One Step on Mars, Part II

Continued from Part I, here.

Out in deep space…

The prove beeped. Its scan reported new activity.

Of course, it paused for a few nanoseconds for a second verification scan. After all, it was designed to avoid false positives. A hundred false negatives were better than a false positive, as they could always be corrected for at a later date.

But the second scan revealed the same presence. Sentients with the same subcomputational patterns were now present on a second planet within their star system.

The probe’s criteria for activation had been met. Continue reading

One Step On Mars, Part I

The probe arrived fifteen days after the first humans set foot in the colonies.

Of course, the colonies were already there and waiting. They’d been there for a while, sitting idly on the surface of Mars, occasionally powering up at regular intervals to perform preventative maintenance and keep their surfaces clean. There were, after all, always more tasks that the robots could carry out. The solar panels needed to be swept clear of dust daily, the supports that anchored the habitats to the thin Martian soil beneath needed to be bolstered and checked to ensure nothing had torn loose, the atmospheric synthesizers that would, one day, lead to Mars possessing a breathable atmosphere had to be maintained, the generators needed the occasional check-up…

So the robotic “minds” of the colonies passed time, waiting for their first inhabitants to arrive.

And somewhere else, out in deep space, the probe waited as well, watching the developments in the Sol system with endless patience… Continue reading

The Tree in the Cave

Biology is a curious thing.  How does a seed, a tiny little cluster of cells with no eyes or brain or neurons or central control, know which way to grow?

The answer comes down to gravity, and light.

The seed on the ground felt the touch of water, enough water to launch its cells into an explosion of action and motion.  This was the signal for which it had waited, enduring dryness and the tumbling external forces that eventually brought it to its resting place.

The cells grew, pushing out beyond their walls, building copies, subdividing in a flurry of growth and replication.  Proteins spun through cytoplasm in a complex dance, uniting and binding with others, and then tearing away once their function had been completed.  DNA spiraled out, unwinding, duplicating, and then recoiling back up like a spring.

The seed’s hard shell cracked, and a root – thin, pale, fragile, exposed – came snaking out.  It searched, quested, found the soil.  It burrowed in, drinking in the water all around it, soaking up that moisture and converting it into more fuel to push itself deeper.

And on the opposite side of the seed, opposite the emergence of the root, a thin little branch emerged, barely even able to support its own weight.

Once exposed from their prison inside the seed, the cells spread out, unfurling, questing for light.  Inside each little cell, dozens of green factories – the chloroplasts – floated, waiting to absorb that dazzling radiance and convert it into food.  The plant didn’t think, didn’t know anything – but those cells ran a desperate race against their dwindling supply of food.

If the supply of food, of high-energy ATP molecules failed, they would have no other options.  They’d die, and the whole organism would die along with them as it starved.

But no – there, light!  The light wasn’t strong, not direct sunlight, but it was enough.  The cells most exposed to the light leapt into a flurry of joyful production, pumping out food to fuel the growth of the rest of the organism.  They worked as a community, creating far more ATP than they needed, exporting the rest to feed their brothers and sisters.

The plant responded to these most productive of its cells, and the entire structure began to shift.  The plant angled itself, growing faster on the side away from the light, angling itself to reach all that it could.  It had to capture as much light as possible, needed all that food!

Eventually, the initial rapid burst of growth slowed.  The cells that had one split joyously in wild abandon, as fast as they could manage, now proceeded at a slower, more stately rate.  The husk of the seed, no longer needed for protection, fell away.  Its remains would break down, eventually reabsorbed by the plant itself.

The plant didn’t know this, of course.  All it knew was that it had light and water, enough to make food.  Enough to exist.

Its stalk thickened, grew out in concentric rings to add more structure and support.  Ridges formed from slight unevenness in the cells’ walls, and the external proteins stiffened, creating defensive bark, a skin beneath which the living cells of the plant flowed and swarmed, passing nutrients up and down.  They sent water up to the leaves, and brought down synthesized ATP, food to feed the growing roots.

