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Horse female bias
I don't know if it's a more general fact, but in most stables I visited, I have observed that there were more mares than stallions or geldings. Typically in a group of ~7 horses I'd notice one or two males, the rest would be females. I think the only place where stallions outnumbered mares was a stallion stud farm, where this was a kind of focus/purpose of the establishment, and I wonder if this is just my confirmation bias or result of some artificial selection, or are horses naturally more inclined to produce female offspring.
Can someone confirm or debunk and explain this observation?

Did you do any research on this, and can you share what you found? I only know from a couple of horse trainers I know that stallions are harder to control. Hence the prevalence of geldings.

It's often the case, as mentioned, that stallions are harder to control, even dangerous - and so people elect not to keep as many (or have them gelded).
For breeding purposes you don't need as many stallions as you do mares, since one is easily able to service several mares.

I can attest to these claims. My grandparents have a (Rocky mountain) horse farm, and he only keeps one stallion (named "Prince") from where it's so aggressive and territorial. No other horses are pinned in the same field as the stallion, and he kind of just does his own thing. Much more difficult to take care of, given these behavioral habits.

@JoeHealey: I'm specifically seeking male:female disparity; I know the number of ungelded stallions is low, but I'm finding male population in general to be small.

@anongoodnurse: female: male populations: Zabierzow stable: about ~8f:3m. "Pegasus" riding club stable: ~7f:2m. Private stable in Kokotow: 3f:0m. Rudawka Rymanowska: 4f:1m. Wernejowka: ~12f:4m. Stable south or Tarnow: 8f:2m. "Natural Horsemanship" stable in Krakow: 6f:1m. Private stable near Lomza: 4f:1m. State stallion stud in Klikowa was a big stable with ~120 horses had about 60% male population but that's a rough estimate, I didn't count. That's different breeds, different purposes, I'm bundling all stallions+geldings as 'male'

The ratio of males to females in stabled horses is irrelevant. You need to look at birth records.

@anongoodnurse: I don't have access to these. This is why I'm asking this question - I know my observations are encumbered with a slew of errors, therefore they can't be treated as anything but a suspicious artifact of data that may or may not be based on an actual trend. And I'm looking for some evidence that either supports or debunks this suspicion. (if I had access to raw data like this I wouldn't need to ask!)

I just googled and found two papers immediately with the answer. You can, too. Try Google Scholar "birth sex ratios in horses".

@anongoodnurse: Just personal experience, but among the people I ride with, it seems like about 3:1 geldings:mares.  Likewise with "horse for sale" ads.  So there must be some human selection going on somewhere between the 50:50 birth sex ratio and the trail.

@jamesqf: "for sale" ads will have an extreme bias of desirability. Example: "Why are all real estate / rent a room ads total crap?" - because the good ones are taken hours after they are published, and the crap ones remain available for years. This effect is accumulating over time (number of crap ads grows constantly, as new ones appear and old don't vanish) so the bias reaches extreme proportions. I don't know about "people you're riding with" though.

@SF.: But I would expect desirability to correlate to price, not numbers.  E.g. if geldings and mares are produced in similar numbers, but geldings are 3x as desirable as a mare of similar age, breed, and training, the mare should be about 1/3 the price of the gelding, no?

@jamesqf: That's what perfect Smith's capitalism would suggest. The reality is the seller dictates the price, and a large part of sellers are quite stubborn and not quite realizing inferiority of their offer and the state of the market. The offers from sellers who are well aware of the market vanish quickly, while bad offers stay up indefinitely long. An analysis of ads as they are listed, over a long time, discarding re-listing would provide a more neutral image. A snapshot of ads from any given moment is severely biased. Even then, breeders will tend to keep the mares and sell geldings.

My guess is the same reason you see a 30 chickens in farmer brown's backyard coop, but only one rooster.
Because, like joe Healy said, stallions and roosters both have testosterone, and that gives them a short fuse.
Also, because a stallion can mate a horse any day of the week, but mares can only have sex when they're not already pregnant or infertile.
Consider the reverse situation. If there are a ton of stallions and one mare, and the mare gets impregnated by one of the stallions, all the other stallions have to wait for the baby horse to be delivered before they can mate again. With one stallion and a bunch of mates, though, you can get as much baby horses as there are mares!

This would be a possible reason if horses were more popular as meat stock; but especially with the new restrictions on transport horse meat industry is a small margin (and I haven't heard of euthanizing male foals - meanwhile on egg farms, newly hatched chickens are sorted and all males are ground up into feeder, almost immediately after hatching.) So while the economy could suggest this bias, that doesn't explain where all these unwanted geldings go.


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What is happening to this spider?
I was trailing through a local bird sanctuary yesterday (central Kentucky, USA) and came across this spider.. it's definitely dead, but what is hanging from the back part of its abdomen? Has some parasite taken home within it, and that is its "nest"?

Upon further analysis of the images, it almost appears as if the spider was bleeding, or leaking bodily fluids, of which, given a potentially higher than not viscosity, has allowed the fluid to become rigid after prolonged interaction with the immediate environment. From there, debris may have been captured on the surface of the leakage, accounting for the change in coloration. Any thoughts?

It is hard to say for certain, but the insect hanging from the spider looks like it may be a member of the family Elateridae, commonly known as a "click beetle". As far as I know, they're harmless and no threat to a spider.
The close binding of the legs with silk suggest that the click beetle(if that is indeed what the insect is) may have been a meal prior to the spider's death, or packaged for later consumption.
Given the amount of debris in the webbing surrounding the spider's corpse, including some pieces of some sort of grass leaves, it seems likely that the webbing become tangled during or after the spider's death.  The placement of the click beetle is likely coincidental, although I suppose it is possible, given the positioning, the size of the click beetle, and what we can conjecture would be the size of the wound if that black material is seepage from a wound on the spider's abdomen, that some force actually punctured the spider's abdomen with the body of the click beetle.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


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How Mitochondria differs from Prokaryotes(probably regarding energy production)?
In other words, what evolutionary advantage is offered by mitochondria to eukaryotes(probably regarding energy production), which prokaryotes themselves cannot evolve or do?(here I am assuming that mitochondria evolved from prokaryotes)
I seemingly found some answers in the below article. Will love to hear the opinion of others regarding the same.
http://blogs.discovermagazine.com/notrocketscience/2010/10/20/the-origin-of-complex-life-it-was-all-about-energy/#.WYXsH4h97b0

Your question is somewhat unclear. Are you asking what selective pressure there was for endosymbiosis?

That's a pleasant article, but you might want to add the relevant parts (the "answers" you found) to the question.

If you mean "why do we have mitochondria instead of our cells doing the work themselves"
Then I can think of several answers.
First, oxidative phosphorylation must take place within an organelle, and requires specialized cellular machinery to occur.
So either a prokaryote can wait a couple million years to evolve these structures, or it can ask its friend to do it, and HE is specially evolved to do just that.
Like the way you hire a plumber when your toilet gets clogged, instead of going to plumber school yourself.
Also, oxidative phosphorylation has to do with oxygen.
Oxygen, when busted apart, can form unstable molecules called free radicals that are essentially bleach.
These molecules zoom around smashing up anything they touch including DNA.
So the host cell says "better you than me!"
Remember how I said you need an organelle for oxidative phosphorylation?
This is why. So all the "bleach" gets contained.
Two very good reasons why we evolved to rely on a separate organism instead of just making our own breathing organelle.

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What is this fruit / nut?
These were found in a park in Pittsburgh, PA. From a distance they looked almost like plums, but they're actually hollow, paper-like covers that contain a hard pea-sized seed.

Thanks for the good description of the fruit, but could you also give an approximate size? And was it a tree or a shrub that you found them on?

Thanks for your edit in astronomy but I could use all your up votes

Most likely a member of the genus Staphylea. Since you are in Pittsburgh, PA, it's most likely Staphylea trifolia L., or an introduced species.

That is it! I've never heard of (or seen) a "bladdernut" before.

By the looks Of it,it mostly is a hop hornbeam Which are indeed found in pittsburghBut i Still cant confirm it because
they are no photos of their leaves and any twigs or the whole tree, this info would be great to identify it and do you mind mentioning the name of the park you've been to
Can you confirm whether the tree looked like this

Ostrya Virginis

Nope, definetly not an Ostrya species.


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What is this? Found in southern Illinois

Found in southern Illinois in the driveway.  What is this?

It looks like a recently emerged periodic cicada that ran into some problems.

Was their grass / bushes around or just rocks?

Definitely a cicada.. it could be prematurely developed which has caused this milky characteristic to most of its body, and/or combined with environmental factors that could have effected it's outer coat. Is that possibly a bubble between the thorax and its left wing? Hmm..

Nice find! It looks to me like a Bush Cicada or scientificly Neotibicen dorsatus. It also looks like its injured, because we can see the white liquid around its wings and abdomen. Bush Cicadas tend to have a yellow or brown color but as shown here there is a wide variaty to the colourations that it might have:
Size (Adult, Length): 35mm to 57mm (1.38in to 2.24in)
Identifying Colors: yellow, brown, white, gold, black
North American Reach (Though Not Limited To*): Arizona; Arkansas; Colorado; Illinois; Indiana; Iowa; Kansas; Kentucky; Louisiana; Minnesota; Mississippi; Missouri; Nebraska; New Mexico; North Dakota; Oklahoma; South Dakota; Texas; Wyoming; Mexico.
Here are and some photos:
Adults:

The cicada is black eyed and green and brown colored. Yours have red eyes, except for one. There are lots of different cicadas, though.

@anongoodnurse And it is extremelly difficult to find a WHITE identical... XD

Many cicadas emerge white. That's not the issue. Your ID is off.

@anongoodnurse Thanks for the edit I will take care for it right away...

Do you have a source for what the fluids of a cicada look like? I wasn't able to find it.

@anongoodnurse I am checking it on the net... Look it sure something like its blood or gastric liquids? Probably..

It looks like a cicada of the Genus Tibicen, perhaps a "dog day" cicada (because of when they come out.)

Here are others of that genus; they're very similar.

