Was Clay the First Life on Earth?

I just finished this book called Seven Clues to the Origin of Life by a biochemist named A.G. Cairns-Smith from the University of Glasgow. He’s got this theory that the first life on Earth was clay. It’s pretty intriguing. I’ll try to explain…

Cairns-Smith is looking to answer the question: how did life spring up on Earth? It’s an elusive puzzle that even the most well respected biologists don’t know how to begin solving.

 Life is highly complicated and organized. Perhaps this could be chalked up to evolution if it weren’t for the fact that the complexity seems to be vital to the whole way that life works. The crucial elements of life (DNA, proteins, lipids, and carbohydrates) depend on each other completely. They are interlocked. You can’t have proteins without DNA, proteins can’t do anything without the energy from lipids and carbohydrates, lipids and carbohydrates are constructed by proteins, and proteins construct DNA which brings you back to the beginning of this sentence.

An analogy that I really like is a stone arch.

You can’t take out one stone without the entire structure collapsing. You also can’t build this kind of arch stone by stone. Similarly, all fundamental pieces of life are necessary to the whole so life could not have evolved piece by piece.

The popular example amongst proponents of intelligent design is a mousetrap, it won’t work unless all the pieces are there simultaneously. They call it irreducible complexity. It’s a pretty valid argument, in my opinion. It’s difficult to imagine how even the simplest life form on earth, a single cell, sprung up out of nothing but the oceans. Why would a bunch of atoms spontaneously and simultaneously organize themselves into a complex system in which every piece depends on the other pieces?

You almost can’t blame people for giving up on this question by just throwing their hands up and saying, “God did it!”. The circumstances that would have been necessary to make the first cells are so unlikely that it’s pretty much preposterous to assume that cells assembled themselves by chance.

Let’s take DNA, for example. DNA is made from nucleic acids. In order to synthesize it in a lab you are going to need a primer, which is a strand of nucleic acid that is used as the starter. In order to make primed nucleic acids there are hundreds of steps that need to be performed in a very precise order. Pouring, stirring, heating, concentrating, agitating…ect.

Sure, you could imagine all of these steps happening on their own in nature. We could imagine a pool evaporating in the sun to create a concentrated solution, lightning striking the pool to agitate it, rainfall to dilute, filtration through rocks… and so on. It’s not that the occurrence of each individual step is too unlikely, it’s that the sequence of hundreds of these events successfully happening one after another is too unlikely. It’s analogous to flipping a coin and throwing heads 10,000 times in a row… if you can make this happen I want to be on your team.

And this is just DNA! We also have lipids, carbohydrates, and proteins to worry about; Each requiring their own long series of steps for synthesis. Not only that but ready-to-go proteins, lipids, carbohydrates, and nucleic acids would have to all be in the same place at the same time in order to assemble themselves into an interlocked cell.

Of course, even extremely improbable events can happen given enough time and all the resources on Earth. However, there wasn’t enough time and there isn’t enough Earth.

What do I mean by this?

Cairns-Smith gives a pretty neat run down of this immense improbability: Let’s say that there are 140 steps to perform in order to synthesize DNA. Let’s also say that the chances of the appropriate event happening naturally at each step is one out of six. Both of these are very optimistic estimates. The chances of, say, lightning striking a certain puddle of chemicals at a certain time, are probably much smaller than one in six. However, if we use one in six we can pretend we are rolling dice, which makes this analogy cuter.

Ok so now we are rolling a dice 140 times in a row and we need the same number to come up every time. This number represents success at each step in the life-making process.

What are the odds of this kind of miraculous rolling actually happening? Since you can roll a 1, 2, 3, 4, 5, or 6, there are 6 possible outcomes for one throw. There are 6*6 possible outcomes for two throws, 6*6*6 possible outcomes for three throws and so on. For 140 throws there are 6 multiplied by itself 140 times possible outcomes.

Put this into google: 6^140. You will get, approximately, 10^109. This is a one followed by 109 zeroes. Try writing that number down just to get a feel for how enormous it is. You will get bored and give up after 10 zeroes, max. Five, if your attention span is slightly longer than mine. The chances of you rolling a dice and getting the same number 140 times in a row are 1 out of this huge freakin number. So, you would need a number of trials that is something like 10^109 in order to hit on the ONE successful trial. 

Well that doesn’t seem like such a big deal…just roll the thing for 10^109 trials. You’ll get the successful one eventually. We have all the time in the world and the whole earth. Sounds feasible…right?

Well, if you were to roll one dice every second since the beginning of earth’s history you can only get through about 10^15 trails. No problem…get more dice. In order to squeeze in 10^109 trails we need to be rolling 10^94 different dice every second.

Turns out 10^94 is a ridiculous number. That’s more than the number of electrons in the observable universe, which means it’s WAY more than the number of atoms that have ever been present on Earth. Earth just doesn’t have enough stuff on it and it hasn’t been around long enough for these kinds of odds.

So, you see what I mean when I say this is a pretty valid argument for intelligent design?

Personally, however, I think it’s quite lazy to assume that cells were prepackaged and handed over to the earth as a finished product. If there is a god I don’t she is as boring as that. As crazy and unlikely as it seems, life has to have started up via natural processes on this planet and I’d like to learn about the ways this could be possible.

Perhaps the very first life was not so interlocked; the pieces not completely dependent on each other. Maybe the stone arch was originally scaffolded, like a wall, and then pieces were gradually subtracted leaving us with the mutually dependent, arch-like system we have now.

Enter this bizarre-o clay theory. I really like it. Maybe you will too!

Let’s start here:

Organisms reproduce by copying the messages that define the organisms. This is what we call passing on genes.  Passing on genetic material that is capable of mutating is all natural selection really requires. Of course, the mutations that are beneficial to an organism’s survival are the ones that get passed on and the ones that are detrimental to survival do not get passed on. This is evolution.

In order to pass on genes, or messages, all we really need are the messages themselves. If the messages can be replicated using readily available materials, then we don’t need all the manufacturing machinery of the cell.

