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  #26  
Old 08-26-2007, 08:16 PM
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Default Re: A Question For The Lone Ranger

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Originally Posted by The Lone Ranger View Post
Strange as it might seem at first, snakes illustrate the circulatory problems associated with an erect posture quite well.

:rattler:

The giraffe information is fascinating too.
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Old 09-10-2007, 01:26 PM
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Default Re: A Question For The Lone Ranger

Dear Lone Ranger

We have a problem in fluid dynamics. If water, or another fluid, flows out of a tap, or other opening, at various pressures, will it always form droplets? Or will it sometimes form a continuous stream for a certain height (and maybe then break up into droplets)?

I'm sure the latter is true but my correspondent claims to have seen high-speed photos that prove the droplet nature of fluids. We don't seem to be able to find relevant web pages.

Yours, Perplexed of Purley.
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  #28  
Old 09-10-2007, 03:34 PM
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When water is flowing through a pipe under relatively low-pressure and at relatively low speed, assuming there are few or no air bubbles in it, it will be experiencing laminar flow. In laminar flow, all the water molecules are moving in more or less the same direction.

This is an "ideal" situation for moving water through a pipe. If you increase the pressure/speed, the water may begin to exhibit turbulent flow. In this case, though the net movement may be in a particular direction, the individual molecules are moving in different directions, making for a very chaotic flow.


To move fluid through pipes efficiently, you want to avoid turbulence at all costs, so it's important to design both your pipes and your pumping apparatus so as to minimize the chances of flow becoming turbulent. (Indeed, if blood flow in any of the major arteries becomes turbulent, the ability of the blood to deliver adequate oxygen to body tissues is severely compromised, and the result is likely to be fatal.)


So, water flowing through water pipes is normally flowing in a laminar fashion. If the tap doesn't have an aerator (which is designed for the express purpose of breaking up the water flow), water will normally exit in a laminar flow if the pressure is low.

If you turn up the tap so that more water flows out at higher pressure, the flow will break up and become turbulent. You can easily see the difference between turbulent and laminar flow.


Lots of hospitals and laboratories have faucets that don't have aerators in them and that are designed to produce laminar flow over a wide range of pressures. The goal is to have laminar flow, because laminar flow is far less prone to picking up airborne bacteria, doesn't splash as much when it hits the sink, produces a constant volume of water at a given pressure, and is more efficient at wetting surfaces.

Here's a picture of a faucet with water flowing out of it in a continuous, laminar stream.



If the water falls far-enough, even if it started out flowing laminarly, it will eventually become turbulent and then break up into droplets. This is a consequence of conservation of mass.

As soon as the water leaves the tap, it is in free fall. So, it will accelerate. Because of the cohesion of water molecules (that is, because of hydrogen bonding between the polar water molecules), they tend to stick together unless enough energy is supplied to pull them apart. You'll notice that as the laminar stream falls from the tap toward the sink, it gets thinner.

This is necessarily so because as the water falls it accelerates. Since the volume of water exiting the faucet is constant but it's moving faster as it moves away from the tap, the diameter of the water stream must decrease as the water's speed increases.

This can go on only so far before the tension caused by the gravitational acceleration of the water causes the stream to break apart into individual droplets. (You can see the same sort of effect in waterfalls, though that water was already flowing turbulently. If the water falls far-enough, the stream of water has completely broken up into individual droplets by the time it reaches the ground.)



So, the short answer is: Yes, many faucets can and do produce laminar flows. But falling water will eventually break up into droplets if it falls far enough, whether it was flowing in a laminar fashion or in a turbulent fashion. (And quite a lot of faucets are designed to break up the water into turbulent flow made up largely of individual drops, so as to aerate it.)


Cheers,

Michael
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  #29  
Old 09-10-2007, 03:59 PM
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Default Re: A Question For The Lone Ranger

Hmm.

One of these days we will find a question that he can not answer.

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Old 09-10-2007, 07:06 PM
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Default Re: A Question For The Lone Ranger

Thanks Michael!

You seem to be saying that slow flow / low pressure allows for laminar flow, but stronger flow will be turbulent - fair enough. Will turbulent flow always separate into disconnected droplets? And will this happen at the tap opening or some distance below?

(In fact very slow flow could also separate into drops due to surface tension - one drop at a time.)

Assuming the fluid in question is electrically conductive, the basic question is under what circumstances could current flow up the stream of fluid, and under what circumstances can you safely piss on an electric fence/electric eel/other hazard? :wink:
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  #31  
Old 09-10-2007, 07:54 PM
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Default Re: A Question For The Lone Ranger

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Will turbulent flow always separate into disconnected droplets?
No. Otherwise a fast-flowing mountain stream (which is most-definitely turbulent) would consist of disconnected water droplets. Most faucets produce turbulent flow, but it isn't necessarily broken up into individual droplets.