Something is not right, though. I can't account for the white opaque liquid; even pictures of injured cicadas don't show it (at least that I can find.)
It looks like yours was dipped in Elmer's glue or something similar; the fluid is pooling under the wings and around the body. They usually hatch from a dry case, so I'm mystified.

About these white liquids you asked me, I checked and found that some cicadas "urinate" after the molt process, but the cicada above is a adult version...

Cicada urine is clear, and usually colorless or lightly colored.

Then I don't know... ran out of ideas.


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Small Pimple like structure in lips?
Is this some  kind of disease ? I saw this in one of my family member
Usually it is totally not visible  but whenever the lips are stretched they are seen

Given that there are so many, thier location (on the lips, where hair is not present), and overall appearance, I'm almost certain that those are harmless, fordyce spots, which are basically just oil producing (sebaceous) glands.
They tend to form (come and go) as someone gets older with age, with nearly 80% of adults experiencing this condition at some point. See here for further details.
NOTE: The link just provided does contain an image of an isolated region of a scrotum.


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What is this bird?
I have found this bird in my house, I live in Haedo, Buenos Aires, Argentina. I tried to take a closer photo but it escaped flying. I am not sure how to describe it, but it's very big compared to normal birds.
This are the photos:

That specimen in your photo seems to be the Southern Crested Caracara, Caracara plancus:

Also your location matches the range of C. plancus, which is from northern Brazil to Tierra del Fuego:

In the US , I would say it could be an osprey , especially if there is a body of water nearby. Or Caracas if in dry grasslands.


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What type of jellyfish is this?
Friends of mine recently came back from a visit in kenya and on the kenyan beach they said they found several jellyfish with "sails" on their head. We tried finding out what they were and found one image online that was exactly the type of jellyfish they found:

What kind of jellyfish is it?
The guide told them that they're dangerous and those are just the corpses without stings or something, but nobody knew it's name.

If the jellyfish your friends saw actually look like this and if they were small (Wikipedia says they're usually less than 7 cm in length), they're likely Vellela vellela or sometimes called By-the-wind Sailors for the way the raised part catches the wind and is blown along the ocean's surface.
Wikipedia writes

...all possess nematocysts, in some species the nematocysts and toxins
  therein are more powerful than other species. V. velella's nematocysts
  are relatively benign to humans, although each person may respond
  differently to contact with the nematocyst toxin. It is wise to avoid
  touching one's face or eyes after handling V. velella, and itching may
  develop on parts of the skin that have been exposed to V. velella
  nematocysts.

Some photos.

Source

Source


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How colon resist to bile
There is a disease called bile reflux which can make damage to the stomach. I just don't know how the stomach can be damaged by bile but the colon (small intestine) can resist with it?


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How does the human ear guess the direction of the source?
Suppose a sound is produced behind you. You can easily tell that the sound came from behind.
Our ear lobes face towards the front and hence traps the sound waves which come from the front. Yet, we can detect   that the sound came from behind.
How does the ear/brain manage to identify the sources of sound accurately?

The ear doesn't actually find the source, it's how the sound is perceived across both ears.
A sound coming from the side is the most obvious case where you get blasted on 1 ear and a relative muffled identical sound on the other ear.
A sound coming from the front is balanced across both ears. Same as behind, except that the forward-biased shape of the ears will distort the acoustics, leaving a distinct distortion signature that tells you the sound is coming from behind you. (For reference, modern 3D video game engines mimic this distortion so you can tell when something is happening behind your character or the camera if you are wearing headphones).
Sound from above or below you will have slightly different distortion signatures due to how the shape of the ears is different from above versus below.


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Does capsaicin in food kill bacteria?
Do foods like spicy peppers have less bacteria on their interior due to their capsaicin content? Probably not, but it seems like they could. Or I guess in other words: does capcaicin provide any benefit from anti-bacterial properties?

I should also note the wording in your title doesn't make too much sense. Based on your description though, I could only assume you were asking if capsaicin can kill bacteria in food.

check this page called " https://www.quora.com/Do-capsaicin-products-have-antiseptic-or-microbicidal-properties " google is great don't you think?

@comprehensible I'm here to find references more credible than a mere quora post.

In 2014, a review article was pushlished by the Department of Food Science and Nutrition at the University of Minnesota-Twin Cities, one that outlines  studies that (collectively) target the top 14 food-borne pathogens in attempts to identifying any potential antimicrobial properties of chili peppers, given that chili peppers can contain high amounts of capsaicin.
From the abstract of the article:

Chili peppers are used worldwide in foods for their pungent flavor, aroma, and to prolong food spoilage. With capsaicin contents ranging from zero to millions of Scoville heat units, the different varieties offer a wide range of options for people all over the world. In addition to their use in cuisines, chili peppers have been explored for their antimicrobial and antifungal properties.

..

This review goes over some relevant research that has already been done in this area. In addition it lays the ground for the new research that is emerging testing new varieties of chili peppers for nutrient content, flavor profiles, and for antimicrobial activities against numerous human pathogens.

The fourteen pathogens that were targeted and tested against were chosen due to their high risk of harm to the general public, most especially pregnant women (according to the FDA). To name a few that are well known, there's: Clostridium botulinum; Escherichia coli; Salmonella (enteritidis and typhimurium); Staphylococcus aureus; and Listeria monocytogenes.

After reading the conclusions of several studies that were provided by the review article (as well as the conclusion of the review article itself), it would seem that the current (as of 2014) consensus is that the efficacy of capsaicin (in chili peppers) as an antimicrobial agent is still to be determined. Of the (multiple) studies that were considered, collectively they produced quite mixed results. The reason for this is because each study has their own method for testing the antimicrobial activities of capsaicin, which makes the comparison of results between tests difficult to perform with confidence.

There are a variety of methods for testing the antimicrobial activities of chili peppers. These methods strongly affect the observed levels of inhibition. Various reasons may contribute in the differences between results, including inconsistency between analyzed plant materials.

..

In these experiments, crude extracts of chili peppers were used; no
  separation of pepper components was done. Based on the data, it seems that capsaicin had a lesser antimicrobial effect compared to other components of chili pepper extracts. Therefore, future studies should try to determine what compounds in the chili pepper gives the spice its antimicrobial properties, and to do so purification of the extracts is necessary. Capsaicin gives chili peppers the ‘hot’ sensation, which some people might not like. It would, therefore, be beneficial if there is another substance in the pepper that could be used in the food industry as a preservative without the pungent taste and hotness.

So, it would seem that, since the idea of using capsaicin as an antimicrobial agent is (fairly) new, there hasn't been a defined method for testing, and because of that, definitive conclusions aren't able to be made yet.

There seem to have been some later studies looking at bactericidal properties w.r.t. Group A Streptococci (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643145/) and Escherichia
coli (http://oaji.net/articles/2016/3556-1474160958.pdf). From the first study: "The present study documents that capsaicin has a promising bactericidal activity against erythromycin-resistant, cell-invasive pharyngeal GAS isolates. Moreover, sublethal concentrations inhibited cell invasion and reduced haemolytic activity, two important virulence traits of GAS."

This 2015 article demonstrated that capsaicin kills streptococci (the bacteria that give you throat infection).
However, relatively high concentrations of capsaicin are necessary to kill these bacteria: The minimal inhibitory concentration was determined to be ~128 µg/ml. given that 6.6mg capsaicin correspond to 100.000 scoville, a bowl (400 ml) full of bacteria-killing chilli would need to contain 7-8 habanero chili peppers - I can't imagine that going down well - particularly not with an already inflamed throat.
Interestingly, the same paper also demonstrated, that lower - more practical - concentrations (8µg/ml or 1/2 habanero per bowl) of capsaicin dramatically reduce the ability of streptococci to enter cells. This means that while capsaicin is likely impractical as an antibiotic, it may actually help your body to fight the disease and/or reduce the risk of contracting a throat infection in the first place.

"Given that 6.6 mg capsaicin correspond..." - I just added that into the Wiki article earlier this week haha. Funny seeing it come up

@Jam good job. IMHO that is the single most important information on that page ;-)

Yes it has some bacteriostasis and antibacterial properties, The only way for you to find it is to do some Agar and similar tests on chillis to find out about their microbes. You will probably find that some chillis have zero bacteria inside them, and that the surface of all chillis have many species. Seeing as it's a weak antibacterial compound, bacteria will probably have evolved to accompany the plant.
hot chillies don't tend to go mouldy on the plant though. they just dry over time.
Fruit generally don't have many bacteria inside them, for example this study shows that a large proportion of tomatoes don't have bacteria inside them, and the bacteria that get in probably do it through the base of the stem.
http://aem.asm.org/content/11/1/7.full.pdf
Humans rarely get infections from eating ou fruit and fresh plants, they are a low microbe environment. even melons, one of the most notorious fruits which are source of deaths and food poisonings, are thought to be from bacteria that grow on the outside of melons.
activities of capsaicin and effects of its antiseptic application to ketchup
http://en.cnki.com.cn/Article_en/CJFDTotal-DLJY200903023.htm
Extract the natural antiseptic material in capsicum [J]
http://en.cnki.com.cn/Article_en/CJFDTOTAL-ZGTW200008001.htm
Study on Bacteriostatic Action of Capsaicinoid [J]
http://en.cnki.com.cn/Article_en/CJFDTotal-SDKX200702008.htm
Study on the bacteriostasis of capsaicin in Capsicum annuum
In vitro activity of capsaicin against Helicobacter pylori
https://www.researchgate.net/profile/Fadile_Zeyrek/publication/267209796_In_vitro_activity_of_capsaicin_against_Helicobacter_pylori/links/5447a8540cf2d62c30508fb9.pdf
Antibacterial activity of capsaicin-coated wool fabric

The OP was asking about foods that contain capsaicin.. you however seem to focus on fruit, of which I myself am not aware of any fruit that contain capsaicin. As for the several sources you provided: they are in chinese, and seem to require an account to access the study, so IMO, your sources aren't helpful (not even an abstract is accessible). Lastly, the formatting of your answer is chaotic, with no logical or linear order. I suggest reformatting your answer, and providing sources that can be accessed, as well as actually address the main concern of the OP.

