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Is Parthenogenesis known as Sexual reproduction or Asexual reproduction?
I have seen that in some books refer to Parthenogenesis as sexual and in others as asexual.
The ones that say it's a form of sexual reproduction,they focus on the fact that meios has happened in the process and also,we are using a sexual reproduction system in that animal to produce the offspring.
The ones saying it is a from of asexual reproduction focus on the fact that although meios is involved,we only have one parent in the reproduction process and we cannot have any new alleles in the offspring than the ones the parent has.(unless we have mutation)
so how can we conclude in the end?which is it ?
and also,what is the evolutionary explanation for this phenomenon(parthenogenesis)?

Could  you add some definition of meiosis? Does meiosis imply crossing over of genes in the context of your question?

Only a matter of definition
It is only a matter of definition. When it comes to sex, there is such a diversity of mating system that it is very hard to make a good definition that won't be challenged by limit cases.
Sexual reproduction can typically be defined based on the presence of meiosis (but again this will lead to limit-cases), on the need for two distinct parents + meiosis, or on the need for two distinct parents which have different gender (anisogamy) + meiosis.
Diversity of reproductive systems
At the end of the day, what one wish to call sexual reproduction does not matter too much as long as the definition is being made clear especially when dealing with potentially limit-cases.
If I remember correctly the intro book to evolutionary biolgy called Evolution by Futuyma makes a good overview of the diversity of reproductive system. Having a vague understanding of this diversity will help you undermine your hope of finding a clearly defined definition for sexual reproduction.
Applying the definition of wikipedia to parthenogenesis
Here is the definition from wikipedia

Sexual reproduction is a form of reproduction where two morphologically distinct types of specialized reproductive cells called gametes fuse together, involving a female's large ovum (or egg) and a male's smaller sperm

Using this definition and applying it to the specific case of parthenogenesis, one would conclude that parthenogenesis is not a form of sexual reproduction (despite the presence of meiosis). Note by the way the even within the term parthenogenesis, there is quite a bit of diversity (see the wikipedia entry for parthenogenesis).

what is the evolutionary explanation for this phenomenon(parthenogenesis)?

I will ignore this question because

A post should always be limited to a single question
This question is very broad
There is not a single answer to this question given the diversity of types of parthenogenesis.

For a start on the subject, you might want to have a look at Jaenike and Selander, 1979 for example.

Thank you very much for your answer.I was still wondering,How can one decide which is more important in the definition ? the presence of Meiosis or the presence of the two parents?

More important for what? Also, it is not that easy to really decoupled the two as as soon as you have two parents, you need some mechanism to merge their genetic information (mechanism which is meiosis). If you are asking "is segregation more important than recombination?", then one first needs to acknowledge that segregation is nothing but a recombination rate of 0.5 at the boundaries between chromosomes (more info about recombination rate and their statistics here)

"... on the need for two distinct parents + meiosis, or on the need for two distinct parents which have different gender (anisogamy) + meiosis..." - Could you add some reference or name some example for two distinct parents that are supposed not to have different gender (no anisogamy)? Some funghi?

"... more important in the definition ? the presence of Meiosis or the presence of the two parents?"  makes we want to set up some answer, are you still interested in the subject? Interestingly, two "parents" is not what the commented answer assumes when citing the textbook definition: it's two morphological different gametes! They might be derived from one single "tree" (blossom male und female, same tree, no two "parents"). Again, very pertaining to differentiate two parents and/or gametes from crossing over of allelic genes. Please let me know if you need any adding answer.

"applying wikipedia's definition...":
"zygote that develops into an organism composed of cells with two sets of chromosomes (diploid)" That should also be addressed, if gametes can be derived from one single cells or, if not, from its mitotic clone without those cells forming "an organism composed of cells", full stop.

@Tarannom As it occurs to me only now after strenously answering it is clearly NOT "the presence of the two parents".

Wikipedia on Automixis says:
"Some authors consider all forms of automixis sexual as they involve recombination. Many others classify the endomitotic variants as asexual and consider the resulting embryos parthenogenetic."
From the last words of this difficult statement  it may reversely be infered that  parthenogenesis is defined as non-sexual. There do exist different definitions of "sexual reproduction". What some authors consider non-sexual and parthenogenetic, others consider as sexual and: non-parthenogenetic. All agree on the term parthenogenetic denoting a-sexual reproduction.
However, it also results from Wikipedia that in the context of parthenogenesis, the existence of haploid gametes, contrary to common definition,  is not a  prerequisite of sexual reproduction, as  with  all forms of automixis  haploid gametes are not involved.
As the question seems to assume there are different opinions on some forms of automixis being sexual, thus parthenogenetic, or not.
To easen up: you must look at the action - what looks like parthenogenesis maybe is not sexual, opinion diverge
Automixis may loosely be used as a synonym for parthenogenesis process and vice versa, the more if parthenogenesis  is seen  as  the opposite of any mating form of reproduction that uses gametes (or is hermaphroditic). As far as some authors consider  automixis that mitotically produces a stage of haploid cells as sexual reproduction, thus non-parthenogenetic  they are looked upon by other authors who do not share that definition as speaking of "sexual parthenogenesis". Some kind of rebuff, I think, as no author defines parthenogenesis as sexual.
Some say that forms of automixis that involve some kind of  - haploid - "gametes" (think of haploid cells as the first stage of a developement of gametes) should not be considered parthenogenesis, but sexual reproduction.
Conversely, automixis and the crossing-over of genes is not a sufficent condition for defining those processes as sexual, thus non-parthenogenetic. All agree that "mixis" alone is no reason to categorize the specific process as non-parthenogenetic.
To easen up:
Standard, normal,  processes of parthenogenesis do not imply the recombination of   genomes, and are termed non-sexual without discussion  (which might come to a surprise and is nothing trivial either, and that might have been one reason to put the question).
Quote from your question: "The ones that say (parthenogenesis is)  a form of sexual reproduction,they focus on the fact that meios has happened in the process..." That denotes the very point where different opinions come together. To easen up: The ones that say so do  not intend to define those "meiotic"/crossing over forms of reproduction as parthenogenic. On the contrary (this is intricate, sorry for being clumsy or "not learned") they want those forms to be counted out. Counter-intuitively, those authors do not see those processes as parthenogenic (without considering them as hermaaphroditic). So there is sexual reproduction with no gametes as cells that have had some life, different lives.
As it occurs only now: those who consider the production of "tiny" haploid cells as sufficient to render the process sexual in charakter, their point of view can easily be reconciled with a more general, common, definition of sexual reproduction that is based on the use of gametes; the concept of gametes is expanded on those haploid "endomitotic" cells that instantenously fuse and are derived from one and the same individual (as it may occur now: the character is hermaphroditic, then!)
You may find that irritating frame shift  in the very first sentence of Wikipedia (to my mind the following quote might have been incited your question):
Wikipedia: "Automixis[...] is the fusion of (typically haploid) nuclei or gametes derived from the same individual.[...] The term covers several reproductive mechanisms, some of which are parthenogenetic." They should not say "are" (parthenogenetic).


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Bird ID (greenish passerine, Sacramento, CA)
Can anyone identify this small, greenish bird I saw in Sacramento, California, in May 2016?  I tried using whatBird.com but wasn't able to come up with anything convincing.
It looks a little like a willow flycatcher (Empidonax traillii) or dusky flycatcher  (E. oberholseri), but their heads don't seem so strongly two-coloured.

(Photo: own work; sorry about the not-great quality)

It could be Eastern wood pewee. https://en.wikipedia.org/wiki/Eastern_wood_pewee.

@SanjuktaGhosh Thanks but, going by the map at whatBird, it's about 2,100km too far west for that.

I see. I didn't go that far with the details. But Eastern wood pewee appeared similar.

This bird looks similar.

The lack of wing-bars and an eye ring would rule out a Least Flycatcher. Sacramento is also too far west of it's range. https://www.allaboutbirds.org/guide/Least_Flycatcher/id

Nope, it is actually green (saw one today) and is more likely a swallow.

Based on the location and picture, this looks like an American Bushtit (Psaltriparus minimus). There are two cues I noticed that led me to this conclusion, the length of the tail relative to the body stands out and the behaviour as the bird is hanging upside down. Tits and Chickadees tend to   hang upside down while foraging unlike other birds such as Flycatchers and Sparrows.
Other features that point towards bushtit are beak, legs, patterning on feathers, relative size of each feature in relation to each other. There is something that does seem off about the picture in the question and that is the amount of white overall in the bird. I found a post on Whatbird.com that talks about identifying a leusistic bushtit, which the bird in the picture may have attributes of. Leucism can have partial effects where only localized portions of the bird will be white.
You can find more information about Bushtits here.

I'm not sure this is quite right but I, too, was starting to think that the greenish appearance of my photo is because of the light reflecting off the tree leaves and not the true cloud of the bird. This bird has the darker colour action on the top of its head starting at the middle of the eyes, whereas mine has it starting higher up.

I agree that the greenish hue to the bird can be an artifact of the lighting, the green leaves do look contrasting different than the back of the bird in your photo. Try looking at different photos of bushtits on google images to get an idea of how variable they can be. They exhibit regional differences in colour as they are not a migratory bird, some can have darker and more pronounced crowns. The supercilium (the area below the crown and above the eye) can be lighter in certain groups. I will add an image from a Bird ID guide to my answer to show the regional differences.

You probably found a Yellow Bellied Flycatcher, which is weird because they are mainly midwest.

I could be wrong, but to me the beak shape looks fairly different, as well as the beak and head coloration (which could be male/female differences, but I haven't heard of different beak shapes in relation to this). Generally I would say the beak in OPs picture looks wrong for a flycatcher.

The above might be a young bird, with the yellow underside of beak.

I don't think this can be it. The yellow lower beak seems to be quite characteristic of the yellow-bellied flycatcher, the head colouration seems wrong and it's so far from its expected range. But thanks for the suggestion -- I really appreciate it!