At the base, the root sank deeper, providing support, and split off to grow in new directions.  It had to stabilize its brothers above, and it fought for every inch against the hard ground, the rocks and other impenetrable items in amid the soil.  Sometimes, its path was stymied, but it always found a way around, chasing after that water.

At the top of the tree, leaves exploded out, each a separate factory to create more energy, to support itself and its surrounding fellows.  They angled towards that precious light, drinking it in.  Each leaf enjoyed its time at the tip of a branch, but the branch eventually moved past it, leaving it as just a side extension.

No leaf complained about this shift in its fate.  They were all a part of the whole, all feeding the greater organism.

Time passed.  The tree measured the passing time, in the rings on its trunk and the growth of its cells, but it didn’t know the meaning of these changes.  It only knew the beauty of growth, the symphony of healthy cells.

Did the tree know that it was alone, away from its brothers and sisters, the sole survivor in this cave, where only happenstance allowed it to grow?  Likely not, even as much as plants understand things.

Besides, the tree would not be alone much longer.  By now, it had enough energy built up, strong enough reserves, to begin the final stage of its life.  It would create seeds, tiny little copies of its own cells, with instructions to go forth, to spread wide, and seek two things:

Gravity, and light.

The tree was alone, yes, but it would not be alone forever – and what is time, to a tree?

The Singularity is Coming, and It Will Be Terrible

Many scientists will talk about an upcoming event called a “singularity.”  This event, championed by very brilliant man Ray Kurzweil, is the point at which machines become smarter than humans.  And once machines are as smart or smarter than humans, the machines can design their own improvements, at an incredibly accelerated rate.  Whether this singularity will happen, and if so what exactly might happen, is a point of significant debate among scientists and other forward thinkers.

I believe that this singularity will happen.  And I believe that it will be absolutely terrible.

I believe that the singularity, this point where machine intelligence surpasses human intelligence, will eventually arrive.  Perhaps not quite within 30 years, as Kurzweil predicts, but it will arrive.  Prediction and heuristic algorithms are growing constantly more powerful, allowing for computers to extrapolate from incomplete data to make predictions.  Even today, Google can take a search string and not just provide a best-hit output, but can integrate keywords, linked phrases, and other information to create a more holistic guess as to what the searcher is after.  It seems like a sensible conclusion that this will eventually grow to at least an approximate facsimile of human thoughts, with a trillion times the background information and references to draw upon for support.

However, unlike Kurzweil, I am pretty sure that this technological singularity is going to prove to be incredibly frustrating.

The internet, for example, is an incredibly disruptive tool that has led to the rise of countless new opportunities.  Yet it also brought new problems and conflict; net neutrality, Comcast-Time Warner oligopolies, the increasing concern of personal security and privacy in a world that is growing more and more digital; all of these problems tag along with this great breakthrough, like remoras attached to a shark.

Even today, in class, we debated Eli Lilly releasing synthetic human growth hormone (HGH), allowing for short children to be treated and to grow to a height more comparable to their peers.  This treatment ran $20k-$40k per year, mind you.  That immediately raised questions of inequality and the growing divide between the rich and poor.

Now, how will people respond to the option to upload a brain, to create godlike robotic bodies, to find new and inventive ways to cheat death?  (How much does one of those robotic bodies cost, anyway?)

One of the wealthiest and most powerful nations in the world cannot even provide an acceptable health care system to its citizens.  Introduce the option to purchase lab-grown organs or brain-scanning nannites, and I cynically imagine that the divide among the populace will further increase.

We are approaching the ability to sequence the human genome for a thousand dollars or less, yet six in ten Americans still don’t realize that ordinary tomatoes contain genes (now that’s scary).

The singularity, a huge leap forward in innovation and discovery, will open up amazing new abilities that previously were believed to be squarely in the domain of miracles.  But that doesn’t mean that they won’t immediately be covered with a fine grime of human pettiness, price gouging, misplaced anger and distrust, and pure dumbfounded incomprehension.

