text:
Why don't we consciously know how our bodies work?
Our brain is responsible for regulating our entire body. However, we don't consciously know how our bodies work — our brain has to learn about biology, medicine, and so on.
Since our brain controls our bodies at the cellular level and below, why do we still have to learn about these processes to become doctors, biologists, etc.? Shouldn't we born knowing about them?

We aren't even conscious about most of what goes on in the brain; consciousness is still a poorly understood phenomenon, but we know that lots of brain activity happens without conscious awareness. Most of the regulatory functions of the body are included in that unconscious activity, but so are some processes closer to what we do in day to day life.
For example, if you are experienced driving a car, you are able to do most of the general functions (staying in a lane, for example, or starting to brake at an intersection) without much conscious input, allowing you to have a conversation simultaneously. You only need to be strongly aware of what's happening in an unexpected situation.
Similarly, muscle movements come from executed programs that are learned through experience (especially for humans; some of these movements are innate). When you raise your arm above your head, for example, there are muscles in your arm that move, but also muscles in your back and legs have to adjust to prevent you from tipping over with the new weight distribution, you might lean your head out of the way, all of this is done without you thinking about each one of those individual muscle movements: you are just conscious of the whole general movement.
Regulatory control of things like your heart rate or digestive system is even less out of conscious control.
Brain-computer analogies are often fraught with peril, but in this circumstance I think it is reasonable to use one. Your computer is able to perform all sorts of calculations, it even has software that allows you to communicate with a network of other computers to bring you StackExchange. But even if you download computer science books onto your computer, it has no idea how to assemble a new computer from scratch. It can display the text that could allow someone else to do it, but it is completely unnecessary for its day to day functioning to know how to replicate it.
So back to your original question: why don't we consciously know how our bodies work? Because it's completely unnecessary to know this for normal day to day operation in the context in which animals evolved.


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What happens during fixation of Nucleic acids on nylon membrane
In Southern blotting technique, fixation of DNA to nylon membrane is a step prior to hybridisation with probe. It is done by baking at 80ºC and according to this cross linking between DNA and nylon takes place.
What I am unable to understand is, if there is cross linking between DNA and nylon then, how does the probe bind complimentarily to the DNA? Isn't cross linking may mask the sites which may form hydrogen bonds?

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text:
What spider is this in Idaho?
I have killed maybe 5 of these solders as I have a 3 year old and dont want her bit.
Details :

Whitish top; brown legs; striped maybe yellow or white on the butt with black
Size of a penny
Seen them all times of the day. Summer (July)

Kinda reminds me of the ant-mimic spider but I am unsure.

And a close up:

Should be able to zoom in quite a bit. Just hold CTRL and hit the plus symbol.

First thought that comes to mind is a Parson Spider, but not quite.. the fact that there's a blemish on the plastic of your vacuum cleaner (lol) makes it a bit difficult to assess the full pattern on the abdomen of the spider.

I'm just about 100% certain that this is a Hobo Spider, which belongs to the species Eratigena agrestis. As stated in my comment, the blemish on the vacuum cleaner's plastic makes it difficult to observe the full pattern on the spider's abdomen, which would have otherwise made for a much quicker identification.
Once realized though, the distinguishing feature for me was in fact the pattern on the abdomen. If you look at the picture I provide and consider at the abdomen, it looks like a face with two eyes, a mouth, some hair, and a beard; i.e., a hobo. Now look at the picture in the OP -- the exact same "face" can be seen, excluding the right "eye" of the hobo (our left), due to the blemish on the vacuum's plastic. The "hair" at the pedicel, the down-turned "mouth", and the "beard", are all visible in both images, and are near perfect matches. The legs, overall body coloration, size & proportionalities, and slight discoloration on the cephalothorax, also match.
I had to maximize the OPs image to 200% zoom to get a detailed enough view of the spider to then make these conclusions.

This species spider is most commonly found in your region, that being north west USA, however, they've also been seen in Asia and Europe. And as for if this is a venomous spider (since you're concerned about your daughter): according to Wiki, this kind of spider doesn't bite unless forced to defend itself, and, the CDC does not consider it to be dangerously venomous.

Well written post. Thanks. However, as Toothpasta mentions in their post, your image is actually of Sergiolus montanus (the stealthy ground spider). Your own wiki link will also confirm this isn't the hobo spider. I would advise adding an update to your answer acknowledging this mistake and perhaps sharing the range and danger status of the correct spider species. Thanks.

If user22020 is 100% sure that's a hobo spider, then I'm 101% sure that's a stealthy ground spider. The source of user22020's picture actually labeled it as such.

 It's definitely in the ground spider family, just like Parsons spiders.
Hobo spiders and barn funnelweavers are more well-known, but both are brown, not black and white, and have vastly different patterning than yours. Stealthy ground spider are not famous because they, like most Idaho spiders, are not dangerous.

Welcome to Biology.SE! Can you elaborate why you think your identification is correct? For example, discuss the key features that helped you come to this conclusion and provide references that support your assertions. ——— You might also want to take the [tour] and then consult the help pages for additional advice on [Answer] questions effectively on this site and then edit your answer accordingly. Thanks!

It seems to be a male barn funnel weaver, according to a quick google search. The main part of this picture that leads me to believe that is the first segment of the leg, closest to the body, is darker than the rest.
This is the a male barn funnel weaver, with the same darker segments. And yes, I looked at the list specifically for Idaho

Answers to species ID questions need a lot more content than this. You need to convince us that your ID is correct, explain why that ID applies over other IDs, and hopefully provide some convincing pictures. Note that species ID is quite difficult, especially for arthropods due to incredible diversity and many similar body plans for distinct species (and even genera).

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Can saltwater fishes survive in sugar solution?
I know saltwater fishes can't survive in freshwater because of osmosis that water would rush into the body of fishes. How about sugar solution? Does sugar solution provide similar conditions as salt water for saltwater fishes?

No, the chloride cells in the gills rely on the relationship  between chloride and sodium to remove salts out of the body against the gradient. Switching the environment to sugar would cause the chloride cells to not be able to maintain ionic regulation. See the below link for basic info on chloride cells: https://en.m.wikipedia.org/wiki/Chloride_cell


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When looking at skulls from early hominids, how do we know their language creation abilities?
If there are no vocal chords left, how do scientists deduce what sounds the specimen was able to create?

Can you provide us with a specific example of where this happened? Because normally, if they do so, I expect them to describe how they did it.

If there are no vocal chords left
The hyoid bone, which is part of the voice box, does fossilize -- at least occasionally -- and can be used to partially reconstruct the larynx capabilities, so this premise is wrong.

We now report the discovery of a well-preserved human hyoid bone from Middle Palaeolithic layers of Kebara Cave, Mount Carmel, Israel, dating from about 60,000 years BP. The bone is almost identical in size and shape to the hyoid of present-day populations, suggesting that there has been little or no change in the visceral skeleton (including the hyoid, middle ear ossicles, and inferentially the larynx) during the past 60,000 years of human evolution.

--A Middle Palaeolithic human hyoid bone

The Dikika australopithecine hyoid body proportions are chimpanzeelike.  ... The Kebara hyoid dimensions (body alone, and articulated body and greater horns) are almost all within the observed range for human hyoids. Discriminant functions clearly distinguish human from African ape hyoids and classify the Kebara 2 hyoid as human  ...  the expanded bulla characteristic of the African ape and australopithecine hyoid body is therefore interpreted as reflecting the presence of such a laryngeal air sac extension. Its absence in the human, Neanderthal, and H. heidelbergensis (Atapuerca SH) hyoids implicates the loss of the laryngeal air sacs as a derived Neanderthal and modern human trait ...

--Comparative Morphology of the Hominin and African Ape Hyoid Bone, a Possible Marker of the Evolution of Speech

Modelling of the potential acoustic capability of Neanderthal VTs [vocal tracts] was carried out by Lieberman et al. [24,25] based on their three-dimensional reconstruction of the La Chapelle-aux-Saints fossil ... A different approach to Neanderthal VT reconstruction was taken by Boë et al. [41] who maintained that the Neanderthal larynx and hyoid bone sat lower in the VT than in Lieberman's reconstruction ... In this paper, we report a new study of the speech potential of Neanderthals, based on reconstructions of the positions of the hyoid and tongue root

--Articulatory capacity of Neanderthals, a very recent and human-like fossil hominin

The description of a Neanderthal hyoid from Kebara Cave (Israel) in 1989 fuelled scientific debate on the evolution of speech and complex language. Gross anatomy of the Kebara 2 hyoid differs little from that of modern humans. ... Because internal architecture reflects the loadings to which a bone is routinely subjected, our findings are consistent with a capacity for speech in the Neanderthals.

--Micro-biomechanics of the Kebara 2 hyoid and its implications for speech in Neanderthals.
As well as larynx reconstruction and anatomic evidence, researchers have other lines of evidence about speech capabilities in Neanderthals and other non-modern humans, such as the genetics (especially the gene FOXP2).


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If cells regularly renew, why do we have scars?
Question may sound bit poetic but I have a pretty basic question here: Often we get a minor wound and cells renew and quickly "cover" it. But when we have deeper wounds, often they leave behind scars. Why does it happen?
I was researching around and saw this comment on a related question:

That's not true - some cells turn over quite quickly, others take months or years, others never replicate.

But how come we get some wounds "completely filled", while others leave scars on almost the same skin/body part? And ok, if a deeper cut has resulted in inner (different type of cells) being damaged, why do we find the scar on epidermis?
Thanks a lot for your guidance.

Scar is mostly collagen( a fibre, not cell)

I think you will get all your answers here. I can add this as an answer if others in the community don't tend to close it as off-topic...