I am still checking different sources.

The bird in the original picture is like no flycatcher seen in North America.

I believe this is a warbling vireo. They white "eyebrow" stood out to me and was missing from any of the other suggested answers.
From the Cornell Lab of Ornithology: https://www.allaboutbirds.org/guide/Warbling_Vireo/overview

Warbling Vireos are gray-olive above and whitish below, washed on the
sides and vent with yellow. They have a dark line through the eye and
a white line over the eye. The lores (the area between the eye and
bill) are white in most individuals. Typically, the brightest plumage
on Warbling Vireos is on vent or flanks. Worn midsummer birds can be
nearly entirely gray above and whitish below.

Pictured bird has a ratio of tail-to-body length that is not consistent with a Warbling vireo. Warbling vireos also lack the white outer tail feathers seen in the OPs picture. Finally, the beak seems much too small for this ID.

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How to prevent blobs under the microscope?
My task is to take photographs of fungus spores under a microscope at x100 using oil immersion.
My problem is that I get all these little blobs. How do I prevent the blobs?
So, I have been instructed to first put the spores on the glass slide, then add a teensy drop of water to it (I use a syringe so I have exact control over the droplet) and then put the coverslip on top of that.  Then I tap the coverslip down with the eraser-end of a pencil to force the excess water out from under the coverslip.  The immersion oil goes on top of that and then I can view the spores and take the photos.
This is what I mean:

All those little blobs aren't supposed to be there.  I can't tell what are spores and what aren't, or if these spores have ornaments or not.  However, I happen know this spore does have ornaments (rhodotus palmatus).

Have you tried stirring the spores into the droplet of water (e.g. with the end of a clean toothpick) before adding the cover slip? I have no idea if it would help, but if the spores float on the droplet, it might give you a cleaner picture.

No, I haven't actually.  Thanks for the idea.

At least some of the blobs that you have appear to be air. Seating the coverslip carefully will help to prevent air-bubbles from forming under the coverslip. Lay one edge against the fluid and slowly ease it down.

You mention using an oil immersion lens. It is possible that water has come into contact with your lens. Oil finding its way beneath the coverslip could also introduce refractory blobs as well.

Hmmm.. I think you probably nailed it with the application of the coverslip - I'll have to try this out.  I don't think the problem is with oil underneath the coverslip because I'm pretty careful.  I'll try slowly easing the coverslip down, as you say.  After I try it, I'll come back here and tell you how it went.

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What is the best way to clean immersion oil from the microscope lens?
My job is to photograph mushroom spores at x100 using immersion oil.
What is the best practice for cleaning the oil from the lens?
Right now I am just wiping it with a cotton swab.

If you want to remove oil from anything, you need an appropriate solvent. Detergent and water would likely work best, and is less hazardous than working with organic solvents like hexane.

Many of our instructors forbidden us to use xylol; though some protocols suggest to use xylol. And really, xylol makes the lens permanently blurry. We were told to use a piece of soft cotton-cloth, moisten a corner of it, and softly rub-out the oil. We used the moist-portion and dry portions quite alternatively as required.

In my experience, any microscope worth using has a minder. I would strongly suggest finding that minder, their opinions about cleaning practice should be respected. Objective lenses can be very pricey so they should be handled with care.
Detergent or water are inappropriate for an oil immersion lens. Detergent is likely to damage anti-reflective coatings on the lens. Water doesn't mix with oil.
My standard procedure with oil objective lenses is to wipe oil off with a good quality lens tissue (Kodak). Do not use facial tissues or a lab tissues, such as kimwipes. They are too abrasive and may sractch the lens. If someone has allowed oil to dry on the lens, I take care to know what solvents are correct for the lens and oil that are being used.

A lens tissue - you mean like those soft cloths used to clean your touch-tablet screen?  I never thought of that.  Seems better than a q-tip (which is what my "minder" recommended to me).

No, they are tissues rather than a cloth. Whatman, Lens Cleaning Tissue 105 lens tissues or these.

The least possible amount of cleaning naphtha, pharmaceutical quality (in German: "wundbenzin") and high grade lens cleaning paper. In the ol' days microscopists used some saliva on a piece of cloth, but that was in the pre-coated optics era.

Welcome to BiologySE... can you add some references or additional information so that others can read more about your answer in the context of this question? We always appreciate referencing answers on the site so that all users can follow along if interested. Thanks

Clean immersion oil from a lens by first pulling a fresh piece of lens paper slowly across the lens, like a bath towel across the back, to absorb the oil; shift to a fresh area of the sheet as required, and use more than one sheet if necessary (although that suggests you my have used too much oil).  Then gently wipe the lens with fresh lens paper with a bit of solvent on it; for the most common Cargille type A and B oils, use a high grade of naptha or xylene (xylol).  Finish by wiping with dry paper.
If a residue persists, and it will at least part of the time, clean the lens with lens tissue after gently breathing on the lens to fog it up:  you want condensed moisture, not saliva.  So it is a gentle, long h-a-a-a-a.  Wipe in concentric circling motion, drifting in or out.  Repeat. This method assures you will not wet and possibly harm the lens.  Dried up oil can be softened with a trace of new oil, or better yet, one of these solvents.  So yes, Always Confused, you still are; you need to remove that final trace of xylol. Don't use detergent. Or water. Ever.  Use Xylol or naptha!
The range of answers here shows the dangers of soliciting online advice.  Look at the online microscope "universities" put up by Zeiss and others, specifically, if possible by whomever made YOUR microscope.  That's where to get the right answer.  Today,even"minders" may not know!


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Is hunting animals, crafting and attacking/defending from enemies intellectually equivalent to learning quantum physics?
Our brains were shaped after natural selection. Which means that, as long as we were being affected by it, our brains were changing, evolving.
Once we stepped out of nature and stopped being targets of natural selection, our brains (structurally speaking) stopped changing.
Civilizations rose, humanities and science developed, and you know the rest of the story.
But the brains that we used to create all that is the same brain that was shaped by natural selection. A brain that was concerned with animal hunting, food gathering, fighting with enemies, relating socially and so forth. It is curious to notice that we used that same brain to develop algebra, geometry, physics, astronomy, arts, and so on.
So, would it be correct to say that all those activities from our ancestors living in nature (gathering, hunting, fighting) are INTELLECTUALLY equivalent to quantum physics, i.e.? Because our brain capacity is limited to what happened to it during natural selection (while we were living in nature), so would it be safe to assume that whatever complex thing we can think of (such as quantum physics) is actually as hard as those activities our ancestors performed in nature?
This may be a very stupid question, but I couldn't find fallacies or wrong assumptions in my thought, but my conclusion seems to be a bit... unexpected? Please, correct me if I'm wrong, I'd really like to know the answer to this.

"Human brains enjoy ongoing evolution"

I have no proper-understanding of quantum-physics; as well, many passionate-people worked on evolution and nature, would say too, they don't know it well. So I'll suggest/ request you to add a small and simple excerpt about why you suspect that process like hunting and gathering is equivalent to quantum physics. As well; 2. we (and our brain) is made of atoms and molecules. So, if atoms and molecules obey quantum mechanics then why our brain will not do? 3. What you mean by 'intellectually equivalent'? did you mean 'conceptually equivalent'?

"Once we stepped out of nature and stopped being targets of natural selection, our brains (structurally speaking) stopped changing." Why do so many people think evolution is "done" and that we're the perfect organism that cannot be improved upon?

Every time a couple reproduces, evolution continues.

On what basis or scale do you intend to compare survivalist strategies and quantum mechanics quantitatively? As a side note, I am reminded of a book I once read about the early expeditions to map the Amazon. Despite having the tools of 19th century science, the explorers quickly changed their attitudes about the "savages" when they realized that the natives' intelligence and knowledge of the jungle far outstripped their own. I think your answer might be more along the lines of "complex tasks are complicated until you know how to do them". It's just hard to compare the two ideas meaningfully.

Huh, we stopped out of nature? I didn’t get that memo. Maybe I need to be online more. // Another comment: the question implies that our brain evolved to do quantum physics well. But in fact our brains struggle mightily with similar enterprises. In short, we are badly adapted to solving abstract problems, and need to impose a rigorous regime on our thought to stop us from fooling ourselves.

It's not that evolution stopped. The 5,000 years or so that humans have been civilized is a blink of an eye in the evolutionary timeline. Give society another 100,000 years or so, we'll see some remarkable adaptations begin to emerge.

Addressing some assumptions/presumptions apparently present in the question (this might be too long for a comment):
First, natural selection has not stopped. The sexual selection might be more active than ever, so there is ongoing "pro-fertility" selection and some segregation "pro-smarts". Not every member of contemporary potplation is capable, even with unlimited attempts at education, of doing something useful with quantum physics.
Second, surviving in the wild and fighting enemies are competitive enterprises. Which means that the task is of potentially unlimited difficulty: the better you are at survival, the more you procreate, the more pressure you put on limited resources of the environment, to harsher climates you spread. With enemies, especially those evolving along with yourself, this unlimited competitiveness is even more obvious.
So, the question could possibly be framed differently: how hard our ancestors, living in nature, made the intellectual part of the task of competing with each other? Apparently, about that hard.

Re the competitiveness and therefore unlimited difficulty: it’s theoretically conceivable for there to be an upper limit imposed by physical constraints. For instance, trees have an evolutionary arms race for height in forests, yet there are various physical limits on how high trees can evolve to grow. For brains, a conceivable limit may be due to the considerable amount of energy we need to expend for our smarts (this is pure speculation of course, but it’s plausible).

