growth!) :

  ab : $ P_{ab} = 0.8, \quad \lambda_{ab} = 1 $

  Ab : $ P_{Ab} = 0.1, \quad \lambda_{Ab} = 1.2 $

  aB : $ P_{aB} = 0.1, \quad \lambda_{aB} = 1.1 $

  Determine the average fitness of the population
  After one generation, what are the new genotype frequencies and the average fitness of the population ?
  What are their values in the long-time limit ?
  Explain clonal interference in this context.

My answers :

Relative fitnesses values - we take the highest as reference (here: Ab):
$$ \omega_{ab} = \dfrac{1}{1.2} = 0.83   $$
$$ \omega_{Ab} = \dfrac{1.2}{1.2} = 1   $$
$$ \omega_{aB} = \dfrac{1.1}{1.2} = 0.916   $$

Average fitness of the population :
$$ \overline{\omega} = p_{ab}.\omega_{ab} + p_{Ab}.\omega_{Ab} + p_{aB}.\omega_{aB} = 0.8556 $$

$$ p_{ab}(t+1) = \dfrac{p_{ab}(t).\omega_{ab}}{\overline{\omega}} = \dfrac{0.8\times 0.83}{0.8556} = 0.776 $$

same for the others frequencies :
$$ p_{Ab}(t+1) = \dfrac{0.1}{0.8556} = 0.117 $$
$$ p_{aB}(t+1) = \dfrac{0.1 \times 0.916}{0.8556} = 0.107 $$

I know that the fraction of the fitter genotype will grow exponentially compared to the genotype of lower fitness. But how do you demonstrate that ?
I learnt that due to the haploid structure of the population, the two new alleles A and B are in competition under natural selection : this will lead to the loss of one of them in the long term (even if they are both advantageous for the organisme). Then how do I explain that we those data ? Does this mean allele B will disappear ?

Any help would be welcomed :)


texts: Consuming animals by slaughtering vs injecting barbiturates?

texts:
In "Least painful way to die" we get an answer ...

Companion animals (e.g., dogs and cats): injected barbiturates are recommended
Laboratory animals (e.g., mice and rats): injected barbiturates are acceptable as are inhaled agents (isoflurane, carbon dioxide).

And assume the butcher guy as soon as he comes to know the animal is gone, he will do the following....

A very sharp knife is used in this process: the point of the knife cuts into the animal's throat and cuts through the dewlap, trachea, esophagus and jugular vein immediately below the jaw-line to allow the blood to flow out.........Animals are bled out before being dressed because it prevents blood from coagulating in the tissues and thus making the meat go rancid. (Source Slaughter Cattle commercial method - Step 6)

Here's my question... What if the animal was killed using 'barbiturates', then is that animal safe for eating by humans or the high levels of 'barbiturates' in that body cause unwanted results in humans too (if they consume it)?

I'm new to biology. :)


texts: Why are spinal nerves considered a part of PNS while the spinal cord is a part of CNS?

texts:
So from my common understanding, CNS consists of brain and spinal cord, and PNS consists of everything else. But the spinal nerves - the nerves connected to the spinal cord - why are those considered part of the PNS? And another clarification - spinal nerves are COMPLETELY DIFFERENT than the preganglionic neurons of the sympathetic nervous system?

Thanks for all your help.


texts: What websites biologists use to check what new plant or animal species have been discovered in the world?

texts: What are the databases or websites that biologists use to check what new plants or animals have been found in the world? The service should list the location of the discovery, time of discovery, image of the new species, the name of the discoverer and other vital information


texts: In Study from Blue Brain they say position of synapses doesn't change even if they modify neurons, only when they change shape of neuron it changes?

texts:
https://medicalxpress.com/news/2012-09-blue-brain-accurately-neurons.html

  We could vary density, position, orientation, and none of that changed
  the distribution of positions of the synapses.....

  They went on to discover that the synapses positions are only robust
  as long as the morphology of each neuron is slightly different from
  each other, explaining another mystery in the brain – why neurons are
  not all identical in shape

My question is why, and how come? Am I understanding it wrong?


texts: Theoretically, what technique would one use to modify a virus so that it only affected a subset of the population?

texts:
I'm writing a novel and i would like to know some of the equipment and techniques involved with modifying a virus.