Scar tissue formation is part of the normal healing process in which fibrous material braces and pulls the wound together, in other organisms (and young mammals) this process is mild and just serves to temporarily reinforce the damaged tissue as new cells migrate in to begin replacing the missing tissue, sometimes to the point of replacing missing limbs in lizards and amphibians. However in adult mammals and birds the process of fibrous tissue is far more exaggerated, creating longer lasting or even permanent scars, Here the wound keeps filling in with more and more fibrous tissue instead of moving on to regenerating what was there originally. This dense fibrous tissue often prevents new cells from easily migrate into the tissue, essentially stalling the healing process. It seals the wound much faster than the more mild deposition of other animals but can often prevents replacement of the fibrous tissue which would otherwise happen as the missing tissues is regenerated. This mass of fibrous tissue is what we call a Hypertrophic scar. this is why scars can also fade, as cells often can migrate in and slowly replace the the matrix but this is severely limited by the dense packing.
Note there is a second rarer form of scar tissue that can form, called keloid scarring. This form of scar spreads beyond the original wound area and seems to be caused by some form of runaway extracellular matrix deposition. It should also be noted adult mammals sometimes do regenerate decent portions of tissue, albeit not well, possibly because some of the controlling cellular signalling machinery has be lost or reappropriated. All the factors that affect this are not understood and are a main focus researched. We do know it varies quite a bit from tissue to tissue and is not terribly consistent.
It is believed that mammals and birds develop this stronger matrix deposition which leads to permanent scar tissue becasue healing fast is more important for them than healing completely since their metabolism runs so much higher. They can't wait around for it to heal they need to get moving as soon as possible or risk starvation,additionally a stable body temp makes for a more inviting environment for bacteria so sealing the wound is paramount. Thus sealing and mechanically reinforcing the wound is more important than regeneration. As you can imagine the worse the injury the more important it is to plug it fast which is why minor injuries are less likely to scar. This is also why lizards and amphibians end up with less permanent scars they can take the time to better regenerate the tissue. Of course this is difficult hypothesis to test, however there has been some success in getting mammalian tissue to regenerate more by removing scar tissue as it forms or just preventing collagen production.
Evolution is one lang story of "good enough" and scar tissue is good enough functionally that the speed at which it can seal a wound favors it over slower regeneration.

@another'Homosapien' It isn't the same meaning as in chemistry. Endotherms are warm-blooded animals. But I don't see any reason to connect endo versus ectothermy to scar tissue formation...

This is a teleological proposal of (perhaps) why scar tissue forms, not an actual answer. Scar tissue formation is not a fast process.

@anongoodnurse it is compared to regeneration. Scarring is just the inflammatory and fibrous tissue formation of the healing process run rampant, it interrupts further complete regenerative healing other organisms experience.

Then write that as your answer, not a teleological proposal. I don't think it's quite "run rampant". Aggressive cancers are "run rampant". Healing is physiological.

@anongoodnurse I did write it up as well as why it evolved in the first place.  The OP asked "why?" which is ultimately a question of what would cause such a seemingly counterproductive mechanism to evolve in the first place.


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how DNA controls properties of cell?
My textbook says:

DNA is the heredity material which controls the properties and
  potential activities of a cell.

I couldn't understand how it controls properties of cell?

I think your best plan is to keep reading.

What it means is that it controls the cells purpose. Skin cells have a different genetic makeup than brain cells.

This question is far to broad. You are essentially asking "what is molecular biology" - like @AlanBoyd suggests, keep reading, probably the rest of your textbook or one you will read in the future is about exactly this.

@BryanKrause,actually I want to understand the fact what is meant by property of cell?and what is meant by potential activities(transcription or translation...yeh??)

The production of all RNAs and proteins in the cell, including RNA and proteins that regulate expression of other proteins, and indirectly all the functions of those proteins. Everything. This is all of biology at the cellular level. That's why your question is too broad.


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Why isn't there 1' to 2' direction or something else except 5' to 3' in dna replication?
I hope i would get logical answers. I  request to post it as soon as possible.

Welcome to Biology Stack Exchange. I would highly recommend to read the tour before asking any questions. You will also earn your first badge. Take the tour here: https://biology.stackexchange.com/tour . Your question is a replication of the following question: https://biology.stackexchange.com/questions/15082/what-does-5-and-3-mean-in-dna-and-rna-strands .. Please check the link provided for answers.

[Source]
DNA is a polynucleotide. The above structure is of a nucleotide which has three components, a nitrogenous base(yellow), a pentose sugar(purple) and a phosphate group. These nucleotides form phosphodiester linkages to form a polynucleotide.

[Source]
These phosphodiester linkages are formed between 3' and 5' carbons of the pentose sugar which is shown in the above image.

[Source]
The end of DNA having a free phosphate group at 5' of pentose sugar is known as the 5'-end of DNA, and the end of DNA having a free hydroxyl group at 3' of pentose sugar is called the 3'-end of DNA.
Here, you can play with the DNA.

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Did the hyoid bone of Australipetichus afarensis have a hyoid bulla?
The hyoid bulla is present in Chimpanzee hyoid bones, and not in Humans. Does A. afarensis have a hyoid bulla?

Short answer:
Yes.
Longer but still short answer:
H. heidelbergensis and H. neanderthalensis have a modern human-like hyoid bone. A. afarensis has a hyoid bulla similar to modern chimpanzees.
The hyoid bone is thought by some to be important in human evolution because of its position in the throat and the possibility that morphological changes in the hyoid were important for the development of speech. However, this view is not without controversy, and it is probably not sufficient to use hyoid bone morphology as a definitive marker for development of speech similar to modern humans, though it may be suggestive.
Some quotes from two references on the morphology of the hyoid of A. afarensis:
Alemseged, et al. 2006:

[the hyoid of A. afarensis] "...is
  most similar to that of juvenile African apes, and unlike that of
  modern humans11,12. The exposed greater horn is slender, and the
  body is expanded anteriorly, forming a bulla that is deep relative to its
  breadth and height..."

Steele, et al. 2013:

"...the Dikika juvenile australopith hyoid is deep for its height (Figure 9) and width and is morphologically chimpanzee-like. This similarity applies both when comparing only subadults from the three extant species (Figure 9A), and when comparing across all observed age classes (Figure 9B..."

References:
Alemseged, Z., Spoor, F., Kimbel, W. H., Bobe, R., Geraads, D., Reed, D., & Wynn, J. G. (2006). A juvenile early hominin skeleton from Dikika, Ethiopia. Nature, 443(7109), 296-301.
Steele, J., Clegg, M., & Martelli, S. (2013). Comparative morphology of the hominin and african ape hyoid bone, a possible marker of the evolution of speech. Human biology, 85(5), 639-672.

Is the A. afarensis hyoid bone in the Steele, Clegg, Martelli paper, from Selam (the 3 year old, aka "baby lucy") found in Dikika ? That's the only fossil remnant of an A. ararensis hyoid bone I've come across (https://www.nature.com/article-assets/npg/nature/journal/v443/n7109/images/nature05047-f3.2.jpg)
From the image, it's difficult to make out a hyoid bulla, and the Steele, Clegg, Martelli paper mentions that they "interpret the morphology", would you happen to know if they go by indirect evidence, and if so, what?

The Dikika specimen was a child also, 3 years old, and child hyoid bones have different proportions than adult ones (https://boneclones.com/images/store-product/product-223-main-main-big-1418687938.jpg)

I think that paper will be the best you get for an answer - as you say, if there are no other fossils, you aren't going to magically find one on Biology.SE. Steele et al. compare the Dikika sample to juveniles of the extant apes. The line about "interpret the morphology" has nothing to do with the type of evidence they used, they are just referring to comparison of all of the extinct samples with the extant species they studied.

A quote from the paper in case you cannot access it: "...the Dikika juvenile australopith hyoid is deep for its height (Figure 9) and width and is morphologically chimpanzee-like. This similarity applies both when comparing only subadults from the three extant species (Figure 9A), and when comparing across all observed age classes (Figure 9B..."

If the extinct sample is one, and its this one https://www.nature.com/article-assets/npg/nature/journal/v443/n7109/images/nature05047-f3.2.jpg
are details, like the hyoid bulla, preserved? just by looking at it, it looks like its not protruding at the anterior end, http://i.imgur.com/BYdjvHx.jpg

It looks to me like it is, clearly moreso than a modern human of the same age (from the article I referenced). Note also that your reference refers to it as a bulla as well. It's possible there is some disagreement in the field, but I see two published sources that agree with each other and no evidence otherwise.

the Steele paper says that "and one (represented by the body only) from the Dikika Australopithecus afarensis (Alemseged et al. 2006)"
while the Alemseged says "the exposed greater horn is slender, and the body is expanded anteriorly, forming a bulla that"
are they not contradicting one another? how can the greater horn be exposed, if only the hyoid body was in the fossil?

@homonidae I can't speak for the authors, but my guess is that Steele is referring to inclusion in their own quantitative analysis, and by their quantitative analysis only the body was fully present for quantification (I agree with you this is not clear in the statement you quoted). The qualitative description by Alemseged would not have that limitation (and Alemseged's own quantification also was based on the body I believe). All that said, your question is about a feature of the body, so I'm not sure why the presence of the horn is particularly relevant.

I'm interested in knowing about the fossil record.
The airsacs, as resonance organs, would have de-evolved as a pharyngeal acoustic chamber formed with the descent of the larynx.
I'm also interested in the semi-aquatic ape theory, and that the larynx descended for inhaling large amounts of air while surfacing. In that universe, the loss of airsacs could have been a later adaptation, as the expanded pharyngeal tract formed an acoustic resonance chamber.