@Charles Peppers are fruits by definition. Capsaicin was even named after peppers (Capsicum sp.) What are you even talking about!?

@Adrian Okay, yes, I misspoke; a pepper is a fruit. The rest of my concerns regarding this answer are still completely valid, including the answer mentioning other fruits/plants that don't contain capsaicin.. why is this answer talking about melons, and tomotoes? You know exactly what I'm talking about; and BTW, your "!" is a bit excessive.

tomatoes are related to peppers. The research papers on bacteria inside fruit and antibacterial actions of capsaicin are pretty relevant, seeing as there are no measurements of bacteria colonies inside chillie pepers on google scholar.  It's a bit of a noob website, bacteria inside of peppers is clearly a research question rather than a complex or general knowledge question that requires experience. It's fine i don't mind learnin fruit bacteriology one day if it helps out a lazy person who doesnt have the energey to do his own research.

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bacterium ability to metabolize a compound toxic to most other organisms, do not know how the bacterium takes up the compound from the environment
A new bacterium is discovered that has a unique ability to metabolize a compound toxic to most other organisms. The microbiologists researching this bacterium do not know how the bacterium takes up the compound from the environment. Design an experiment to determine whether uptake is passive or active.

Please refrain from copy-pasting your homework questions in Biology.SE, instead try researching the answer yourself to show some effort and then frame a question that helps you understand the concept.

Assume that the toxic compound is some form of liquid (water or oil soluble).
Take a sample of the bacteria and irradiate them (inactivate them permanently). Immerse the inactive bacteria in the toxic liquid for a certain amount of time.
Remove the bacteria later, "wash" them off (against a sieve designed to filter bacteria) for toxin traces that could be on the membrane or cell wall, then liquefy the bacteria and test for presence of the toxic compound. If the uptake is active, there shouldn't be any of the toxic compound in the bacterium.


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Botany inquiry about tropism
Can anyone explain the mechanism of hydrotropism and what kind of plant hormone involved?
Our teacher says that it hasn't been proven yet. I looked up many data only to find about the phenomenon of this effect.


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If I receive dopamine only from doing difficult things will I eventually enjoy them?
I've recently read a post from reddit about how dopamine affects our motivation. Author states:

Dopamine is pleasure. Your brain craves more pleasure. You get too
much pleasure and your brain adapts to feel like tons of pleasure is
less pleasure then everything else becomes more boring. Cut those big
pleasure spikes out and everything else becomes more pleasurable. Your
dopamine receptors change to interact with less dopamine when you have
too much and when you cut down on dopamine, your dopamine receptors
change to interact with more dopamine. This makes boring stuff fun. Do
boring things long enough and endure until it becomes pleasurable via
dopamine receptors. And remember, think in terms of dopamine the next
time you feel like not doing what you need to do!

He advises to stop listening music, playing video games, watching porn, digital entertainment intake. He says:

This will make your dopamine receptors less dull over time and more receptive to lower levels of dopamine so doing things that are boring now will eventually feel not-boring if you can cut out big dopamine spikes.
Then, you keep doing the things you know you need to do but don't feel like doing long enough until your dopamine receptors become used to less dopamine and those things will feel good to do.

Some people accused author because of bro-science in his post. Can someone prove the theory or debunk it?
Will I enjoy doing difficult things which don't give me pleasure now if it's my only dopamine source?

Reddit is not always a reliable source. Have you done any research into this? What have you found?

Perhaps it's just a language issue, but 'difficult' and 'boring' are vastly different.  Backcountry skiing, flying your plane into short mountain strips, or playing a musical instrument can be difficult, but not boring - at least to me.  OTOH, video games, porn, and digital entertainment are boring to me.  And though I've scrubbed my toilet regularly for all my adult life, it's never become pleasurable.  So it seems that there's a major flaw in the argument :-)

I recall times when I found anything boring except activities which author advises to give up. Since the moment I quit playing video games I became interested in many things which previously seemed to me very boring and uninteresting.
For clarification, by difficult things I mean things you [have to]/[need to]/[should to] do but they seem boring and uninteresting and you don't enjoy them. Interesting things can be challenging, but if I enjoy them they aren't difficult to me. So difficult - hard to bear.


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Estimation of species range fragmentation
While discussing species distribution patterns along spatial, temporal or functional gradients one often finds a hump shaped species richness pattern.
This is well documented in many taxa and spatial scales and known as the   mid-domain-effect (e.g. Colwell & Lees 2000 ).
These patterns also arise stochastically (depending on the species range frequency distribution). So random distribution of species ranges midpoints are used as null models to test for these mid-domain-effects.
However, these models assume unfragmented species ranges. With a highly fragmented species range the pattern would look quite dissimilar.
So I don't want to start a discussion on the validity of this concept but rather ask:
Given a gradient and known species occurences on that gradient.
Has anyone read an article about (or has an idea) what would be a good/unbiased* estimator for species range fragmentation?
Thanks
*e.g: One that doesn't over- or underestimate fragmentation for rare or abundant species

Good equestion. However, I think this might be hard to answer since fragmentation is used in a number of quite different ways (so methods to estimate them may differ). For instance, are you referring to fragmentation at the landscape scale (e.g. as a result of logging previously continuous forest), or to "fragmented" species distributions at the country level (e.g. a species that is found in five areas/regions of a country with large gaps in between)?

I didn't think that the premise of the question was black and white kind of clear, In fact It seems that you wish to have a clear answer to a difficult to measure and define topic. Species range fragmentation is ephemeral and a . quote. hump in species richness pattern is difficult to associate with fragmentation measures.

Very interesting question +1. I don't know the literature on the subject very well but I did not find much by looking for it. I know that a number of methods exist when you have genetic data (STRUCTURE or some of the work of J. Novembre probably).
Here are two possible solutions
Fitting $x$ distributions
You could be fitting 1, 2, 3, ...., n normal (or uniform) distributions to the observed data. Each time, compare their maximum likelihood (for which you might need a MCMC with 2⋅x parameters, where $0≤x≤n$ is the number of distributions you're fitting) and select the "best" model with some information criterion such as AIC or BIC.
The number of fragments is just the $x$ value associated with the lowest AIC.
Logistic regression
Another (faster and simpler) solution would be to fit a logistic regression to your data.
Iteratively fit a logistic regression of degree 1,2,3,...n and then again use some information criteria to select the 'best'.
To find the number of fragments, you can then either use the number of degrees in the model or even better use some threshold on the the probability of getting a zero (which you could compute with the package effects in R).
Notes
It will probably takes you a day or so if you're at ease with these methods and have intro knowledge in programming.
You might want to get opinions from stats.SE as well.

Very interesting answer as well! I will have a look into both approaches. About the Opinions from stats.SE: Is it possible to link this question in crossvalidated or do i have to post a new thread over there?

Many people don't like cross posting. I would advice to accept the current answer here before and then ask your question on stats.SE while making sure to add a link to the current post on stats.SE. You can also link the stats.SE post here.


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Role of neuraminidase in preventing polyspermy in humans
Neuraminidase is a hydrolytic enzyme present in the acrosome of human sperm. It removes neuraminic acid (salic acid) from glycoproteins. I have read in a book that due to this reason it (the enzyme) prevents polyspermy. Can anyone corroborate both of these statements?


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How much time can a human survive only drinking water and eating sugar?
If a person only drinks water and eats glucose, how long could they survive before getting any symptoms? When would the damage become irreversible? When would that person die from lack of minerals, proteins and vitamins? Also, can this "process" be sped up by drinking distilled (pure) water?

You may want to look at so called "Muselmann" created in german concentration camps, becasue their diet consisted of nothing but carbohydrates(vegetable broth and bread) and water.  Protein deficiency seems to be the most important factor.

According to WP, symptoms of vitamin C deficiency (scurvy) will appear after 1 month.

@John Actually there's at least one study I'm familiar with where a 27yo male fasted for 382 days with no ill effects (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2495396/). He had vitamin and nutrient supplements but no protein. I'm pretty sure the cause of death will be related to a vitamin deficiency.

What about vitamin deficiencies that weaken your immune system and tend to lead to death from infection? Would those count?

Almost a duplicate of https://biology.stackexchange.com/questions/8279/how-long-human-can-survive-with-just-drinking-water-everyday (but without the sugar)

The type of sugar matters a lot in this case, since muscovado, jaggery or other non-centrifugal cane sugars contain vitamins and minerals (https://en.wikipedia.org/wiki/Muscovado#Nutrition).

@arboviral fasting does not mean zero calories, you have to look at the type of fasting, many are only a restriction on on one type of food or to a specific calorie count. You also need to look at the patient, for a 800lb patient has a much larger reservoir.   If a normal person did not eat for 300 days they would be dead, your body would literally run out of calories to operate.

@john Agreed, but in this particular case it seems the only calories taken were those forming part of the glucose tolerance tests required during fasting. The patient was 456lb at the start but OP didn't give any restrictions on starting weight. It is an unusual case, but that's why they wrote it up as a paper (and presumably why it was entered into the Guinness book of records). The full text is available at the link I posted above.

Depending on the weight of an individual, about 3 weeks or longer. Sugar will not ward off starvation.


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What is the resting human stomach pH?
This article in ThoughtCo.com claims we have a resting stomach pH of 4-5.
Unfortunately, there are no references, so I can't verify what it says.
I am slightly confused, however. The study says
"Results are given as medians and interquartile ranges: fasted gastric pH, 1.3 (1.1-1.6); gastric pH during the meal, 4.9 (3.9-5.5)"
This other one says
"In the fasted state, the median gastric pH was 1.7"
This article in UCSB Scienceline says "The normal human stomach has a pH which can range from approximately 1-3 but is usually closer to 2.". Unfortunately, they too don't provide any references, so I can't check their claim.
So what is the pH of a human stomach at rest? If it is about 2, then did the article in ThoughtCo.com get it wrong? If it is about 4-5, then what did I misunderstand in the two studies I cited?

It feels to me like your two papers answered your question. The pH of fasted stomach as around 1.1 - 1.8 and it is around 3.9 - 5.5 during a meal.