Think about when you had to teach your grandmother to send emails.  Now, try and imagine explaining to her that cell-sized computers are going to create a digital backup of her brain to transfer into a robotic artificial intelligence.

Imagine the cries of “class warfare” when the ability to create real-life save points is released – for the low, low cost of $7 million per year in equipment, processing power, implants, and data storage.

The singularity is coming, and it’s going to be terrible.

How it works: Mendelian Inheritance!

Today in How It Works, we are going to take a step away from the molecular areas of genetics, and are going to instead talk about evolution!  More specifically, we are going to talk about this dude:

Look at those glasses.  Has to be a scientist.

This man, who lived back in the 19th century (1822-1884, to anyone who’s interested), is named Gregor Mendel.  Growing up in Austria, he worked on a farm as a child, and chose to join the Augustinian monks to help afford his studies, as the monks would pay for his education.

At the university where he studied, Mendel chose to focus on heredity – a hot topic at the time!  He started off breeding mice together to track their traits, but the monks weren’t comfortable with him observing animal sex (squeamish lot, those monks), so he switched over to plants.

What Mendel observed, as he bred together pea plants while looking at certain traits, is that it was possible to create what were known as inbred lines – that is, lines that always showed a certain trait!  Back then, there wasn’t a clear understanding of the existence of genes, so scientists could only observe the phenotype – that is, the physical appearance of the organism in respect to a specific trait.

Mendel, in true scientific fashion, tried to only focus on a single trait, figuring that the fewer variables he had to track, the better.  For this example, let’s take pea pod color (which comes in two flavors: green and yellow).  If Mendel bred some wild-type plants together, he would get a mix of greens and yellows.  But if he kept on breeding only green or yellow plants together, he eventually found that all the offspring would be 100% green or yellow, matching the color of the parent.

Now, that’s not too interesting.  If you keep on selecting for a trait, eventually you only see that trait.  Awesome.  But when things got really interesting was when Mendel decided that, after creating an inbred line of green peas and an inbred line of yellow peas, he was going to breed the two different inbred lines together.

The first generation of offspring from this cross (usually referred to as F1) was all green peas.  Pretty dull, although it’s interesting that green seemed to dominate over yellow.  But not yet willing to give up, Mendel decided to go ahead and cross this F1 generation to itself.  The results from this cross were surprising.

Mendel saw that in this next generation (the F2 generation), he would see three green pea pods for every yellow one.  And no matter how many times he tried this F2 cross, he still saw this remarkably stable ratio of three to one.

From this, Mendel deduced that there were two alleles that represented these two colors.  The green allele made pea pods green, while the yellow allele made them yellow.  Whenever a plant had one of each allele, it would show green; the green allele is dominant to the yellow allele!

The big conclusion that Mendel drew, along with the existence of these alleles, is that these alleles were given to offspring independently.  This is known as the Law of Independent Assortment.  Here’s a handy chart to show how it works:

In this case, the big G corresponds to the allele that makes the pea pods green, while the small g corresponds to the allele that makes them yellow.  As you can see, the F1 individuals each have one big G allele and one little g allele; because the big G is dominant, they are green.  When they are bred together, 3/4 of the resulting offspring will inherit at least one G allele, and will thus be green.  But the last 1/4 will inherit a little g from both parents, and thus will be yellow!

One way to think about Mendelian inheritance as a set of rules:

  1. All genes have two forms: a dominant form, usually represented by a capital letter, and a recessive form, usually represented by a lower case letter.
  2. If a dominant allele for a gene is present, that is the phenotype that will be shown by the organism.
  3. The only time a recessive allele will create the phenotype is if there are no dominant alleles present for that trait!
  4. There is an equal chance for a parent to pass on any allele that it has.  In the above example, each parent in the F2 cross has a 50% chance of passing on a big G allele and a 50% chance of passing on a little g allele.
Makes sense so far?
Now, there are a ton of other factors that can influence inheritance, things like co-dominance, suppression, partial penetration, and haploinsufficiency.  But these will come into play later.  Mendel’s discoveries, although lost for many years, created a stir in the scientific community when they were rediscovered and shown to be correct.  