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Do Cooper Hawks eat fish?
I have seen a Cooper hawk sitting on a low branch above my small Koi pond 3 times in 4 months. The books and net say they eat birds and some mammals but I wonder if he is looking at my fish ? Or snakes or frogs ?  As I write this I had a thought, song birds come down to a shallow part of the pond, that may be what the hawk is after. But I still wonder about the original question.

Birds learn new tricks very often, using roads to crack nuts, opening foil milk bottles (tits), and Hawks are known to catch Koi.
These pages say that Cooper Hawks specifically do catch fish: http://forums.gardenweb.com/discussions/1997093/hawks-taking-koi
http://www.outdooralabama.com/coopers-hawk
Here is a cooper hawk catching a duck and swimming around with it: https://www.youtube.com/watch?v=A08jxYinAG8
if you put cooper hawk pond into youtube, you will find 10+ videos of them bathing in ponds, and 2 videos of them scouting at a pond.
My aunt saw a buzzard, Buteo Buteo 50cm tall, catching a yellow Koi right out of the water while I was out for the day. The Koi was 30cm long, 12", it dived on the water and flew away with a fish on the wing. The Koi had indeed vanished as my aunt had said.


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Why do I want to urinate when I touch water?
I've noticed that whenever I come in contact with running water (especially when I do my dishes), I have a desire to urinate. A quick Google search (link,link) gave me few different hypotheses:

Cold diuresis. Being in contact with cold water reduces temperature on the skin, which then constricts blood vessel to reduce heat loss, thereby increasing blood pressure and prompting the bladder to release excessive fluid.
Afferent innervation. I wasn't able to comprehend all the details of the process, but it seemed like this hypothesis is pertaining to the nervous system than circulatory system, hence different from first hypothesis.
Learnt psychological response. Second article linked above argues that this is a conditioned reaction, where even the sound of tap water triggers the desire to urinate. While it did not mentioned specific details of how this happens, I'm also assuming that this hypothesis is different from aforementioned hypotheses, because this hypothesis sounds more like a psychological response than biological reaction.

Which one of these hypotheses accounts for the desire to urinate when in contact with water? How exactly does it happen? If there is any other reason, feel free to add in the answer.

All three are probably contributors to some degree, although the third is a learnt psychological one and not physioly as you said.

@comprehensible I find it a little hard to believe in the first hypothesis. It's bewildering to me that such a limited time of exposure to cold water in a small surface area (hands) will result in such a drastic change in blood pressure that will prompt bladder to release excessive fluid. Is there any studies done for this?

@comprehensible I'll also be interested to see why the people will learn to have desire to urinate at the sound of tap water. Is there any reason that for that?

The blood pressure is a direct response to your body being supported by gravity, or when it is weightless in water and in fact your upper body pulls upwards. It would be interesting to see when the pee reaction arrives, because, it's normally strongest above the groin up to the solar plexus, the visceral nervous response. There are some more answers here. https://www.quora.com/Why-does-swimming-make-you-need-to-pee

Your point, and the article that I've linked to, seems to point to the case when the body is submerged in water. I guess this does not fully answer my case of washing hand, but your point certainly is true to body in swimming pool.

I came to this thread while I was doing some google search about the first theory because this applies to me. I have noticed that if I come into contact with cold water, I feel the sudden need to urinate. This is the reaction of my body and I don't have control over it. My body does not react the same way with hot water. This could be a complex mixture of biology and neurology (speculating). Some years back at the college, I learnt that part of the waste (e.g. salt) that comes out in the urine, also goes via the sweat through the skin pores. So the more we sweat, the less we feel the need to u

FIRST PART:
I am writing this answer with an analogy.I have analogised your question to a childhood habit developed by our mothers-when she would want us to urinate all she had to do was to take us to the toilet and make a "siiii" "siii" sound to mimic the sound of running water(more or less)
Since I have analogised in that way I think the third hypothesis (referred in your question)is more apt.
SECOND PART:
What fascinated me more about your  question was your comment-"I'll also be interested to see why the people will learn to have desire to urinate at the sound of tap water. Is there any reason that for that? – Hosea Jul 14 "
Indeed there is because we still have our mirror neurons
[SOURCE]
What I wanted to understand is if mirror neurons contributed to Pavlovian reflexes.The answer was yes
Furthur I could find out from sources that the micturition process has centres in the brain stem which are controlled by higher centres in the brain.One of them was the "medial frontal cortex".
Read the following article:

The Pontine micturition center (PMC, also known as Barrington's nucleus) is a collection of neuronal cell bodies located in the rostral pons in the brainstem involved in the supraspinal regulation of micturition. When activated, the PMC relaxes the urethral sphincter allowing for micturition to occur. The PMC coordinates with other brain centers, including the medialfrontal cortex, insular cortex,hypothalamus and periaqueductal gray(PAG). The PAG acts as a relay station for ascending bladder information from the spinal cord and incoming signals from higher brain areas.[source]

From the outline in the following lines I could conclude that there are mirror neurons in this region which 'may' be involved in the micturition control:

Yoshida et al. [26] recently recorded from neurons in the medial frontal cortex, some of which selectively responded to self or observed actions within a social context
[source]

Although research has confirmed that mirror neurons contribute to Pavlovian reflexes no such pathway has yet been discovered which can directly help us to confirm  and understand its relation to urination urge in contact with water.

I asked my doctor about this issue. I had noticed the effect after age 65 and I remember my mother putting my younger siblings when they were just a year or two old, on her insteps as she sat down, and imitated the sound of running water - like a half whistle - soothing sound. And pee came. Now when I do dishes, I immediately feel to pee although I did not really want to before. I know this happens to most older folks. My doctor said maybe it is nerve anticipation that activates the urethral muscles, and too, maybe the instinct of a baby in the womb of the mother surfaces again. I did not quite get that part. I think it is a psychological thing where we respond to brain-nerve-urethra instinctive coupling, something we have no control over. I have started to empty my bladder before going to do dishes. When you shower, it is natural to pee when the water hits you, even if you had no urge to pee before. This is no fancy explanation but I just thought it might contribute.


text:
What kind of bird did I hear at three AM in Germany
I woke up at three AM from some sort of industrial noise outside. In addition to the noise I heard some creaking like from a stuck door. After the initial noise had ended, something that sounded like birds calling continued for at least 30 minutes.
The most common call sounded like staccato tweeting that lasted for about a second and increased in tone height. This call I heard many times. There were also some slower, non staccato beeps but no continuous singing like you'd hear from a blackbird.
I'm in southern Germany, in a city near a park. The area is brightly lit. It could conceivably be bats, but in my experience they don't tweet loudly and they dont make a staccato noise.

Try to listen on line a nightingale, maybe it was a far away one and you could hear only the most characteristic notes which are similar to what you describe. Are you south or north of Munich (roughly south of the city there are not breeding nightingale).

It could be a bird that is normally not out and about at that time, but also disturbed by the industrial noise.

A bit North of Munich. I think birds decide whether to sing by whether it's light out, so I think it should be a bird or bat that normally sings early, even if the noise woke it up.

Bats are quite out of question. You would not be able to hear most of their sound, and they definetly wouldn't remotely remind you of a blackbird.
Re: nightingale, try http://www.xeno-canto.org/species/Luscinia-megarhynchos - but I have my doubts.


text:
What is the name of this plant or shrub?
I just found a plant in India.

Here is its leaf.

I tried looking it up on flowers of India & wikipedia, but both databases are too
much to read manually.
Physical description:
Each Stem has 6 leaves on it, Leaves are opposite & Elliptic shape, Entire margin & Pinnate veins on it.
I am thinking it is shrub, not a tree.

I replaced night time images with day time. Hope this will help to ID this species easy.


text:
Control of neural systems
It turns out that my work in nonlinear dynamics directly maps to Integrate and Fire models and could even provide a new way to control them (manipulate the firing rates). However, it is unclear to me if my findings are interesting or just old news.
I am looking for literature on the intersection of control and neuroscience. Specifically I am interested in any research, theoretical, experimental or simulation-based that dwells on the control of neural systems.
I am especially interested in any work that takes a mathematical point of view on this issue and on any work that summarises the state of art in this field.
Forgive me is this seems trivial to you, but coming form complex systems theory I did my best and found nothing.

I think this is a very interesting field but I don't think your question is very well-suited to Biology.SE. You don't have any specific question, you are just asking for some literature that would effectively describe the entirety of the field of theoretical and computational neuroscience. I will say though that the fields of control theory and computational neuroscience are closely intertwined. I don't know what search terms you are using but I am surprised you aren't finding anything. Try adding "neural" to any searches you would do in your field.

It seems to me that I am a little more specific than this, I am not looking into the entirety of theoretical and computational neuroscience but merely its connections with control theory. Perhaps this is still a huge field, in that case there could be for example a textbooks worth mentioning? I deeply thank you for your input, neural is in my list along with control.

Yes, applications of nonlinear dynamics to neural control is still too broad of a field to make an answerable question.

https://scholar.google.com/scholar?hl=en&q=control+theory+neuroscience

https://scholar.google.com/scholar?q=control+theory+neural

Ok, so how should I proceed? remove the question?
Personally, I think it still has something to teach. A person in my situation would be actually benefited a little but by finding out that he has to pinpoint the question further. Please let me know the canonical course of action and I will follow it immediately.


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Microorganisms in Louis Pasteur's experiment of beans
Louis Pasteur's experiment proves that microorganisms do not grow from non-living matter, he discovered that microbes can cause food spoilage.
So, where do microorganisms come from? Do they come from the environment?

So, where do microorganisms come from? Do they come from the environment?