What confuses me is why the ThoughtCo article says we have a resting pH of 4-5

It is not a peer review document so they might as well say anything 2. I don't where they got these numbers from but it actually match well with the 3.9 - 5.5 estimates of Russel et al. 1993 that you found.

true, but I thought ThoughtCo was a generally respected website, so I was surprised to see them get something wrong. 2. yes, they match well, but seem to be reversed: Russel et al. says our stomach pH is approx 1-2 fasted and 4-5 during a meal, while ThoughtCo say it's 4-5 at rest (I guess they mean 'fasted'?) and 1-2 after a meal.


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Does cortical nephron has just thin ascending loop of Henle?

Guyton and Hall , South Asian edition states that, in Table 76-1 that ascending limb of loop of Henle has thin segment only. But, none diagram in book or internet explain this.
Can any one explain this difference in text and diagram please?

Note: AK Jain Textbook of physiology 6th edition. states on Table 55.1

The descending limb of loop of henle contains a thin segment whereas ascending limb contains a thick segment.

This does explain diagram a bit.
This makes Guyton contradictory.
Edit: From comments, no where the table states part of loh in medulla.

https://goo.gl/Yiz7f5 ascending limb is 'thick' not thin only. See the diagram.

@JM97 So, is the given information on table wrong?

There is also no link on wikipedia or anyother site for cortical nephron ,I could find.

@Anubhav Goel no! that is not what it implies.for the cortical nephron only the thin limb is present in the medulla but both thick and thin limbs are present in the medulla for the juxta medullary nephron so it provides for functional diffrrences between the nephrons.REFER TO THE DIAGRAM ON PAGE 463.(Fig-76-5)

@CATHARANTHUS It is no where written in table part in medulla.

@Anubhav https://ntp.niehs.nih.gov/nnl/urinary/kidney/index.htm see the figure 3.

Most probably the wording is wrong.

@JM97 Ok, you can add that whole as an answer, if you wish or have time?  Thanks for help.

@Anubhav Goel JM97 is correct...besides its a table to help you memorise not understand concepts...thats why i precisely mentioned the diagram in your edited question.

@CATHARANTHUS A table memorising wrong things actually.. Well,  thanks for your efforts.


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Why is the Red Fox colored bright orange?
They're not poisonous or anything, so it can't be aposematism.  As far as I know it doesn't come from diet like the flamingo.  They're not apex predators, so they can't get away with it (like tigers), and honestly it seems like a big risk factor given how many species prey upon them.  As well as something that would make hunting more difficult for them.  I understand they prefer dense brush, and I think hunting during low light hours, but orange against green is about as starkly contrasting as it gets.  So does that just leave sexual selection?  One of their sexes thinks it's pretty, basically?  Or is there some other reason for it, one that might have something to do with the rest of the odd coloring?

The orange colour isn't really all that bright. Photographs that make them look intensely orange (such as this one on Wikimedia Commons) have typically had the colour saturation cranked right up (notice that grass in that photograph is unrealistically intense green).

Most mammals don't have good color vision.  They're dichromats rather than trichromats like primates (including humans).  So you have to figure out what that red/orange color is going to look like to its dichromatic predators & prey.  Orange on green might be good camoflage to them - consider tigers :-)

Consider also that foxes are mostly crepuscular hunters... the low light levels around dusk and dawn mean that the orange/green clash is even less important. So maybe it really is just down to foxes like a nice orange mate.

Of possibly partial interest (given what I thought you might be asking from the title of your question -- "Why is the Red Fox coloured bright orange") is that at one time, English didn't use the word "orange" for the colour we now recognise as orange.  As this Wikipedia page notes, red deer, red hair and the robin red breast were all named "red" even though they were more orange than red.

The tiger doesn't just "get away with it" - it is very well camouflaged

Their fur colour is actually a pretty good camouflage

Ahahaha, I love how simple, and yet indisputable, this answer is :D

Good camouflage indeed

The difference between the name and reality is a linguistic rather than a biological issue. The word "orange" is a relatively modern English word. In the past "red" would have been a term applied to other creatures which are also the same colour, the "red" squirrel for instance, along with people with copper coloured hair who are said to are "redheads" and not "orangeheads".

From the question title, I also thought he was asking about the naming, until I read the body. :)


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New evidence about the beginning of life?
The cover story of the August Scientific American is about new evidence suggesting "volcanic pools" as the location for "first life" as opposed to deep sea smokers like "The Lost City".
I was under the impression that one of the strong arguments for the deep sea vents is that the DNA of the life there is some of the "oldest DNA" on the planet. I'm wondering how the authors would explain that. (Maybe life spread to every "nook and cranny" in a geological blink of an eye?)

Can you please give some reference to support your claims. You could add 1) the link to the article from the August Scientific American 2) a source that support your claim that strong arguments for the deep sea vents is that the DNA of the life there is some of the "oldest DNA" on the planet. especially so that the term "oldest DNA" is very unclear.

Really, if you want to know how the authors of an article explain something, ask them. The question is really not on topic here, given the wooliness of your statement about "the oldest DNA on the planet". This is a Q&A forum for precise answerable questions about biology.

It's an interesting question, but I agree with David that the idea of "the oldest DNA" is a bit strange. The parts of origin-of-life theories about geology are generally about how to create the basic molecules of life (bases, sugars, lipids, etc). These molecular parts don't have an 'age' - so I would not expect to be able to date DNA to any particular location on Earth.

Ah, reading the Sci. Am. article (https://www.scientificamerican.com/article/did-life-first-evolve-in-geothermal-pools/), I see it is about the chemical 'signature' (sodium, potassium, zinc) - that makes sense, as that's about the only way you could infer the geology of life's origins. Perhaps the question could be re-framed as "What do we know about the geological origins of life?" or similar.[ here is the paper, btw : http://www.pnas.org/content/109/14/E821.abstract ]

Okay, now that I've been wrung thru the wringer. I'm not sure what my original source was, but I probably worded my statement incorrectly. I think where i got the "oldest DNA" idea is from articles like this one http://www.pnas.org/content/110/27/11067.full.pdf supporting the idea that the "Last Universal Common Ancestor" came from a high temperature (ie. deep sea smoker) environment. I see upon further reading that this is still up for debate and I suppose "volcanic pools" were high temperature environments.


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white blood cells and cancer cells transport through lymphatic vessels
It is a well-known fact that both of these cells can reach the lymphatic vessels from interstitial space. How does it do so physically? Are there any mathematical models describing this process? It seems like there are endothelial cells along the lymphatic vessels that act like valves, so I would assume that these "valves" open, the cancer cells/WBCs would fit through to reach the lumen?
This question is also a reference request. I am looking for papers that describes the process of intravasation of WBCs and cancer cells into the lymphatic capillaries? Mathematical models are preferable but this is such a niche topic that probably there are no mathematical models.

good question +1 specially on the cancer cell part.looking forward to an answer.

The "valves" are basically one way valves that just prevent backflow of interstitial fluid from the lymph into the interstitial space, so they do not specifically affect the flux of WBCs, cancer cells, etc. into the lymph vessels. In terms of a mathematical model of flux into the lymph vessels, you could use Poiseuille's law to determine the flow rate of interstitial fluid through the "valves", then multiply by the concentration of WBCs, etc. in the interstitial fluid to get the flux of the given cells into the lymph vessels. Of course, that is just one possible model for one parameter (cell flux).

I am looking for more of a biomechanical/fluid dynamics model. Also, you haven't explained how the WBCs/ cancer cells go through the valves...


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Spatiotemporal patterns in neural networks
It turns out that my work in nonlinear dynamics directly maps to a close variant of the Integrate and Fire model. My model produces spatiotemporal patterns that resemble foam. I have to stress that this is  the result of an exceedingly simple model of neuronal activity.
The plot below visualizes the voltage levels of a network of neurons. Yellow is high, purple is low.

I am wondering is these patterns are relevant to the computational neuroscience community. To this end, I am looking for literature describing spatiotemporal patterns in (preferably biological) neural systems.
I am especially interested in any work that  proposes metrics that characterise such patterns since this would allow for a quantitative comparison with my results.
Forgive me is this seems trivial to you, but coming form complex systems theory I did my best and found nothing.

Maybe look at the neural correlation literature? It often involves looking at statistical structures (patterns) of population codes.

I will take a look as you suggest.  The term population codes is very useful to me. Can you make your direction more precise (specific book/paper)? I know I am asking for a lot.

Unfortunately, I haven't looked at this sort of literature for a long time, but here are some thoughts with which to start.
Your question is about "spatiotemporal patterns" of neural systems. One of the first things that comes to mind is neural oscillations (e.g. alpha waves). This is essentially looking for the presence of "frequency patterns" in the neural system. This has a huge amount of literature.
Another methodology that comes to mind is the graph-theoretic approach. In essence, functional or anatomical activity is used to build a graph, which can be analyzed for patterns (i.e. special properties of the graphs of neural systems that are, say, shared across species). One paper: Complex brain networks: graph theoretical analysis of structural and functional systems by
Bullmore and Sporns.
Separately, I might think about the neural correlations literature. Essentially, this is analyzing a neural population by examining the correlation structure of its members, and looking for patterns within it (i.e. that characterize the population code of the system). Two review papers: Neural correlations, population coding, and computation by Averbeck et al
and Measuring and interpreting neural correlations by Cohen and Kohn.
For a review on population codes, see Information processing with population codes by Pouget et al.
This notion is sort of orthogonal to the notion of sparse coding in neural networks, more prevalent in sensory perception.
Sorry if this is broad, but then again I feel the question is quite broad as well. If you have more specific questions, let me know.

This is broad, just like the question is. As someone coming form a different field, this is what I wanted, general directions. Thank you.


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mRNA synthesis for in vivo injection
I found a commercial reagent called in vivo-jetPEI® from Polyplus-Transfection that is able to delivery mRNA in vivo. I'm planning to do an experiment with it, but I'm worry about how to synthesise mRNA and purify them clean enough to inject to living body.
I also found a recommended Kit called HiScribe T7 High Yield RNA Synthesis Kit that can help me to synthesise mRNA but I'm not sure if I can use the final product for an in vivo injection. Anyone have any experience with it?