Quote:
And will this happen at the tap opening or some distance below?
If you turn your kitchen tap to a very slow, laminar flow, such that there's a very small volume of water flowing, you can see it shatter into individual drops maybe 6 inches to a foot below the tap, depending on the flow volume. This assumes that the flow is sufficient that the water does not separate into drops because of surface tension (as you pointed out), and come out one drop at a time.

If your tap allows for laminar flow with a greater volume of water (i.e., it doesn't have an aerator), the column of laminar-flow water will remain intact all the way down to the sink. What causes the column of water to eventually "shatter" into droplets as it falls (whether the flow is turbulent or laminar) is mostly the tension created by gravity pulling on the water column, though air resistance doubtless also plays a role, since it will magnify any deviation from perfect smoothness in the column of water, making the flow more turbulent and hastening the "shattering" of the column.


Quote:
Assuming the fluid in question is electrically conductive, the basic question is under what circumstances could current flow up the stream of fluid, and under what circumstances can you safely piss on an electric fence/electric eel/other hazard?
Electricity would flow through any electrically conductive fluid that was in laminar flow quite nicely, since the molecules are more or less in contact. It would also flow quite nicely though any conductive fluid that was in turbulent flow, so long as it hadn't shattered into droplets.

If you wanted to safely urinate on an electric fence, the trick would be to be far-enough from the fence that the urine stream had shattered into individual droplets by the time it reached the fence -- and that the droplets had moved far-enough apart, on average, to prevent the current from "jumping" from one droplet in the stream to the next.

If you're standing on an elevated platform and urinating onto a fence 20 feet below you, my guess is that you'd be perfectly safe. I wouldn't want to try it from a distance of 2 feet, though.

It depends on the voltage of the fence, too. The greater the voltage and the amperage, the larger a gap the electricity can jump. Urinating on a high-voltage electric line -- even from a considerable distance -- would be a very bad idea.

Cheers,

Michael
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Last edited by The Lone Ranger; 09-10-2007 at 08:12 PM.
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  #32  
Old 09-10-2007, 08:35 PM
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Default Re: A Question For The Lone Ranger

On Mythbusters, they tried pissing on an electric fence and an electrified 'third rail' (as used by some subway trains).

The conclusion was that you wouldn't get electrocuted unless you were very close, as the stream of piss breaks up into droplets after just a few inches (due to gravity accelerating it as TLR described).
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  #33  
Old 09-10-2007, 10:46 PM
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Default Re: A Question For The Lone Ranger

That must have been what Ding was referring too.

... How close to reality were the mythbuster experiments? :whoa:
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  #34  
Old 09-10-2007, 11:02 PM
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Default Re: A Question For The Lone Ranger

They equipped 'Buster' (a crash test dummy) with a 'bladder' and a valve. The diameter of the urethra was deliberately made on the large size to give 'a really good flow rate' at the upper end of the range for a large human male. Then they propped him up next to a railroad track and arranged for him to pee on a live rail. He was equipped with a sensitive ammeter that could measure any current that flowed up the urine stream (they used real human urine, I think). There was no measurable current while the crash test dummy remained in a standing position. Slow motion photography showed that the urine 'stream' actually consisted of separate droplets, and that the gaps between the droplets formed a total air-gap that was large enough to withstand the several thousand volts available at the rail without arcing across. The program did stress that although they had 'busted' the myth, this was still not a sensible thing for anyone to actually try for real.

For the electric fence test, Adam did actually pee against a live electric fence. He eventually got real close, and then did get an electric shock, though he said it "wasn't too bad". From 'normal' range (whatever that means) he didn't get a shock.
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  #35  
Old 09-12-2007, 07:50 PM
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Default Re: A Question For The Lone Ranger

By the way, here's a neat video that demonstrates an important difference between laminar flow and turbulent flow.

[YOUTUBE]http://www.youtube.com/watch?v=X4zd4Qpsbs8[/YOUTUBE]


The reason it works is this: the fluid into which the dye is placed is very viscous. So long as you stir it slowly, flow is laminar and all the molecules are moving in the same direction. So, if you're careful, you can reverse the direction of stirring and get your original drops of dye back.

This works because by stirring in reverse, you're reversing their direction of movement and returning the molecules to where they started. So long as you stir slowly and in a precisely reverse pattern to the original stirring that dispersed the dye throughout the fluid, fluid flow remains laminar and so you can reverse the process by which you dispersed the dye through the viscous fluid and get your dye drops back.

We used to do this trick in a Biomechanics class I took; we'd put drops of dye into corn syrup, stir it up to disperse it, then reverse the direction of stirring to get the drops of dye back. It was always a fun trick, and it really impresses people who aren't expecting that sort of thing. (You can win money off people by betting them you can "unstir" a mixture.)


The trick, though, is to use a very viscous fluid and not to stir too fast. Otherwise, fluid flow becomes turbulent and the molecules are not all moving in the same direction. You cannot unstir the mixture if flow becomes turbulent.