Yes!
There is no spontaneous generations. Microorganisms (virus, bacteria, unicellular eukaryote, small multicellular eukaryotes) just like macroorganisms (big-enough to be seen by the naked eye multicellular eukaryotes) are not recreated out of nothing. Abiogenesis happened a long time ago and as far as we know, it is not happening today.
This means that if there is a micro-organism somewhere, it must have come from the environment. It did not pop up out of nowhere.

That is the biggest question to be answered in biology, as of today we do not know where microorganisms originated from. What is known is that they outnumber us by combined weight and population. There are some interesting theories of their origin, one is called "panspermia" which proposes that life might have seeded the Earth from other planets. And considering that some bacteria are capable of surviving extreme levels of radiation        (D. radiodurans), it is not unreasonable to think they could have achieved interplanetary travel via space rocks.

The question is not about the origin of organisms, but rather how it is that microorganisms become present in food to spoil it.

This is one of the questions "So, where do microorganisms come from?"

and that question is immediately followed by a more specific form of that general question: "Do they come from the environment?".  That shows the question is about the presence of microorganisms at the time of Pasteur's experiment, not hundreds of millions of years earlier when they originated.


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Is there any artificial species (in particular, an artificial species of animal)?
Dogs were artificially selected from wolves, but a dog and a wolf can produce fertile offspring, and thus are of the same species. I had heard that the aurochs and cattle were different species, but I could not find this information anywhere. I had heard also that some artificially selected flies are considered to be a new species.
Is there any human-made species (especially a species of animal) which is not able to produce fertile offspring witch any other species, in particular with the one from which it evolved?
EDIT: (A similar question in different words.) Is there any human-made animal lineage which was conceived by artificial selection and which is broadly accepted as not being a race or subspecies, but a species on its own.

You might consider the horse, there aren't any wild horses that don't trace their lineage back to the domestic horse rather than a shared ancestor & though they can be bred with some of their closer relatives (notably donkeys & zebras) the offspring are almost invariably infertile, so they may fit your criteria?

Artificial selection leading to new species - Domestication
As you talk about dogs in your intro, let's consider them.
You will fail to breed a great dane and chihuahua for obvious mechanical reasons. You will also fail to breed a chihuahua with a wolf. So, yes artificial selection have lead to reproductive isolation.
Artificial selection leading to new species - lab experiment
Artificial selection have also lead to reproductive isolation in non-domesticated species. See for example the post Have we ever observed two drosophila lineages that evolved reproductive isolation in labs?
Concept of species
As a side note... Above, I consider the so-called 'biological species concept'. For a discussion on the definition of species, please have a look at this post.

There is not clear delineation for speciation, but think more along the line of a spectrum. When I compare the bacteria S. Pyogenes (flesh eating bacteria) and S.Dysgalactiae (commensal pathogen) they are very similar in a lot of their genes but they have also acquired qualities that helps us distinguish these as different species. Still, when found together, they readily undergo bacterial conjugation and exchange genes.
So to comment for the first part of question, the ability to produce fertile offspring does not imply that species are identical...rather compatible.

The OP clearly refers to the so-called 'biological species concept', so it is, IMO, possible to answer the question without getting lost in a semantic argument on the definition of the term 'species'. For such discussion have a look at this post.


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What is the use of ampulla in Scoliodon?
What exactly is the use of Ampulla of Lorenzi in Scolidon?
It posseses eyes for seeing prey, so what is the use of Ampulla?

Welcome to Biology.SE! What research have you done before asking it here?

I am just a student of class 12 and this question is very much important for my knowledge.

very frankly, being a student of class 12 does not give you liberty to ask here questions lacking prior research effort. The question might be important, and interesting as well, but as long as you don't show an attempt to answer it yourself, we are not willing to help you out. You need to, at least, google about it and then tell us what you have found so far, and how that does not help you :)

Ok ok , thanks for giving me the exact procedure of asking questions. I'll try to work on this topic in google.

@Abhijit Have you checked Wikipedia? It says quite a lot of stuff, which should probably be enough for a 12th grader (no school is going to make you right a thesis or something on this topic).


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How long can algae survive with no air recycling (closed bottle)
In a small bottle nearly filled of Chlorella in water and grow medium, how long would it take for them to die (with or without light).
Thanks in advance ;)

Calculate the oxygen in the bottle, calculate how much oxygen the Chlorella will use all together per second = time.  Best I can give you with no specifics provided.


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Garden Mushroom Identification

Could someone please identify this mushroom?
Found in a garden situated in a mild Western European country.

Looks like shaggy ink cap, Coprinus comatus, to me.
Blacksmith37's answer suggests that shaggy mane is the usual common name. I hadn't heard that name until I looked at the Wikipedia page. In the U.K. it is shaggy ink cap, inkytop, inkhorn or lawyer's wig.
Update
This is a good general source of information. Also comatus (Latin) means hairy.

I think the more common name is Shaggy Mane , related to "inkies" and "micas". It is too old to eat when it gets pink, then black liquid. In the Midwest US they come up early spring and fall in the same spots. .... Sorry,I meant to imply that was the name in the US. It is a good beginner mushroom ; hard to confuse with anything poison.

Re: "too old to eat" (or rather, the implied inverse). The standard disclaimer applies: Never rely on identification from random people on the internet to determine if a mushroom is safe to eat. Also, never consume any mushroom you're not 100% sure is edible.

^^ from the wikipedia article on the mushroom: "The mushroom can sometimes be confused with the magpie fungus which is poisonous."

So... Does the goo actually act as a stable pigment?

@TheNate No - in fact the inkcap fungus is unusual, in that if it is harvested, or after it has shed its spores, the whole "cap" turns into black goo and auto-digests itself! But they are good to eat if they are picked young and eaten as soon as possible after picking.

By the way, don't eat this mushroom and consume alcohol. There is a substance in the mushroom (marketed as drug under the name Antabus) causing a prolonged hangover.


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Is this an eastern hemlock (Tsuga canadensis) seedling?
I recently planted a few seeds gathered from a Tsuga canadensis cone in soil gathered from a garden full of weeds. I can't tell if what I have growing is a hemlock seedling or just another weed. See photo:

This is not a Hemlock seedling but a young specimen of the family Amaranthaceae, almost certainly an Atriplex, known in English as Saltbush or Orache.
You can tell by the shape of the opposite leaves and the 'frosty' look (not sure if frosty is the correct English word)
This specimen looks quite similar to yours.

Taken from here
As North America is very rich in species, I don't think anyone can be more exact than Atriplex.
Atriplex grows in salty soils such as deserts and seashores, but also in moist environments. Most species prefer bare soil, so are also well adapted to grow between crops, so yes, this might be called a weed.

No, this is not a Tsuga canadensis seedling.
A hemlock seedling should look something like this:

http://www.uky.edu/hort/propagation-canadian-hemlock


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Methods to evaluate gene expression
I was wondering what method should i use if i want to evaluate if a gene is being expressed or not. The first method that came to my mind was Western blot , but i don't know if i could use others.
I wanted to know if western blot , specifically , is a good method to evaluate that and , also , if there other methods equally good to evaluate gene expression.
edit : I edit my question and asked about Western Blot , specifically , and asked about more general methods do evaluate gene expression.
I don't really know why my question got down voted that much , I apologize for any inconvenient.

"Best" depends on what you are doing. For over expression of a heterologous gene in E. coli, I'm content with a dark band of appropriate molecular weight on SDS-PAGE that is not present in the control. That's certainly better than a western in this particular case.

Perfectly good question! Lots of possible options depending on cell type and whether we are interested in RNA levels or Protein levels. The question might be improved by either asking for a specific system or explicitedly ask for general methods.

Thanks @JeppeNielsen i edited my question. I also do think this is a perfectly good question.

If you really want to know if your gene is being expressed up to protein, then go with western blot. mRNA based methods are good, but they will be limited in the sense that they will not account for RNAi.
This seems to be a good reference on the subject of RNAi.

RNA based methods, while certainly useful in many circumstances, won't account for any kind of non-degradative post-transcriptional regulation.

Sorry, I should have written RNAi. Take a look here

Thanks luis. One more thing : If someone says "express" , they mean the production of a certain protein or if the protein is working properly ? I think i just got confused about this concept.

@user158657, I found some questions on SE that might be interesting for you. Please check: Q1, Q2, Q3, Q4, Q5 and Q6. I would only add that, personally, I do not think that it is wrong to use gene expression when referring to gene transcription as it is commonly used in the literature. But it is certainly inaccurate.

@user158657, you could also check these references on non-coding RNAs and epigenetics: ref1, ref2 and ref3.

GFP or other flourescent proteins fused to gene products of interest can work very well, in C. elegans changes of protein expression can be tracked at cell level in live worms.  In situ hybridisation can also be used to detect RNA expression levels of targets, in indivdual cells or in whole mounts, like commonly used D. rerio.


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Yeast transformation plate confluent with growth
I have problem with yeast transformation. I tried to transform pyes3-tryp(my insert inside) into INVsc1 yeast cell by following the protocol in the manual for few times but failed(confluent with growth). In the manual, it states :INVSc1 will not grow in SC
minimal medium that is deficient in histidine, leucine, tryptophan, or uracil.I tried 2 media: selective media+ amino acids except tryp and selective media + amino acids except the 4 amino acids. There are confluent growths, no single colony on both of the plates including on the negative control plate( only yeast cell no plasmid).However, the confluent growth is less severe in the plate without the 4 amino acid. Everything i used is sterile except the old DMSO in my lab which had been opened outside of the laminar before. So, is it due to contamination by bacteria or...??.

Resuspend some of the cells from the plate in water and look at them under a microscope - it's easy to tell the difference between yeast and bacteria. What happens if you try streaking out your untransformed yeast strain on your selective media? Do you get any single colonies? (You shouldn't.)


