Friday, March 15, 2013

An Atom In The Universe

Re-Posted from:

By Ethan Siegel

“The atoms come into my brain, dance a dance, and then go out – there are always new atoms, but always doing the same dance, remembering what the dance was yesterday.” -Richard Feynman

Here you are, a human being, a grand Universe of atoms that have organized themselves into simple monomers, assembled together into giant macromolecules, which in turn comprise the organelles that make up your cells. And here you are, a collection of around 75 trillion specialized cells, organized in such a way as to make up you.

But at your core, you are still just atoms. A mind-bogglingly large number of atoms — some 1028 of them — but atoms nonetheless.

Those two things — you and an atom — may seem so different in scale and size that it’s hard to wrap your head around. Here’s a fun way to think about atoms: if you broke down a human being into all the atoms that make you up, there are about as many atoms that make up you (~1028) as there are “a-human’s-worth-of-atoms” to make up the entire Solar System!

All the matter in the Solar System, all summed together, contains about 1057 atoms, or 1029 human-beings-worth of atoms. So an atom, compared to you, is as tiny as you are in comparison to the entire Solar System, combined.

But that’s just for perspective. The 1028 atoms that are existing-as-you-right-now each have their own story stretching back to the very birth of the Universe. Each one has its own story, and so today I bring you the story of just one atom in the Universe.

There was a time in the distant past — some 13.7 billion years ago — when there were no atoms. Yes, the energy was all there, but it was far too hot and too dense to have even a single atom. Imagine all the matter in the entire Universe, some 1091 particles, in a volume of space about equal to that of a single, giant star.

The whole Universe, compressed into a volume of space that one large star takes up.

Yes, back then it was too hot to have any atoms at all. But the Universe didn’t stay that way for long: it may have been incredibly hot and dense, but it was expanding and cooling incredibly rapidly back then. After less than a second, the quarks and gluons had condensed into stable protons and neutrons, the building blocks of all atomic nuclei.

The atom we’re thinking of started out as a neutron. Protons tried to fuse with it to create deuterium, but the Universe was too hot for that to happen, and each time it formed deuterium, it was blasted apart less than a nanosecond later.

After about three minutes, a few of the neutrons had decayed into protons, but this one remained, and finally the Universe had cooled enough so that nuclear fusion could proceed. The neutron quickly formed deuterium, then Helium-3, and finally found another deuteron to become a Helium-4 nucleus. Only about 8% of the atoms in the Universe became Helium-4 like this one; the other 92% were just plain old protons, also known as Hydrogen nuclei.

It took another 380,000 years for the Universe to cool enough for this to become a neutral atom, and for two electrons to join this nucleus. The Universe — despite its rapid expansion and cooling — remains 100% ionized until the temperature drops to just a few thousands of degrees, which simply takes that much time.

Over the next hundred-million years or so, this atom found itself caught up in the gravitational pull of the Universe, which began to form stars and galaxies. But the vast majority of atoms — more than 95% — weren’t a part of the first generation of stars, and neither was this one in particular.

Instead, when the first stars formed, they kicked the electrons out of the atoms that surrounded them, creating ions once again.

It was only by luck that this atom we’re following wound up in a dense molecular cloud, shielded from this radiation. After more than a billion years in this collection of neutral atoms, it finally found itself pulled in by gravitational attraction to what would become a giant star.

This atom lost its electrons and fell to the core of the star, where it lay dormant for millions of years, as hydrogen nuclei fused into other helium nuclei just like this one. When the core ran out of hydrogen fuel, helium fusion began, and our atom fused with two others to become a carbon nucleus!

While other atoms even closer to the center of the star fused further, carbon was as far as this particular atom went. When the core of the star collapsed and the star went supernova, our atom was blown out into the interstellar medium, where it resided for billions of years.

While billions of other stars went through the life-and-death cycle, this carbon atom remained in interstellar space, eventually picking up six electrons to become neutral. It found its way into a gravitational collection of neutral gas, and cooled, eventually getting sucked in to another gravitational perturbation, as star-formation happened all over again.

This time, the atom didn’t find its way into the central star of its system, but rather into the dusty disk that surrounded it. Over time, the disk separated into planetoids and planetesimals, and this atom found itself aboard one of those.

It first joined together with four hydrogen atoms, becoming methane, and went through millions of different chemical reactions over time.

After life took hold on Earth, it became a part of a bacterium’s DNA, then a part of a plant’s cell wall, and eventually became part of a complex organism that would find itself consumed by you.