Cairns-Smith proposes that the very first organisms were “naked genes”, genetic material without a cell. He suggests that the atomic structure of crystals served as the very first genes.

I’ll explain. Crystals “reproduce” by making layers. The layers are simply repeating patterns of atoms and ions.

A single layer of kaolinite crystal looks like this:

Due to the sizes and charges of each of these particles, only certain atoms and ions can stack up on top of this layer and become the next layer. Think of it like legos…not just any lego can go on top, it has to have the right hole size. Take it one step further…think of it as legos with positive and negative charge. You can’t stack two like-charges right on top of each other. Therefore, the next layer of legos (atoms) is pretty much determined by the first. Starting to sound like DNA yet?

If your family wasn’t as dorky as mine and you didn’t get a grow-your-own-crystal kit as a kid here are some cool videos of crystals growing:

http://www.youtube.com/watch?v=DKJmBuh-5eg&feature=related

http://www.youtube.com/watch?v=zwqst0aR8D0&feature=fvw

http://www.youtube.com/watch?v=jrKThzpJ5hQ&feature=related

http://www.youtube.com/watch?v=D9OLLrMLdAU&feature=related

http://www.youtube.com/watch?v=QwiPplYoH7Q

Don’t they even kind of look like they are alive??

For a crystal to grow like this it’s necessary for the environment it’s in to be in a state of super saturation. Super saturation is just when there is more stuff dissolved in a solvent than can usually be dissolved… sugar in water, for example. If you add sugar to water while stirring it will dissolve, of course. But if you keep adding sugar the water will get to a point of saturation where nothing else will dissolve. However, if you heat the solution, then EVEN MORE sugar will dissolve and the water will stay more sugary than it ought to be even after cooling… It’s become super saturated! 

All we need now is a seed- a small crystal from which a large crystal can be grown. Put a little crystal fleck in the solution and in no time you will have grown a dazzling crystal! In a super saturated solution, crystals can be added on faster than they are dissolved away. If your saturation level is high enough you don’t even need a seed crystal. Spontaneous seeding can happen on little flecks of dust or on the surface of its container.

Sometimes, especially if the saturation level is very high and crystals are forming fast, the units will add together in the wrong way. When this happens the resulting crystal bit becomes destabilized and it will dissolve faster, not allowing more crystals to grow on top of it. Or maybe the crystals will add together in a way that strengthens the crystal and allows it to last longer. This “mutation” will then repeat itself because, remember, the next layer is determined by the one that came before it. Ahem…evolution by natural selection much?

But even with perfectly constructed crystals, when the stacks of crystals get too heavy they will break off, exposing both ends for continued growth. The crystals “breed” by breaking up as they grow and providing new seeds for more crystals to grow on. So now we have a mechanisms for crystal birth and mortality!

Ok, but eventually the solution is going to run out of stuff to give, right? The crystals can’t keep growing and reproducing forever because sooner or later everything that was dissolved in the solution will be deposited on the crystal. There will be nothing left to make more crystals from.

This is why we need a continuous crystallizer! A continuous crystallizer is a vessel system that allows for inflows and outflows. It just so happens that the whole earth is a continuous crystallizer for clay materials. The earth makes clay all the time…and lots of it!

I know we probably aren’t used to thinking of clay as a crystal but that’s just because the crystals are so small we can’t see them. Here are some pictures of clay way close up:

This is Smectite

Kaolinite

Dickite...haha. God. What am I, 12?

See how there are tiny uniform units that get repeated and stacked up? That’s the signature of a crystal.

Ok, well this whole analogy is cute and all but it doesn’t change the fact that CLAY ISN’T ALIVE. Our genes aren’t made of crystals…they are made of organic molecules. What gives?

Is it possible that modern organic genes could have evolved from crystal genes?

Cairns-Smith thinks so!

It just so happens that certain organic molecules could be very useful to an evolving crystal organism. Not only that, but clay is very good at holding onto organic molecules. Let’s look at some of the important life molecules and how they could be of use to clay crystals. Amino acids and formic acids could be used to control acidity and promote crystallization in clay. Sugars, like polysaccharides will soften and harden under certain circumstances and could serve to control the sliminess of the clay, which is useful if the survival of the clay crystals depend on not being dried out. Nucleotides could be used to bind clay crystals together in certain ways. Perhaps the very first DNA molecules were constructed to interact with clay and lock the pieces of the crystals together.

Now that we have a mechanisms for all these organic molecules to interact, it’s not so difficult to imagine the organic molecules starting to use each other as templates for reproduction instead of the crystals. DNA-like molecules could have come along to help amino acids join up into chains, all the while being protected and promoted inside the “membrane” of a clay crystal. Sooner or later, cell membranes would have had to evolve to replace the clay cradle and proteins would evolve to aid in the assembly process. All this could have been accomplished with more and more sophisticated crystal growth. Remember, the more well-constructed the crystal, the more likely it is that there will be lots of them.

As organic organisms become the more high-tech and efficient organism, one that can construct itself from air and sunshine, they eventually replaced crystal organisms. This would have happened via genetic takeover.

I found this diagram here. It represents a secondary gene type taking over the original gene type.

Is this what really happened? Was our very first ancestor really clay? Hell if I know. Aren’t there some religious stories about humans being created from clay? That might add a whole layer of beauty and humanity to this theory.

There are certainly criticisms of the clay theory but it seems that most of them have to do with the lack of evidence. Unfortunately, we can’t go back in time and watch as the very first life began to evolve. Life springing from clay has also never been demonstrated in a lab setting. Of course, this whole process of evolution from clay to cells would have taken a VERY long time so perhaps it’s not feasible to recreate it in a lab.

Maybe we’ll never know how life began on this planet. And isn’t that great? In a way? Maybe?

Well that’s enough nerding out for now!

But before I go….

I doubt that anyone really reads my blog this closely but I have a few updates and follow-ups. From my alternate biochemistry blog: I got that book, Extraterrestrials, A Field Guide for Earthlings and it’s AWESOME! Tons of cool pictures and hypothetical aliens! It was definitely worth the one penny I paid for it on Amazon, even worth the $4 of shipping. I recommend it.