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Why do humans not have a powerful sense of smell?
It seems like a useful ability to be able to detect many different things about, say, another organism. A lot of mammals have this ability. Why not humans? Did we evolve it out or never develop it?

Note that human smell might not be as poor as thought: http://news.rutgers.edu/research-news/human-sense-smell-it%E2%80%99s-stronger-we-think/20170508

Humans' poor sense of smell is a myth, borne of 19th century speculation rather than actual data. This is described in an excellent recent paper in Science , "Poor human olfaction is a 19th-century myth" by John P. McGann. Quoting from a recent blog post of mine,

The myth dates to the work of the pioneering and hugely influential
  anatomist and anthropologist Paul Broca, who concluded that the
  relatively small olfactory bulbs in humans and other primates enabled
  the occupancy of this space by facilities of intelligence and even
  free will: “…it is no longer the sense of smell that guides the
  animal: it’s intelligence enlightened by all the senses… This is the
  cause of the atrophy of the olfactory apparatus of primates." This
  presumed “atrophy” and poor sense of smell however, were not based on
  any actual data on primates’ sense of smell! The myth propagated and
  expanded in the 20th century, becoming dogma. Back in the 19th, even
  Freud weighed in, noting that the lack of a strong sense of smell
  contributed, in humans compared to other animals, to sexual repression
  and mental disorders.

Humans, when trained, smell quite well, and can for example follow scent trails through grassy fields. Interestingly, the number of olfactory neurons is very similar in humans and other mammals (plotted in the aforementioned post).

Your first link is broken. But, please don't just mention the link. It's better if you some words of the link so that we can have a gist of what you want to say.

@Mockingbird. Good points -- I've edited the post. About the link: I don't know why it doesn't work; I've given a partial reference, also, so it can easily be Googled.

In that case, how come hunters often complain that their prey can smell them from dozens of meters, yet you hardly ever hear of a human hunter tracking his quarry by smell?

There are several factors in human.

we are upright, which brings the nose just about as far away for scents as it can get, you want your nose as close to the ground as possible for the most efficient use scent. This is not in and of itself a deal breaker but it is an important factor which made smell less important for us.
Our large brain is competing for space with our sinuses and nasal cavity. So in turn we have lost a great deal of our nasal cavity as our brain has increased in size, some even speculate this is why we have a protruding nose becasue part of the function of that cavity is thermoregulation and air filtering and the protruding nose helps compensate. The shrinking of our face and snout has pushed this even harder. the less space you have in the nasal cavity the less space you have for olfactory receptors, which reduces the number of distinct smells you can detect.
primates in general have poorer senses of smells than other mammals , they have much better vision however, so the lose of smell was an evolutionary  trade off. So humans  were starting with a handicap to begin with.

Keep in mind humans still get a lot of information from out sense of smell, but not all of it is conscious. Nearly everything you think of as "taste" is actually smell.

The order of senses from strongest to weakest or more important to less important is basically opinion based. Some would say smell is less important, other would say hearing or some might say taste.

"The sense of smell is not powerful in humans" is absolutely false. They are very powerful as it seems and can be considered as the most powerful sense in human beings. Check this Youtube video which explains why smell is the most powerful sense in organs. What makes sense of smell most powerful is due to its spontaneous ability to trigger and revive memories and emotions. According to this site:

The sense of smell is closely linked with memory, probably more so than any of our other senses.  Those with full olfactory function
  may be able to think of smells that evoke particular memories; the
  scent of an orchard in blossom conjuring up recollections of a
  childhood picnic, for example.  This can often happen spontaneously,
  with a smell acting as a trigger in recalling a long-forgotten event
  or experience.
In addition to being the sense most closely linked to memory, smell is
  also highly emotive.  The perfume industry is built around this
  connection, with perfumers developing fragrances that seek to convey a
  vast array of emotions and feelings; from desire to power, vitality to
  relaxation.
On a more personal level, smell is extremely important when it comes
  to attraction between two people.  Research has shown that our body
  odour, produced by the genes which make up our immune system, can help
  us subconsciously choose our partners – read more here.  Kissing is
  thought by some scientists to have developed from sniffing; that first
  kiss being essentially a primal behaviour during which we smell and
  taste our partner to decide if they are a match.

Smell is closely related to association and was the first sense to get evolved.

The sense of smell was probably the first sense to evolve in a living
  creature. In many animal species, smell can play a critical role in
  finding a mate, communicating with other animals or helping them to
  survive by finding food. Clearly, though, in humans, smell does not
  carry the importance that it does in other species.

But the sense of smell is overshadowed by other senses particularly vision because it is most well develop and important sense in human beings.(here, here, here, here) but actually smell is the powerful of them all.
The weakest sense in human beings would be taste.(here, here).

This is a question relegated to evolutionary biology.  Our sense of smell is as it is because that is part of our evolution and it is what works best for us. Also consider that you used the word "powerful" The word is arbitrary when comparing the sense to other animals. The more sensitive sense of smell in dogs for example is tied to their survival


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To which SCOP Class corresponds the following secondary structure?
I need to classify this protein into one of the SCOP class (all $\alpha$, all $\beta$, $\alpha +\beta$, $\alpha/\beta$, or small protein).

I'm having difficulties understanding the difference between $\alpha +\beta$ and $\alpha/\beta$. I would have said, that it belongs to the group $\alpha/\beta$, due to the fact that presents an alternated combination of $\alpha$-helices and $\beta$-sheets, where the $\beta$-sheets are mainly parallel, but I do not know if I'm understanding the concept right.
Has anyone a tip to identify the differences quicker?


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DNA as a digital storage medium; sequences algorithmically avoided for safety reasons (or should be)?
Safety for the environment is probably implicit here as well, but the focus should be on the people who may come in contact with large amounts of synthetic DNA used to encode information as a data storage medium.

The idea of using DNA as a digital storage medium is not new. Two papers are listed below but there are many others.
Recently the concept has been further highlighted by the news of a "movie" being encoded using CRISPR-Cas. A Harvard University video explains the process:

In this video, Wyss Institute and Harvard Medical School researchers George Church and Seth Shipman explain how they engineered a new CRISPR system-based technology that enables the chronological recording of digital information, like that representing still and moving images, in living bacteria. Credit: Wyss Institute at Harvard University
For more information, please visit: https://wyss.harvard.edu/taking-cells...

below: a GIF showing the original data, and the "movie" interpreted from the recording in DNA. From the Los Angeles Times:

DNA DVR? Scientists have uploaded a short movie of a galloping horse into the DNA of living bacteria and were able to retrieve it with a 90% success rate. (Seth Shipman)

The immediate application in the Harvard Wyss Institute work seems to be (based on my understanding of the video) in-situ data logging, where information relevant to an experiment is recorded in the DNA of cells involved in the experiment. So the use of a moving image is a way to bring home the key point of "chronological recording of digital information".
Other uses involve the DNA itself, stored outside of living cells, as simply a mass storage medium.
QUESTION: I'm wondering if there are sequences that are likely to become algorithmically avoided as standard practice for safety reasons (or should be) when using DNA as a digital storage medium. The DNA may be handled by IT personnel rather than trained biologists, or shipped, or otherwise not be treated with the same diligence to safety that synthetic DNA is handled by researchers today.
Some other discussions of DNA as a storage medium:
Next-Generation Digital Information Storage in DNA, Church, Gao, Kosari, 2012. doi:10.1126/science.1226355
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA, Goldman et al. 2013. doi:10.1038/nature11875

For further background on the temporally encoded data work, see the excellent answers to the question What does it mean to “write an image and GIF into the DNA of bacteria”?
edit: I'll quote a comment here just to make sure that the word safety isn't misinterpreted as data integrity or the safety of the bacteria:

When speaking of safety issues related to the handling of biological or biomolecular samples, it's the safety of people that we worry about. Safety rules, safety procedures, safety courses, safety glasses, these are for the safety of the human, not the safety of the sample.

An identical or near-identical question to this has been posted before, but I can't find it, maybe it was deleted. Just a reminder in case anyone else can find it...

@BryanKrause There is a deleted question which was similar. Here I've used some of your helpful suggestions and also removed the less-relevant material which seems to have been distracting. However please don't assert that I must prove DNA is dangerous before I can ask if DNA would be treated with caution.

Oh okay that was your question. Do you have the paper you cited there? It might be the Church one you have here, that sounds familiar. I seem to recall that paper describing exactly this issue. I'm wondering what answer you are expecting beyond what they said.

@BryanKrause I seem to remember that there is one sentence in this one five year old paper. The field of molecular biology moves quickly, so that doesn't make it the last word on the subject going forward. Is there something about this question you find unsettling? Can you let it go for a day or two and see if some informative answers are posted? Possibly post one yourself? Stackexchange is about getting answers for ones self, but also the generation of answers that can be read by many.

I'll try to write an answer when I have more time, but the two answers here are examples of why I was asking you about Church. Neither of the writers of these answers seem to have read Church, because they are ignoring all of the issues that paper raises. If you included that information in your question and made clear what about those issues you are interested in, you would get better quality answers.

You might br interested in this

@another'Homosapien' Lots of goodies to read there - I'll add a reference to that in my question. Thanks!!

@another'Homosapien' thanks for the edit - looks better!

DNA data can theoretically be used as malware: http://dnasec.cs.washington.edu/

Yes, there could be sequences that a DNA based system could not store handle/very well: repetitive DNA sequences.
Not only do such sequences make a lot of problems during the sequencing ('reading of data'), but they are also more prone to form secondary structure elements like loops, since repetitive DNA can bind to itself in various different ways. This means that similar to natural occuring repeats they are more likely to mutate during DNA amplicifation (the number of 'copies' can quite easily change), which makes the 'data' more instable.
A possible way to solve this problem would be to use specialised data formats that avoid as much Repetition of data as possible (similar to how zip or jpg files work)
Otherwise I agree with Nathan, that DNA by itself is not dangerous (since it won't do anything outside of cells, and the bacteria used in molecular biology are generally harmless unless you start eating them in large quantities or otherwise getting them in your body). The possibility that the DNA could somehow code for toxic proteins is very very low, and you could just check that the 'data' in the DNA does not form a protein by chance anyway.