Cheers,

Michael
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  #36  
Old 09-12-2007, 10:55 PM
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Default Re: A Question For The Lone Ranger

Our electric fence has high voltage, something like 24,000 Volts, but very low amperage. It won't kill you, but I do know from experience direct contact is unnecessary, it will arc to anything halfway decently grounded within a 1/4 to 1/2 inch or so of the wire. Even though I now know Mythbusters busted that myth, I'm still not going to test the theory. It might shock my peener, making it go hide up inside. It took years to get it out of hiding after living though four Wyoming winters.
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Old 09-13-2007, 01:10 AM
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Default Re: A Question For The Lone Ranger

It is probably highly dependent on the voltage, and third rails have voltages of not more than about 1000V. I wouldn't try it with overhead lines.
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Old 09-13-2007, 08:10 AM
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Default Re: A Question For The Lone Ranger

My original cautionary comment in the other thread was based on personal experience. I don't know what the voltage of the fence was, but here is what happened.

I was visiting a friend in rural Alabama. I went behind the barn to take a leak. I really had to go quite badly, so the initial stream of urine was quite strong. There was a sheet of roofing tin leaning up against the fence (which I did not know was electrified). I pissed on the tin from a distance of probably not more than two or three feet. I received a very definite and painful shock. Not severe enough to cause me any real harm, or immobilize me (I backed off damn quick I can tell you) but still quite painful and unexpected, comparable to getting kicked in the balls. This is definitely not an urban myth. If it were a myth at all it would be a rural one.
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Old 09-13-2007, 01:43 PM
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Default Re: A Question For The Lone Ranger

We could investigate this issue in numerous trials with different voltages, volunteers, pressures, peeing techniques, etc. Maybe circumcision plays a role in determining the shape of the flow too. We could get the Ig Nobel Prize for this.
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  #40  
Old 11-26-2007, 08:00 PM
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Default Re: A Question For The Lone Ranger

I am currently reading Darwin's Children by Greg Bear. It's a sequel to Darwin's Radio. In the books a new disease is caused by Endogenous Retro-Viruses (ERVs) and turns out to be a new step in the evolution of humanity. Meanwhile the mummified remains of two Neandertals are found together with a Homo Sapiens Sapiens child and it is suggested that this is their child as a result of the same rapid evolution through ERV.
Anyway, my question is: is it true that parts of our 'junk DNA' consists of 'captured' viruses? That these viruses can become active again and cause diseases?
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Old 11-27-2007, 12:16 AM
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Originally Posted by Watser?
Anyway, my question is: is it true that parts of our 'junk DNA' consists of 'captured' viruses? That these viruses can become active again and cause diseases?
The short answers are: yes, probably not, and probably not.

And not all ERVs are part of “junk DNA”; some of them have evolved to become not just functional, but vital to our survival.

Perhaps a brief discussion of what DNA and RNA are and how they function is in order, as well as what viruses (specifically, retroviruses) are, and how they function.


For all the hideous complexity of molecular biology, the central concepts regarding DNA, RNA and proteins are actually very simple indeed; almost everything boils down to the complementary nature of the nitrogenous bases.


First, we need to know what proteins are, and why they’re so important. Any molecule that is made by stringing together many similar smaller molecules (these small molecules are called monomers) is called a polymer. A protein is a polymer of monomers known as amino acids. There are only about 20 amino acids in living things, so what distinguishes one protein from another is simply the number and the sequence of the amino acids. Here are the 20 amino acids found in living things, shown below. Notice that the only difference between any two of these amino acids is what happens to be bound to the “alpha” carbon’s 4th bond. (These 20 different chemical assemblages are known as the amino acids’ side chains, so the only difference between 2 amino acids is the makeup of the side chains.)



If you bring two amino acids together, the amino group on the “left” side of one molecule (the H3N+) can bond to the carboxylic acid on the “right” side of the other molecule (the COO-). This bond is called a peptide bond. Consequently, a long chain of amino acids bound together by peptide bonds is known as a polypeptide.

Once a polypeptide is formed, further bonding between different portions of the very large molecule (a polypeptide can be made of many thousands of amino acids) causes it to fold up into a distinct, three-dimensional shape. This molecule is a protein.


The importance of proteins to living cells cannot be overstated. That’s because proteins are the primary structural molecules of cells. That is, they make up a great many of the internal structures of cells. Further, many proteins function as catalysts, and can greatly speed up the rates at which chemical reactions take place in cells. (Proteins that function as catalysts are known as enzymes.) A cell could not survive without these enzymes, since they regulate the chemical reactions that keep the cell alive.



What has this to do with DNA? DNA is the molecule that stores the “information” the cell needs in order to manufacture proteins. A section of a DNA molecule that contains the “information” for making a particular protein is called a gene.