From my brain waves blog: my eccentric (in the best way) mother bought herself a Mindflex…remember? That maze toy that you control with your brainwaves? It seems to work! I tested it out by doing math problems while the probe was on my head and I made the ball levitate pretty high. Then while I was zoning out and watching TV the ball would fall down. Maybe it has a delay of a few seconds…but overall, I’m a believer! How cool will it be when we develop technology that is even better at measuring and responding to brain activity so that we can begin to control things exterior to our bodies with nothing but thought? YAY! THE FUTURE! Well, someone’s gotta be jazzed about it, right?

OK see ya next time!

Alternate Biochemistry

This topic was suggested to me by my awesome friend Thaddaeus Buser who is studying marine biology in Alaska.

Cool for four reasons: First of all, Someone reads my blog?! Awesome! Secondly, DUH. Aliens and extremophiles are my favorite thing to nerd out about…of COURSE I want to learn about hypothetical alien biology. Also, right in the middle of my research for this blog THIS hit the news. Relevant. Finally, remember that meatball looking cave alien in Star Trek the original series? That was my favorite alien in all of sci fi! It was called the Horta and a huge theme of that episode was that is was not carbon based, it had alternate biochemistry.

God, and that scene when Spock mind-melds with it and feels all it’s pain and suffering makes me want to cry every time. The only clip of it I could find on youtube has a bunch of fart sounds over it. Way to ruin a beautiful moment of cross-species connection, youtube jackass.

Here it is if you are curious.

But you should probably watch the episode Devil in the Dark sans fart sounds if you haven’t already.

Anyway, I’ll try to break this down with my meager knowledge of biology…

Life (as we know it) requires at least one cell. Cells need four things:

-carbohydrates (provide the cell energy)

-lipids (also called fats. They store energy and make up structures like the cell wall )

-proteins (the machines that do all the work of the cell. They are made up of amino acids, one of which is pictured here. )

-nucleic acids (DNA is a nucleic acid. It’s the master blue print that tells the proteins what to do.)

There is no need to fully understand what those diagrams mean, I certainly don’t. But I do know that the letters stand for elements and I see lots of C’s for carbon.

All four of these things have one element in common: Carbon. It’s what forms their backbones.

There are a few good reasons why life seems to have chosen carbon over any other element.

First of all, carbon’s main gig is forming compounds and carbon is good at what it does.

Here’s why:

Elements can bond with other elements via sharing electrons. All atoms want to have eight electrons in their outer shells and carbon only has four. That means it’s going to want to get close to other atoms and share electrons with them so that everyone has eight.

Having four slots for other atoms to go into makes carbon very versatile. It will bond with all kinds of stuff; hydrogen, oxygen, nitrogen…whatever, it’s not picky.  It helps that carbon is just the right size to nestle into lots of different kinds of molecules without pushing too much stuff out of the way.

Carbon will also readily bond with other carbon atoms to form long chains or rings. The bonds in these structures are strong and stable and carbon atoms can keep being added on to give you as big and complex a molecule as you need. 

This is important because it means we can make lots of different kinds of proteins which have all kinds of different functions. Remember, on the most basic level, proteins are what is doing all the work your body does and proteins with different arrangements of atoms will have different functions.

Here is a cool video I found of proteins doing lots of different jobs. My favorite parts are at 2:48 – 3:09 when they are all forming some kind of chain and then the severing protein comes and breaks it and at 3:41 when the motor protein comes walking by. It really walks along like that!

But seriously, proteins are the reason we can digest food, fight off illnesses, store memories, move our arms and legs…ect. Our body has about 50,000 different kinds all made up of carbons assembled into different combinations.

 And a final reason for basing life on carbon: there’s a lot of it. It’s the fourth most abundant atom in the universe because it’s easily made in the cores of stars.

 Welp, sounds like carbon is the right one for this job. But could any other atoms do the same sorts of things carbon does? Could life be based on something other than carbon?

Silicon might do the trick. Check it out, it’s right there underneath carbon on the periodic table.

 It’s in that spot because they both have 4 valence electrons…4 slots for other atoms to fill, so it will react (form bonds) with lots of the same stuff that carbon reacts with.

Just like carbon, silicon will form long chains with other silicon atoms. These are called silicates (the silicon analogy to carbonates). So a silicon based life form would have proteins that are made up of silicates instead of carbonates.

If silicon were to be the basis for a life form, lots of the molecules we know and love would be changed a little. For example, the carbon reactions take place when humans take in food and air would be silicon reactions. Allow me to explain: chemicals break apart and make new bonds inside our bodies to turn food into energy and air into whatever we get from oxygen (I don’t actually know, will someone tell me?). Our uh, “exhaust” gasses are carbon dioxide (We breathe it out. It’s a carbon and two oxygens: C02) and methane (FARTS. It’s one carbon and four hydrogens: CH4). Silicon can form very similar molecules: Silicon Dioxide (A silicon and two oxygens: SiO2) and Silane (A silicon and four hydrogens: SiH4). If a silicon based life form metabolized in similar ways that we do, by that I mean…eat food (as we know it) and breathe oxygen, then silicon dioxide and siliane would be some of it’s waste products in the same way that carbon dioxide and methane are our waste products.

Silane is what silicon based life forms might theoretically fart out, then. It’s what’s called pyrophoric, which means it will spontaneously burst into flames in the air! Can you imagine if that’s what farts were like??! It would be way harder to get away with, that's for sure. 

Silicon dioxide is what they might exhale. The thing about silicon dioxide, though, is that it’s a solid at earthly temperatures. It’s pretty too! Look:

It’s melting point is at 1,650 degrees Celsius, or 3,000 degrees Fahrenheit…HOT. So, silicon based life would either “exhale” a solid crystal, which might prove to be a bit of a respiratory problem, or maybe they would exist somewhere where the temperature is much hotter so the silicon dioxide could be in gas form. 