Is it feasible for a virus to be engineered to only affect certain people? It doesn't have to be possible, only sound like i know what i'm talking about. I have been trying to research the subject but nothing i have found will tell me the basics of what is involved with virus modification.
Thanks.


texts: Why do cyanide and arsenic smell like almonds and garlic, respectively?

texts: Why do humans smell arsenic as garlic or cyanide as almonds? Do both smells activate the same receptor? Is there any reason why our brain interprets these smells the same?


texts: How are new chromosomes replicated into the next generation via sexual reproduction?

texts:
If an individual has a new chromosome, which is very unlikely to happen, he will not have any luck in finding a sexual partner with this same trait. How will the offspring inherit this trait. And given that extra/fewer chromosomes are often undesirable traits (e.g. Turner Syndrome) how can it propagate?

I assume that humans and rats have different number of chromosomes, so a common ancestor must give a lineage where some individuals had a different number of chromosomes than their parents.


texts:
It is a classical result that the expected time for a neutral mutation to occur and to get fixed is $2 N \mu \frac{1}{2N} = \mu$, where $N$ is the population size and $\mu$ is the neutral mutation rate (wiki).

I am not sure I understand what this actually mean. What is the probability of (at least) one fixation event to occur in $\frac{1}{\mu}$ generations? Is it 0.5? Could we calculate the probability that (at least) one fixation event occurs in $n$ generations? For example after $n=\frac{\mu}{10}$ generations, is the probability of observing (at least) one fixation event equal to $0.1$ or is it more complicated?

UPDATE

Following @DanielWeissman comments:

Let's consider we are starting with an initially monomorphic population (population of clones). In addition to that, let's consider that the population is relatively small $N\mu < 1$


texts: What industry regulations protect the privacy of DNA results in the US? (UK, or EU wanted as well)

texts:
I am writing computer software that allows users to learn more about their own DNA and (optionally) allow some of that data to be used for research purposes.

I'm very concerned about a future/theoretical situation in which an insurance company uses that DNA data to disqualify someone on the basis of pre-existing conditions.

Question

What privacy regulations exist that would assure users that there is no insurance risk in a collecting information about one's own DNA? (Primarily interested in the USA, but UK and EU would be valuable)
Outside of legal regulations, what should users look for when shopping among providers? (for quality, scope of services provided, etc)


texts: For emphysema, which of the respiratory volumes is affected?

texts:
It could be the tidal volume because it affects how a person inhales and exhales normally.
It could be the residual volume and functional residual volume, because it increases its amount. Because it traps air.
On the other hand it also affects the Forced vital capacity because it decreases the amount of air that can be forcibly exhaled immediately after one inhalation.


texts: Can parts of a human brain be asleep independently of each other, or vary in the times required for them to fall asleep?

texts:
I know that some birds and marine animals can continue complicated activity (swimming, flying?) while one hemisphere of their brain is asleep.

I'm interested if human brain has some parts of it that can be asleep while others are awake? In other words, can a human brain be only partially asleep while experiencing insomnia or similar sleep disturbances?

If human brain can have different parts "sleeping" independently of each other, is it possible that the times to "fall asleep" vary between these different parts of the brain?

I would appreciate research articles on the topic or just the names of brain regions that may exhibit behavior described above.

Update: I've taken a look at R&K "principles and practice of sleep medicine"' and it mentions the following parts as involved in sleep:

Medulla, preoptic area, hypothalamus, thalamus, entire neocortex involved in NREM.

Neurotransmitter systems: histaminergic, orexinergic, serotonergic, noradrinergic

Sleep factors: adenosine, interleukin-1 and other cytokines, prostaglandin D2, growth hormone releasing hormone, nitric oxide, all promote sleep in or around preoptic area.