DNA is a molecule known as a nucleic acid, as is RNA. Nucleic acids are polymers of subunits known as nucleotides. Each nucleotide has three components, a phosphate group, a pentose (a 5-carbon sugar), and a nitrogenous base.

In DNA, the pentose in each nucleotide is a sugar called deoxyribose. (So, DNA stands for deoxyribonucleic acid.) There are four different nitrogenous bases that can be present in any DNA nucleotide. They are adenine, cytosine, guanine, and thymine. So, the four different nucleotides found in DNA molecules look like this:



RNA is only a little different from DNA. Instead of deoxyribose, RNA has ribose for its pentose. (Hence, RNA stands for ribonucleic acid.) The four bases present in the nucleotides of RNA are adenine, cytosine, guanine, and uracil. Here are the four nucleotides of RNA:




Now, about the complementary nature of those nitrogenous bases. A strand of DNA (or RNA) consists of a whole bunch of nucleotides bound together. Because of their structures, adenine is strongly attracted to thymine (and also to uracil), and cytosine is strongly attracted to guanine. This is what is meant by the “complementary” nature of these molecules.

So, if you assemble a strand of DNA, it will more or less automatically assemble a second, matching (but “mirror-imaged”) strand. This is true because the nucleotides containing adenine will attract and bond to complementary nucleotides containing thymine, the nucleotides containing thymine will attract and bond to complementary nucleotides containing adenine, the nucleotides containing guanine will attract and bond to complementary nucleotides containing cytosine, and the nucleotides containing cytosine will attract and bond to complementary nucleotides containing guanine.

The reality, of course, is a bit more complicated, but that’s the gist of it. That’s what makes DNA such an excellent “information-storage” molecule; it’s very easy to copy. Just split a DNA molecule down the middle – this is called “unzipping” it – and each half assembles the missing half. So you wind up with 2 identical DNA molecules. [I tell my students that reproduction almost always begins with the unzipping of genes, one way or another.]

Also, because of the complementary nature of the nucleotides, DNA is more or less self-repairing if damaged.


When the “information” in DNA needs to be copied in order to manufacture a protein, the relevant section of the DNA molecule is “unzipped” and this time, the nucleotides of RNA bond to the DNA. So, the relevant “information” is copied to make a molecule of RNA (the uracil in RNA bonds to the adenine in DNA, just as thymine does). After the RNA molecule is assembled, it is released. It then travels out of the nucleus of the cell (where the DNA is stored) and to a ribosome, where the “information” it contains is used to assemble a polypeptide chain.


But how is this “information” encoded, you ask? Each sequence of three nucleotides in a DNA molecule forms what’s known as a codon. Each of these codons specifies a particular amino acid. This is what’s known as the genetic code.

Since there are four different nucleotides in DNA, and since each codon contains three nucleotides, there are 43 = 64 possible combinations of codons. Since there are only 20 amino acids but 64 codons, we say the genetic code is redundant. That’s because each amino acid is coded-for by more than one codon. (The exception is tryptophan; for whatever reason, there’s only one codon that codes for it.) The genetic code is not ambiguous, however, because each codon codes for one and only one amino acid. That, again, is because of the complementary nature of the bases – the fact that adenine will normally bond only with thymine (or uracil) and cytosine will normally bond only with guanine.

Incidentally, there are three codons that don’t code for any amino acids. Since they don’t code for any amino acids, the assembly of a polypeptide chain stops when one of these three codons is reached. They are, therefore, referred to as “Stop” codons.



Now we’re in a position to understand how proteins are made. Basically, there are two major steps – transcription and translation.

In transcription, a gene is unzipped and the nucleotide sequence in one of the DNA strands is copied to make a molecule of RNA – specifically, a molecule of what’s known as messenger RNA or mRNA for short. Each DNA codon, naturally, has a complementary codon of mRNA.

After the mRNA is made, the DNA releases it and zips itself back up. The mRNA travels out of the nucleus of the cell and binds to a structure called a ribosome. (The ribosome itself is largely made of RNA.)

At this point, yet another type of RNA, transfer RNA (tRNA for short) comes into play. A given tRNA molecule has an anticodon at one end, which can bind to a complementary mRNA codon. At the other end, it has an amino acid.

Since a given tRNA has a particular anticodon at one end (an anticodon that will bind only to the appropriate complementary mRNA codon) and a particular amino acid at the other end, the sequence of codons in the mRNA determines the sequence of tRNA molecules that will bond to it – and, therefore, the sequence of amino acids that will be assembled. Since the tRNA molecules, when they bond to the appropriate mRNA codons happen to bring amino acids into close proximity, those amino acids will form peptide bonds, and so in bonding to the mRNA, the tRNA assembles a polypeptide chain. Since there are no tRNA molecules that will bind to a “Stop” codon, when one of those is reached, the polypeptide chain is released. It then folds up to become a protein.

This process, in which the “information” in the mRNA is used to assemble a polypeptide chain, is translation.