Here’s a cool picture of what the authors of the book, Extraterrestrials, A Field Guide For Earthlings thought that silicon based life might look like.

There are lots of used copies of this book on Amazon for a penny. I ordered one just cause I’m hoping it has lots of cool pictures. I’ll let you know if it’s worth the penny.

Following the reasoning that life is all about having four bonds, every element that is in the same column as carbon could theoretically be a basis for life.

However, there are some pretty serious problems with some of them.

Germanium, being the next one down, is a good place to start. Germanium COULD, theoretically, act like carbon. By that I mean, there is a germanium analogy to methane and carbon dioxide (germane and germanium dioxide), and germanium can also form long chains with itself. The pitfall is that germanium is RARE. Which makes sense, I mean…I never hear about germanium in anything, do you? This poses a problem because life needs LOTS of atoms. The likelihood of enough germanium atoms being in one place at one time to assemble into a cell, let alone a creature with trillions of cells, is pretty small.

However, germanium based life might be possible in the future! Heavy elements are fused in the cores of stars. As more and more stars die and new ones are born, the universe is getting more and more metallic. Maybe someday there will be enough germanium around to base life on it. Maybe life will slowly evolve to be based on heavier and heavier elements! Or maybe, due to the present state of the universe, we are in an era of life that will never occur again. Who knows?   

The next ones down the column: tin, lead and ununquadium (yes, that’s it’s name!) have the same abundance problems as germanium. There just isn’t that much of them around. Also, it’s hard to imagine how a life form based on such bulky elements would get around. I mean, think about being made of tin or lead…it would pose a pretty serious moving problem, wouldn’t it? I would think it would require lots of energy to move your body because it would be very heavy. Sounds like a pretty inefficient life form to me.

It has also been suggested that life could be based on nitrogen or phosphorus because these two atoms have the tendency to form long chains just like carbon. I couldn’t find out as much about these elements as a basis of life. The fact that no one has really done any google-able research on it makes me think that it’s probably not very likely, but I would love to hear about it from someone who knows more about biochemistry than me.

All in all, carbon seems to be the atom best suited for life, so it’s really no surprise that all the life we have ever heard of is carbon-based. Furthermore, it’s quite likely that carbon is the only element that can fill this role. I’ve heard people argue that it’s arrogant to assume that all life in the universe must be similar to life on Earth, but I really hate that argument. Here’s why: if we don’t make that assumption then we really don’t have much to go on. What are we supposed to be looking for if not what we know works? Perhaps life could be totally different than us elsewhere in the universe, but how would we recognize it if we saw it? And if we are going to make the argument that the basic chemicals of life are unnecessary, why not make the argument that most things attributed to life as we know it are unnecessary? For example, why should life require cells? I mean, when you think about it…our definition of “life” is pretty vague and sticky. Anything that is able to create offspring that are slightly mutated in order to better survive its' environment counts. Or more specifically, anything that evolves via natural selection. Using that definition of life, is a computer virus life? It certainly mutates and evolves. Is a crystal life? It grows and “reproduces” with altered offspring.

Life, it’s nature, it’s origin…everything about it, is obviously a major source of contention amongst the human race. I think religion is probably the most poignant example I can give here. But whatever you believe, I think it’s safe to say that no one understands life completely. All we can really do is speculate. Which is awesome because it’s a great chance to use those wonderful imaginations we’ve been blessed with!

Ok, well that’s enough nerding out for now. See you next time!

Cosmic Rays

Did you know that you are getting showered by particles as you read this? Even if you are inside…even if you are hundreds of feet underground!

Violent events in outer space (super novae, storms on the sun…ect) are constantly sending high energy particles into our neck of the galaxy. Sometimes they even come from outside of our galaxy.

Here’s what happens: a really speedy proton will come zooming in from an explosion in a distant part of space and reach our atmosphere. Our atmosphere has LOTS of stuff in it. Chances are pretty high that this proton is going to slam into one of those nitrogens or oxygens that we have hanging out up there. When this collision takes place some crazy stuff happens…

When a high-energy proton from outer space runs into an atmospheric molecule it creates a shower of secondary particles.

Turns out that if you want to know what something is all about, what you have to do is pummel it. Pummel the nucleus of an atmospheric molecule with a high energy proton and it will release all kinds of things that it’s been holding onto.

This is a diagram of the collision:

    

 See the things labeled with the pi symbol? Those are pions! They were a big freakin deal when they were discovered because they had actually been predicted a decade earlier by Japanese physicist Hideki Yukawa.

The reason why Yukawa thought these things needed to exist is because he was running with the idea that every force has a particle associated with it. There are four fundamental forces in nature: Gravity, the electromagnetic force, the nuclear strong force, and the nuclear weak force.  The nuclear strong force is the one that we care about here.

Here’s a run down on the nuclear strong force: We know that like charges repel each other, so protons are not going to want to live next to each other. YET, they do! They are tucked in very close together in the nucleus of atoms. So there must be an entirely different force holding them together that overcomes this electrostatic repulsion force. This is the nuclear strong force.

Yukawa argued that pions are the particle associated with the nuclear strong force. Since every particle can be modeled as a wave (wave-particle duality, heard of it?), and since pions have a wavelength that acts within the teeny dimensions of an atomic nucleus, and the wavelength of a particle depends on the mass of a particle… he was able to accurately predict the mass of the undiscovered particle! Bet he felt cool when a particle of exactly that mass was found 10 years later.

Ok, SO… pions are created in the upper atmosphere after protons from outer space disturb the nuclear force field of an atom in the atmosphere by smashing into it. But pions are very unstable and they decay within a tiny fraction of a second into other particles called muons and neutrinos. Then the muons decay into an electron (or a positron) and neutrinos. Here is a picture of it happening in a lab:

This is a particle explosion inside of a streamer chamber. All this chamber is doing is recording the tracks of charged particles as they move along. The scientists who took this picture launched a positively charged particle in from the left and watched as it collided with a neon atom. The starburst in the middle is where the neon atom released a bunch of pions because its nuclear force field was disturbed.