How it works: miRNA!

So previously, I was talking about the DNA to protein pathway.  But in real life, things aren’t nearly as simple as this; there are many different mechanisms for feedback, for controlling how, when, and how many proteins are made from DNA synthesis.  Keep in mind that the raw genetic code in all of your cells, from skin to muscle to bone to organs to brain, is the same!  And yet somehow, these cells are able to differentiate, taking on many different shapes and roles.  How do they do it?

One way is through micro RNA, or miRNA!

Previously, I talked about messenger RNA, or mRNA, which is the intermediate stage between DNA and proteins.  DNA is transcribed into mRNA, which is then translated into protein.  A fairly simple two-step pathway.

But there are other types of RNA!  At least three other types that are well known, at least.  The first type is known as rRNA, and forms a specialized structure called a ribosome, which turns mRNA into protein.  The second type is known as tRNA, and is the structure that carries individual amino acids to the protein as it is being built by the ribosome.  And the third type is called miRNA, and suppresses the formation of proteins, preventing them from being translated at all!

So how’s it work?  It’s simple!

miRNA starts off just like any other RNA – it’s transcribed from DNA.  But remember how RNA is single-stranded, while DNA is double-stranded?  And the bases in DNA match up with each other, leading to complementary binding that holds the two strands together?

Well, miRNA starts off as a single strand of RNA, about 70-90 bases in length.  The bases at either end of the strand match up with each other, however, which causes the strand to fold in half and form a loop, similar to a hairpin!  (In fact, these loops are known as hairpins in scientific terminology.)  This hairpin structure can also be known as a stem-loop.

Once a stem-loop has formed, an enzyme called Dicer approaches, and slices off the “loop” part of the stem-loop.  After this piece has been sliced off, the miRNA appears as a short little sequence, about 20-22 bases, and is double-stranded.

The next step after this is the formation of the RISC (pronounced like “risk”) complex, a group of proteins that latch on to the double-stranded little miRNA.  At this point, one of the two strands is discarded, so the RISC complex contains a single piece of RNA, about 20 nucleotides long, sticking out from the big mass of proteins like a comb.

Now, that little miRNA contains a specific set of bases, and 20 bases means that this miRNA will only bind to sequences that are complementary matches – balanced opposites.  And it just so happens that certain, specific mRNAs have that exact complementary sequence!  The RISC complex uses its miRNA as a key to find matching mRNAs, and then binds to them and prevents them from being translated.  Instead, they are degraded, and that protein is not produced by the cell!

And thus, miRNA is able to lower the amount of, or down-regulate, the amount of a very specific protein in a cell, by preventing it from being made in the first place by destroying the mRNA.  Seems easy enough, doesn’t it?

How it works: The DNA to Protein Pathway!

In this installment of How it works, where I talk about various different aspects of science, I am going to focus on micro ribonuclease, also known as miRNA!  These tiny molecules have often been confusing to scientists – for clarity, read on!

One of the most important, if not the absolute most important, pathway in a cell is the creation of proteins.  Proteins are the building blocks of life, and make up most of your cells, carrying out various functions, providing structure, support, helping to create new molecules, digest food, fight off disease, and many more functions!  But where do they come from?

First an introduction: we all know about DNA, the building blocks of life, the code that contains the instructions for creating any organism, the double-stranded helix that looks like an incredibly long and twisted ladder.  But how does DNA turn into a baby, or a dog, or a palm tree?  Well, it needs to go through some conversion!

The first conversion step is the creation of RNA, which is very similar to DNA.  While DNA is double stranded and made up of the bases A, T, G, and C, RNA is only single stranded, and instead of using T (thiamine), it uses U (uracil).  The creation of RNA from DNA is known as transcription, while the conversion of the RNA into proteins (which make up the various parts of the cell and are what makes it ‘tick’) is known as translation.

This may seem confusing, so let’s use an analogy!