This makes me hypothesize that drugs that modify the effects of these systems (ex- caffeine affecting adenosine) could result in sleep- related disturbances in these systems, potentially causing them to fall asleep later that usual. But I'm looking for more info to fihre out if this is true


texts: Lower optimum temperature of plant Catalase

texts:
Most resources give an optimum temperature of 35° C for Catalase. after performing the AP Catalase enzyme lab in school, using blended potatoes, our results gave a greater reaction rate at a room temperature of 25° C. we hypothesized that this is due to the fact that potatoes cannot regulate body temperature, so catalase works better at room temperature. The only source we could find that backed up its claim was an excerpt from a Pearson textbook: Here

Do plants have a lower optimum temperature like the textbook suggests, or was something wrong in our experiment?

(75 students, half did potatoes, half did liver)


texts: We as individuals die when we get old. But why are cells affected by time? We are constantly providing energy to the cells through food, but the cells die after a certain time. Why does this happen?


texts: Image analysis of GFP-tagged protein localization bursts

texts:
I'm reading an article (full text here) that analyze the dynamics of localization of a GFP-tagged transcription factor (Crz1) over the time at the single-cell level, by taking movies in a fluorescent microscope.

In Methods section they say:

  Fluorescence cell images were segmented using a Hough transformation algorithm in Matlab, provided by Sharad Ramanathan. Localization score was determined by the difference between the mean intensity of the 5 brightest pixels in the cell and mean intensity of the rest of the pixels in the cell.

The segmentation process here seems to be the identification of cells over the background. They then calculate a localization score, for each frame of the video, for every cell. Now there's the part that I can't understand:

  Bursts were identified by thresholding traces at >1 standard deviations above background noise, estimated from the lowest 20% of values.

I searched some definitions of "background noise", but I can't figure out what does it mean in this particular context. Moreover, "lowest 20% of values" of what?

Is it plausible that they define it for the lowest 20% of values of localization scores over the time, at the cell each time considered?

Maybe can be useful a screenshot of a single cell in a photogram of the video:


texts: Evolutionarily speaking, why do humans have 46 chromosomes

texts:
In humans, each cell normally contains 23 pairs of chromosomes, for a total of 46. Monkeys, chimpanzees, and Apes have 24 pairs (twenty-four pairs), for a total of 48.

What caused humans to have 46?

EDIT:
@TomD is right, I was asking why we have one less chromosome pair than chimpanzees (for example) [23 pairs instead of 24].


texts: How to conduct PSI-BLAST for a given protein sequence against bacterial protein database only?

texts:
I have a list of 100+ proteins and I need to conduct psi-blast for each one of them against "bacterial proteins" only.

I went to NCBI's protein blast tool, but couldn't figure out how to select/limit the targeted database.

Here are the 2 configs I tried:

Database: pdb, Organism: bacteria (taxid:2)
Database: landmark, Organism: bacteria (taxid:2)

Can anyone tell me if either of the approaches is correct? If not, please point the right way.

Edit 1 - add more details

All of my data is from "Supplementary Table 10" of paper "Comparative genomics of the neglected human malaria parasite Plasmodium vivax".

About 5% of all my protein sequences are ISS predicted. Remaining sequences are IEA predicted


texts:
Why does yawning seems to be contagious?
Is this similar to laughter being contagious or does it has a different reason?


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

texts: Found this interesting insect hiding behind the thin branch of flower (the diameter of the branch is 3-4mm) in my garden in Kuching, Sarawak, Malaysia


texts: Color van der waals bonds in swiss PdbViewer

texts:
I'm trying to color certain amino acid's van der waals bonds as in the following picture:

can anybody please describe the steps to accomplish that?


texts: Synthetic construct with multiple ORFs not expressing

texts:
I designed a synthetic construct on paper and got it synthesized from a company. The objective was to make a vector which can be used to study both transcriptional and post-transcriptional regulation by different cis-elements (2-3 different cis-elements can be studied simultaneously).