My favorite is the positively charged pion that sweeps up counter clockwise because we get to watch it decay into a muon. The muon is the one that makes the big spiral. When it got to the middle of the spiral, you can see that the path breaks off because the muon decayed into even smaller particles. Since it was a positively charged muon, it decayed into a positron (the anti-matter twin of the electron, it's labeled e+) which went off to the right, and a neutrino which went off somewhere unrecorded by the streamer chamber because neutrinos don’t have a charge.

So this is what is happening a few miles above our heads. (Except for the spiral pattern…that only happens because of the magnetic field inside of the streamer chamber, in the atmosphere these things go in straight paths).  But you get the jist… particles are careening in from space and smashing our atmospheric atoms into little bits and these little bits quickly decay into other little bits that rain down on us.

Muons are the evidence of cosmic rays that we detect down here near sea level. You can think of them as big fat electrons because they have electron charge and are about 207 times the mass of an electron.

I really like muons because I’ve spent a lot of time with them. Two years ago I did this experiment for a physics lab class at WWU where we (my lab partner and I) were trying to measure the lifetime of a muon. This was our apparatus:

And this is a schematic of what it looks like inside of that big shiny tube and in the box under the computer that says Muon Physics.

Inside of the aluminum tube is a scintillator and a photomultiplier tube (that’s the thing that says PMT). The muons come in and hit the scintillator, which is just a luminescent material that converts the energy of the muon into light. The photomultiplier amplifies that light and sends the signal off to the rest of the stuff that I don’t really care about.

All I know is that the first signal (a muon hitting the scinitillator) will start a timer, if a second signal occurs within 20 micro seconds, then we know that the muon that hit the scintillator also decayed in the scintillator. This is what we want! Both of those flashes are sent off to the read out software on the laptop and the time between when they occurred is measured. This is the lifetime of the muon. Zing!

If you look at what you are getting from the photomultiplier tube with an oscilloscope it might look like this:

The first blip is the muon hitting the scintillator and the second blip is the muon decaying.

Do this enough and you can find the average life time of a muon. It works out to be something like 2 microseconds (split a second into a million pieces and take two of those pieces…pretty short). It’s an easy experiment!

Using this lifetime and some assumptions, we can figure out how many muons should be able to make it from their birth place in the upper atmosphere to sea level. We can do this because we know how fast the muons are traveling. We know how fast they are traveling because we know how far a charged particle of a given mass and speed can go through matter. We know the mass, we know how far it goes through the scintillator…we’re in good shape. We found that muons have speeds of .9950-.9954 the speed of light. In case you don’t know…light is really fast! 99% of the speed of light is haulin ass.

But here’s the catch: the lifetime of a muon is so short that they don’t have time to make it from the upper atmosphere to the surface of the earth before they decay…even if they are traveling at the speed of light. BUT they DO make it to Earth. Lot’s of muons make it to sea level. A muon goes through an area the size of my finger nail every minute. Sit still long enough and thousands of muons will go through you.

So they don’t have time to make it to earth, but they do… How are they doing this?

This is Einstein’s theory of relativity at work. Because the muons are traveling so fast, they are experiencing time at a slower rate then we are. This is called time dilation. It’s where the fast moving clock runs slower. If you had two clocks that were perfectly synched up and then accelerated one of them to near light speed and let it cruise around for a while, when it comes back to earth you would find that years have passed on the stationary clock while only a few minutes have passed on the moving clock. This happens in Planet of the Apes, remember?  

I like to talk about the muon time dilation experiment because I get the feeling there are lots people that think relativity is just some hypothetical, unsubstantiated, frou frou, magic, pretend physics. But no, it’s not. Time dilation happens and the fact that so many muons make it to earth is proof. I think people have a hard time relating to it because relativity only really matters when you are traveling at speeds close to the speed of light. We can’t speed ourselves up to a significant fraction of the speed of light, we are too massive. It’s pretty easy to accelerate a dainty little thing like a muon to near light speed, however. Therefore it’s pretty easy for them to experience time dilation. And they do!

In fact, if you divide the observed muon lifetime by the lifetime we think we should be observing if there were no effects due to time dilation, you get 1/9. This means that muons are keeping time at 1/9 the rate that we are. Nine years in your life is one year in a muon’s life.  Neat, huh?

Other cool things about muons:

You can do astronomy with muons! Remember, they are the grandchildren of a short fling between an extraterrestrial proton and an atmospheric atom. If you trace back the trajectory of these incoming muons you can figure out where these high energy proton grandparents came from in the first place. Turns out lots of them are coming from the direction of a cluster of galaxies in the constellation Virgo. Inside this cluster is a giant galaxy called M87 which is believed to have a super massive black hole at its center. 

You can even see the shadow of the moon in muons!  

Also, muons can cause lightning! As they are making their trek from their birthplace in the upper atmosphere to the surface of the earth they strip away electrons from atoms in the lower atmosphere. This creates a separation of charge and thus, a strong electric field. When the field strength becomes too high, a discharge occurs. This is lightning!

Well, that’s enough nerding out for now. See ya next time!

Brain Waves

After thinking up that brain alien at the end of my Europa blog, I realized I really have no idea what brain waves are all about.  So this is me finding out what I can about them!

The wordnet definition is: “rapid fluxuations of voltage between parts of the cerebral cortex that are detectable with an electroencephalograph”

Holy crap, so many questions need to be answered about that statement.

Ok, first of all. What is the cerebral cortex?

Turns out it’s the biggest part of your brain. It’s all the wrinkly stuff I think about when I think about brains. Actually, it’s a 2mm layer of gray matter that covers the outside of your cerebrum, the walnut-looking part of the brain, shown below.

Peduncle?! Really?
That's the cutest word I have ever heard. 

The cortex is made up of neurons and glial cells. Glial is greek for glue, this is the stuff that is sticking it all together and maintaining the structure of the cortex, it’s good stuff but the neurons are the important part for brain waves. They are cells that use electricity to get shit done.

