Monday, December 27, 2010

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:

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


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!

Sunday, December 5, 2010

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!