Think of DNA as the blueprints of a skyscraper.  These blueprints are very valuable, since they contain all the instructions for how to build this massive building!  Also, because they include every single detail of the construction, there are a lot of pages of blueprints.  There’s only one copy of these blueprints.  Now, if all the construction workers building the skyscraper had to keep on handing off this giant book of blueprints to each other, things would very quickly get disorganized and not much work would be accomplished.

So, what if we made things a little easier on our construction workers?  Instead, let’s just make photocopies of the relevant pages, and give each worker the pages for his specific assignment, copied out of the blueprints.  This way, you can have tons of copies of the blueprints floating around, each one short and to the point, and the workers can destroy their copies when they’re done, keeping the original blueprints intact.

In this case, all of those copies are like RNA!  This RNA is actually referred to as messenger RNA, or mRNA, because it carries the message of how to build a protein.  So, there’s a guy sitting next to the blueprints in the main building making photocopies – what he’s doing is known as transcription.  All the workers that get the copies then go on to build parts of the building – just like mRNA leads to the creation of proteins.  This is known as translation.

Still with me?  Good!

As I mentioned, there’s only one copy of the DNA.  In humans, this isn’t quite true – there are two copies, one copy coming from each parent.  Sorry to lie to you about that.  But still, 2 copies for an entire cell is not a lot, so the DNA remains inside the nucleus of the cell, where it is safe and protected.  Inside this nucleus, a protein known as RNA polymerase (remember this from our discussion of PCR?) is responsible for reading along an exposed strand of DNA and synthesizing the single-stranded RNA copy.

That single-stranded RNA copy isn’t ready to be turned into a protein yet, however.  It needs to have some modifications made to it!  One step is that some parts of the code may be unnecessary, and certain protein complexes will chop out these unnecessary sections (known as introns) and reattach the two ends of the RNA.  Also added on to the RNA is a “cap” at one end, that helps keep the RNA from being prematurely broken down by enzymes.  At the other end of the RNA is a “tail”, which contains instructions about how the RNA should be processed, as well as sites for miRNA binding (more on that later).

After the newly made mRNA has had these edits made to it, it is considered to be a mature mRNA, and is ready to be sent out into the big, wide world outside the nucleus!  So out it goes, into the cytoplasm.  Here, it floats around until it encounters a large protein complex known as a ribosome.  The ribosome attaches onto this RNA and, like a computer program, reads its code!  I will talk more about DNA code in another update, but the code specifies a specific order of amino acids.  As the amino acids are assembled in this order, they coil together and become a specific protein.  So this ribosome reads the RNA code and assembles the amino acids in the specified order, thus creating a protein.  This is translation.

Now, that mature mRNA hangs around for a while outside the nucleus, constantly being used by ribosomes to make copy after copy of protein.  But it can’t stay forever, or else the ribosomes would waste all their energy making extra copies of the protein that it specifies!  So, over time, that tail is shortened more and more.  The tail is representative of the mRNA’s age – the shorter the tail, the older the mRNA.

Eventually, that mRNA has such a short tail that its code is exposed!  At this point, another protein, known as RNase, steps in.  This enzyme, RNase, is designed for the specific purpose of destroying RNA without a tail.  It latches on to the mRNA and chops it up into pieces, which are then recycled and brought back inside the nucleus, where they will be reused to make new mRNA!

And that, ladies and gentlemen, is the pathway for making proteins, from the DNA (the blueprints) to immature mRNA (the unedited blueprint copies) to mature mRNA (the copies with proper notes for the workers) to protein (the actual product specified on the blueprints).  Not that bad, is it?

How it works: SDM!

Welcome to How it works, a new and (hopefully) illuminating series on many of the techniques that I, as a biologist, am familiar/somewhat familiar/not at all familiar with!  Read on, but be prepared to learn!

So, in the last How it works, I talked about PCR.  PCR, as you may recall, stands for Polymerase Chain Reaction, and is a way of making a lot of copies of DNA, very fast!  Seriously, once you know your sequence and have a couple strands of the DNA, you can go from 2 strands all the way up to 20,000 strands, all identical, in an hour or less.