I really like to imagine neurons as little tiny Electros from Spiderman. Try it, it’s way funnier than reality:

http://www.youtube.com/watch?v=gjAbg9tmKAE&feature=fvst

Anyway, here’s what they really look like:

They kind of look like Electro

 And here’s a diagram of what you are looking at in the above picture:

All neurons have these basic parts but the shape, size and characteristics will vary depending on what type of neuron it is.

There are three types of neurons

-Sensory neurons: these are the ones that are responsible for basically everything we experience in the physical world. Pain, heat, cold, taste, touch, sound, vision, smell…any way you can physically experience the universe is totally up to the sensory neurons.  

The dendrites (little spider leggy things) of the sensory neurons in your tongue, for example, gather information from either chemical interactions (how food is reacting with your taste buds) or physical processes (you bite your tongue and the pressure in the tissue activates the neuron). Neurons take whatever information the world gives them and convert it to an electrical signal that shoots out through the axon and is transmitted to the spinal cord and on to the brain.

Aside: I just found out that the pain signal is transmitted to four different areas of the brain in order to sort this experience and compare it with other experiences. IE: Have I bit my tongue before? Is this time worse?

One of the areas that is put in charge of sorting this stuff out is the limbic system which is the emotional center of the brain. That’s way pain can make us cry!

Anyway, sensory neurons are the reason we can relate to the world outside of our bodies. SO FREAKING COOL. Can you imagine, if a person’s sensory neurons were wired just slightly different from everyone else’s, the entire world might smell like chicken? Or what they interpret as green might be what I see as pink. And who is to say that doesn’t already happen? I could turn this into a real stoner blog about reality and authentic experiences but I think I’ll leave it at that.

However, I will throw in the interesting fact that there are neuroscientists that believe diseases like schizophrenia, a mental disease that makes it difficult to tell the difference between real and unreal experiences, has lots to do with how the sensory nerves are wired. We have no idea what really causes schizophrenia but it’s definitely an interesting theory.

Anyway, long story short: our entire perception of reality is balancing on the electrical activity of our sensory nerves. This deserves it’s own blog. Maybe I’ll get to that someday.

OK…back to the different types of neurons and then hopefully back to brain waves!

Motor neurons transmit impulses from the central nervous system to our muscles and glands. These are the the middle management types underneath the brain who are telling your body to move. The motor pathway is your spine. That’s why spine injuries can paralyze you: motor neurons no longer have a way to communicate with your arms and legs.

Interneurons are pretty much what they sound like. They translate certain information from the sensory neurons to the motor neurons. Sounds like a lame job, but it's an important one. There is so much sensory information constantly bombarding us, the interneurons are the ones that decide what is going to get paid attention to and we are going to act on. 

So, from what I gather it goes like this:

1.)  Slam your fingers in the door

2.)  Sensory neurons tell interneurons about the change in tissue pressure that you are experiencing

3.)  Interneurons tell your brain and motor neurons about the sensory neurons’ message. Sometimes the brain can be passed up entirely and motor neurons will fire without permission from the boss. These are called reflexes.

4.)  Motor neurons stimulate your muscles to make you physically react to the pain- ie: get your fingers out of the door, scream…ect.

All of the communication that gets done is via electricity, the language of the nervous system.

This four step process goes for every experience, smell, sight….ect, it’s just that pain is the easiest for me to understand because the cause and effect chain seems much more direct. The intricate processes that go along with what your brain tells your body to do based on what you see or hear or smell are way more complicated.

Ok, so now that we know a little about neurons…what do these have to do with brain waves?

Well, as should be obvious, your brain is constantly responding to millions of bits of sensory information. As you are reading these words, sensory neurons are transmitting the light that reaches your eyes into electrical impulses that your brain interprets as written words, the same goes for the feeling of the chair you are sitting on, the smell of the room, the taste of the inside of your mouth, and all the noises around you. With all these neurons firing at different times and places, your brain is FULL of electrical activity constantly.

What’s surprising to me is that some of this electrical activity is periodic. By that I mean, it repeats itself in a predictable pattern. Every certain amount of time there will be a spike in electric potential.

What is electric potential?

Perhaps some of you have seen those gadgets that measure the how good a battery is? They are called voltmeters and are used to determine the electric potential difference between the positive and negative terminals. A greater potential difference between the two terminals means a more charged battery.

What’s happening inside the brain is that there will be a large separation of positive and negative charge caused by brain cells allowing sodium ions to enter their membranes. Since ions have charge, this creates a high potential difference, then suddenly a discharge of ions which lowers the potential difference. This “action potential” gets propagated throughout the brain and happens again and again in several different brain cells.

That’s all I could really find out about the cellular mechanism of action potentials without delving into journals with too much jargon for me to read. If anyone has a better understanding of the action potential and can explain it to me, please do!

Anyway, regardless of exactly why it happens, a graph of this electric potential activity might look something like this:

The y axis is volts (how strong of a battery your brain is) and the x axis is time.

Neuroscientists have classified the different types of brain waves based on how often the spikes occur, this is called the frequency of the waves.

Each unique frequency is associated with a different type of thought process.

Delta waves are the slowest ones, 1 to 4 pulses per second. We emit them when we are deep in dreamless sleep.

Theta waves are of frequencies around 4 to 7 pulses per second and they are associated with reduced consciousness. You might emit theta waves when you are day dreaming. If you are walking around or driving and suddenly realize that you can’t recall the last few minutes…you were probably emitting lots of theta waves. We also emit lots of theta waves when we are doing repetitive tasks.

Alpha waves, which are characterized by frequencies of 7 to 13 pulses per second are associated with mental relaxation. Someone emitting alpha waves is aware of their surroundings but not really concentrating on anything in particular. We probably emit alpha waves while we watch tv.

Beta waves have the highest frequency in the above graph and they are associated with concentration and problem solving.

There are even higher frequency brain waves called gamma waves that come out when a thinker is involved in cross-modal sensory processing. Meaning, they are combining information from two different senses like sight and sound.

When we are sleeping our brain waves sink to lower and lower frequencies; from beta to alpha to theta and finally to delta waves. When we wake up, the process is reversed.