Okay, so that’s a quick and dirty summary of the importance of DNA and how proteins are made. What does any of this have to do with viruses?

A virus is not a living thing. It is a bit of nucleic acid (either DNA and/or RNA) surrounded by a protective protein coat. Most viruses contain DNA. If a virus gets into a living cell, it can “subvert” the cell’s own machinery by integrating its DNA into the host cell’s DNA and thus “forcing” the cell to make viral proteins and DNA – that is, to make many copies of the virus. Often, it kills the cell in the process.

A retrovirus is sneakier. It has RNA instead of DNA. It also has an enzyme called reverse transcriptase. When a retrovirus gets into a living cell, it uses reverse transcription to convert its RNA to DNA (the reverse transcriptase allows it to do this, naturally), and then it splices that DNA into the host cell’s DNA. After that, it does what a virus normally does – it forces the cell to copy its genetic material.


A virus isn’t necessarily harmful to a cell. It may do nothing more than quietly co-opt the cell into making a few proteins and nucleic acids that it wouldn’t have made otherwise, without harming the cell in the process.

So, viruses can become incorporated into an organism’s cells without harming them in the process. They can even be passed on from parent to offspring, if they’re in the host organism’s gametes (sperm or ova).



An endogenous retrovirus is a retrovirus that long-ago infected organisms of a given species and become incorporated into that species’ genome, and so is passed on in the sperm/eggs to offspring. Obviously, the original virus must not have been too harmful, or the original hosts wouldn’t have survived long-enough to pass it on to their offspring, and so it wouldn’t have become incorporated into the genome of the entire species. Once a virus has managed to become incorporated into a species’ genetic makeup, it’s subject to mutation just like any other gene.

As such, virtually all ERVs have long-since suffered “knockout mutations” that rendered them incapable of “escaping” and becoming infective again. It’s exceedingly unlikely that any sort of “back mutation” could occur that would once-again make the virus infective.


Interestingly, once the virus has become part of a species’ genetic makeup, it’s just as likely that it will be subject to a beneficial mutation as is any other bit of genetic material. As such, not only have many ERVs been incorporated into the genetic makeup of humans and other species, some of them now perform important – even essential functions for us.

For instance, in all placental mammals, ERVs function to strengthen and maintain the placenta. Of equal importance, several ERVs seem to function to suppress the mother’s immune system during pregnancy; this prevents the mother’s immune system from attacking and destroying the developing embryo. As such, it’s unlikely that any of us would survive long-enough to be born were it not for ERVs.

In that sense, ERVs do play a function (sometimes a major function) in evolution. It’s likely that placental mammals arose when – quite by accident – some early mammals were infected by a retrovirus or retroviruses that a.) happened to suppress females’ immune systems, allowing them to carry embryos inside their bodies longer and thus give birth to larger, better-developed offspring, and b.) happened to get itself incorporated into its bearers’ genomes and so was passed on to those offspring.

On the other hand, as mentioned above, it’s exceedingly unlikely that an ERV could re-evolve infectiousness.


Hope this helps!

Michael
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Last edited by The Lone Ranger; 11-27-2007 at 05:25 PM. Reason: Fixed broken link.
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  #42  
Old 11-27-2007, 12:44 AM
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Default Re: A Question For The Lone Ranger

Thanks Michael :thankee: that was very interesting (though I'll probably only remember a bit of it).

BTW: this bit
Quote:
Interestingly, once the virus has become part of a species’ genetic makeup, it’s just as likely that it will be subject to a beneficial mutation as is any other bit of genetic material. As such, not only have many ERVs been incorporated into the genetic makeup of humans and other species, some of them now perform important – even essential functions for us.

For instance, in all placental mammals, ERVs function to strengthen and maintain the placenta. Of equal importance, several ERVs seem to function to suppress the mother’s immune system during pregnancy; this prevents the mother’s immune system from attacking and destroying the developing embryo. As such, it’s unlikely that any of us would survive long-enough to be born were it not for ERVs.

In that sense, ERVs do play a function (sometimes a major function) in evolution. It’s likely that placental mammals arose when – quite by accident – some early mammals were infected by a retrovirus or retroviruses that a.) happened to suppress females’ immune systems, allowing them to carry embryos inside their bodies longer and thus give birth to larger, better-developed offspring, and b.) happened to get itself incorporated into its bearers’ genomes and so was passed on to those offspring.
is explained in the second book, it is pretty high in science (though I keep forgetting most of that too).
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Old 11-28-2007, 02:55 AM
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You're most welcome, Watser?!


Aw, come on, nobody thought the "unzipping of genes" joke was funny? I may have to go pout now.


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Michael
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Old 11-28-2007, 05:17 PM
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[youtube=GkdRdik73kU]Molecular Biology's Central Dogma[/youtube]

Youtube has a movie about replication and transcription, it's one of my favorite science movies. Like many other molecular biology movies, it shows as though molecules themselves were magically seeking out each other even that's not actually the case. But then shortcuts have to be taken to show the really important features.