Have you read the discussion of safety issues in the paper the OP cites? This answer suggests you haven't. Biology.SE prefers researched and cited answers. Although you have a couple links in your answer, neither are directly related to the issue at hand.

Thanks for taking the time to post. You've actually answered an interesting question that I didn't ask but wish I did! I've asked about safety and you've discussed data integrity or stability, which is probably a more interesting topic.

Given the quantity of storage, with no avoidance system, you will eventually encode toxic or dangerous proteins.  But the system would have no molecular machinery to even transcribe it into proteins, let alone what may be necessary for proper secondary processing so that the protein would be active.  Now if they started somehow storing data into proteins as a final form, we'd have to be a lot more careful.

Data written on a discarded floppy disk (remember those?) or hard drive or thumb drive in a landfill has no hope of its data getting into the bacteria in the landfill, but the fate of data stored in DNA is less certain. In DNA written without safety rules, there may be sequences that bacteria or phages could find not necessarily toxic, but instead "very interesting" or even helpful. That's one random scenario.

Even if DNA drives (to give it a name) are being handled by IT professionals instead of trained biologists, we can still expect the environment to be clean enough so that no organism would tend to be affected by it. Also, as @nathan points out in the other answer, free DNA cannot do anything on its own. Its just like an open book, you can't get anything from it unless you have a reader (protein) for it. There have been no reports claiming that foriegn DNA (called cell-free DNA or cf-DNA for humans) has ever caused any health issues. In fact, there are no reports of cf-DNA even being transcribed by humans. You might also want to have a look at this to find out more. However, as pointed out by @AlanBoyd in comments, organisms residing inside humans can take up free floating DNA from their surroundings. For example, Heliobacter pylori has been shown by Stingl et al, 2009 to take up free DNA from its surroundings. Keeping that in mind, there are chances that DNA drives could be harmful (if, by chance, the drive contains some genes that might provide some antibiotic resistance to the pathogen). Some microbes show a phenomenon known as natural competence i.e. they simply take up plasmid DNA from their environment, break it into parts by restriction enzymes and add it into their genome. These organisms, which generally possess sex pilli for DNA take up, can be a major threat to the use of DNA drive if the users of DNA drives show carelesness while handling and mainpulating DNA since some of this DNA might provide them with antibiotic resistance or capability to infect humans. However, we can prevent this from happening by making sure there are no restriction enzyme recognition sites in the DNA of the drive, so that the organism cannot cut the DNA for ligation into its own genome.

This looks like the beginning of a fascinating answer! As I mentioned in this comment (and obliquely in this comment) sequences that might be avoided for data integrity might be a more interesting question, but I've asked about safety. Maybe you can divide these various items into data integrity and safety categories or somehow make it clear which would need to be avoided for reasons of safety?

@another'Homosapien' my understanding of the question is that DNA sequences created solely for data storage might inadvertently contain elements that are biologically unsafe - is this so, and what precautions would need to be taken to avoid this?

When talking about safety issues related to the handling of biological or biomolecular samples, it's the safety of the person that we worry about. Safety rules, safety procedures, safety courses, safety glasses, these are for the safety of the human, not the safety of the sample. There may be a bias that DNA is "safe" so the word must be talking about something else, and of course data integrity is more interesting and easier to answer. I can clone this question and re-ask specifically about safety, and change this one to data-integrity if it works with all the answers here, what do you think?

Or leave this as safety (and stress the human part more) and clone the question and make it about integrity and you can move the integrity part of your answer there. Whatever is most accommodating to those taking the time to post the answers.

Are you prepared to post an answer, citing recent authoritative sources that "...there are practically no dangers working with DNA drives"? Because this is what I'm asking, and I'd like to see how an answer like that fares - general agreement and lots of up votes or concerns and criticisms. I'm asking and looking for a proper SE answer, because I'm not sure, so I'd like to see perspectives from those more knowledgable than I, and then follow up by reading the linked sources.

It doesn't answer the question, it's an opinion. Do you understand why an answer of "I can't think of any related issues" is not an answer to a request for an authoritative source? You're saying that you think it's safe because you don't happen to know of a reason why it isn't. I'm looking for some scholarly work that addresses the safety issue as might be expected in an SE answer, and I've reinforced that again in my comment in the Bounty banner.

'none of the organisms that I know tend to just take up free DNA from their environment' many bacteria do this such as Helicobacter - see this paper for example

@alanboyd dude thats a very nice point 'bacteria inside humans could take up DNA'. I don't want to take the credit of this idea from you, but thanks a ton for that :D

Do you want me to post a separate question about data integrity where you can move the data integrity part of your answer and I there's some chance it will be the accepted answer?

So far you've really given me only stated your personal opinion regarding safety, and support your opinion with a few links on other topics and certainly not related to DNA synthesis for data storage. Then you have a much longer section which is unrelated to the question. This is not a good SE answer to my question.

Comments are not for extended discussion; this conversation has been moved to chat.

I would say no for two reasons.
The first is I don't know of any DNA sequences that are in themselves infectious.  You'd need the proper cellular machinery to make anything out of them.  If I'm not mistaken even most prokaryotes have varied defenses against random pieces of DNA getting incorporated into their systems.  Otherwise they'd never have stable cores. Viruses and bacteria etc have to use strategies to get around those defense systems.
The second reason, even if I'm wrong on the first, is that this system must be designed to be as free as possible from outside influence.  A system designed to minimize external influence also inherently minimizes influence to the outside, at least in this case.
This wouldn't be handled by IT people unless it was somehow massively automated.  Again no clue on the final form, so hard to say.

Have you read the discussion of safety issues in the paper the OP cites? This answer suggests you haven't. Biology.SE prefers researched and cited answers.

Thanks for your thoughts. Infectious proteins took science by complete surprise decades ago, and it took a while for people to agree it was happening. However, as you point out, since DNA is primarily information, it probably doesn't have much ability to induce molecular changes on its own. Instead, it usually needs to be accepted into, or forced into a transcripting environment.

@uhoh Exactly.  If you've never tried to transfect e. coli in a lab, I can tell you that it is nontrivial, at least for an undergrad who only does it a couple of times.  I wasn't able to access the Nature paper so if there is a list of other safety concerns I did not consider, my apologies.  Infection was just the first thing that popped into my mind as far as safety.  I guess other than that I would think all the other safety issues would be related to standard DNA sequencing work, which is pretty well OSHA'd up.

I'm wondering if there are sequences that are likely to become algorithmically avoided as standard practice for safety reasons (or should be) when using DNA as a digital storage medium.

I don't think the sequences themselves are the concern here, so much as the procedure used to integrate them into bacteria for data storage, which I don't think is of direct risk to humans.
In the Shipman-Church paper, video frame data are encoded into chunks that are 27 bases long, interrupted by short PAM spacers and barcodes to aid in resequencing (for time-directed data readout).
The larger 35-base oligonucleotides are administered into the host bacteria via electroporation — effectively shocking the cells, which opens up the cell membrane to allow the oligonucleotides to get in for the bacteria's existing Cas1/Cas2 system to integrate into the genome.
Electroporation can be used for delivering oligos in vitro, into human cell cultures, but not typically to live humans. Lab safety and contamination protocols are used to prevent exposure to reagents and limit risk of electrocution.
Even so, shocking people wouldn't be enough as the sequences themselves are not enough to be the risk. Efforts at CRISPR human gene editing in vivo typically focus on the Cas9 system. Human cells don't express Cas9, so that bacterial protein would have be delivered along with the target sequence, which would use delivery techniques not used in this paper (e.g., injection or lipid-based delivery).
It may even have to be done in such a way as to get around immunity to Cas9 protein, or be directed at stem cells or other cell-specific population to have a desired effect.
A 27-base sequence could theoretically target genes critical for health — say, deletion or insertion of some 27-base sequence within an oncogene or tumor suppressor gene, for example, delivered with the CRISPR-Cas9 platform. But to administer this, you'd need an entirely different protocol than what the Shipman-Church paper describes, in order for this storage medium to begin to create the possibility of a safety hazard for humans.

Going to the (paywalled) Goldman-Birney paper, they do not store their data in bacteria, but simply synthesize DNA oligonucleotide strings and effectively store them in blobs of fat (literally). When they want to do data retrieval, they do shotgun sequencing with high coverage to get back the original sequence.
As such, there is no real risk of incorporation into human cells, short of microinjection, and so no real direct risk from subsequences being transcribed and translated into pathogenic proteins or virus particles, etc.
While the sequence data could itself contain pathogens, your IT fellow would need to bring their own protein machinery and protocols to have anything nefarious happen. Sequencing is what is done to affect data retrieval, not transcription/translation, and sequencing does not activate any code in the underlying sequence.


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Evolution of autophagy and apoptosis
Autophagy and apoptosis are both necessary for survival of a multicellular organism. I have some information on evolution of autophagy and apoptosis.
However, the key difference between the pathways struck me as - autophagy is for self survival whereas apoptosis is for survival of the population. Given this, is it logical to assume that autophagy evolved earlier than apoptosis ?
Edit1:
I thought of a reason for autophagy to precede apoptosis. Since apoptosis requires mitochondria for its initiation and was acquired as endoymbiosis, I assume that:
$1)$ The primitive organisms taking up primitive mitochondria were eukaryotes.
$2)$ These were already sophisticated enough to have preliminary autophagy.