For in-vivo injection do you mean to inject into the bloodstream? Or micro injection into cells?

@alec_djinn Hi! I mean 'inject to the bloodstream' of living organism. Like living human, living rat for therapies.

Have you ethical clearance to inject mRNA into humans? I would very much doubt it if you are unsure how to prepare the mRNA.

@David Hi David! thank you very much for your reply and concerns. I'm not testing on human yet, I just planning to make an experiment on mice. Everyone have their first time, this is the first time I make an experiment on mRNA so there are some problems I need to elucidate before doing it.

You should purify your RNA after transcription from any buffer/enzyme contaminants. There are several kits available in the market for that. One is GeneJET DNA & RNA Cleanup and Concentration that uses standard silica-beds packed columns to absorb nucleic acids. You can then elute them in pure water and you should be ready to go. Once the RNA is purified you will use the vivo-jetPEI for the delivery.

Thank you very very much! I just take a look at it and planning to purchase it. I hope it will work well, many thanks to you!

My preferred method is to use the Ambion T7 Megascript kit, but I haven't made a full comparison to other kits. They should all be more or less the same. But the transcription itself may not be enough.
Be sure that the mRNA contains a 5' cap. This is needed to bind the translation machinery and produce protein. You can include this in one of 2 ways, a cap analog, or capping enzymes. The cap analog is easier, because you just put the analog in the transcription mix. But this reduces yield, because you typically need to replace 80% of the GTP with your analog. You also won't get 100% capping, the best case scenario would give you 80% capping, but typical results are often much lower than that. If you use an older cap analog, half of the caps will be inserted the wrong way, but ARCA will prevent that. The Capping Enzymes are usually more efficient, but not cheap, and adds an extra reaction and purification step to your protocol.
A good mRNA also needs a 3' PolyA Tail. This can be added enzymatically, or it can be built into the DNA template. The enzymatic method isn't hard, it just uses E. Coli PolyA Polymerase and ATP, and can often be added to a mRNA reaction without additional purification in between. But the tail length would be a little random. Building the tail into the DNA offers more control over length, and eliminates an additional reaction step. But ordering a DNA with 100 to 200 consecutive A's is a little difficult, because quality control is hard with consecutive bases.
Finally, the RNA needs to purified. The method alec_djinn describes isn't bad, but I prefer to use Phenol:Chloroform extraction and isopropanol precipitation. It's rigorous, but it takes more time and uses potentially dangerous chloroform. You can find details on the internet, or just ask me for instructions.
I've made lots of RNA this way, and injected that RNA into a lot of mice. But I'm skeptical of JET-PEI, or any PEI product, for in vivo use. Protecting mRNA in vivo is very hard, and the simple ionic interactions between PEI and mRNA fall apart in the bloodstream. PEI is probably better than nothing, but take a look at the data on that page. The RNA all goes to the lungs. This behavior is typical of a cationic particle that aggregates in the blood, and these aggregates get trapped in the narrow capillaries of the lungs. If this was normal PEI, that mouse would die. Also, they're using 50 µg doses of mRNA. I was doing my work with 1 µg doses, but I was using a different type of transfection reagent and hydrodynamic injection. I also don't see any numbers reported on their bioluminescent imaging data. It's pretty easy to make that data look better than it is by adjusting the scale.

Extremely enthusiastic answer! I don't know why you don't have any name, i really really thankful to your answer. Actually, I found this publication by Huang et al., 2015 using in-vivo-JetPEI and modified mRNA to delivery to the cardiac organ. They also use Ambion T7 Megascript kit as your recommended so it's a good point to start with. Outside of that article, i can't find any other publication about inject mRNA to the bloodstream for delivery to all organs. Could you please tell me which type of reagent are you using to delivery?

@joe I prefer a certain level of anonymity, which is why I can't tell you much about the transfection reagent we used. Our lab invented it, and we were the only ones to ever use it. The paper you mention injects the RNA PEI mix right into the heart tissue, which avoids the requirement for circulatory stability. Injecting any particles into the blood stream typically leads to accumulation in the liver, spleen, kidneys, or lungs, but mostly the liver. Unfortunately, this accumulation is usually through a destructive pathway that degrades the RNA before it can make protein.

I hope your lab will commercialize it as soon as possible so anyone can use it. That's so bad if I cannot delivery mRNA to all organs. Anyway thank you very very much!  I will find more information or/and contact them to elucidate this issue before I buy this reagent.


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Do Pthirus gorillae remain in gorilla leaf nests after gorillas migrate and abandon them?
Gorillas build leaf nests to sleep in. Do the lice which parasitise gorillas, Pthirus gorilla, remain in gorilla leaf nests after gorillas migrate to new regions (and abandon the old nests)?

From the Wikipedia page on Pthirus gorillae: "Researchers theorize that humans acquired the parasite while butchering or scavenging on gorilla corpses, or sleeping in the abandoned sleeping nests of gorillas".
So yes, they are believed to remain.


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Is there variation in which olfactory receptor genes are functional in humans?
According to wikipedia humans have around 400 functional olfactory receptor genes and 600 pseudo genes. Most mammals have higher numbers of functional OR genes.
My question is whether it has been studied how the number or subset of these functional ORs varies between humans.

Can you elaborate on what you mean by "vary between humans"? Which characteristics amongst humans are you trying to associate with differences in the number of OR genes?

My question is whether two randomly chosen humans have different numbers and different subsets of functional OR genes or whether they are very likely to have exactly the same subset of functional OR genes. I'm not trying to associate any characteristic to this subset, though of course one could assume that it might result in a specific range or acuity of olfactory sensing, but that's not very important to my question.

Perhaps the most dramatic example of variation in olfactory abilities in humans is anosmia, or the inability to smell. However, this isn't always due to broken olfactory receptors -- some total anosmias are due to cilia (small hairs) that don't function properly. (This paper mentions that.)
Specific anosmias, or insensitivities to particular smells, are probably closer to what you're asking about. The textbook chapter I linked to below talks about how proportions of the population lack the ability to smell certain odorants -- for example, about 1/10 people cannot detect ethyl mercaptan, which is the scent given to natural gas leaks. These specific anosmias are generally restricted to just one odorant (smell), which suggests that it is likely a receptor deficit. (EDIT: The comments below have even more examples of scents that vary from person to person.)
Interestingly, many conditions are associated with a decline in smelling ability and range, like Alzheimers, diabetes, and taking certain medications. These declines can be because of fewer olfactory receptors or because of deficits further along in sensory processing.
I couldn't find any papers assessing smell variation across all humans -- doctors rarely think to assess smell, so there isn't much data on "normal" populations. Also, it doesn't seem like the genes controlling olfactory receptors in humans have been characterized well, so it would be extremely difficult to do a comparison on the genotypic level.
In sum, there are definitely differences in the ability to smell a wide range of scents. To my knowledge, this hasn't been characterized in an especially systematic way. (If it has, I hope somebody on here knows otherwise!)
This chapter of Purves' Neuroscience gives a basic run-down of olfaction and some possible variations in it.
https://www.ncbi.nlm.nih.gov/books/NBK11032/

Hydrogen cyanide would NOT be used as a natural gas odorant, since it is highly toxic, quite aside from the fact that many people can't smell it.  Mercaptans are generally used instead.  Another instance of something smelt differently by people is the flower alyssum: to me it has only a faint grassy odor, while my ex thought it had a strong and very pleasant fragrance.

Coriander (fresh leaves, not the dried seeds), which is a common spice in asia, is percieved as 'soapy' by some people. There is an article, that also liks this to genetic variants.

@jamesqf : oops, I misread the a paper. Ethyl mercaptan is added to natural gas and some can't smell it. Some people can't smell hydrogen cyanide and that's dangerous because it could kill them. Editing now.


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What is the reason for cats not liking water?
I have two cats myself, a Siberian and a Maine Coon, neither of which like water. In fact, they detest it - like most cats. I was wondering what the reason for this was and if any of you have any interesting theories as to why this is the case.
Thanks in advance!

Quick note here : I agree with the questioner, and the accepted answer. I don't like to bring an old question out of zombie land but ... I recall seeing images of a tiger (i think it was) very happily charging into a pool of water when chasing after prey. No hesitation. So I wonder if different species have different levels of fondness? I know this is the case for dogs ~ we had a newfoudland, and she was impossible to keep dry if even the smallest puddle was seen, she was in it ! Other dogs are somewhat less aquatic, we now have a chihuahua that only likes to paddle ~ she doesn't like rain !

First, some cats do like water. But it seems true (from personal observation and most people's opinion) that most cats don't.
The question has already been asked many times online. Just Google your question!
I doubt one will find peer-reviewed papers on the question but below is a summary of what seem to be the most often mentioned possible reasons I could find. Of course, these bullet points are very hypothetical and I don't know of any research presenting evidence for or against these hypotheses.

Their fur is not really adapted for the water and will very quickly become waterlogged and heavy making it uncomfortable.
Cats are generally speaking quite skittish
Cats may not like the odour of chemicals we put in the water.
Cats love to groom themselves. It is an aweful lot of work to do the grooming after a bath.

Note also that domestic cats are descendent from cats living in very arid areas. The most closely related species with cats are the African Wildcat living in Northern Africa, the Near East and around the periphery of the Arabian Peninsula.
Source
My non-peer reviewed sources are

http://www.petful.com/behaviors/why-do-cats-hate-water/
http://www.animalplanet.com/pets/healthy-pets/do-cats-really-hate-water/
http://www.petguide.com/blog/cat/why-do-cats-hate-water/

Thanks a lot for this helpful and comprehensive answer :)

@Remi.b Your answer is literally copied from the following page, of which to me, is not credible and has no scientific basis whatsoever: http://www.petful.com/behaviors/why-do-cats-hate-water/

@Remi.b "One is that the cat’s fur becomes waterlogged, which weighs down your cat ... your pet will be uncomfortable" ... "some cats may not like being submerged in water simply because they have never experienced it before, and cats are naturally skittish." ... "Cats are also sensitive to odors, and it is speculated that your cat may not like the scent of chemicals from tap water."