Does the movie get all of the process details correct? I have a couple of questions, I've noticed in my molecular biology reading that sometimes it seems like they're talking about different kinds of DNA replication machinery all doing the same thing, I was wondering are they comparing various different replication enzymes from different species or are multiple redundant replication machinery at work in human cells? The other question, are the mRNA strands driven by random Brownian motion to move by themselves out of the nucleus into the cytoplasma to be united with a ribosome? Or are there helper molecules which ferry the mRNA from the transcription grounds to the ribosomes?

Your talk about ERVs made me think of a certain company's research aimed at eradicating HIV. They've developed a drug designed to accelerate the rate of mutation in HIV by tricking the reverse transcriptase into incorporating nucleotide analogues in the DNA chain. Fascinatingly, the drug causes random multiple point mutations in order to drive the virus into extinction by causing multiple knockout mutations over successive generations.

If the clinical trials bore out, then HIV could become another ERV in the humans infected by it. Who knows maybe it'll end up driving another evolutionary phase in humanity in the distant future.
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Old 11-28-2007, 07:00 PM
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Originally Posted by cappuccino View Post
Youtube has a movie about replication and transcription, it's one of my favorite science movies. Like many other molecular biology movies, it shows as though molecules themselves were magically seeking out each other even that's not actually the case. But then shortcuts have to be taken to show the really important features.
I left out a lot of details regarding DNA Synthesis and Protein Synthesis for that reason too. I figured that, for example, an explanation of how mRNA is processed before it's released and allowed to leave the nucleus would be pointlessly complicated and wouldn't be helpful in understanding the basic processes involved.


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Does the movie get all of the process details correct?
From what I can tell, it's pretty good, aside from some forgivable oversimplification.

I had trouble with it on my computer; it doesn't play very well. It appears, though, not to have any narration. That may be because it's intended to be played while someone explains what's going on. Otherwise, some of what you see won't make any sense. For example, DNA polymerase can only copy DNA in the 5' → 3' direction. This means the leading strand and the lagging strand of a DNA molecule are copied differently during DNA replication. They actually show that in the animation, but if you didn't know it beforehand and therefore what to look for, you'd never be able to make sense of it.

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I have a couple of questions, I've noticed in my molecular biology reading that sometimes it seems like they're talking about different kinds of DNA replication machinery all doing the same thing, I was wondering are they comparing various different replication enzymes from different species or are multiple redundant replication machinery at work in human cells?
I'm not entirely certain I can answer. As far as I know, DNA polymerase works more or less the same in all eukaryotes. As mentioned though, the leading strand and the lagging strand are copied differently. You have to keep this in mind when thinking about DNA replication; that might be a source of confusion.

Also, DNA replication works a bit differently in prokaryotes than it does in eukaryotes. (Also, transcription and especially translation work a little differently in prokaryotes and eukaryotes. This is largely because prokaryotes don't process their mRNA after it's synthesized. Eukaryotes, by contrast, heavily process their mRNA after it's synthesized, but before it leaves the nucleus.)

In any event, DNA polymerase and RNA polymerase are far from the only enzymes that take part in DNA synthesis/protein synthesis, so that might be a source of confusion. If a textbook or an instructor makes a random reference to helicase, for example, without explaining its role in DNA replication, that could easily lead to confusion.

It's also worth keeping in mind how big a molecule DNA is. Several different DNA polymerase molecules will be simultaneously operating during the replication of a DNA molecule -- otherwise, copying the molecule would take much more time. So you'll have lots of (more or less) identical molecules performing the same tasks during DNA replication; if this isn't understood, random reference to "the other" DNA polymerase molecules will be terribly confusing to the listener.

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The other question, are the mRNA strands driven by random Brownian motion to move by themselves out of the nucleus into the cytoplasma to be united with a ribosome? Or are there helper molecules which ferry the mRNA from the transcription grounds to the ribosomes?
Random Brownian motion plays a big role, but it's a bit more complicated than that. "Mature" mRNA (that is, mRNA that has been processed and has had its introns spliced out, etc.) can bind to nuclear export proteins (is there anything proteins can't do?). Unprocessed mRNA typically won't bind to nuclear export proteins.

The mRNA apparently can't pass through the nuclear pores and thus into the cytoplasm unless bound by nuclear export proteins ("exportins"). Unbound mRNA is far too large a molecule to have much of a chance of passing through a nuclear pore on its own. I don't know off the top of my head how exportins work, but I'd guess they cause the mRNA to fold into a more compact shape that can more easily pass through a nuclear pore. The mRNA/exportin complex diffuses out into the cytoplasm (as far as I know, no active transport is involved), and the proteins are eventually released. The mRNA, should it encounter a ribosome, can then be used for protein synthesis. If it doesn't encounter a ribosome, it will sooner or later be degraded by RNases and broken down into its component nucleotides.