People that hit snooze over and over go through this entire cycle several times every morning. It’s possible for people who do this to stay in the theta state for an extended period. Apparently, this can be a very productive and creative time where the snoozer has a free flow of ideas, memories, and plans. SO THERE, ex’s who got mad at me for hitting snooze 5 times in a row…my brain was doing good things! I definitely have the weirdest dreams during my snooze hour. 

Well, this is all fine and good but let's get to the real question, how can we use brain waves in a capitalistic society?

Turns out, there are lots of toys that have to do with brain waves!

I was working as a math tutor for this kid whose parents bought him this thing:

Jedi Trainer

It measures your beta waves. If they strong enough, a fan will be activated under the ball and the ball levitates. This kid had practiced a lot and could levitate the ball. I was really curious about it so I had him try it while I distracted him by clapping and yelling his name right next to him. He couldn’t levitate it while I was doing that. He also couldn’t get it to levitate while he was watching tv. I tried it for a while and couldn’t get it to work. He was telling me I needed to focus on one part of the ball and think about it really hard. Couldn’t do it. Guess I’ll never be a jedi L

This one is pretty cool...Check it:

Mind Flex

The Robert Schneider from Apples in Stereo did some electric engineering magic to turn one of these into a synthesizer. Check it:

http://www.wired.com/underwire/2010/10/robert-schneider-teletron/

I am very suspicious of this. What you would have to be doing in order to change the frequency of your brainwaves is descending from a state of deep concentration to a state of day dreaming. You couldn’t do this by concentrating on making a pitch go up or down because concentration in general is associated with one type of brain wave, beta. Beta waves aren’t going to change depending on what you are concentrating on, just whether or not you are concentrating.

 So if he’s really doing what he says he is doing and controlling his brain wave frequency, then when he is pointing down he must be concentrating less and when he’s pointing up he must be concentrating more. But it wouldn’t work if he were concentrating on making the pitch go up and then concentrating on making the pitch go down because in both cases he would be concentrating. Make sense?

Anyway, if he really is doing what he is saying and controlling the synthesizer with his mind, then he is very good at going from concentration to day dreaming just like that. 

Either way, if you don’t already love Apples in Stereo you should probably go download their album New Magnetic Wonder and surrender to an hour of pure pop bliss. They are fantastic.

You know who would have a hard time playing with any of those toys? ADHD patients. People with ADHD show a beta wave deficiency.  NASA psychologist Alan Pope has actually done research on video games that might treat ADHD.  An ADHD kid will have an electroencephalogram (electro-IN-seff-el-o-gram) probe on their head to measure the frequency of their brain waves. The joystick that controls the game will work better if kids can produce higher frequency brain waves, ie: more beta waves.  So kids can play their favorite game and learn how to pay attention at the same time.

Pretty cool!

When my electrical engineer dad was in college his senior project involved brain waves. In preparation for this blog, I asked him about it and this is what he said:

Hi Val,

Yes, my senior project at Virginia Tech, back in 1978, was to design an EEG Telemetry device. The unit I designed accepts the output from up to 20 EEG (Electroencephalography) electrodes (typically at ~10 microvolt levels, 0 - 1000 Hz). These signals were amplified by high-gain differential amplifiers, and then used to modulate 20 Intermediate Frequency subcarriers, then placed on a frequency modulated (FM) 100 MHz RF carrier, thus allowing the signal to be transmitted wirelessly on the commercial FM radio band. The purpose of this unit would be for use in emergency situations, for example head injuries, where the EMT's on-scene could attach the probes, and transmit the EEG to a doctor in the hospital, where he could begin his diagnosis before the patient is delivered to the hospital. We had plans to test the operation of this unit on a cat, but did not get that far with the testing.

My design was entirely analog, as that was the only technology readily available at that time (1978). Digital processes / electronics and wireless communication technology have come a long way since then. These days, this type of instrumentation almost always digitizes the signals fairly early in the signal chain. Then there are many more options for channelizing and transmitting the data.

As far as what information about brain activity can actually be derived from brain waves (EEG) -- sorry to say, I am not much of an expert on that, but I'm sure there is lots of info out on the web about that.

Love,

Dad

It’s probably not good to post someone’s private emails without their consent but I’m pretty sure my dad isn’t going to sue me, he sounds smart anyway.

Obviously, this thing never got built. But if it did I wonder how useful it would be. I’m not sure how much about a person’s state of being we can really interpret from the waveform of action potentials in their brain besides whether or not they are concentrating.

How freaky would it be if we could tell exactly what someone was thinking by analyzing their brain waves? Sounds like an Asimov story. 

Well, there is clearly lots I still don’t know about the mechanisms of the brain.

The brain is intricate and invaluably crucial, definitely the most important organ. But what is it that is telling us that the brain is the most important organ? Oh yeah! The brain! Self preserving propaganda? 

Read Tom Robbins, Even Cowgirls Get the Blues for the full philosophical rant on this one.

And while you are at it, if anyone can tell me why cats seem to be the popular animal of choice for brain wave experimentation, I would be interested in knowing!

Well, I think that’s enough nerding out for now! See you next time.  

Europa

As promised in my extremophiles blog, here is the Europa blog you’ve been waiting anxiously for.

What is Europa?

It’s a moon of Jupiter!

Europa is one of the (at least) 63 natural satellites of Jupiter. Galileo spotted it through his telescope in 1609 and you can see it too if you look at Jupiter through a telescope. Here’s what you might see:

That’s Jupiter and the three other Galilean satellites: Io, Ganymede, and Callisto. These are the big ones, some of them are even bigger than planets in our solar system.

Europa is about the size of our moon which makes it bigger than Pluto and about 70% of the size of Mercury. Not too big but still, it’s got lots going for it.

I’ll tell you straight up, the reason I like Europa so much is because it’s the best candidate for life (as we know it) in the solar system. Check out the close-up:

See the cracked blue surface? That’s ice. Water ice! It’s been hypothesized that underneath the icy crust, there is a wide spread liquid ocean warmed by volcanic vents. On Earth there are entire communities of species that thrive near ocean-floor hydrothermal vents. It’s entirely possible that the same thing is going on under Europa’s ocean.