But wait!  What about if you want to make a couple small changes to your DNA?  In order to explain this, I’ll lay out a nice, hypothetical example:

You’re a researcher, working on, for example, fingers!  You go out and take a bunch of DNA samples from six-fingered people (this condition is actually called polydactyly), and compare the DNA sequence to that of normal, five-fingered people.  You compare the DNA using sequencing, which will be explained in another episode.

Now, you find that the DNA is almost identical – except in one spot, instead of there being an A in the DNA, you find a T instead!  (Remember, DNA is made up of only 4 bases, A, T, G, and C, combined in long strings, a bit like computer code.)

So, you hypothesize, if a person has a T in this spot on their DNA, instead of an A, they grow six fingers instead of five!  But you can’t just call it quits now – you don’t have any experimental proof, nothing to show that this isn’t just coincidence.  So you decide to do an experiment!

Now, first off, you can’t go around giving people extra fingers (unless you’re a mad scientist or something, in which case feel free).  So instead, you look at mice, and notice that they have this exact same gene.  Great – there’s no problem with giving mice extra toes!

So, you now have 2 different directions your research could take.  You could:

  1. Search through millions of mice until you find some that have extra toes, and extract their DNA and see if it shows that same mutation A -> T.
  2. Take normal mice, use a technique called Site-Directed Mutagenesis, or SDM, to change DNA from them to have the T instead of the A, and see what happens when you put it back into new mice.
Do you know which path is best?  Here’s a hint: we want the method that doesn’t involve searching through millions and millions of mice, counting toes.  We’re taking door number 2!
As you recall, PCR works by separating the two DNA strands, attaching primers to each strand as starting spots, and then synthesizing the rest of the DNA in the complementary strand, building off the primer.  SDM works almost exactly the same way – but with one difference.  Another primer is included!
This third primer is made to cover the spot where the mutation should occur.  Remember, primers are usually 7-10 bases long, so even with one base in the middle altered (to create the mutation), it will still bind very strongly to the DNA.  It might look something like this: 

On this picture, ignore the red circles, but look at the two strands of DNA (black lines) with the SDM primers (blue lines) attached.  See how the blue lines have one base that is incorrect, making them kink away from the DNA?  That’s intentional!  
Now, after the first round of DNA synthesis, the new strands, made from these primers, will have that mutation, that single changed base, as a part of them!  And because every DNA strand will be made with these altered primers, 99.9% of the DNA from the reaction will be mutated, just as you wanted, instead of containing that original A instead of T.
(Can you see why this process isn’t 100% effective?  If you guessed that it’s because of the original strand of DNA, you’d be right!  That strand is unchanged, and so it will still have the A instead of the T.  Since we’ve made thousands of copies, though, the chances of that original strand being the one used is very low, however, so we don’t worry about it much.)
So after reading this, hopefully you’re starting to see a bit of the power of PCR – not only can it make thousands of copies of a single piece of DNA, but it can also be used to introduce very specific changes at exact locations!  And all of this can happen while you take your lunch break, you productive researcher, you.

How it works: PCR!

Author’s note: This is part of an installment on how many methods and techniques in biological sciences work, written for educational purposes!  Hopefully, this blog will rise to be something more than silly short stories.