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Your talk about ERVs made me think of a certain company's research aimed at eradicating HIV. They've developed a drug designed to accelerate the rate of mutation in HIV by tricking the reverse transcriptase into incorporating nucleotide analogues in the DNA chain. Fascinatingly, the drug causes random multiple point mutations in order to drive the virus into extinction by causing multiple knockout mutations over successive generations.

If the clinical trials bore out, then HIV could become another ERV in the humans infected by it. Who knows maybe it'll end up driving another evolutionary phase in humanity in the distant future.
I've read of this. It's a brilliant idea, in my estimation, and may prove the best way to deal with HIV.

Cheers,

Michael
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  #46  
Old 01-25-2008, 07:45 PM
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According to local folklore, we need a cold winter to cut down on insect pests during the summer months. If the winter is too mild, we get swarmed by the pesky critters. If the winter gets and stays cold enough, we'll get a normal number of them in the summer.

First, how much truth is there in this belief?

Second, if there is any truth to it, how cold does it have to get and for how long?
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Old 01-25-2008, 09:54 PM
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There is truth to the belief.

Insects and other small arthropods have various ways of dealing with winter cold. The main problem, of course, is preventing their body tissues from freezing – or, from freezing in such a way that the freezing process will kill. There are conditions in which an animal can freeze without being killed in the process.


If you dissolve a substance into water, this causes freezing point depression. That is, the temperature at which the water freezes is lowered. This is why, if you live near the ocean, the salty seawater can remain a liquid at temperatures that cause nearby freshwater ponds and lakes to freeze. That’s the same principle behind antifreeze in your car. Ethylene glycol (commercial antifreeze) has a freezing point of about -13 degrees Celsius. Water, of course, has a freezing point of 0˚ C. Mix the two and you depress the freezing points of both liquids, so you get a mixture that won’t freeze unless its temperature is lowered to considerably less than -13˚ C. (The exact freezing point, of course, will depend on the proportions of water and ethylene glycol in the mixture.)


It’s worth keeping in mind that there’s no such thing as “cold.” “Cold” is merely a relatively lack of heat. The warmer something is, the faster its molecules are moving; the colder it is, the slower its molecules are moving. A refrigerator or freezer, therefore, doesn’t work because it adds some magical substance called “cold” to your food. It works because it removes heat from it. Similarly, it gets colder in the Winter because less energy is being delivered by the Sun than is escaping to space.

As a substance cools, its molecules move more and more slowly. Eventually, if it’s a liquid, the molecules will be moving slowly-enough that, when they happen to bump into each other, they won’t have enough energy to overcome their electrostatic attraction. So, they’ll stick together, forming crystals. As more and more molecules stick together, the liquid freezes.

It’s thought that the reason for freezing-point depression is that as you dissolve one substance into another, the molecules of the solvent necessarily become more widely-spaced. This means the molecules of the solvent are less likely to bump into each other and start sticking together to form ice crystals.



So, many small “cold-blooded” animals secrete sugars and/or proteins into their body tissues during cold weather that have the effect of lowering the animals’ freezing points. As such, they can avoid freezing in sub-zero (Celsius) temperatures. As an illustration, just a couple of weeks ago, while out for a hike in sub-freezing temperatures and with nearly a foot of snow on the ground, I counted three spiders and a couple of moths walking along (slowly, to be sure) on the snow.

So, the widely-believed notion that “cold-blooded” animals cannot survive – much less function – in sub-freezing temperatures simply isn’t true. Most people don’t notice spiders and moths and whatnot when hiking in the winter because they don’t think to look for them.

Even so, sufficiently prolonged exposure to sufficiently cold temperatures will kill any animal.



Most arthropods don’t remain active during the winter months, of course. In many, many species, the females lay eggs in the autumn, preferably in some well-insulated place. The eggs, jam-packed full of sugars and proteins that will prevent them from freezing in all but the most extreme of conditions, will survive over the winter and hatch out new critters in the spring.


A variation on this is that many insects enter a pupal stage during the autumn. Again, the insect generally seeks out a well-insulated place (say, under the bark of a tree or down in the ground) where temperatures are unlikely to fall too low.

Some insects (e.g. dragonflies) have aquatic larvae. The young insects will survive just fine through the winter, so long as it doesn’t get cold-enough for the ponds or lakes they’re living in to freeze solid.

Many insects can survive the winter as adults by going dormant. It’s not all that uncommon to find adult insects hibernating under tree bark or in the soil, for instance. Again, they tend to choose well-insulated sites, and so long as the temperature doesn’t go too far below freezing, they’ll survive just fine until warmer temperatures when they can again become active.