The construct is like this:

SmaI-RES1-CMV-RES1’-GFP-MCS1-SV40PA-Linker-RES2-CMV-RES2’-RFP-MCS2-SV40PA-Linker-RES3-CMV-RES3’- YFP-MCS3-SV40PA-ΔLinker-SmaI

where:

RES1 = KpnI [GGTACC]
RES1’= SalI [GTCGAC]
MCS1 = EcoRI+BamHI [GAATTCTGGATCC]
RES2 = ClaI [ATCGAT]
RES2’= NheI [GCTAGC]
MCS2 = SpeI+HindIII [ACTAGTAAGCTT]
RES3 = XbaI [TCTAGA]
RES3’= PvuI [CGATCG]
MCS3 = NotI+SacI[GCGGCCGCGAGCTC]
Kozak consensus sequence = GCCACCATGG
Linker (100bp) = AATTCTGGATCCTGCAGCTTATAATGGTTACAAATAAAGCAATAGCATCACAAATTTCACAAATAAAGCATTTTTTTCGAATTTCGATTCCACCGCCGCCTTCTATGAAAGGTTGGGCTTCGGAATCGTTTTCCGGGACGCCGGCTGGATGATCCTCCAGCGCGGGGATCTCATGC

GFP, RFP and YFP are fast turnover variants with MODC pest sequence. I took the sequences for these proteins from Evrogen website. I took the Sv40 polyA signal sequence from one of their vectors in order to avoid any event of incompatibility. Kozak sequence was also taken from those vectors only. The total size it ~4.8kb. For CMV promoter I took the standard sequence used in most vectors.

With this vector I could clone any post-transcriptional regulatory sequence between stop codon and SV40PA, and could change promoters as well.

With the CMV promoter and no 3'UTRs I see a very faint expression of GFP, but could not see any RFP expression. I used pMaxGFP and dsRed as a control for filter sensitivity.

I transfected the plasmid in Hela and Neuro2a and at various concentrations (1-5μg) using lipofectamine. The controls express well (transfected 1μg each) but I see very faint GFP expression and dont see any RFP expression.

I checked the sequencing QC report given by the company and there were no indels or other mismatches. I am clueless about why the construct fails to express.

Is the linker a problem; is 100bp not sufficient ?


texts: Probabilities in calculating the kinship coefficient

texts:
I've been reading up to try to understand how the kinship coefficient (or coefficient of coancestry) is calculated. https://brainder.org/2015/06/13/genetic-resemblance-between-relatives/ this is the best explanation I've been able to find so far. However, I've not been able to find an explanation that makes a clear distinction between genes and alleles.

In my initial reading of the above I factored in this fact and assumed that often when the author wrote gene he/she meant allele (an assumption which I now think is incorrect), and thus that identity by descent of a single allele between individuals would be enough to satisfy kinship in the context of the definition of the kinship coefficient. This lead me to confusion upon reading the kinship coefficient as mathematically defined from the condensed coefficients of identity:

D1 + 1/2(D3+D5+D7) + 1/4(D8)

Surely, I thought, the kinship coefficient should merely be the sum of the probabilities of all the possible ways in which the two individuals may share the same allele. And thus there is no reason to multiply the sum of D3, D5, and D7 by 1/2 and D8 by 1/4.

Finally to my question; Kinship coefficient is defined as the probability that two individuals are identical by descent at a single randomly selected gene. Remembering this, is the reason it is calculated in this way because in order for the gene between individuals to be fully identical in the case of D3, D5, and D7, an additional identical allele is required from one parent (an event with a probability of 1/2), and in the case of D8 additional identical alleles are required from both parents (an event with a probability of 1/4)?

I'd be very grateful if someone could clarify for me why it's calculated in this way.


texts: What is optical density in Lowry's protein estimation method?

texts:
I have a few questions:

What is an OD value?
Why do we use blank solution in Lowry's protein estimation method?
If The OD of a protein is 0.01, what does it mean?

Thanks in advance.


texts: How Anopheles crop doesn't digest gametocytes of P. vivax?

texts:
Background

According to my A-level textbook: When Anopheles mosquitoes inject their proboscises and suck up blood from human host of malaria agent, they suck all stages of malaria parasite present in the blood like merozoites, cryptozoites, gametocytes etc.
But, Anopheles mosquito's crop digests all other stages of malaria schizogony except the gametocytes.