You seem to think that living in the natural environment is "easy". But, even when the climate helps, even when you have no war to fight or defend against, even so you have to know the habits of the animals which you will hunt, the fishes you fish, the proper season of the plants (fruits, fibers, roots...), which of them could be toxic, which could be medicine; when planting you have to know the season for planting, the season for harvesting, not to mention which plants grow well near which others, and which grow sick close to which others, what are the proper soils and proper irrigation for each species, how to deal with pests, etc.
As you can see, if you try to do those things, you will probably acknowledge that they're not necessarily easier than modern science. After all, nobody created the whole of "quantum physics" out of thin air. There were many different discoveries developed by independent researchers over a long time, with many trial and error in between, etc. And all this, of course, was only made possible after the extreme specialization that - in the end - probably turned us "modern civilized people" into the least healthy and more emotionally tormented version of our species.
So yes, to be human is enough challenge for anyone. To be a single mother is probably more difficult than any dry and tedious mathematical equations.

It may not be easy but it can obviously be done without any symbolic reasoning at all, for example by a worm or a fly. And even with symbolic reasoning one could argue that memorizing plants is not the same as contemplating curved space time or Riemann's conjecture. What you say may be right; but the argument is not rigorous.

@PeterA.Schneider Worms and flies only eat what their instincts have prepared them for. Even ants that tend aphids are not able to learn what "genetical enhancement" might be. Our brains have the biggest ability to learn, and we did this to domesticate dogs, horses, plants... The first man who thought he could mount a wild horse and fall, and mount again and fall again, until he finally tamed it, has surely had some "symbolic reasoning", didn't he? My point is, if we have room for symbols, this must have arised in the old past of our species.

I don't think this is really a biology question; philosophy, maybe. Or for the history and philosophy of science.
The main problem is: what does "INTELLECTUALLY equivalent to" actually mean? What sort of equivalence is it? There isn't a convenient Mohs scale we can use to measure the hardness of problems.
We don't actually have a good biological model of what it means to think about something. We know it involves neuron activation, and you've probably seen the use of fMRI to map exposure to various thoughts to rough activation patterns in the brain, but it's not a model we can replicate yet nor describe in truly precise detail.
We don't have a clear enough description of what it means to think about something to say which animals think and which don't. We know that crows understand object permanence. Some chimps can understand symbolic reasoning. Does that imply some equivalence with human cognition?
"stepped out of nature and stopped being targets of natural selection" is also an assumption which I'd like to question. When do you think this happened? The earliest I think you could possibly justify would be the invention of antibiotics in the 20th century.
It's possible that something like Turing equivalence applies to thought; once a particular level of symbolic reasoning is reached, from there the entirety of mathematics is reachable given enough time and effort.

"stopped being targets of natural selection" happens gradually, of course, and is not finished (one can still die from cancer before procreating). But physical resilience was less and less needed with the growing degree to which we shape our environment (build shelter, heating, grow food) and help each other (support the weak, heal the ill, technically fix issues like myopia).

I won't address all the assumptions/propositions you offer in your answer, just the basic question:

would it be correct to say that all those activities from our ancestors living in nature (gathering, hunting, fighting) are INTELLECTUALLY equivalent to quantum physics, i.e.?

Yes
What do you need to live in prehistoric times?

Observe your environment
Understand what is happening (beyond basic animal instincts)
Form plans of how to survive better
Enact those plans (possibly as a community)

What do you need to do quantum physics?

Observe your environment (=read books, go to university)
Understand what is happening (=understand the mathematical formulas etc.)
Form plans of how to make it better (=have intiuitions about where to go for new developments in QT)
Enact those plans (=actually work out full-fledged new theories and successfully run them past the QT community)

(You can think of more points, for example "storing/accessing knowledge" and probably more).
Analogy: computers
There is an excellent analogy with computers. Since we developed the "Von Neumann architecture" for computers, computers basically did not develop much further. Yes, there were vast, unbelievable improvements in capacity and speed, but that's about it. Fundamentally, every computer you have today, including laptops, smartphones etc., are conceptionally exactly the same as the first computers around the middle of the 20'th century.
The achievement was to build a general computing device that can be applied to any problem whatsoever, without even knowing what the problem is. Once you are at that point, you're basically "done".
The same goes for the brain: once you reach the point where you have all the basics (understanding, reasoning, communication etc.), you're all set. You "only" have to increase capacity/speed to achieve almost anything. Obviously we cannot really scale capacity/speed of a single human brain; I would say we achieve this today by making fields like physics, mathematics, electronics etc. ever more compartmentalized. The time where a single human could know everything humanity has learned about a topic is long, long gone. But basically, it is the same.

Could you provide some references?

@Ebbinghaus, for which part of the answer do you need references? I believe it's pretty self-explanatory and general enough to not need any? The "Von Neumann architecture" is the only term requiring explanation, but it is quite ubiquitous, and any Google hit for it will suffice.

I think you are underestimating the intellectual capacity needed by prehistoric humans to perform all their activities; in short, to survive. It is true, prehistoric humans did the same things animals did. But they did it in a fundamentally different fashion.
Animals are largely driven by instinct. By contrast, we humans have very few instincts — perhaps none! — we cannot overcome. We can choose not to follow even the most basic survival instincts: We can voluntarily hunger to death, refuse to procreate, go out in the cold and freeze to death, with a warm home in sight. We can even actively end our lives.
But this freedom from pre-cast behavior has enormous benefits: It enables us to adapt to environments to which we are physically not well suited. Too light-colored people inhabit the Sahara; fur-less humans dwell in the arctic. We grow food in arid places, by means of irrigation. What makes this possible is a system of knowledge and customs commonly referred to as culture. This puts humans in a unique position among animals. Our survival depends on our mental capacity, not any longer on our instincts or our physical shape.2 This shift is what characterizes us. This shift was made possible by a change in our brains.
Some time in the evolution of homo sapiens something astonishing happened. It is the ability for symbolic reasoning and reflection. We see things not only as what they are; we imbue meaning in them which isn't obvious at face value. We tell stories about ourselves, about our ancestors, and about everything else we see. We keep memories of the past, and tell them to our children. We have rites which reinforce these memories and our sense of belonging, belonging to the place and to each other. The stories we told (like heavens full of scheming gods) were often much more complicated than the reality they tried to explain (like rotating balls on elliptic trajectories). We could create an adaptive symbolic working model of ourselves and our environment; one which was elaborate and complicated, and often poetic and beautiful.3
This ability proved an evolutionary advantage in times of rapid environmental changes and allowed us to survive where other species went extinct. We developed a brain that's "almost entirely plastic" (Feynman)1.
This unique ability to create internal models of the ever-changing world around us allowed us to make Gedanken-Experimente, predict the consequences of our actions. We could be strategic. Ockham hadn't been around yet, and the Ptolemaic way of making sense of it all was blossoming.
This ability to create and manipulate mental models with a high degree of freedom (not hard-wired to specific inputs or instincts) is key to our humanity. The result of our evolution was a brain which is almost completely unshackled. It is aggressively designed to invent stories and see patterns. We are the zoon politikon as much as we are a zoon poetikon, a story teller and singer.
Our mind is not modeled for a specific environment. We can live everywhere we can physically go — and beyond! This enables us to do things that seem very removed from what we did when we evolved. We are physical explorers as much as we are mental explorers. The very advantage of this particular line of evolution, its very essence is that it is not only ready for the unknown, but actively seeking it.
Stay tuned.

1 The lady whose leg he pulled responded: "No, really!?"
2 In fact, our instincts, for example our aggression, appear to become a danger to our survival rather than a requirement.
3 As an example for sophistication and information content consider Australian Aboriginal mythology with stories possibly describing events thousands of years ago.

Unlike the other answers, I'd like to focus on the issue of intellectual performance. If you're trying to ask whether the hunters and gatherers used to use their brain capacities as much as we do, assuming we haven't evolved much since then, the answer is yes. Though, it hadn't been the same type of brain performance. Most of the knowledge needed for hunting is procedural (implicit) information, something you can learn by watching and repeating your parents' techniques. In nature you have to be careful not miss any predator's noise and you have to be always prepared to run. This characteristics fits the brain condition today known as adhd. And, indeed, this hypothesis of the origin of ADHD as an regiment from the times of hunter-gatherers is currently being confirmed by the genetic research.
So if I got you right, I think your hypothesis is right, we use our brain capacity as much as the hunter-gatherers did. But, as can be seen on adhd, non-adhd people are better equipped for the conditions of the today's world (therefore it's called a deficit, they usually score worst in IQ tests) but people with ADHD might have better chance of survival in the wild (because they use more of their brain capacity focusing on potential danger).


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Are there any animals that are both poisonous and venomous?
From my layman understanding, animals that inject venom into the bloodstream by biting or poking are venomous. And ones that harm you when you eat them are poisonous.
Are there any animals (or plants) that fit both descriptions?
I'm guessing eating a venomous rattlesnake will give you an upset stomach but not cause enough damage to be classified as poisonous. And I'm pretty sure poisonous tree frogs don't bite into their prey and inject them with anything.

Any stomach upset from eating rattlesnake is likely to be purely psychosomatic.

What is poisonous depends on who (what species) is eating it, so you might want to specify if you are specifically interested in animals that are poisonous to humans.

Anecdotally, people consume the venom sac of cobras in cognac. Apparently this causes some mild hallucinations (and if you happen to have a cut where it enters your bloodstream before the venom is neutralized by your stomach acids, it kills you)

Eating rattlesnake is pretty common. They're not at all poisonous.

@WayneWerner - ...and now, across America, thousands of idiots will start raising cobras for their venom sacs...which should, predictably and in short order, raise the average intelligence of Americans.

If a poison kills you through the bloodstream but not through digestion, it means that it was digested, nothing more. Rattlesnake venom is a protein that denatures in the stomach long before it reaches the bloodstream - it's not really different from eating any other kind of protein. Others may be destroyed through cooking through the same basic mechanism. Contrast this to e.g. alkaloids, which pass through the stomach unhindered.