My answer is inspired from three different sources (incl. the one you cite), none of which are peer-reviewed. I doubt one will find a peer-review paper on the question. Nothing is presented as a fact but is rather hypothetical. I doubt one could find a peer-reviewed document on that question. The question has been asked thousands of times online so I guess we can either vote to close as homework question (as it lacks effort from the OP) or rephrase an answer along the same lines as other answers online. I just tried to clarified these points.

If the question can't be answered with science then it shouldn't be answered at all, is my understanding of this forum. Purely opinion based answers aren't welcome (again, from my current understanding of the site's policies), and just because a question is asked often, that doesn't grant violation of these guidelines. Yes, I vote to have this question be closed, due to the inability to provide a scientifically based answer.

A series of hypotheses has never been considered uncacceptable as long as they are logical, plausible, not based on false opinions and is clearly presented as a series of hypothesis and not as supported by any evidence. Consider this post for example.

@Remi.b All you did was regurgitate what the author of that page thought. I came across the exact same page when researching for this answer, and chose not to answer because of it having no scientific basis, at all.

Well, I am sorry you chose not to answer. Hypotheses are accepted as answers here (if labelled as such). Regurgitating what others say, is pretty much what we all do when answering a question. This is the whole point of saying things that make sense. We just have to be clear about whether we are giving hypothesis, loosely supported hypothesis or extremely supported hypotheses. IMHO, this is pretty much the only  type of answer one can provide. Btw, I read more than one webpage and their hypotheses were often quite related.

You can open a meta.biology.SE post if you want to discuss whether my answer is on-topic by its nature or not but let's not further our discussion with more comments. It'll be interesting to see how other users see this issue.

Please see the following link for further discussion of this question/answer regarding the concerns that have been expressed in previous comments. https://biology.meta.stackexchange.com/questions/3739/if-a-question-has-no-scientific-findings-available-for-answering-is-it-okay-to

@Charles I added the sources. These are not the original webpages I used (I just don't quite remember what source I first used) but they are making the same claims and all are using the same vocabulary. The main interest in adding these sources is to avoid to be called for plagiarism.

@Remi.b Great, thanks. After reading the response of canadianer, I agree that your answer is (now) acceptable. I reversed my vote on your answer, given the recent addition of sources, and most especially you noting that they aren't peer-reviewed. :)


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What kind of spider is this?

Found in my house in a Beltsville Maryland

It looks like a brown recluse spider

@SonicSplasher I strongly disagree. IMO, the only resemblance that spider (in the picture) has with a brown recluse is the abdomen shape. The head, thorax, leg lengths, and overall color doesn't match.

I disagree with Trachelas.  Two points stand out for me - the chelicerae are forward-projecting, rather than the flat face of the sac spider; and the rather odd knock-kneed appearance of the front pair of legs is a bit unusual for Trachelas.
There is another two-toned, red-and-tan spider that also turns up in houses in the spring and fall - the European import Dysdera crocata aka the Woodlouse Hunter.  That's what this is, I believe.

I agree with Dysdera crocata from the generally-longer shape and because of the shape of the chelicerae

I'm 90-95% certain that the spider in question is a Trachelas tranquillus, more commonly known as a "Broad-faced Sac Spider".
Broad-faced sac spiders are quite distinct in coloring; they have a dark gray/brown head (cephalothorax) with tan/light-gray abdomen, orange/red legs, and distinct pincers (which can be seen if you look closely). These spiders are also quite common for your area, and aren't a major threat to humans.

EDIT: I would like to mention that the images I provided (most likely) have enhanced lighting, and/or are much closer to the spider, so the leg color is (expected to be) lighter than what's depicted in your image.


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Strange white strings on cherry tree leaves
What could be the cause of these white strings on the leaves of our sour cherry tree? Is it some kind of fungus or an insect?

Also, i don't know if it's related or not, but on the other side of the tree brown spots started to appear also on the leaves:

I live in Hungary, if the climate is relevant.

The picture is too blurry for an exact determination.
From what I see it might be Metcalfa pruinosa or a related species, which is an insect of the order of the Hemipteri.
It's a widespread parasite of ornamental plants.
Here a page about it
http://ag.udel.edu/research/delphacid/species/Metcalfa.htm
if true, what you posted are the nymph, and you might be able to find the adults around

This sort of thing happened to one of my plants.  When I took a closer look at the plant, it was a group of white aphids.  The brown coloration of the leaves of your cherry tree was relevant because aphids can sometimes kill the entire plant that they feed off of.
I did not take a picture of the plant, but I found one online: https://entnemdept.ifas.ufl.edu/creatures/trees/shivaphis_celti03.jpg

Woolly Aphids.
They suck the juices out of the leaves of certain trees such as cherry trees and rose plants —to name a few.
Best way to treat them, is gather a plethora of Lady Bugs (or maybe two) to feed off these parasites naturally. Alternatively, try using Neem Oil. It is derived from the leaves of an Indian tree with amazing properties —so your trees/plants won’t be affected. You may need a spray bottle. Just add a little water to dilute for the spray. Make sure you get under the leaves as well. Best wishes!

welcome to the SE Biology. Please feel free to verify your claims, and it will be good answer. But notice that if you dint get any sources  it would be taken like only claims and might potwntionaly get donw vote.


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Why do humans cook animal meat
Why do humans "need" to cook animal meat?
It seems there's an aspect of safety to it: are other animals (eg, house cats, dogs) not vulnerable to the same diseases we get from modern food processing of meats?
But it also seems there's something else to it: is raw animal flesh is harder to digest for us, no matter how fresh or processed?
I've read so many conflicting things about it, like how cooking is really a way to avoid disease, but that the human body is capable of processing protein from raw meat just the same. An example is how other countries eat raw meats that Americans would not. But then I've also read things about how cooking meat is what allowed humans an energy advantage early in our development as a species (I'm not clear how more calories are "unlocked" by cooking) or how denatured protein plays some role in usability. I also know that my person experience with raw meats doesn't help me understand it, because sushi seems to be fine but raw eggs will upset my stomach.

Possible duplicate of Why cooked food considered nutritious if proteins decompose at much lower temperatures?

"I've also read things about how cooking meat is what allowed humans an energy advantage early in our development " -- Cooked food requires less energy to digest, not that it contains more calories. Currently I'm not able to find the source, but if my memory serves me, it's ~10-15% less energy demand.

Because in general (sushi &c excepted), it tastes a lot better?

Humans do not "need" to cook food, but in general cooking food facilitate digestion and absorption of nutrients.
Heat cause denaturation of proteins. Once denatured, proteins are more susceptible to the enzymatic digestion. Thus, more nutrients are absorbed. There are also macroscopic phenomena in play, for example, a cooked piece of meat is more tender than the raw one, making mastication easier and less energy consuming.
The fact that you may feel your stomach upset because of raw food is probably due to the fact that you were never used to it. Your intestinal flora has been selected during the year to deal with the food you usually eat, any "new" food may cause the same symptoms. Humans that eat regularly raw food will not feel the same way.
Generally speaking, cooking food help killing bacteria, so your body does not need to deal with lots of infections that would occur otherwise. This, on the other side, makes your body weaker compared to the one of a wild animal, for example, that is used to deal with such bacteria. Of course, many animals also die because of food poisoning or food-related infection, only the "stronger" survive so there is a strong selective pressure in wild animals to have "a strong digestive system" (and a strong immune system as well). This selective pressure is less pronounced in modern human society but it is still present in less modernized areas.

Taste is relative. Some likes raw food more than cooked one.


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What are some online databases that I can search to find the pathways for sythesis of Lignin, Cellulose, GAX?
I am trying to obtain the pathway information for synthesis of Lignin,GAX and Cellulose in Sorghum. I am quite new to biology and genetics (EE background). I would appreciate it if y'all can provide me with some websites or books where such info maybe available. I have already looked in KEGG. Thank you very much.

KEGG would be the first choice for pathway data (also/especially for specific species). If KEGG does not give you the data you need, maybe describe what else you need, to give people a better idea in which direction to go.

The other big metabolic database site besides Kegg is MetaCyc which certainly responds to searches for lignin and cellulose.
The problem with lignin is that it is a very complex molecule, so in both Kegg and MetaCyc there are a many reactions involved in its synthesis. Cellulose is less complex and I have no idea what GAX is, despite an internet search. If you are so new to biochemical reactions and metabolic pathways that you cannot handle the results of a MetaCyc search on lignin you should easily be able to find articles devoted specifically to cellulose and lignin, perhaps using Wikipedia as a start.

I'd guess it is supposed to be a subscript x, so that @Adi means the various form of Gibberellic Acid: GA3 and etc..


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can anyone identify this plant please?
Seen in the med and have it in my garden

Please specify where you are located in the world, and if this plant was acquired locally or not. :)

It is a houseplant, not a common wild plant. Your question might be a better fit on gardening.SE.

This flower is some type of mandevilla.

The question states "seen in the med" which I assume means the Mediterranean.

This is a climbing plant from the Genus Mandevilla. It's a genus native to the Americas.
Here is a photo for comparisson:

However, since the Genus Mandevilla has more than 150 species (let alone cultivar and hybrids), narrowing it down to a particular species may be very difficult in your case.


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Optimization of Signal Peptides
We are looking at modifying the signal peptide of a receptor in a common immortalized human cell line.  The cell line already expresses an unusually high amount of the protein, but much of it is not surface expressed.
When we compared the sequence of the signal peptide in the cell line (in this specific case the first 19AA), we found 2 mutations vs the wild type (WT) sequence.  One obvious idea, which we will do, is to restore the peptide to the WT version.
But I've been curious about options that increase trafficking to the plasma membrane over WT.  When I've looked up groups that have actually done this, it's normally been with large screens against every possible mutation in the signal peptide.
Are there targeted approaches to choosing a small number of signal peptides to increase surface expression?
I'm playing around with swapping it out some viral peptides that are totally unrelated to see if we can get increased expression with a receptor that's still (semi) functional.

Is there any evidence for the idea that the signal sequence is the cause of the lack of surface expression? Do you know where the rest of the protein (not at the surface) actually is located?