Some insects and even some small vertebrates (e.g., some amphibians and reptiles) can be supercooled to well below 0˚ C without freezing. This only works for relatively small animals, however. If it isn’t disturbed water that’s pure or nearly so can be chilled to nearly -40˚ C without freezing. This is called “supercooling.” So long as nothing disturbs the supercooled water, it will not freeze. The reason that water normally freezes at 0˚ C is because “impurities” in the water act as “condensation nuclei.” Water molecules will adhere to small bits of matter suspended in the water column, other water molecules will stick to those water molecules, and so on.

But if you can purify water sufficiently and keep it still, even at temperatures of -20˚ to -30˚ C, water molecules will collide with each other and stick together too infrequently for ice crystals to form, and so it won’t freeze. But even a slight disturbance – say, shaking the container or dropping in a single crystal that can act as a condensation nucleus will cause the entire mass of water to freeze almost instantly.

Supercooling normally works for only relatively small volumes of water because, the greater the volume of water, the greater the chance that some water molecules will happen to collide and stick together, thus initiating rapid freezing. That’s why insects and frogs can be supercooled, but not bears.


How to accomplish this? Some animals can actively transport large amounts of glucose or similar sugars into their body cells (glucose cannot cross cellular membranes on its own, and so will not “leak” out again), until their body cells have practically no water in them. By transporting sugars and proteins out of the blood and into body cells, they convert the blood to nearly pure water. So long as the animal remains absolutely still, neither the body cells (which have very little water in them, so don’t freeze because water molecules are too widely-separated to come into contact) nor the blood (which supercools because of the lack of condensation nuclei) will freeze. Of course, anything that disturbs the supercooled animal will cause it to freeze more or less instantly, killing it in the process.




Anyway, regardless of how they manage to beat the cold, insects can only carry this so far. Exposure to sufficiently-low temperatures for sufficiently lengthy periods will kill any animal.


Where the animal in question is and what the weather conditions are will play a major role. Animals that burrow deep underground to overwinter will rarely experience lethal temperatures unless it’s an exceptionally cold and snow-free winter. (Snow acts as an insulating blanket. A prolonged cold spell accompanied by snow on the ground will kill many fewer burrowing insects than will a cold spell in which the ground is bare.)

Similarly, for those of us living more than 23.5˚ north of the equator, the Sun is always in the southern part of the sky, especially in winter. This means south-facing hills, trees, etc. receive more sunlight (and, therefore, more warmth) than do those facing north. So, an insect that burrows into the bark of a tree on the south-facing side will survive a much colder winter than will an insect of the same species that happens to choose the north-facing side of the tree for shelter.


***

So, the short answer to the question is that there’s no way to say exactly how cold the weather must be or for how long. Each species’ tolerances will be different. However, as a general rule, the colder the winter and the less snow there is, the fewer insects will manage to survive it, including those that plague us in the spring and summer months.

Cheers,

Michael
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Old 01-25-2008, 11:23 PM
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How about bacteria? I thought they could survive for many thousands of years at very low temperatures? Also plant seeds?
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Old 01-25-2008, 11:44 PM
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Under the proper conditions, you can freeze single cells for indefinite periods of time. Bacteria have been found in permafrost that were at least 10,000 years old. Upon thawing, they immediately began to swim about.

Small-enough organisms can be frozen without killing them, under the proper circumstances. It generally has to do with avoiding the formation of ice crystals, since those crystals will rupture cells, killing the organism in the process.

Generally, the trick is to freeze the organism fast-enough that the water solidifies without the formation of sharp crystals that will rupture the cells. Since a living thing is made mostly of water and since water has a tremendously high heat capacity, this means that it's not physically possible to remove enough heat from a sufficiently-large organism fast-enough to freeze it without ice crystals forming that will rupture its cells and kill it. That's why you can freeze an embryo but not an adult human.


Some plant seeds have virtually no metabolic activity if either frozen or dehydrated, and so can survive for years or even centuries under the proper circumstances, only to sprout when conditions are favorable. Many seeds have impermeable, waterproof coats, for instance, and the embryo inside remains in a dormant, dehydrated state with virtually no metabolic activity for years. If a fire then sweeps across the soil and heats the seeds sufficiently to weaken the protective coating, water can then infuse into them. Metabolic activity will then resume and the seeds sprout. That's one reason why it's not unusual to see plant species growing after a prairie or forest fire that haven't been seen in the area for decades. (Plant conservationists often use fire as a tool for restoring grasslands, since so many grass species have fire-resistant seeds that can remain in the soil for years until they're "activated" by a surface fire.)

Cheers,

Michael
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Old 01-26-2008, 01:35 AM
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But if you can purify water sufficiently and keep it still, even at temperatures of -20˚ to -30˚ C, water molecules will collide with each other and stick together too infrequently for ice crystals to form, and so it won’t freeze. But even a slight disturbance – say, shaking the container or dropping in a single crystal that can act as a condensation nucleus will cause the entire mass of water to freeze almost instantly.

l
Cool! (no pun intended)

Does the same thing apply to heating a liquid?
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