The amazonian giant centipede has a venom that is injects with bites, but it also exudes a poison that really will only give you a rash but i believe is classified as a poison.

That is certainly an interesting question!
First, to clarify definitions:
To be considered venomous the toxic substance must be produced in specialized glands or tissue. Often these are associated with some delivery apparatus (fangs, stinger, etc.), but not necessarily.
To be poisonous, the toxins must be produced in non-specialized tissues and are only toxic after ingestion.
Interestingly, many venoms are not poisonous if ingested.[1]
I know of at least three species that produce both poison and venom. One is a snake (although not a rattlesnake, which are, in fact, edible): Rhabdophis tigrinus, which accumulates toxins in its tissues, but also delivers venom via fangs.[2] The other two are frogs: Corythomantis greeningi and Aparasphenodon brunoi, which have spines on their snout that they use to deliver the venom.[3]

[1] Meier and White (eds.). 1995. Handbook of clinical toxicology of animal venoms and poisons. Boca Raton, Fla.: CRC Press, 477p.
[2] Hutchinson et al. 2007. Dietary sequestration of defensive steroids in nuchal glands of the Asian snake Rhabdophis tigrinus. PNAS 104(7): 2265-2270.
[3] Jared et al. 2015. Venomous frogs use heads as weapons. Current Biology 25, 2166-2170.

Interesting, I got different answers when I asked for the difference between "poison" and "venom" on english.SE.

But not too surprising. Try asking the definition of significant on english.SE and Cross Validated and see how disparate the answers can be. English.SE is concerned with general parlance, whereas, biology.SE is (generally) more concerned with the technical conventions. That is a good object lesson that definitions are only definite within a field.

Can you please add links to your sources? I don't know if the book is available on Google books or some other resource, but the two journal articles will be available via PubMed. This will very much help people who want to check your claims, as well as those who wish to learn more. If Wikipedia articles (or some other better resource) are available for the animals you mention, you should link to them as well.

@svick Most of the answers to your question cite no sources. Interestingly, those that do actually align quite nicely with this answer.

The answers in english.SE are not that different... Still, of course there is a difference between scientific use and regular use. But I would call it difference in the details.

@MattDMo I've added links. Luckily, Meier and White (1995) is available on Google (it is also available at any library with inter-library loan service). I think you'll find the claim you are wanting to check on page 3, first sentence.

Your definition of poison seems rather narrow. I don't think poison frogs would meet it as stated.

@CodesInChaos Can you explain why you don't think Dendrobatids conform to the definition.

Although it fits the question, isn't "To be poisonous, the toxins must be produced in non-specialized tissues and are only toxic after ingestion." a bit narrow?  After all there are animals (like some frogs and toads, as well as many insects) - as well as some plants (poison ivy) - that are poisonous to the touch (causes rash and maybe allergic reaction) or have poisons (often on the skin) that start working as soon as they're in your moth (so you spit it out).  These are not venom, since it's not injected into the blood... but nor are they toxic in the sense that the poison must be ingested.

@BaardKopperud, I think you are coming at this question from too anthropocentric a viewpoint. Organisms may produce topical reactions in human skin, but it is unlikely, in most cases, that this was the selective impetus for developing that chemical. They probably evolved those toxins in response to predation, and the topical reaction of hair-less apes (recent new comers in most cases) is just collateral effect.
Also, there are plenty of things that taste bad (e.g. sour citrus, spicy peppers, bitter greens) that evoke a taste aversion response, but are harmless to ingest (so, not poisonous).

I once read something about a type of tiger snake that was poisonous to touch and has a venomous bite.
Edit: I found the species Asian Tiger Snake, Rhabdophis Tigrinus
Rattlesnake meat is the same as any snake just don't eat the head.

authors: Bob Jarvis - Слава Україні


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How screeching affects the body?
Most times when I hear a screech (such as moving a sharp object on a chalkboard thereby causing such unpleasant noise), my body twitches. There are also other unpleasant sounds that causes the twitching, but whenever it sounds only my dad, my brother and I that feels it, but my two sisters and my mum says they don't feel anything. My question is:
Is there any scientific term for this feeling?
Is it hereditary?
What happens in the body or brain when the sound is produced?

Me too feel this; but rarely on chalk-board. It is more common if I slide a stainless-steel-spoon on a stainless steel dish. The sound is not bad but it induce a strange "uneasy" or "discomfort" feeling on my palms, thumbs, the ventral surface of hand, armpit, the side of body; and sometimes includes chest, interior of hands, spine, legs etc. I don't know why this happen; but many others report this. The susceptivity to this, varies from day to day, and sometimes only the vision (not even sound) before the screatch, induce this sensation.

This also happens to me if someone screetches finger on paper (for say while someone is reading or demonstrating from a book) when I was unprepared to follow the finger of the reader. Also the strength of this sense in me depends upon the 'look' or 'pattern' of finger-holding of the reader. I don't know is their any name or identification of it; but it really happens. It might be some sort of illusion. These illusions were much stronger when I was kid. I was scared of it.  With age, these irritating illusions became much milder.

Why this downvote?

This is the answer: http://www.livescience.com/16967-fingernails-chalkboard-painful.html.


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Why WHO has not eliminated chicken pox like smallpox?
Chicken pox is a viral disease, so why then has the World Health Organization (WHO) not eliminated chicken pox like smallpox?
Smallpox still exists in labs.

The answer to this could be too opinion based, and can raise a lot of conspiracies... But I think, and don't take my word for it, since I don't base it on anything. I think the reason to keep a deadly virus alive, is to study it. Experiment with it. I mean, how else can we improve our knowledge? Or test out new antibiotics/medicine/vaccination or maybe even in the future some nano technology? (the last one I think is still sci fi, but keeping an open mind and a good imagination is the way for new and better things)

Eliminating a virus from the world is an immensely costly undertaking. As with most things in real life, cost vs. benefit (and feasibility) need to be taken into account. Unfortunately, there is a limited amount of money available to fight disease.
The overall mortality rate of smallpox is about 30%. That's a very high mortality rate, one that shaped history significantly.
By contrast, of a yearly 4 million people who contracted chicken pox (in the US, before the vaccine), only 100 to 150 died each year.
The death rate of smallpox: 30%. The death rate of chicken pox: .00375%
Maybe someday chicken pox will go the way of small pox. But our limited monies need to be devoted to eliminating viruses that cause greater harm, e.g. polio and others.
Also, not all viruses are equally "eliminatable", e.g. H1N1, HIV, etc.
Smallpox Vaccine: The Good, the Bad, and the Ugly
Monitoring the Impact of Varicella Vaccination

As well as the risk associated with the viruses (as explained in anongoodnurse's answer), chickenpox isn't a good candidate for elimination because of its lifelong carrier state. With smallpox (like polio and measles, which are also candidates for eradication) there is no carrier state, so eliminating the virus at one time point means the virus will not return.  With chickenpox, you could eradicate every active case, and next week an adult carrier will start shedding the virus again and start new rounds of infection.  There is as yet no way of eliminating the virus from carriers, so it's impossible to eradicate chickenpox or any other virus that enters a similar long-term latent/carrier state, which includes all the herpesviruses, HIV, adenoviruses, etc.

I like the complement this answer provides but references would be important. Biologists never trust anything said without references ;)

True, but every unvaccinated generation that dies reduces the risk. Also, there is a zoster vaccine that greatly reduces the chance of shingles. Additionally, shingles is far, far less contagious (direct contact with vesicles or a surface recently in contact), so what you say is misleading. None of that is to say, however, that it would be very easy to eliminate varicella-zoster even if money were no object.


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The human brain in numbers I: neurons
Even though knowing the number of neurons in a functional unit or with the same function is not of main importance, it may be interesting to know their orders of magnitude, especially in the human brain. For example:
|------------------|------------------|
| cerebellum       | 100,000,000,000  |
| cortex           |  20,000,000,000  |
| telencephalon    |  10,000,000,000  |
| brainstem        |   1,000,000,000  |
| sensory neurons  |                  |
|          haptic  |     500,000,000  |
|          visual  |     100,000,000  |
|        auditory  |           2,000  |
| limbic system    |                  |
|         amygdala |      10,000,000  |
|------------------|------------------|

Surely, for many parts of brain you will find a reference where the number of its neurons is estimated (e.g. for the amygdala) - when you search hard enough. I also found The Human Brain in Numbers where some numbers are given. But I am looking for a reference where many of these numbers are given in a systematic way, ideally in a table like the one above. Is there any?

For which parts do you want such numbers? The more detail you go into, the more likely you are to get nothing. It would be, say, easier to get info on the 4 lobes than on hundreds of areas. So, do you want info on simply the 4 lobes?

As many as possible;-) My interest is not specific but general. And please do not ask, why I want these numbers: I just want to know which ones exist or are known (approximately).

A related question - yielding a partial answer - can be found here: What are the estimates in total neurons and average connections per neuron for each of the processing areas of the visual cortex?

First of all, let me clear out that these numbers are calculated, not observed (obviously, nobody has counted the number of neurons in any part of brain). So, take these with a grain of salt.
I was unable to find any report that collects and displays all numbers together (Bio Numbers too didn't yield significant information). So I will compile here all the numbers I have found so far (and keep adding as I find more):
|----------------------|------------------|------------------------|
|PART OF BRAIN         |NUMBER OF NEURONS |               REFERENCE|
|----------------------|------------------|------------------------|
|The human brain       | over 120 billion |  Herculano-Houzel, 2009|
|Telencephalon         |  12-15 billion   |           Shariff, 1953|
|Cerebellum            |   101 billion    |    Anderson et al, 1992|
|Cerebral cortex       |  21-26 billion   |      Pelvig et al, 2008|
|Amygdaloid complex    |    12 million    |    Schumann et al, 2005|
|Hippocampus (CA1)     |  11-24 million   |        West et al, 1990|
|Brainstem             |   < 1 billion    |  Herculano-Houzel, 2009|
|Visual cortex         |   140 million    |       Leuba et al, 1994|
|Auditory cortex       |    1 billion     |University of Washington|
|Corpus callosum       |   200 million    |          Healthline.com|
|Spinal cord           |    1 billion     |University of Washington|
|Cortical minicolumn   |      80-120      |               Wikipedia|
|Cortical hypercolumn  |   5,000-10,000   |               Wikipedia|
|----------------------|------------------|------------------------|

I will continue adding more numbers as I find them. Again, nobody will claim these numbers to be exact, these are just estimates from calculations. Even different sources show different numbers. For example, the Washington University page puts the number of neurons in visual cortex to 528 million. Thus, don't expect these numbers to be anywhere near exact.