Firstly, it is important to note that, while autophagy's primary role is to 'shut down' the cell in hopes that reduced function will aid its return to homoeostasis, there is evidence of it being used as a primary method of programmed cell death in certain animals, where periods of massive cell elimination are required (e.g. insect metamorphosis). Source (Nature Review)
Your question is somewhat difficult to answer, as there is fairly limited research in the area, to my knowledge. For extrapolation purposes, it's also necessary to establish what we should consider as autophagy and apoptosis in simple organisms - how similar do the mechanisms of the processes have to be in a rudimentary form in primitive organisms to qualify as such? There is evidence of an apoptosis-like process, as well as autophagy in a range of protozoan bacteria. PLOS article (Evolution of apoptosis-like programmed cell death in unicellular protozoan parasites, Kaczanowski et. al) (Metamorphoses of Malaria: The role of autophagy in parasite differentiation, Isabelle Coppens) Additionally, based on genomic investigations, macro-/micro- autophagy are likely to be present in all non-parasitic primitive eukaryotes. (Origin and Evolution of Self-Consumption: Autophagy
Timothy Hughes and Tor Erik Rusten)
Based on some reading I did during my first degree, it is likely that both apoptosis and autophagy both developed from a precursor process that was present in prokaryotes (some bacteria, such as Myxobacteria, undergo a type of programmed cell death). An older nature article extrapolates that, based on prior research, it is likely eukaryotes came to possess the rudimentary processes of apoptosis (and likely autophagy) through the absorption of multiple strains of bacterial genomes. (Origin and evolution of eukaryotic apoptosis: the bacterial connection, E V Koonin and L Aravind)
Ultimately, I feel it's difficult to state which developed first, if, indeed, they did so separately. Assuming they originated from the same initial mechanism, which seems likely, there is a distinct possibility of them developing alongside each other. If this is the case, it's a bit of a 'chicken and egg' situation - at which point would you consider apoptosis apoptosis? There is evidence of both occurring in yeasts, as well as protozoa, so assuming these processes are indeed precursors to what we observe in multicellular eukaryotes, simultaneous development seems most likely.
Please excuse me posting the names of some articles, rather than links - I have limited use of them at the moment.

Much appreciated. I will wait for other answers and in their absence your answer deserves to be chosen as accepted.


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Role of the pupil response in night vision
What are the things that affect the reaction time of pupil light reflex? What I mean to say is, if you are in a bright room, and the light suddenly turns off. The time you spend to see things in the room (i.e.., night vision) is the reaction time.

pupil dilation and contraction (the pupil light reflex) and retinal production for night vision (a it room suddenly going dark) are very different things, which are you asking about?

Short answer
Pupil responses have little effect on dark adaptation. It is the retinal processes that govern the bulk of the dynamic range of the eye's light sensitivity.
Background
You are referring to dark adaptation of the eye, which is, according to the Universty of Calgary:

This change is called dark adaptation and refers to the process by which the eye becomes more sensitive to light under conditions of reduced illumination. [C]ones are primarily responsible for resolving fine detail (acuity) and colour vision in good light, while rods allow us to see more effectively in dim lighting conditions. The recovery of sensitivity in dark adaptation involves the regeneration of photoreceptor photo-pigments as well as neural changes.

See figure 1. The rods are way faster in gaining sensitivity than the photon-hungry cones.
In a typical clinical setting for diagnostical purposes of e.g. rod function, a typical dark adaptation period is about 20 minutes or so, which fits the below graph quite well. At the end of dark adaptation, the eye is about 100,000 times (i.e., 5 log units) more sensitive than it was at the beginning of the test, a level called dark adapted sensitivity (Universty of Calgary).
In contrast, the pupil response has only a minor effect on light sensitivity in  dark adaptation. It does change its diameter in the dark for sure, but the amount of light that passes through doesn't change too drastically. Pupil diameters range between about 2 and 8 mm (Spector, 1990), say a factor of four. In terms of surface we are talking about 3 and 50 mm2, respectively using (pi*r2), hence a factor of 16, as opposed to 5 orders of magnitude in the process of retinal adaptation.

Fig. 1. Light sensitivity adaptation of rods and cones. source: Uni Calgary
Reference
- Spector. The Pupils. In: Walker et al. (eds.) Clinical Methods: The History, Physical, and Laboratory Examinations. 3rd ed. Boston: Butterworths (1990)


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Do some colors trigger more neural activity in human brain?
On this webpage I found this:

The study found that “globs” in the brains of monkeys reacted differently to colored
  stimuli, and reacted based on color. The brain was most triggered by specific colors
  (red, then green, then blue) and colors with the most saturation. What this tells us is
  that these colors immediately impact a user and draw attention.

Question: Do humans show similar increased neural activity to some colors?
Then I found a perception curve in this webpage

While this curve tells that yellow and green are seen before other hues while red and violet are difficult to perceive; I am not sure if yellow and green elicit more neural activity in the brain.
Anything to say on this matter?

The paper from Stoughton & Conways (2008), where the linked Design Shack webpage refers to, explains that in the visual nucleus in the brainstem (LGN) as well as in the primary visual cortex, most of the color-selective neurons are selectively responsive to colors in the red-cyan axis (Fig. 1).

Fig. 1. RGB color space. source: Commodore 128 forum
This indeed means that these colors evoke more brain activity in these regions of the brain.
Note that a perception curve mentioned on the linked D'Source webpage is nonsense terminology

Why do you think it's nonsense?

D Would you elaborate on why do you think its nonsense?


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What does it mean to "write an image and GIF into the DNA of bacteria"?
BBC News recently published an article saying that:

An image and short film has been encoded in DNA, using the units of inheritance as a medium for storing information ...
  The team sequenced the bacterial DNA to retrieve the gif and the image, verifying that the microbes had indeed incorporated the data as intended.

The news article shows an image of a hand (shown above) and a short film (not shown here) of a horse rider that was encoded into the DNA "using a genome editing tool known as Crispr [sic]".
My question is, what does this mean? Did the scientists break down an image into 0's and 1's and (install?) it into bacteria?  How does a scientist (download?) an image into bacteria and then (redownload?) the image later?  How does DNA hold information of a picture that can be (downloaded)?

I'm just going to migrate this to [biology.se], I believe you'll get a better answer there. By the way - the BBC article links to the Nature journal article in which this work was published. That's the first place you should start trying to read from (although I wouldn't blame you if you didn't understand it).

It's refreshing to see the actual CRISPR part of the CRISPR-Cas system being used.

"Did the scientists break down an image into 0's and 1's" Digital images are already 0s and 1s. No need to "break down" anything.

Just an off-topic note: Stating a "short movie of a riding horse" I think its probably the first movie made in history "Race Horse" which actually was just were several stringed pictures. https://movies.stackexchange.com/a/42182/20039

Just to add what might have been missing in the beautiful answer by @iayork. I just want to give a more simple picture of the encoding done in the E. coli DNA.

First for the rigid strategy in which 4 pixel colors were each specified by a different base, suppose we have a sequence:
AAGCCCTGGTCAGCT
Ignore the first AAG and start with C. Now, each base of DNA can represent a 2-digit binary number, and each number then corresponds to a color, like:
C = 00
T = 01
A = 10
G = 11
With this strategy in mind, the sequence CCCT would give 00000001 pixet (or pixel set), and so on as the sequence grows. This pixet would define the color of four pixels in the image. Thus, each base corresponds to a pixel in the image, and the base defines the color of the pixel in a 4-color image.
Now, lets come to the flexible strategy. To begin with, see the table again:

Here we are using standard 3-base codons. From the predefined value for each color (1 to 21), we can find the color using the codon. For example, from the same sequence:
AAGCCCTGGTCAGCT
Ignore AAG again and start with CCC. From the table, CCC encodes a value of 1. Move to next, TGG encodes a value of 16, TCA encodes 10 and GCT encodes 7, and so on for longer sequences. So, now we get an image with 4 pixels i.e. 2 x 2 with the pixels having color code 1, 16, 10, 7. In this way, each pixel can have a color from predefined values. On extracting this data, the image comes out as (from gizmodo):

The above part talked mostly about the single image of a hand. Now, talking about the horse-riding GIF, the process is almost the same. Here, we have to encode 5 images instead of one. Scientists encoded these 5 images in 5 different cells. After culturing them for some generations, they extracted the information of all images (using standard bioinformatics tools) and compiled them to get the GIF back. The initial and final GIFs look like this (from wired.com):

What do these rigid and flexible mean?
In this technique, the terms rigid and flexible are more about individual base rather than the codon. In the rigid strategy, the value of each base is fixed i.e. rigid. For example, in any sequence, C will encode the value '00', whatever the next or previous base is. This means that in both CCCT and GGTC, C has its rigid value '00'. So, for a 4-color image, where each base rigidly corresponds to the color of a pixel, we get as many pixels as the bases in the sequence.
On the other hand, in the flexible strategy, the individual bases do not have a fixed value, and the overall value of a pixet is defined by all the bases encoding that pixet. For example, TCC encodes a value of 6 while CCC encodes 1. The value of individual base is degenerate (or flexible), hence the name flexible strategy.
Thus, in a nutshell, while the rigid strategy is more efficient since one pixel is defined by one base (whereas in flexible strategy, one pixel is defined by one codon), the flexible strategy is better suited for getting more colored images since you get more color options by increasing the number of bases in a codon (whereas you only get 4 colors in rigid strategy, defined by 4 bases).
Why are we ignoring AAG?
As @canadianer points out in their answer, AAG is a PAM i.e. Protospacer Adjacent Motif. According to Wikipedia:

Protospacer adjacent motif (PAM) is a 2-6 base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system. PAM is a component of the invading virus or plasmid, but is not a component of the bacterial CRISPR locus.