Question

Well, how does the digestive system of Anopheles distinguish the gametocytes from other stages of malaria parasite?
Or, is there any protective mechanism for gametocytes to stay untouched in face of digestion in Anopheles crop?


texts: How can a recessive allele propagate until they manifest?

texts: Suppose a specific gene has two possible alleles. In a given population all members have only the dominant one. By a mutation on member receives the first recessive allele of that population. Is it possible that one day the descendants of this population have this allele manifested? I think it's very unlikely that this allele survive until another similar mutation occurs and they get manifested in the phenotype.


texts: Sometimes after a nap, I wake up in a state of grogginess. I learned that this is actually called sleep inertia. I'm able to find lots of methods to overcome this, but what causes it in the first place?


texts: Why is an HIV infection considered "incurable"?

texts:
My biology teacher told me that if one caught HIV, they cannot be cured because it was near to impossible to be completely virus-free. She said this was because HIV keeps on changing its glycoprotein coat.

Can someone please explain what she meant by "keeps on changing its glycoprotein coat" to me?


texts:
Is there an effective way to use cellulase(s) and/or lignase(s) to remove unwanted plant debris from a sample?

I'm working with a series of fresh water grab samples for environmental assessment. The objective is to separate out the benthic invertebrates as a proxy for biodiversity and habitat health. We use 500 micron mesh to remove the bulk of the sediments but this leaves several liters of fine plant material in a variety of stages of decomposition. While searching through yet another petridish of rotting sphagnum I wondered if there might not be a better way to do this?

Is there an effective protocol for decomposing the plant matter using some mixture of cellulases and lignases? Or am I barking up the wrong tree?


texts:
Is the ribosome found in mitochondrion and choloroplast formed of 30S and 50S subunits as in prokaryotes. I couldn't find any information on internet concerning it.
The general wikipedia page has no information about it though it says

  The ribosomes found in chloroplasts and mitochondria of eukaryotes also consist of large and small subunits bound together with proteins into one 70S particle.[9] These organelles are believed to be descendants of bacteria (see Endosymbiotic theory) and, as such, their ribosomes are similar to those of bacteria.


texts:
I have a biological puzzle that's been perplexing me for years.  Can you review my logic and tell me where I'm wrong or if I'm on to something.

As I understand it, most, if not all genetic engineering uses a marker gene to identify transformed bacteria.  This marker gene was/is usually an antibiotic resistance gene so the transformed bacteria will be the only ones that can grow on an antibiotic laced culture medium.

So, every (most) GMO will contain a copy of a bacterial antibiotic resistance gene.

Also, I believe that bacteria are able to spontaneously aquire DNA from their environment and / or other bacteria.

So, is it a fair question to ask if the unnatural proliferation of antibiotic resistance genes in the wild due to the commercial propagation of GMOs might be at least partially responsible for the increase in multiply resistant organisms that we are seeing?

Has anyone, for example, mashed up GMO matter, added non antibiotic resistant bacteria, grown the mix up overnight, added the antibiotic used as a marker in the GMO, incubated for a few days and then seen if any bacteria survived?


texts: What evolutionary process has provided humans with the ability of feeling electric current? Besides lightning and electric eel, what natural hazards include electricity that poses a threat to humans?


texts: Does a generator potential pass along a nerve the same way an action potential does?

texts: I have read that a generator potential is a localized depolarization of a membrane. Does that mean that it does not pass along a neuron the same way an action potential does ? If not, then how do generator potentials from multiple rods in our eyes add up (converge) and trigger an action potential in a sensory neurone ?


texts: What cell types produce immunoglobins and where are those cells found?

texts: I know B cells found in bone marrow produce immunoglobin G.  But IgM is produced in mucosal cells at least in the gut.  Can you find immunoglobin expressing cells in other tissues in the human body?  Are B cells or IgG mRNA ever found in blood or tissues?


texts: What is this flying animal that hovers like a hummingbird?

texts:
What is this animal?

Characteristics:

Has a long curved bill.
Has green upper body and a dark black lower body.
Likes petunias.
Hovers like a hummingbird but is a bit smaller.
Has small rear feather-like tufts and is very odd shaped.
Moved quickly from flower to flower.