From staining it seems to mostly be diffuse through out the cytoplasm, not really in puncta as I would have thought from miss-folding.  We also know that what is surface expressed is functional.

Further I'm interested in the general case if there is one, type-I transmembrane proteins if a type is needed.  I will say that interested in any particular modification, even if it's a signal peptide not found in the host (eg viral).  I'm trying to get my tech transfer guys to clear me asking about the specific protein.

I don't have an answer to the question but I'm intrigued by the problem. Do the mutations look like they might affect SP function? Meanwhile here is a paper on overall design principles that you may not have seen. It's old, but it's by G von Heijne.

@AlanBoyd Any von Heijne is worth reading regardless of application. That was the main source that lead me to ask the question.

Also, the mutation is a serine mutation so I think it probably changes things

You could upregulate the transcription of the receptor gene you are interested in. More receptors being produced = more receptors being expressed on the cell's surface.


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What is this web-like organic matter?
I saw this on my window couple of days ago. Does anyone know what it is? I have tried google image search with no luck.

Do you have any idea how long that's taken to develop?

scale would help a lot. I could be looking at an arctic oil spill satellite image.

Hi @Charles I would say it appeared out of no where I was out in the front lawn and noticed this it would have definitely caught my eye if it was developing and in its early stages

@John, I cropped the image but this is on my front bay window (outside) it is roughly 2 to 3 inches in length.

@Irfarino Just out of curiosity, where are you located in the world?

This is a slime mold of the genus Stemonitis, and I'm thinking the species is axifera. They tend to form on dead wood, of which seems to be the case in your picture (assuming that we are in fact looking at the wall just next to your actual window, since the bottom left of your window can be seen at the top right of the picture).

that sounds pretty close, the picture I posted is the outside of the window it is on the aluminum capping and the gray area is the caulking but there is wood underneath the capping just like any other windows. The mold seem to be forming on aluminum in my case. Is this harmful to humans?

@Irfarino I'm fairly certain it's harmless.


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What is carbon in the soil?
I often see the term "carbon in the soil" (example) but I cannot figure out what it is. It's a positive goal too - people want agricultural techniques that do not deplete it.
What form does this carbon exist in and what are the major sources? How does it help plants and other organisms who use the soil?

CaCO3 can be a major constituent of soil, i.e. Chalk, so mountains can be made of carbon in large amounts. Environmental Scientists study mountain weathering's effect on the climate, with sulphuric acid and absorption of CO2 carbonic acid into alcaline soils. Carbon in the soil conversely, refers to carbon fixing by plants adding to the soil, and plant matter being consumed and returning to the air. There is mineral and organic carbon. soil technically is not often mineral, it is normally a living matter of organic and mineral.

It refers to organic carbon, i.e. the carbon present in proteins, carbohydrates and other molecules as consequence of the metabolism of living creatures. Carbon rich soil is an indication that microorganisms, insects, and worms are living in the soil. They are the basis for the soil ecosystem and boost the flow of nutrients that ultimately will support plant growth. A soil with low content of organic carbon indicates that it's a harsh environment where living organisms struggle.
Some articles on the matter:
https://en.wikipedia.org/wiki/Soil_microbiology
http://www.nature.com/nature/journal/v501/n7468_supp/full/501S18a.html
http://mbio.asm.org/content/6/2/e02527-14.full

How does agriculture deplete it?

Why the downvote?

@aitchnyu It depends on many factors. The use of chemicals for pest control of fertilizers may affect the ecosystem, for example, causing a cascade of reactions that it's hard to predict. Also, intensive cultivation may deplete the soil nutrients too fast, "starving" the biota.

If you take an average soil sample, it contains lots of organic matter, unless it is completely mineral like desert sand. Oganic matter always has C, H, O elements, and often N. Peat bogs for example, are classed as a type of soil and can contain almost only organic matter, with many kilos of carbon per cubic meter, rainforest soils are sometimes meters of peat, it can catch fire due to carbon content. Humus in forest soils is also mostly organic. If carbon fixing life is removed from a carbon rich land, soil carbon will often slowly return to a mineral state, often as a function of temperature (hot soil mineralizes faster) carbon products get turned into simpler more volatile lower energy compounds, by being eaten by biota and respired as CO2.

Carbon in the soil would be what's left of anything that died in there, or any animal feces.
Carbon in the soil may possibly benefit bacteria that live in the soil, which may fix or otherwise convert nitrogen, but the plants don't use it.
However, let's imagine a dog is walking around and dies. It will rot into a gooey paste as maggots eat it, and then will liquefy into a putrid mess and eventually what's left of it will turn to dirt.
The dirt will have lots of carbon in it, which bacteria will probably use,
The dirt will have lots of minerals in it, which the plants DO use
They get their carbon from co2.


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Identify this bird
I have attached below the image of a bird that I see everyday from my balcony. Since I do not have a good camera, I searched the image of the bird on Google. It feeds on insects. I live in Satna (Madhya Pradesh), India.

You are probably seeing an Indian Roller (Coracias benghalensis).

Which is similar but not the same to the picture you posted; which is a  racket-tailed roller (Coracias spatulatus) a similar species of Roller  found in Africa.
However in India do occur other 2 species of Roller, the European Roller and the Dollarbird. You can check pictures of this other 2 species online and compare them with the bird you see every day.

Your guess is that the bird in question is an Indian Roller. However, you also said that there are two species of rollers found in India. Therefore, what I want to ask you is whether the Indian Roller is different from the European Roller or the Dollarbird?

Yes they are different as you can quickly see from a rapid google research. I guessed based on the most common species given in your area and asked you to check.


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What is this creature I found on my house?
What is this creature and what species is this?
I found this on my balcony.

It's a caterpillar but please add your approximate location, it helps a lot the id.

Well, your question ended up being closed... If I understand it correctly, you simply asked "what is this creature?" and, after that, you asked "what species is this?". That being the case, the question seems to be clear enough to me.
Therefore, let's see:
What is this creature?
It's a caterpillar of a moth from the Genus Orgyia.
What species is this?
The Wikipedia link above lists more than 40 species. Here is, for instance, Orgyia antiqua:

And Orgyia leucostigma:

But my guess is that your specimen is Orgyia australis (specially if you live here down under):

Adding your location will greatly improve the chances of defining the species inside that genus.
Conclusion
That's simply a caterpillar (larva) of a moth from the Genus Orgyia. Narrowing it down to the species depends on you adding more information to the question, specially geographic location.

Based on his name I would hazard a guess he's from India. There are Orgyia australis in India, particularly around crop fields.

@JohnBell Don't forget the other Indian Orgyia not yet described.

And that not every Indian person gasp lives in India...but good job, everybody, on the quick ID. Distinctive little guys. It's usually O. leucostigma here in south Texas, I think.


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Specific examples of signalling pathway using logical 'OR' and 'AND'?
I have read here that
"signals from two different pathways may be needed to activate a response, which is like a logical "AND." Alternatively, either of two pathways may trigger the same response, which is like a logical "OR."
But no example is mentioned. I want to know some specific examples in which cell signalling uses logical OR and Logical AND. Any references will be appreciated.

There are thousands of examples, here I list just a few.
1) Macrophage activation. This is a complex case with many proteins acting as AND/OR. The following paper depicts a nice scheme that helps to understand the circuit.
https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-2-36
2) The Lac operon that follows the logic:
if low_glucose AND lactose:
    express(lac_genes)

if (high_glucose OR low_glucose) AND no_lacotse:
    inhibit(lac_genes)

if high_glucose AND lacotse:
    express_at_low_level(lac_genes)

https://en.wikipedia.org/wiki/Lac_operon
https://en.wikipedia.org/wiki/Synthetic_biological_circuit
3) Phosphorylation and ubiquitination pathways. For example,

... proteins primed through phosphorylation by one protein
  kinase are often phosphorylated processively on the N-terminal side of
  the priming phosphate by GSK3 at a series of Ser/Thr spaced by three
  residues, with the cluster of phosphates regulating protein activity
  (e.g., glycogen synthase, β-catenin). If the two sites are
  phosphorylated by different protein kinases, then this can in
  principle provide a logical AND gate in a downstream response.

http://www.sciencedirect.com/science/article/pii/S1097276507007988
4) Neurotransmitter signaling pathways.
Figure 2 of the following paper
http://www.sciencedirect.com/science/article/pii/S0022519306003675
describes the boolean logic underlining the signaling pathway

Tyrosine hydroxylase activates itself in this model.
  There is an “AND NOT” gate between
  tyrosine hydroxylase and COMT to activate dopamine as
  tyrosine hydroxylase and not COMT activates dopamine...
...adenylate cyclase is activated by dopamine
  receptor 1 and not by dopamine receptor 2, which has been
  represented by the “AND NOT” gate between the input nodes.
...
DARPP32, is activated by protein kinase A, and
  not by calcineurin, therefore protein kinase A “AND NOT”
  calcineurin activates DARPP32.
DARPP32 inhibits protein phosphatase1, which is
  represented by the “NOT” gate from DARPP32 for protein
  phosphatase1.
  ...
  The activation of glutamate receptor, needs the presence of both
  protein kinase A and the ligand, glutamate therefore, a
  “AND” gate between protein kinase A and glutamate, “AND NOT”
  protein phosphatase 1. ...

Here the link to a database of natural and artificial biological logic gates and here the article presenting the database
To conclude, I would like to highlight this work on the engineering of a biological transistor.

In the paper linkI find this statement TSC2 can be directly phosphorylated by both ERK and ERK-activated ribosomal protein S6 kinase (RSK) on S664 and S1798, respectively, as well as by AKT (on S939 and T1362. in figure 4. Can you please advise if this is an example of OR where TSC2 can be phosphorylated either by RSK and ERK or by AKT. In case if it is not do you know any such logical signalling in cancer metabolism.

If you consider phosphorylation in general, it is an OR. But since you get different residues phosphorylated by different enzymes then I would rather consider them separately. What is the output you are looking for in this case?

If my 1 at output means to phosphorylate and 0 means not to phosphorylate then can it be considered as an OR Boolean logic?