Ok, but why do we think there is an ocean?

First of all, there is lots of evidence that Europa is resurfacing.  IE: water is seeping up through those cracks and freezing on the surface.

For instance, compare Europa to our moon:

See all the holes and dents? Those are craters from meteor impacts. Europa should look like that too as it is just as likely to get hit by space stuff as the moon. Even more likely, in fact, because it’s next to Jupiter which is so massive that it sucks lots of passer-byers into it’s orbit. The fact that it doesn’t look all pock marked is evidence that the surface is relatively new. The craters have been washed away.

Want some more evidence for resurfacing? Ok, well…Europa has a much higher albedo than the other icey moons around it. That’s science talk for it’s much shinier. Ice darkens in space over time. It shouldn’t be that shiny unless the ice is new.

What other evidence is there for an ocean?

Europa has a significant magnetic field. You don’t get one of those unless you have an electrically conducting liquid on the inside. Earth’s magnetic field comes from our molten iron core. It’s possible that Europa’s magnetic field is caused by a very salty ocean, with the ions from the salts providing the conductivity. Either that or it’s got a molten core…also good for the case of an ocean warmed by under sea volcanoes.

We can get clues about Europa’s interior structure based on what kinds of chemicals are present on the surface.

How do we know what chemicals are present on the surface?

Well, every element has a certain “finger print”. You can tell what you are looking at based on it’s emission spectra, the light it’s giving off, basically. This has to do with the way the electrons lose energy and eject a photon on their way down to a lower energy state. I talked about this a little bit in my transparent aluminum blog.  The amount of energy that an electron loses as it falls back down to a ground state is exactly the energy of the photon it ejects. The energy of a photon is what determines its wavelength. Each element emits a combination of different wavelengths that is completely unique. This is because each element has a distinct electron configuration.

So the moral of the story is: want to know what your looking at? Look at the wavelengths it emits or absorbs.

Here is the emission spectra of Neon, to give you an idea:

This is the combination of colors (wavelengths) you are looking at when you see a Neon sign. Overall, it will look red due to the domination of red wavelengths. If you see a sign that is not red, it’s got a different inert gas in it but we still call them Neon signs for some reason. Argon and Xenon make blue, Krypton is white, Helium is purple.

Anyway, now that y’all know how it works…using spectral analysis, we’ve found carbonates and sulfates (both salts) on the surface of Europa. The saltiest areas are the also the ones that appear the freshest. I’ll spell it out for the dummies: salt water seeped out of the cracks and refroze into these fresh spots! Well, it’s possible anyway.

Hey, wait a sec…did I say carbonates? Carbon! The basic building block for life (as we know it) is present in abundance on Europa. That. Is. Rad.

So, what kind of life would we find on Europa?

Well, it couldn’t depend on photosynthesis because it’s way too far from the sun – plants just won’t grow there. Chemosynthesis would have to be how life gets by. This is a process of producing energy utilized by several organisms living near hydrothermal vents on the bottom of Earth’s ocean. Basically, biomass gets created from the oxidation of the chemicals spewing up from the volcanic vents. It’s a way of getting energy that has nothing to do with the sun.

Bill Nye named chemosynthesis as one of the 100 greatest scientific discoveries of all time. Probably because up until the 70s we had no idea that life could exist that didn’t depend on photosynthesis. I mean, when you think about it…EVERYTHING lives because of the sun. Meat eaters eat animals that eat plants that photosynthesize due to sunlight. All the food chains we knew about begin with photosysthesis. When scientists first discovered all the life on the bottom of the ocean that is surviving independent of the sun, it was a total shit show.

Aside from chemosynthesizing, Europan life would also have to be mobile. Since volcanic vents don’t last forever, they would need to be able to migrate from vent to vent. 

We might get a clue for what kind of life could exist on Europa by studying Lake Vostok, a huge fresh water lake underneath 13,000 ft of ice in Antarctica. This lake has been completely untouched for 5 million years, so whatever life might exist down there has evolved independently of everything outside of it. But before we drill into it and check out what kinds of creatures are down there, we need to get to work on developing ultraclean technology so we don’t contaminate the unspoiled, ancient ecosystem.

Maybe once we have that ultraclean technology we can take it to Europa!  Probably not anytime soon though... proposed missions to Europa have been haunted by budget cuts and pushed so far into the future that it seems unlikely that we’ll ever get there. I guess it’s way more important to spend money on war.

Anyway, if we did send a probe to Europa, here’s what some artist thought it might look like:

But I like to think it would look like this:

I labeled things for the people who aren’t able to correctly interpret my breath-taking artistic abilities. The blue things living near the volcanic vents are the central nervous systems of a chemosynthesizing species I have conceptualized. They are basically soft brain matter protected by a shell. They communicate with the detached, moving parts of their body via brain waves. The moving parts swim around swiftly by moving their flagella and bat-like wing-fins. The central nervous systems are capable of modulating the brain waveforms to give the detached body parts any order. It’s similar to the way our brains tell our arms and legs to walk or dance or kick, except it’s a signal that is transmitted through the water rather than being directly connected to the brain by a nervous system. The part of the detached body that receives the brain wave signal is shaped like a star.

There is also a predatory species that grows downward from the bottom of the ice. These predators look like long tentacles and are able to control their interior pressure to create dramatic pressure differences between the outside and inside of their bodies. They can create near-vacuum inside of their bodies and suck in whatever unfortunate Europan creature happens to be swimming by. They digest by putting their captured prey under high pressure and squeezing out all nutrient-rich liquids. Their waste products are what the brain species mold their protective shells from (after super-heating by the volcanoes and reforming).

The brain species are a highly intelligent and sensitive life form. They are able to interpret brain waves of not only themselves but of any other species. As an artifact of what is basically telepathic communication, they are capable of deeply understanding the needs and desires of other living creatures.  They have lots of valuable wisdom to share with the universe.