References:

Herculano-Houzel, 2009
Shariff, 1953
Anderson et al, 1992
Pelvig et al, 2008
Schumann et al, 2005
West et al, 1990
Leuba et al 1994
University of Washington
Healthline.com
Wikipedia Cortical minicolumn
Wikipedia Cortical hypercolumn

Just great! More than I did expect.

It would be great if the table was hierarchically organised (where possible): top level: the human brain. Way down: the amygdala,...

@hansstricker again, I don't get you. How are you categorizing them to get a hierarchy? From front to back? Number of neurons?

I mean hierarchized by being-part-of. Doesn't this make sense, at least sometimes? I mean, some parts of the brain are immediate parts of the brain (cerebrum, brainstem, cerebellum), others are parts of parts, and so on.

May I add the numbers for cortical minicolumns (ca. 100) and cortical hypercolumns (ca. 100 x 100) in your table?

@hansstricker with proper citations, why not? Every answer, including mine, on Biology.SE is open for improvement! Right now I am quite busy, so will not be able to help anyone out much :)

@HomoSapien: This is a hierarchy which I have in mind: https://en.wikipedia.org/wiki/List_of_regions_in_the_human_brain . It would be great to have this with the acoording number of neurons.

120 billion? I always thought it was closer to 90 billion.

@forest however surprising it is, its just a scientific claim. You never know until you count them all :P


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What is the exact concept of "Repulsion" and "Coupling" (Genetics)?
From all sorts of books including standard books (like those by Tamarin, Griffith etc) as well as internet; I could not clear-up many things about "Repulsion" and "Coupling". Such as:-

Is "Coupling" an exact synonym of "Linkage" ? and is "repulsion" an exact synonym of "recombinant"? No-where I could yet found mention of it.
What are they telling as coupling-"phase" and repulsion-"phase"? Are there 2 different "step"s or "time-frames" or "generations"?
Coupling and repulsion- are they indicating to a "phenomenon"? or the Genotypic "state"?
according to Griffith's introduction to genetic analysis (7th Ed)

Now let us consider what may be learned by repeating the crossing experiments but changing the combinations of alleles contributed as gametes by the homozygous parents in the first cross. In this cross, each parent was homozygous for one dominant allele and for one recessive allele. Again F1 females were testcrossed:

  The following progeny were obtained from the testcross:

  Again, these results are not even close to a 1:1:1:1 Mendelian ratio. Now, however, the largest classes are those that have one dominant allele or the other rather than, as before, two dominant alleles or two recessives. But notice that once again the allelic combinations that were originally contributed to the F1 by the parental flies provide the most frequent classes in the testcross progeny. In the early work on coupling, Bateson and Punnett coined the term repulsion to describe this situation, because it seemed to them that, in this case, the nonallelic dominant alleles “repelled” each other—the opposite of the situation in coupling, where the dominant alleles seemed to “stick together.”

From this paragraph; it strongly seems to me; repulsion is not opposite word of coupling; rather it is synonym of coupling; where we started the breeding experiment with such parents those contained Dominant allele on one locus and recessive allele in the other locus for all the chromosomes.  As a result; parental combination  Pr+ and vg trended to stay together "coupled" (965 progenies at testcross output) and similarly parental combination pr and Vg+ stayed "coupled". Have I understood it correctly? or I'm missing certain significance of the concept of repulsion?

I guess the confusion is stemming from trying to fit the phenotypic terms coupling and repulsion to their genotypic basis.
Coupling and Repulsion are both used considering the phenotypic profile of the progeny, and hence, takes into consideration only the distribution of the dominant allele. If, in the progeny of the test cross, the percentage of double dominant is less than that the average percentage of single dominant, that would be what we call repulsion, as in the two dominant traits tend to be separated. The opposite, percentage of double dominant being greater than the average of individual dominant, is coupling.
This said, it is clear what would be the corresponding genotypic states. If the chromosomal states are $Pr^+/Vg^+.. pr/vg$, coupling would be observed if the $pr$ and the $vg$ loci are linked, since for individual dominant phenotypes to appear, recombination is necessary which is rendered less probable due to linkage. A genotype of $Pr^+/vg..pr/Vg^+$ would result in the phenomenon of repulsion in a test cross. The case you cite, has the latter, and hence, we observe repulsion.
Now to your questions.

Is "Coupling" an exact synonym of "Linkage" ? and is "repulsion" an exact synonym of "recombinant"? No-where I could yet found mention of it.

Neither. More accurate would be to consider both coupling and repulsion as consequences of linkage, differing in the configuration of the linked gene (see above).

What are they telling as coupling-"phase" and repulsion-"phase"? Are there 2 different "step"s or "time-frames" or "generations"?

Although this is difficult to answer without knowing the context, I belive that the author here might be referring to the variable possible configuration of the alleles, as in, if they are in a coupling-phase, they are so oriented that the resultant progeny will show the coupling phenomenon. The phase may change to repulsion if a recombination event occurs. (again, see above.)

Coupling and repulsion- are they indicating to a "phenomenon"? or the Genotypic "state"?

Not to argue much in this semantic mashup, they are best viewed as differing phenomenon (as in the different obtained progeny phenotypic ratios) resulting from varied genotypic states.

(1 of 2). From your statement; "takes into consideration only the distribution of the dominant allele."; to me it seems "takes into consideration only the distribution of the dominant allele in whole cell and not in chromosomes". Did you meant that? hmm then i see the F1 hybrids out of 2 sort of experiments (1. pr+pr+/vg+vg+ X pr-pr-/vg-vg- ; and 2. pr+pr+/vg-vg- X pr-pr-/vg+vg+) gives rise to F1 progenies both having the exactly same notation pr+pr-/vg+vg-; though they are actually different. Image. (contd...)

(...contd) (2 of 2) so I guess, probably to  distinguish between these 2 sorts of F1-hybrids of exact same notation; people used the term coupling and repulsion. (and also your second paragraph tries to ‘define’  coupling and repulsion by test-cross-result, on the F2 progeny). So I could guess; the terms “coupling” and “repulsion” is basically for distinguishing or classifying that 2 sort of F1 progeny. Is so? If so, then everything is crystal clear to me.

Btw later-on you could add some authoritative reference to your answer.

@AlwaysConfused I think you have the right idea. And while the terms are not defined only for test crosses (corrected in the question), test crosses provide the clearest distinction between the two phenomena. In other cases, it might be difficult to put the observed results into one of these.

I could not understand your last sentence: "In other cases, it might be difficult to put the observed results into one of these." is not clear to me. Could you write it a bit more clearly? (sorry if I'm not fluent in English).

What do you mean by "other cases"?

You wrote "corrected in the question". But my question is yet un-edited (by me or any other).

Consider this case ($pr+/vg+..pr/vg$ X $pr+/vg..pr/vg+$). The observed frequencies will make it difficult to classify the result into one of the categories. I meant corrected in my answer. Sorry for the typo.

@AlwaysConfused Does that solve your question?


text:
Would a hole in a heart make it unsuitable for transplantation?
Would a hole in a heart instantly make it unsuitable for transplantation? Or could it be possible for a heart with a congenital defect to still be suitable for use is someone else's body?

I am assuming you are referring to a patent foramen ovale.
A Google Scholar search for donor heart "patent foramen ovale" returns many results about transplanted hearts with PFO, which suggests to me that this is not a contraindication for donation, though that may be up to the transplant team or hospital. In most cases, PFO is not symptomatic; it could also be potentially repaired at the time of transplant if it was deemed significant.


text:
Extremely Scientific Sexual Education Material?
I'm trying to prepare material for 'the talk' about sex and reproduction. I know there's plenty of great books and resources out there for young readers, which I'll use to start with, but I'm also looking for something overbearingly scientific.
Essentially, I'm looking for an academic-level resource that is as close as possible to a literal play-by-play second-by-second explanation of puberty and the entire reproductive cycle. This is partly to polish my understanding, and to prepare myself for unexpected questions.
For example, it should explain the mechanics that sperm/egg cell(s) use to get around, how sperm penetrates the ovum, the process of breast development, and how they become lactation-ready, how the milk is made, what controls where adult body hair grows, the chemical process leading to feelings of lust, etc.
I was mentally reviewing my knowledge of this the other day and realized I know a lot of 'what' but not 'how' or 'why', so here I am.
Multiple books/resources is fine.

Why not some high-school biology textbook? Sex-education is a very broad term. Maybe a single book entitled 'sex-education' or 'sexual awareness' etc. would not be enough. You may need to consult basic genetics books and teachers to know topics like why birth successive girl-child can't be depend on the mother. To know about sexually-transmitted disease you may need to consult peoples expert in microbiology and parasitology. To know about menstrual health and hazards of early pregnancy etc. you need to know about human physiology especially, reproductive-biology and endocrinology, as well

you may take advice from medical professionals, and gynaecology books and nursing training books may add some help. For psychological aspects, you may require training about psychology and counselling and even sociology. Very much interdisciplinery question.