Yes, if you consider "just phosphorylation" then yes, it's an OR. Indeed you will have 1 as output as long at least one among ERK, RSK and AKT, are active.


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Sub-saharan africans (Andamanese, Semang) have the ancestral hair-type, do they also have pediculus humanus capitis lice?
Do humans with the ancestral hair-type also have pediculus humanus capitis lice? Pubic hair lice, Pthirus pubis, are adapted morphologically to cling onto
coarse body hair, and originates from Pthirus gorillae via a host switch 3.3 Ma1. Pthirus pubis is also, at times, found at the eyelashes of infants.
The ancestral hair type is coarser than the derived, longer and thinner hair type. Is it parasitised by pediculus humanus capitis, or, by a lice that is adapted to cling onto the coarser hair, possibly related to Pthirus pubis?

The ancestral hair form is frizzier and much shorter. It survives in sub-Saharan Africans and in other groups whose ancestors never left the tropics, notably the Andamanese, the Semang, the Aeta, and the natives of Australia and Papua New Guinea. The latter groups are descended from humans who spread out of Africa along the southern route into South and Southeast Asia.2

References

Reed, D. L., Light, J. E., Allen, J. M., & Kirchman, J. J. (2007). Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice. BMC Biology, 5(1), 7. doi:10.1186/1741-7007-5-7
Frost, P. (2015) Evolution of Long Head Hair in Humans. Advances in Anthropology, 5, 274-281. doi: 10.4236/aa.2015.54021


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Affinity for oxygen and carbon dioxide in animals
I'm currently reading Treatise on Invertebrate Paleontology (A) and don't understand the following fragment:

The affinity for oxygen in lower animals is many times that in higher ones, whereas conditions are the reverse with regard to carbon dioxide.

What does it mean by "affinity"? Affinity of hemoglobins (in blood)? Affinity of oxygen-transporting molecules, whatever they are? Something else? The book doesn't provide a source of its claim here.
EDIT: @Will - I'm more interested in what kind of affinity they are speaking about in regards to carbon dioxide (I can't comment due to not having enough reputation yet.)

Can you include more of the surrounding text to help with context?

@AlanBoyd "Their [i.e. aerobic organisms'] needs vary according to degree of activity and environmental conditions. In any given case, oxygen requirements can be extremely different, and such variations are usually determined by the affinity of special hemoglobins for oxygen. [The quote above is here.] Humans require an oxygen to carbon dioxide ratio of 250 to 1. In contrast, Arenicola marina needs only a ratio of 50 or 70 to 1. Many lower organisms, especially polychaetes, can tolerate considerable decreases in the amount of oxygen that they take in without the slightest organic damage."

In your comment it says "affinity of special hemoglobins for oxygen".  That is not the same block text as your question.    I think they are speaking to the ability of worms and the like to scrounge O2 out of environments that would be much too hypoxic for vertebrate life.  They can do that because their hemoglobins have greater affinities for O2.  You can read up on bloodworms for an excellent example.

In English "A has an affinity for B". We know what B is (oxygen) but you are expecting us to be able to guess what A is. I'm afraid that you are not supplying enough information for anyone to be expected to help you.

The phrase "lower animals" is so vague as to be completely useless.


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What are the chemicals of betel leaves that may react with estrogen?
Im conducting this experiment about pregnancy testers.Im not quite sure what extract method i can use regarding this experiment.any thoughts?? please help me..


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Seeing with one eye, why intensity doesn't get half?
Today I just closed one eye(for finding blind spot), and as usual some of the visual field is lost, but I wonder why is not intensity of light(brightness) reduced to half?
Shouldn't it be since our brain is now getting only half impulses?
Does our brain instantly reduces the threshold of rods and cones when one of the eye is closed?

Never experienced, but removing one earphone surely reduces sound intensity that is perceived.

The intensity of sound that's experienced by the ear with the earbud would still be the same. The overall experience may change, but if you are experiencing sound at a level of 10 (arbitrary measurement), then after an earbud is removed from one ear, a level of 10 will still be experienced by the other ear that still has the earbud in place.

So, to more directly relate this analogy to sight.. perhaps when listening to a song with earbuds, the vocals are being played in the left speaker, and the instruments in the right. If you take out the left ear bud, only instruments will be heard, but the intensity will still be the same. And so with eyesight, if you are looking at two people standing in front of you, and close one eye, one person may disappear (just like the vocals), but the other will remain, and you will still be able to see them with the same intensity of light (just like with the instruments in the right speaker).

Consider two tuning forks are being vibrated one at each ear, now removing one will certainly reduce the intensity of that same frequency.

Well of course it will because of increased amplification due to the sound waves having the same phase (if I'm remembering my physics correctly). I don't think that analogy applies to this scenario though.

Okay , take this example, put one ear in water bath and let other in the air. ask someone to make some noise, now remove the ear, the noise will be increased.

Again, I don't think that analogy applies either. I think we should just wait for someone who wants to give an all inclusive answer. I myself am at work and about to go to lunch, otherwise I might be inclined to do so. Or, we can move this discussion of "most appropriate analogies for this given situation" to chat.

Let us continue this discussion in chat.

This is actually a very interesting question! (Binocular neurons will change their activity when you close one eye by definition.)

Think of eyes as cameras producing an image at a given framerate. If you have 2 cameras and shut 1 of them off, that doesn't change the amount of light incoming to the other camera.
Your question is one of signal interpretation rather than receiving signals and adding them. Given that the 2 cameras have different perspectives, adding their respective pixels makes no sense. Instead, the dual images (if both cameras are on) are post-processed for spatial reference relevant to perspective.
In the case where a camera is shut off, then the spatial reference becomes a null picture and the post-processing can be skipped.
(For reference, if you took incoming data from both eyes and added them, the result would be an incoherent and largely unusable mess)

Experiment 2
Aim: Effect of intensity on two eyes
Requirement : Two eyes, a dark transparent glass, an object to glance.
Procedure :
1)Sit in a lit room
2)Look at fan with only right eye
3) Look at fan with only left eye through dark glass.
4) Look from both eyes( keep dark glass in front of left eye)
Observation : Brighter in only right eye, darker in only left and medium brightness with both eyes.
Result: Intensity do add when are different. Or more correctly they rather average out.
In your actual experiment, the intensities in two eyes just averaged out, that was mathematicaly equal to single eye.
Theory:
Three principle

1) Brightness is transferred via frequency principle. Greater the intensity of light, greater the frequency of AP transmitted.
2) [Action Potential ][1]

Action Potential has a fixed depolarising potential.

3) Each spatial point, in space, of vision, is represented on a single spatial point in occipital cortex.

Two action potential caused by same image pixel reach their representative point on occipital cortex area 17.
They are then sent to visual associative Area 18 for matching.

“Fusion” of the Visual Images from
  the Two Eyes
To make the visual perceptions more meaningful, the
  visual images in the two eyes normally fuse with each
  other on “corresponding points” of the two retinas.
  The visual cortex plays an important role in fusion. It
  was pointed out earlier in the chapter that corresponding points of the two retinas transmit visual signals to
  different neuronal layers of the lateral geniculate
  body, and these signals in turn are relayed to parallel
  neurons in the visual cortex
  Source: Guyton and Hall, chapter 51.

Same impulses from same spatial point are sent to same interneuron.
The action potential cannot rise further.(Principle 1 above)
This fused signal reaches next neuron for further processing. Intensity is judged.
Same amplitude as of one eye reached, so same intensity was percieved by even two eyes.
If fused signal is of intermediate frequency, intermediate brightness is observed.


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How to choose the most appropriate measure of genetic distance
I am conducting a phylogeography study of a fish species and am trying to construct a phylogenetic tree to describe population structure and ancestry. I have constructed trees using various measures of genetic distance, such as Nei's DA, DS, and Edwards Chord distance. The answers I get between these measures are conflicting, but each explained by a sound hypothesis, and so I must carefully and objectively choose which measure of genetic distance is to be most trusted given my data.
So my question to the community is not, "which should I choose?" but "how should I choose?" I am interested in an answer or (ideally) resource that describes what factors I should take into account and that may bias my result.

Just curious, but is there a reason why you didn't mention/aren't concerned with Centimorgans? I only ask because I'm uneducated in phylogenetics, but when I was studying genetics (in university), that was the unit we used to measure relative chromosomal "distances".

I think we are at cross purposes: cenimorgans describe the statistical distance (linkage) of markers from one another on one genome. What I am interested in is the distance in terms of divergence between multiple genomes (population samples) for the same marker or set of markers.

Yes,  I remember we were studying linkage analysis at the time of that unit being introduced. Makes complete sense!

Have you looked at Rogers, Deriving Phylogenetic Trees from Allele Frequencies: A Comparison of Nine Genetic Distances?


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Pros and cons of amino acid structure vs DNA sequences for evolutionary comparison
This is an analysis question for a lab on the amino acid differences in beta globin amongst different primates, and using such differences to construct a cladogram and infer evolutionary relationships from it. Any input is greatly appreciated!
Question:
What do you see as the strengths and weaknesses of using amino acid structure of proteins for evolutionary analysis? In your opinion, would it be more useful to use DNA sequences for this type of evolutionary comparison between living and extant species? Why or why not?

Since this is homework/coursework, youre usually expected to show your own effort first. But to give you a hint, the real key is in the redundancy of the amino acid sequence.

Amino acid (protein) structure has its advantages over raw DNA.
Protein structure already has introns (noncoding regions) trimmed out which aren't obvious from a plain DNA string.
A protein can have different shapes (such as unbound/bound) or even folded/misfolded (as in the case of prions). DNA doesn't have a way of encoding these changes as they are dependent on substrates, environmental factors and available energy.
Visualizing the 3D structure of a protein can give insight into its functionality that you can't read off a DNA string.

But in the context of this question, we want to use either the DNA or amino acid sequence to build something like a phylogenetic tree. I'm not an expert in phylogenetics, but I assume that important information would be in those introns, because they usually have more freedom to mutate than exons. So two species could have a protein with the same amino acid sequence, but different DNA sequences in their introns. You could use those differences to help identify how they are related.