In simple terms (avoiding technical details), PAM is required for the CRISPR to function, but is not a part of the sequence itself. Much like a punctuation, it is necessary for proper functioning of CRISPR, but it is not to be read for encoding/decoding purpose. For the Cas9 found in E. coli (and is the most popular one), the sequence AAG serves as a PAM and is thus not used for encoding purpose here. Scientists also avoided to use AAG in their pixets so that there wouldn't be more than one recognition site for integration (ignore this point if you're unaware of the working of CRISPR).
Reference: Shipman, S., Nivala, J., Macklis, J. and Church, G. (2017). CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature. http://dx.doi.org/10.1038/nature23017

Just a note: The AAG sequence is a PAM for a specific Cas protein. There are Cas proteins from different bacterial species and they have different PAMs.

Why doesn't CAS9 read AAG?

Nice addition, but there is no Cas9 in BL21. In this paper, PAM recognition for protospacer acquisition is mediated solely by the heterologous Cas1-Cas2 complex. Internal AAG is avoided so that there isn't more than one recognition site for integration.

You might also mention the benefits of a degenerate code that are discussed in the paper, especially avoiding repeats and internal PAMs.

A digital picture has many pixels on different sections. But is there any way to locate pixels of specific location of a picture on this method. Or the scientists designated different bacterias for different sections?

@mockingbird AFAIK the only way is to count. Nope, scientists encoded one full image in one cell, only different images were incorporated in different cell. As for your first question, Cas9 does read AAG, but its more of a signal, so we don't take the risk of using it as pixet. See canadianer's first comment.

@Mockingbird I think they just wholesale sequenced the entire CRISPR locus, which is really not overly interesting. To me, the neatest part of this research is how they used CRISPR to integrate the information into the genome.

I don't understand what you mean by "wholesale sequenced the entire CRISPR locus". Do you mean that the entire CRISPR locus is encoded for one image? But an image has many pixels. How did they maintain the order?

@Another Can you include a link to a paper regarding this phenomenon which is not behind paywall?

@another'Homosapien' Yes, just finished ;)

you write - Now, each base of DNA can represent a 2-digit binary number. Why 2-digit? why not 1 or 3 digit?

@user1993 because there are only 4 bases, too many for 1 digit (2) and too few for 3 digits (8)

But what is not clarified in the answer was the use of the word "GIF" - did the researchers actually encode the image in the CompuServe Graphics Interchange Format, or is "GIF" being used intentionally as a misnomer because it's a more familiar way of saying "animated image"?

@oldmud0 I won't consider it either. They just broke the GIF (i.e. a group of images) into individual images and encoded it. Later, they extracted the data for individual images and merged it to get the GIF back. So, its neither being encoded in the GIF format, nor is GIF a misnomer. It does seem perfectly fine to me :)

@another'Homosapien' Then, it would be more professional and correct to refer to a an animated image not as a GIF, but rather as an animated image, no? A GIF itself was not written to the DNA, nor is the format of the animated image important ("graphics interchange format") in the experiment.

Frankly, yes it should be so. But people not so familiar with computers and formats often fail to understand the term 'animated image' since this is what they refer to by the term 'GIF' (ironic, I know, but I've seen this many times)

@oldmud0 Without reading the paper again, I guess the correct description would be that they transcoded a GIF into their novel DNA code.

The image was not in the DNA as such, only as an abstract representation that could be converted into an image from knowledge of the code.  Briefly, they encoded the image into DNA, using a couple of different strategies in which DNA represented pixels -- either with a single DNA base representing a pixel, or with a triplet representing a pixel.  Knowing the code they used, they could then extract the information and turn it back into an image.
Quoting from the original article, CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria:

We began with an image and stored pixel values in a nucleotide code ... We first encoded images of a human hand using two different pixel-value-encoding strategies: a rigid strategy, in which 4 pixel colours were each specified by a different base; and a flexible strategy, in which 21 possible pixel colours were specified by a degenerate nucleotide triplet table ...  To distribute the information across multiple protospacers, we gave each protospacer a barcode that defined which pixel set (denoted as ‘pixet’) was encoded by the nucleotides in that spacer. Four nucleotides define each pixet, and the pixels of a given pixet are distributed across the image ...

Their 21-color strategy is outlined in this figure:

Note: The paper isn't open-access. If you want a full-access version, Church often puts freely accessible versions of his papers on his web site; this paper, #441 on his list, is still shown as "in press" there, but check back at intervals and maybe it will be available there

For clarification, if I had a square image of lets say 9 pixels (3x3), I would assign "arbitrary" bases to each pixel lets say, line1: [G A T], line 2: [T A C], and line 3: [A A A].  And I make an arbitrary rule stating this 3 line code of bases is equivalent to this 9 pixel picture. I then install this code using CRISPR method into bacteria and read it back. Simply put, is this what the scientists did?

Just to be clear to the OP, this isn't conceptually any different than encoding images in binary, except there are 4 possible states instead of just 2. Effectively, each base in DNA is 2 bits.

@PiratePi  conceptually that's pretty much right. You describe arbitrary encoding for a full image, they did it using arbitrary (but consistent) encoding per pixel, but that's the only difference.

Just to add an explanation of one point that may not be clear (and might usefully be incorporated into the answer). GIF is a format for colour images that allows images of up to 256 red-green-blue colours (2^8). A colour table defines what colour corresponds to each of the 256 number values. The genetic code will only allow a maximum of 64 colours to be defined from a DNA sequence. These 64 colours can still be interpreted by software that can interpret GIF image encoding — the fact that the other 192 possibilities are not used is irrelevant. Likewise for 21, rather than 64.

Though there's nothing stopping them from using 4-base "codons" to get 256 colours.

@canadianer Indeed; for this purpose there is nothing any more special about using 3-base codons than there is using 8-bit bytes.

Is there a reason that AAG doesn't map to a number?

"The image was not in the DNA as such, only as an abstract representation that could be converted into an image from knowledge of the code" Right, which is what encoding means. The image absolutely was "in the DNA" ... and the subsequent faithful extraction proves it.

@AndrewPiliser This would be a great, separate question. AAG is the PAM used by E. coli which is necessary for protospacer acquisition, or at least greatly increases acquisition efficiency.

What's exactly a protospacer?

"Four nucleotides define each pixet, and the pixels of a given pixet are distributed across the image" Are these 4 nucleotides are the 1st base of a triplet codon?

The mentioned paper isn't free accessible.

@Konrad Rudolph they did both.  "a rigid strategy, in which 4 pixel colours were each specified by a different base; and a flexible strategy, in which 21 possible pixel colours were specified by a degenerate nucleotide triplet table"

@Mockingbird The four-nucleotide approach was a different, simpler but less flexible, strategy from the triplet strategy.

@iayork Thanks for the clarification, turns out I misread the comment that that [the comment that I criticised] was replying to.

I hate to pile on with more comments here, but I should correct my previous statement that there is "nothing stopping them from using 4-base codons". In fact, I see in the paper that they were already concerned about the cost of synthesizing all of these oligonucleotides.

@LightnessRacesinOrbit I'd suppose if the image was encoded in the DNA, then the bacteria would be able to construct some protein which would look like that image. Alas, it wasn't, even remotely. Instead, it's just that the DNA was used as a medium for storage of image data, which is much less exciting.

Since a few people asked why the AAG triplet is avoided in the code, I thought I'd add this in addition to the other answers. The interesting part of this research is not necessarily the image encoding but rather how they utilized the CRISPR system to integrate the encoding DNA into the genome. It may be a surprise to some that the image is not encoded in one long string but rather, due to the nature of the type I CRISPR system of E. coli, in 33 base pair chunks called protospacers (of which 27 bases are used for the actual encoding, which gives 9 pixels per spacer). Thus the entire 30x30 pixel image required stable integration of 100 protospacers (though not necessarily in a single cell). These protospacers (oligonucleotides) were chemically synthesized and then introduced into cells by electroporation.
Integration of these protospacers into the genomic CRISPR locus utilized overexpression of heterologous Cas1 and Cas2 endonucleases. These proteins recognize exogenous DNA preferentially when it is flanked by a protospacer associated motif (PAM), which in the case of the CRISPR system in question is AAG. The complex recognizes the PAM and cleaves the exogenous DNA to form the 33 bp spacer which is inserted into the genome. Simplistically, it could be pictured something like this:

However, consider a situation where AAG is used to encode a pixel:

This creates an internal PAM that could lead to loss of information, depending on which PAM is recognized. Actually, the major benefits of having a degenerate code is to avoid certain triplet combinations that lead to internal PAMs or sequence repeats (which are error prone in replication).

References/Further Reading:
Amitai G, Sorek R. 2016. CRISPR-Cas adaptation: insights into the mechanism of action. Nat Rev Microbiol 14:67-76.
Shipman SL, Nivala J, Macklis JD, Church GM. 2017. CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature.
Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y. 2015. Structural and mechanistic basis of PAM-dependent spacer acquisition in CRISPR-Cas systems. Cell 163:840-853
PS: For anyone that cares, those images are not technically correct but, at the moment, I don't feel like changing them. In reality, the PAM is not part of the processed spacer.

Good enough, +1! Yet I feel you should expand the second paragraph a bit :P

@another'Homosapien' I tried to avoid too much mechanistic detail since I expect a lot of the people interested in this question are not extremely well versed in the intricacies of CRISPR-Cas (and neither am I, for that matter). I'm open to suggestions, though.

Without a little jargon, how is anyone supposed to assess the credibility? ;)