If you’ve ever worked in a biology lab, you’ve probably heard professors, researchers, or even other students talking about PCR.  But what in the world is this strange acronym?
PCR stands for Polymerase Chain Reaction, and is a method for amplifying DNA!  This process can take a few strands of DNA, or even a single strand, and turn it into thousands of (nearly) identical copies! Although it has a few limitations, it is a very rapid, powerful tool, and has many different uses.
So, you may be wondering, how does PCR work?  It’s simple, and all depends on temperature.  But first, a little refresher on DNA.
DNA is made up of two strands, each of which is complementary to the other.  Because they are perfectly complementary, they fit together, bonding perfectly.  Think of it like ripping a piece of paper in half – the two pieces of paper will perfectly match up together, unlike any other ripped piece of paper!  Same thing with DNA.  Once enough complementary bases are in a strand of DNA, it will only fit perfectly with its exact match.
Even though DNA normally sticks together, it does separate – when heated up!  In order to separate the DNA, the solution containing the DNA is heated up to between 95 to 98 degrees Celsius, near-boiling.  At this point, the DNA peels apart into the two different strands, but doesn’t fall apart quite yet.
Now, the enzyme that copies DNA is known as polymerase, and it’s a big, complex protein.  Polymerase attaches on to an exposed single DNA strand, and builds the complementary strand of the DNA.  Bam, DNA copied!  Unfortunately, it’s not quite that easy – there are a couple requirements of polymerase, however, that make it a little tricky to work with.  
The first issue, which made PCR impossible for a long time, is the fact that polymerase is heat-sensitive.  If you heat the protein up too much, it acts a bit like a spaghetti noodle – it falls apart, and no longer performs its DNA-copying function.  Even if you cool it back down, it is still broken.  Now, when you have to heat up the DNA to separate the strands, this becomes an issue.  
The way to solve this problem is actually rather ingenious, in terms of biology.  In some hot vents, such as those found in hot springs in Iceland or at the bottom of the ocean, certain bacteria (known as thermophilic bacteria) are able to thrive.  In order to survive in the boiling-hot water, they have evolved special forms of enzymes that remain stable at very high temperatures.  The polymerase used in PCR comes from one of these bacteria, T. aquaticus, and is thus known as Taq polymerase.  It doesn’t break down in hot water!
The other issue with polymerase, however, is that it can’t start on just a single strand – it needs to start on a double strand.  This means that if you chop a bit out of a double-stranded piece of DNA, the polymerase can copy that area missing its complementary strand.  If you have a single strand by itself, however, there’s no place for the polymerase to attach.
Now, in order to get around this problem, two different short pieces of DNA, known as primers, are added to the mix for PCR.  These primers are usually 8-10 bases each in length, and are specially selected to perfectly fit the DNA strands at either end.  This means that the primer forms a very short section of double-stranded DNA, allowing the polymerase to attach!
The last thing needed for a PCR to work successfully is the raw ingredient – the bases that DNA is built from!  These are easily synthesized, and are added to the mixture so that the polymerase has raw materials to use to build its strands.
So, PCR goes through three steps – denaturing (where the DNA separates into single strands), annealing (where the DNA is cooled off enough for the primers to bond to either end of the single DNA strands), and elongation (where the polymerase attaches to the DNA at the double-stranded primer, and then builds the second strand down the rest of the length of the strand).  Each of these steps is performed at a different temperature, so a PCR machine, also called a thermocycler, rotates a sample between the three temperatures.  Although temperature can vary, denaturing is usually around 96 degrees, annealing happens around 58 degrees, and elongation is generally at 72 degrees.  The thermocycler simply keeps on cycling the temperature of the sample between the three programmed temperatures.
Because the primers/Taq polymerase combination makes a copy of every single-stranded DNA molecule, each cycle should, in theory, double the amount of copied DNA!  Here’s a quick example:
Start with 1 strand.
After 1 cycle, you have 2 strands.
After 2 cycles, you have 4 strands.
After 3 cycles, you have 8 strands.
After 4 cycles, you have 16 strands.
After 5 cycles, you have 32 strands.
As you can see, the amount of DNA grows very rapidly!  Of course, this growth stops if you run out of primer pieces of DNA or raw bases, but in general, this method allows for millions of copies of DNA to be synthesized in a half hour or less.
PCR has a couple other limitations.  Because polymerases don’t copy DNA instantly, there is a limit on how long the copied DNA strands can be.  The maximum length of DNA that can be copied by PCR is about 10,000 base pairs, although some methods can go up to 40,000 base pairs.  PCR also has occasional errors, as the Taq polymerase has an error rate of about 1 in 10,000 bases.  Sometimes, the copied DNA strands aren’t perfect – and that, of course, means that future strands copied from those are also flawed.  
Despite this, however, PCR is a very powerful tool, and is used all the time in biology labs!  And now, you know how it works!