@Moderators good interdisciplinery question requiring expertise from various fields. Bio or health ; which will be more appropriate?


text:
Does heating proteins before a SDS-PAGE gel effect gel result?
I need to isolate a protein that a bacteria has excreted into an agar plate. My plan is cut out parts of the agar, heat the agar to melt it and then concentrate the protein through some purification kit, and then run SDS-PAGE to see if I was successful in isolating the protein.
However, I am not sure whether heating the unknown protein before SDS-PAGE will effect the gel run in anyway. Does anyone know? I know if might denature the protein in some way, but I am doing that anyways with SDS.
Thanks.

I think this depends strongly on the kit you are using for the purification. Agarose doesn't need to be heated until boiling, usually they get liquid around 60°C. Or you could try to use some low melting agarose in a higher concentration. These melt around 37°C.

I guess the next question is what is the most effective way of extracting proteins from LB agarose. Are there any pre-defined methods for this?

Not that I know of. It also depends on your agarose.

I will have to be using LB Miller Agar

Could you just make a liquid subculture and isolate your protein from the medium?

As far as I know, it has an effect. If you denature your protein before running the gel, you do a normal SDS-PAGE and seperate the proteins by their size. Since you use SDS, the charge of the protein doesn't have any influence on your gel.
If you don't heat your proteins before, you do a so called native PAGE. Here the size of your protein doesn't matter so much, because you also seperate for charge, folding, pH and so on. You may have a look on this methods paper for more information.

It's native PAGE, using SDS is by definition not native. I guess a typing error?

I changed it to native PAGE :)
But SDS is the most common used, so the most will understand it.

It's not the heating per se that separates native from SDS PAGE. It's the SDS in the gel and the running buffer and the presence of denaturing agents in the preparation of the samples. Native gels you do after you know a few things about your protein and you want to get more information. But the first step in isolating and potentially identifying a protein from a culture (among SDS and native gel) is most probably the SDS PAGE as you would be able to separate all the proteins by size and as monomers.

If I use regular PAGE, how do I extract the protein from the agarose that the bacteria are growing on?

It would depend on the temperature and how long you keep it there. For SDS-PAGE we normally do it at 95 degrees Celcius for 5-10 minutes. Keeping it much longer could degrade the protein and fragment it.
You could try to do your culture on agar of lower concentration.
Alternatively, you could aim for liquid cultures, as it would facilitate handling before the SDS-PAGE.
(The whole story changes if you expect your protein to be heat-tolerant - as it could be the case that your bacterium is a thermophile)

I am not sure. I am seeing a zone of clearance around the colonies in the presence of silver, which makes we suspect that some exoenzyme is being released.

You mean you add silver in the agar? Can you add it in a liquid culture and see what extracellular enzymes you can detect in the SDS PAGE afterwards?


text:
What happens if you mix brain waves?
I was learning about brain waves, i.e. gamma, alpha, beta, etc., and was wondering what would happen if you mixed them together - e.g. I listened to Gamma waves and Delta waves at the same time. Would I get some sort of brain damage or is the brain able to handle that?

Your question is very unclear. What do you mean by "listening" to brain waves? Do you mean hooking someone (yourself?) up to an EEG and using software to translate the various types of waves to sound? The only damage you'll get is to your ears if the volume is too high. Why on earth would you get brain damage?

how it is possible to 'mix' some brain waves? as well; isn't we naturally get all- ranges of neural-rhythms (alpha, beta, delta, theta, etc) on same-scalp at same time?

Everyone has a mix of ongoing oscillations, of brain waves, at any given point. Some frequencies of waves are more or less likely to co-occur with other types of waves.
In general, brain activity follows roughly a power law distribution - that is, there is more power at lower frequencies and that power decreases in a predictable way as you go to higher frequencies.
When researchers talk about brain waves at a particular frequency, they are talking about a deviation from power law at that frequency - if they say "gamma waves" what they really mean is "there is more energy at gamma frequencies than we would expect if things were random."
Some of these deviations are predictable with changes in brain state - for example, low frequency (delta) activity is greater during sleep, and higher frequency (gamma) activity is higher during cognition.
It should also be understood that these terms really come from a method of data analysis such as Fourier analysis that breaks a signal down into component frequencies. It isn't necessary that a signal is actually produced by combinations of sine waves to break that signal down into component sine waves and describe it that way.


text:
Allergies - congenital situations or created and developed over the years?
This is probably an easy question, but I've yet to find an answer.
Recently I felt under the weather more and more often, especially at the time I was waking up. I assumed this was an allergy-related thing so I did an allergy test and found out that I am allergic to dust-mites. This does explain my condition after waking up, as these mites mostly reside in the mattress and thus affect you during sleep. However, it doesn't explain why this allergy hadn't affected me at all until now and why it suddently appeared after 20+ years. So the question is, is this (and more generally other allergies) a congenital situation, or was it developed due to my way of life, (non) cleaning habits etc.?

Have you read this quite good article? What don't you understand after reading it?

@MattDMo well, wikipedia articles are always explanatory, but in this case, I can't spot any part that refers to weather dust-mite allergy or allergies in general are inherent or not..

Allergies are caused by one's immune system.  If you had never been exposed to the allergen, you would not experience any symptoms.  So they are not innate or inherent.
Why do people develop food allergies after repeated exposure?  I have not read any convincing explanations for the biology behind this.  When you look at the heavy-chain switching that takes place in B-cells, the IgE that are responsible for allergy symptoms are the terminal switch, so those antibody variable regions have already been selected during your life history up until that point.


text:
What organisms are Chloroperoxidase enzymes found in?
Are they found in humans? I'm wondering because they display a structural similarity to glucose-6-phosphatase, which is an important enzyme in gluconeogenesis.

Could you add some details of the structural similarity - from a quick search, I see that chloroperoxidases has a 3-layer sandwich (alpha-beta hydrolase) fold and G6P has a number of subunits.

I can look for more on that but my primary question is what organisms they are found in.

A good start is to look for the EC in RCSB  : http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=2F987A5C there's an 'organism' box on the left hand side

It is only found in an ascomycetes which is named Leptoxyphium fumago, also known as Caldariomyces fumago.
It isn't found in any other specie that we know of yet as searched on the RCSB PDB and Uni-Prot.
In researches that uses it they extract it from the organism, it is also available to buy from companies like Sigma Aldrich who extract it from the ascomycete too.
Sources:
Improvement of activity and stability of chloroperoxidase by chemical modification
Over-expression of chloroperoxidase in Caldariomyces fumago.
RCSB Protein Data Bank
Uni-Prot


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Will dead cells in culture media have any significant impact on Live cells during incubation?
I am generating stable cell lines and have something like 25+ culture flasks to take care of. Ideally I can let dead cells sit in the media with the live adherent without rushing to change media constantly - Will this affect growth of live cells - I don't want to hinder them as they are already sitting in high[] Hygromycin

I think, you should change the medium in a normal frequency, so every 2-3 days. But I don't think, that you have to change it every day. The cells shall die so in the end you have small populations which fit your purposes.

I'm not sure if this is linked to the actual dead cells, but I've found that not changing the media on plates while trying to generate lines from primary cultures can lead to contamination. Again, I haven't determined if this is because there are dead cells available for contaminants to derive nutrients from, or if it's just because changing media removes contaminants before they can grow too much. You might want to keep that in mind, though. I've found that changing media every 3 days is good enough.
Also, it depends on what you want to use your lines for. If you're hoping to study cell signaling or polarization (like if these are immune cells), it may be a problem, as the dead material will activate immune cells, and alter their signaling patterns. This has less to do with your worry about overall growth and more about you developing a good model for whatever you're doing.
To be fair, these signaling shifts can modulate proliferation in culture, but that's really going to vary from cell type to cell type. Sorry for being a bit vague! It's just that all cells are different- I happen to work with immune cells that are fairly finicky. There are other types that are a lot more robust, however, like fibroblasts, that you could probably spit on and they'd be fine.
If changing the media every 3 days really is too cumbersome, you could try splitting off small subcultures and doing a mini-experiment to see if changing the media vs not impacts confluence after a week or so? That would tell you how flexible your cells are when it comes to this.
Edit: Here are some publications that discuss the effects of dead cells in culture and differences between cell types. I also recommend that if you're using a cell line, looking up information via the ATCC website and reading their datasheet and some of the top references they site that likely describe how the line was isolated and best practices for culture.

"Inhibitory effects of persistent apoptotic cells on monoclonal antibody production in vitro" - a good example of how a lack of dead cell removal in vitro can impact cell function/phenotype and highlights the differences between different cell types.
"Cell death in mammalian cell culture: molecular mechanisms and cell line engineering strategies" - a good review that touches on the actual molecular mechanisms to which I was alluding. I particularly recommend reading the section "Induction of cell death in mammalian cell cultures", as it summarizes and links to several primary resources that show how increases in cell death can affect things like productively, growth, and cell number. It also does a good job of touching on the different kinds of cell death, which is important to understand but may be a bit too in-the-weeds for the original question.
"Links between metabolism and apoptosis in mammalian cells: Applications for anti-apoptosis engineering" - similarly good as the previous source, but looks at it through a more metabolic lense, which I think is helpful when considering the realities of cell culture.

Thanks for the answer... but could you please include some sources?  In biology we can't just take you'r word for it; we'd like to see some peer-reviewed articles / books from which you can defend your response.  Thanks!

Thanks for the hot tip. There's a lot of sources relating to the effects of cell death on different pathways, activities, and functions, so I picked a good primary example and two reviews so that it's easy for OP to get a good overview and find more information if they so wish.


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Why is freezing bacteria not a problem?
I have a follow up question to this question: Does freezing microorganisms such as probiotics kill them?
If freezing bacteria kills some of them, then you are effectively putting selective pressure on bacteria when you freeze them (the bacteria more resistant to low temperatures survive, bacteria less resistant die). Why then is it a good idea to freeze bacteria?

When you freeze bacteria, you slow their reproduction. Example: Bacteria, as well as enzymes etc. need the correct temperature and environment to function properly. Is it something like this that you want to know, or are you searching something more in-depth?

Mutations usually occur after a bacteria has divided into two, and usually not within an already existing bacteria. If the bacteria cannot multiply, then how can it mutate or build up resistance?

Hmm ok you have a point. So bacteria are killed in a non-discriminant way by freezing? i.e. some just happen to die during freezing while others survive.

If the cold shatters or ruptures the membrane, then that ought to weaken the bacteria or kill it.

I was thinking of heterogeneous bacteria, but that's not correct it seems.

I don't understand why selection like this would be a problem, even if it occurred. What's the issue with having more cold-resistant bacteria? As Hallur mentioned, even if the bacteria survive being frozen, they won't reproduce at such cold temperatures, so it wouldn't be a problem for food safety. And I don't think anyone uses freezing to try to sterilize things.

I was thinking about its use in research. If you selected for cold resistant bacteria then it could possibly confound your experiment.

The ice crystals that form tear and shear the bacterial cells, unless you add a cryoprotectant (for example, glycerol) to the cells beforehand.
Remember, when water freezes its volume increases.  This is why a closed soft drink can that you put into your freezer to chill faster, will burst if you leave it in until the contents are frozen.
Exactly the same thing happens to cells (animal cells, plant cells, yeast cells, etc.) if they are frozen without a cryoprotectant.

This does not answer the question.

@mdperry Your answer contain valuable relevant information but you should write it as a comment otherwise it may be deleted in future.

@AlwaysConfused I'm not so sure about it being deleted, since mdperry's answer does contain intelligible, accurate & [somewhat] relevant information. A downvote, however, would be a reasonable action to take, should you think the response deserves it.

The long-term effectiveness of freezing or incinerating bacteria is rooted in how brutal and difficult to withstand such actions are.
Freezing generates ice crystals which, as mdperry points out, "tear and shear the bacterial cells."  In theory this could create a selective pressure to survive these temperatures, and indeed akinetes are known to survive the freezing process.  However, that is a non-trivial evolutionary step.  To fit such a state into the lifespan of a bacteria would call for a substantial mutation.  Freezing bacteria for a few hundred million years will likely be sufficient to "teach" them how to survive!  Without such a step, it's just not reasonable to survive the abuse.
The same goes for incinerating.  Once you get hot enough, the chemistry of organic molecules starts to become a permanent terminal issue.  Evolving to beat this is simply really hard.  In fact, an autoclave is enough to kill virtually everything, though one strain of Pyrolobus fumarii did survive at 121C in an autoclave.


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

It looks like the chick of a Moorhen (Gallinula chloropus) or Coot (Fulica atra), probably the former. Both species are common on ponds.

The moorhen chicks on the picture here indeed have this similar German/Belgian flag coloured beak: https://upload.wikimedia.org/wikipedia/commons/9/9b/Gallinula_chloropus_-Regents_Park%2C_London%2C_England_-chicks-8.jpg

it's a chick of Common Moorhen. Shape and color of the bill allow to tell it apart from the coot's one.
Also the behaviour can help: the moorhen often walks on floating vegetation whereas the coots prefer to swim.


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Help with molar ratio
What is meant when asked write molar ratios in 3 parts? For example I am currently assembling a vector that requires annealing several oligos to two pcr fragments prior to ligating them into my vector; which will be used for future transformations. I was told to "assemble the annealed oligos with the 2 pcr fragments. Use a 100:1:1 molar ratio of annealed oligos:each pcr fragment." I'm thinking this means- concentrated oligos:diluted pcr frag #1:diluted pcr fragment #2. I am confused about how to determine the final concentrations of my pcr fragments in relation to the concentrated/undiluted annealed oligos. Why? Because I only know their concentrations as ng/uL not as 5x, 2x or 1x. Should I calculate it as 1(part) divided by 102 (whole) for each fragment? Then multiply that number by the actual concentration of my pcr fragments.
I am sure the answer to this is probably simple but I'm sorry I don't understand it and am hoping someone helps me with understanding calculations of this sort. Thanks.

The whole point of this problem is that for each 100 molecules of annealed oligos, you need to have one molecule of each fragment.
You need to take into account the following:
The MW of each fragment is approximately proportional to the length of the fragment. Thus if you divide the concentration by the length of each fragment, you can get a value that simulates the molarity, meaning that you can use these values to fix to the ratio that you are asked between the different fragments.
For example, if the fragment1 is 100 bp and you have 10ng/µl, fragment2 is 200 bp with the same concentration, then you need to add 1 volume of fragment1 and 2 volumes of fragment2 to get the 1:1 molar ration.
In a similar way, you can calculate the amount of oligos added to have 100x more (of the ratio of concentration to bp length) than the respective fragments.


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Which leads are abbreviated typically as channel ECG 1 and ECG 2?
I want make sure about the fact in the documentation of MIT-BIH NSRDB here.
They just say ECG 1 and ECG 2 but not what particularly.
I think they are the frontal plane channel and transverse plane channel but in which order, I do not know.
In their other database (MIT-BIH Arr.), #1 Channel was about MLII, but #2 Channel about V1.
So I am confused.
Normally, I get data which says leads are this and this. Display channels can be this and this. Etc with this device, very clear manual.
Ticket: https://github.com/MIT-LCP/physionet/issues/21

I'm voting to close this question as off-topic because it is about electrical schematics, not biology. Please take the [tour] and carefully read through the [help] to learn more about the site, including what is on-topic and what is not, and how to ask a good question.

Can you just ask them?

Answer in the ticket but it is still little open because it does say which lead is ECG1 and which ECG2

These records are from Holter recorders and the leads are not in
  standard precordial positions. As a general rule one lead is
  approximately a V5 position or a modified lead II (recording from
  right pectoral area to the cardiac apex), and the other lead is
  generally close to a V2 position.


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The difference between the two ways of glycine represntation
I'm confused because I see now two different way to represent the glycine amino acid. while I understand the first way of the representation the second one I don't understand at all. I believe that both represent the same amino acid but I see that some of the componenets are absent in the second way (no COOH and no carbon). I would like to know the explanation.
This is the first (and the simplest way):

and this is the form that I don't understand:

This is a chemistry question. In organic chemistry, the skeletal representation of molecules does not explicitly label the carbon atom. Line endings, angles and vertices denote a carbon atom. Likewise hydrogens are also not labelled because carbon is by default assumed to be attached to hydrogens if not labelled otherwise.

I hope this co-relation would help.

@industrious If you are an industry-related person; then you have to also stay aware that aminoacids could occur in D and L forms. Both have same bond connectivity so their structural formula is exact-same. But the 3d structure of the 2 type of molecule is different and that can have severe difference of biological effect. (see wikipedia, Natural proteinogenic aminoacids are L-type).

@WYSIWYG, isn't it _bio_chemistry. I don't think the hold is appropriate, there is overlap with chemistry SE but biochemistry is central to the study of biology as well.

@Michael_A This does not specifically concern Biology. It is primarily about organic chemistry and how organic molecules are represented on paper. If you really think this is an on-topic question then vote to reopen. Let's see what others think about it.

The first method of representation is the regular way, where all groups, including carbon and hydrogen are shown.
The second method is the "skeletal form", where every bend in the line means a carbon group, and the hydrogen atoms attached to the carbons are implied. It does seem a little tricky to visualise, but it is easier and faster when you come to larger groups.
Check this out.

Thank you for your answer, but I didn't understand where are the hydrogen atoms in the 2nd diagram that I showed (skeletal form).

@Industrious like Malhar Khushu explained, hydrogen atoms attached to carbon atoms are implied in the skeletal form, which means they are not showed.

See, @Industrious, carbon atoms, in organic compounds have 4 bonds. If, in a skeletal form, a carbon atom isn't showing 4 bonds, then there are hydrogen atoms attached there.

The skeletal diagram omits labels of carbon atoms. This lewis structure of glycine includes carbon atoms and makes the structure of NH2 and COOH a bit clearer as well;

Thank you for your answer, but I didn't understand where are the hydrogen atoms in the 2nd diagram that I showed (skeletal form).


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Why are archae and bacteria grouped into separate domains?
Archae and bacteria are both Prokaryotes. Why are they group into two separate domain?

have you tried google - there is plenty out there for you to discover about this...google "why are archaea in a different domain from bacteria"

Homework questions and questions that show little or no prior research effort are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy.

Reducing your question to its fundamental misunderstanding
Similarly one could ask "Mammals and birds are vertebrates. Why are they grouped into two separate taxa?" (Bacteria and Archea include all procaryotes unlike my example). Or even better, one could ask "procaryotes and eukaryote are all alive. Why are they grouped into two separate taxa?" At the end of the day, your question boils down to why do we group lineages together?.
Why do we group lineages together?
Population tend to diverge through time. For this reason we end up with a multitude of different lineages. As humans we can enjoy grouping lineages as we like to. One might group all yellow flowers together for example. However, a grouping which is of particular interest is one which represent evolutionary relationship. Insecta for example represents a group that include all currently living insects and all of their ancestors until the most recent common ancestor of all insects (that is the individual toward which all currently existing lineages coalesce). Such groups are called monophyletic.
You should have a look at this post where I made an intro to phylogenetic.
In short, to answer your question,

[W]hy are [Bacteria and Archea] grouped into two separate domain?

Because they represent two separate lineages.
Phenotypic differences
Of course, different lineages often have distinct phenotypes which makes their grouping intuitive to a naturalist. For Bacteria and Archae, it takes some knowledge in molecular biology to tell how different they are phenotypically. This document from Colorado University does a good job in introducing the similarities and differences between Bacteria and Archae

I would add to this that an important element of this classification is that bacteria and archea are at least as different from each other as plants and animals; our bias as eukaryotes might be to split the eukaryotes into all sorts of classes and lump prokaryotes together as just being sufficiently different from us, but if we try to be slightly less biased it is clear there is just as much (and by most definitions more) variation within the prokaryotes.


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How do spiders get silk from their spinnerettes?
I'm 13 and writing a report on spiders. How do they use the silk protein gel from the spinnerets? How does it get from the spinnerets to the web? P.S. I know how silk is created, all the way up until the tapering duct
As I currently understand it, the silk proteins are created, then dissolved into a liquid/gel, and stored. Then it is put through a funnel into the tapering duct, liquid is removed. I'm missing an understanding between the removal of the liquid and formation of the silk. Could someone fill in the gap?

Welcome to SE Biology. There is an expectation that you research your question before asking it here. Updating your question to include details of your own research will help people to provide specific answers. It will also ensure your question isn't downvoted or closed for being a homework question.

A: This isn't homework because I'm homeschooled (just to clarify.)

B: My dad tried to install security software and search engines are down. I can only use websites I've been to. Although I do know that silk proteins are created, then dissolved into a liquid/gel, and stored. Then it is put through a funnel into the tapering duct, liquid is removed..... And then I don't know what happens with it......

The link in my initial comment outlines the homework policy, which is broad enough to include your question. You can ask homework questions here but you need to show that you have researched the question. The following quote from your comment satisfies that criteria and it you should add it to your question; Silk proteins are created, then dissolved into a liquid/gel, and stored. Then it is put through a funnel into the tapering duct, liquid is removed..... And then I don't know what happens with it

The term "homework question" is used as an umbrella term for the whole bunch of things like: Homework questions, assignments, low effort questions, not researched questions and so on. And your questions clearly falls under it at the moment, so please edit it accordingly.

As we actually have a homework tag we should not be to fast saying homework questions are off topic. This question has an open answer which could be interesting in other contexts than homework, it just needs more clarification. It is not too broad and definitely answerable by someone knowing more about spiders than I do.

@skymningen They are not off-topic when the person asking shows some effort to solve this by themselves. This varies of course between a 15 year old and a student of an university.

@Indigo2003 Your question has been edited to avoid deletion. You may further edit according to your needs. Besides here's a link, I would suggest you to go through before you post another homework question. biology.stackexchange.com/help/homework

I've seen earlier that exam-questions/ book-exercise questions or any-such type of evaluation-questions (which are usually not fundamental questions) considered as homework question.

I think if a spider expert sees this they will know exactly how to answer it. I urge other closure reviewers to leave the question open. Good luck with the report!


text:
Online phylogenetic tree of human lineages
I am looking for a source of information about the diversity of human lineages and their relationships.
With a quick google search it is easy to find this type of tree

A perfect online resource would...

Contain a lot of lineages going to the most detailed lineages
Contain links to wikipedia or other source of information that could help someone to:

identify a group
have an overview of their culture

Contain visualization of their current (or past) geographic range.
Contain visualization of migration patterns
As mtDNA and Y chromosome may typically show different story, it'd be great if the resource would differentiate these and highlights specific cases where the two tree differ.

Can you recommend some online resources?
A review paper with nice graphs would also be welcome.

Related:

The post The best free and most up to date phylogenetic tree on the internet? recommend resources for visualizing the tree of life.
This webite offers a pretty amazing tree of religions.

Note that the structure of the human evolutionary tree depends on the kind of markers that are considered, male and female lineages don't necessarily have the same history, so SNPs from the mtDNA and Y chromosome will tell a different history, at least when looking into the details.

@bli Good point! I forgot about it. Following your comment, I added a bullet point in my list of descriptions for a perfect ressource. Thank you

Great link about the Tree of Religions!

Such a "tree" actually also has gene flow across branches. Related: Human migration by haplogroups, World map of Y-DNA haplogroups, Early human migrations, Simplified interactive map, Other

Trees for haplogroups
See

https://www.eupedia.com/genetics/phylogenetic_trees_Y-DNA_haplogroups.shtml
https://www.eupedia.com/genetics/
focus on Europe: https://www.eupedia.com/europe/origins_haplogroups_europe.shtml

and many pages linked therein such as https://www.eupedia.com/europe/Haplogroup_J2_Y-DNA.shtml#subclades

and so on.

More detailed for mtDNA (female lineage):

https://en.wikipedia.org/wiki/Human_mitochondrial_DNA_haplogroup

and many links therein

More detailed for the Y chromosome (male lineage):

https://en.wikipedia.org/wiki/Human_Y-chromosome_DNA_haplogroup

and many links therein

https://en.wikipedia.org/wiki/List_of_Y-chromosome_haplogroups_in_populations_of_the_world and links therein
https://isogg.org/tree/index.html
and the Google Sheets linked therein
https://www.yfull.com/tree/

"Trees" for populations
Note that the trees are for genes/haplogroups, whereas such a "tree" for populations actually also has gene flow across branches. Imagine overlaying the tree for mtDNA (female lineage) with the slightly different tree for Y-DNA (male lineage).
Geography of migration
Migration and geographical distance played a key role in the emergence of distinct populations. See

maps of migration by haplogroups: Human migration by haplogroups, World map of Y-DNA haplogroups, Early human migrations, Simplified interactive map, And so on.
maps of distribution of haplogroups: mtDNA in Europe, Y-DNA in Europe, many of the links listed here, and so on

Also check out how theories about migration are changing. For example about mutation M174: theory around the year 2010 vs. theory since at least 2016.

There are a lot of very good resources in your answer. Thank you!

I have used this online tool it has many of the features you are looking for.
http://itol.embl.de/shared/ivica
You can see some example in this page.

How to use this website, where exactly are human lineages?


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If a dead animal is electrified, will it decay?
I was walking past some power lines today, and a flying fox (like a small furry bat, for those who don't know Australian fauna) had grabbed onto two adjacent power lines, closing the circuit, and as such died due to electrocution.
That got me thinking about whether or not the animal would decay in this situation. As far as I understand it, decay is caused by bacteria and other micro-organisms. Could they survive in this high-voltage environment? If not, will this poor flying fox be perfectly preserved until the next blackout occurs?

even if all the bacteria on and in the flying fox die, as soon as he hits the ground there will be plenty more organisms joining.

That is really interesting thought! I've read about microorganisms that can live in extreme conditions like strongly acidic/ alkaline/ salty/ boiling-hot environment; but never read about electrified environment. Thanks for asking!!

probably the OP is asking if it is not grounded; i.e. electric current continue to flow through that organism, then what will happen.

Environemental factors will degrade it (wind-water etc.). For the decaying part, good question sir. But from what I know, electricity will follow a certain shortest path inside the body to close the circuit. The rest shouldnt be electrified and bacteria will be alive.

Then the question could be edited and broadened as; "are there any extremophilic organism that can thrive in presence of high electric- voltage or current?"

@Always Confused "but never read about electrified environment". Bioelectrochemistry is actually a field of research. Microbes can exchange electrons with solid electrodes. If interested, you can search for Microbial Fuel Cells or Microbial Electrolysis Cells. Of course it's rather low voltages and currents, but still, there are a lot of exciting applications.

Degradation doesn't necessarily require bacteria to start. Death would stop oxygenation and feeding of cells, cell lysis would occur, and decomposition would start. add surviving/environmental bacteria and nature takes its course.

Environemental factors would degrade it (wind-water etc.).
But from what I know, electricity will follow a certain shortest path inside the body to close the circuit. The rest shouldnt be electrified and bacteria will be alive.
Bacteria are indeed not resistant to high levels of electricity and would die of it. The current would need to traverse the Entirety of the animal to kill every single bacteria which is highly improbable. Leave one alone, it will reproduce fast.
From what I researched, a constant electrical current of the power of an electric line would cook the animal in a short time. The flying fox you saw probably didnt have live current traversing him anymore and died from a quick jolt (this is a guess only).
Even in the extreme case that 100% of the bacteria would die, the dead animal would be recolonized by bacteria really fast. Even in the wires, wind or animals would carry bacteria.
Power lines are probably protected from arcing this way through anything that could touch them. Imagine if they werent, trees touching them would burn, shoes you throw and hang on them would be calcinated etc.
Off-topic: Are you sure he wasn't only sleeping on his improvised power-line hammock ? :P
Sources:
Conduction of Electrical Current to and Through the Human Body: A Review
Effects of high electric fields on microorganisms I. Killing of bacteria and yeasts

https://www.youtube.com/watch?v=eczDpGiULLo

Note that that paper used 25 kV/cm (2.5 mega V/m - the si unit) - this is way way higher than all but the very highest voltage transmission lines. I think you will find that the reason is purely cooking (high temp) and then desiccation. Trees that touch powerlines can indeed burn and short out lines.

Let me first point out what is harmful about electric current:

alternating (ac) current in the range of 20-200Hz is dangerous, because (even for miliampere current values) it may interfere with the oscillations of heart, causing fibrillation and subsequent death, if the normal blood circulation is not restored within a short period of time. This is typically the cause of death in the domestic accidents associated with electricity (leaving apart falling form a ladder when getting shocked).
direct (dc) current is harmful only at high values, such as 1 ampere and greater. These are rare in domestic conditions, but not uncommon in industrial setting. In this case the current flowing through the body simply paralizes miscles, leaving the eprson conscious, but unable to release the wire. The harm results from being heated by currents, resulting in lethal burns.

Touching the electric power line certainly involves the ac effect, and in some cases may imply the dc effect as well. If the animal simply died from the heart fibrilation, the damage to its tissues due to the current is virtually non-existent, and it will decay normally. If the current was high enough to cause burns, then the current stops once the tissues along its path carbonize and stop being conducting. Burned tissue is inorganic matter, which is of little interest to micro-organism. However, anything that was not burned, will decay normally.
Some also these relevant posts:

Why does electric shock freeze up muscles?
Why does an electric shock contract the muscle?

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