The atom is currently in a red blood cell of yours, where it will remain for a total of about 120 days, until the cell is destroyed and replaced by a different one.

Although the cell — and all cells in your body — will be destroyed and replaced, you will remain the same person you are, and the atom will simply take on a different function, whether in your body or out of it. The atoms in your body are temporary, and can all be replaced — unnoticed by you — by another of the same type.

And each of the 1028 atoms in your body has a story as spectacular and unique as this one! As Feynman famously said,

“I / a Universe of atoms / an atom in the Universe.”

The story of the Universe is inside every atom in your body, each and every one. And after 13.7 billion years, 10,000,000,000,000,000,000,000,000,000 of them have come together, and that’s you. The Universe is inside of you, as surely as you’re inside the Universe.

You, a Universe of atoms, an atom in this Universe.

Wednesday, March 06, 2013

A Sample Size Of One and The Search For Life (part 4)

In September 2011, researchers with the Oscillation Project with Emulsion-tRacking Apparatus or OPERA for short, reported an astonishing observation. They saw what they believed to be particles, muon neutrinos, travelling faster than the speed of light! This was startling because nothing, not even muon neutrinos, are allowed to travel that fast. Even before attempts to repeat the observations were conducted, the findings were met with criticism and skepticism, even from within the ranks of the researchers themselves! Five months later, they found the cause of the anomaly; a loose fiber optics cable. Repeated experiments with the same equipment, and around the world, failed to find any faster-than-light traveling by anything.

Why did the researchers doubt their own eyes? Why were the most vocal critics of the finding those who found it? Because the Universe and everything in it must abide by laws; laws that were elucidated by asking deep, probing questions to discover how the Universe works. They are powerfully explanatory. You had better make damn sure you know what you are talking about before you propose changing them because without them, it would be hopeless to discover anything about ourselves or our place in the Cosmos.

Life too must adhere to the laws of this Universe --chemical and physical-- and it’s those laws that place real limits on what’s possible and what’s impossible. For example; we know that life must be bounded; made of cells. How can we know this? Everything --the stars, planets, you-- are all made of the same chemical  stuff. Life itself is the emerging property of complex chemistry. That chemistry must exist in sufficient concentrations to allow for reactions fast enough to interact and integrate  with other reactions and to changing external conditions. Unbounded chemicals diffuse, lowering their local concentrations, which slows their rates of reactions until eventually they go so slow that they essentially stop. Life everywhere must be packed inside of cells.

We can also say something about what those cells will look like; for example, their size is not limitless. There can be no single celled organisms the size of cities. Giant blob-like creatures are not permitted in this Universe. Why? Life everywhere is an open system. Closed systems run in one direction only; towards equilibrium (2nd law of thermodynamics). Once there, chemical reactions stop. Living systems are constantly in a state of disequilibrium, powered by a constant inflow of new material and energy (negative entropy). This requires a boundary that is capable of being selectively permeable and has enough rate of exchange to keep the internal chemistry at disequilibrium. Since surface area increases at a slower rate than the volume, cells larger than a critical size would effectively be “closed”. The cellular material would be used up faster than it could be replaced and the system would eventually stop running. This fact explains why elephants and fruit flies are made of cells that are the same size. Large organisms are not made of large cells. Cell size is limited by law.

Given that life is chemistry of encoded genetic information, storing, replicating and passing on error-prone protein building instructions generation after generation encased in a selectively permeable membrane of relatively small size, and given that life's chemistry requires a liquid medium of water to run, we can begin to strategize where to look. Follow the water used to mean looking only in the Goldilocks zone of planetary systems --not to far from a Sun, not too close, just right for liquid water to be present. But now we know that liquid water can exist almost anywhere in a solar system. For example, the distant moons Europa and Enceladus, under the tidal forces of their large host planets (Jupiter and Saturn respectively), can generate enough geothermal energy to have liquid water at remote distances from the Sun. 

Once we locate the water, what kind of life can we expect to find there? Worms? Jellyfish? Algae? People? Ironically, the start of life is the easiest to predict. The first cells were likely simple. Very similar to our bacteria. But from here, any resemblance to life on this planet is pure speculation. There is simply no way to predict beyond that first instance of life what will follow. Even the history of life on this planet is not repeatable. If you rolled back the clock  to the first cell, and let Natural Selection play out all over again anew, none of the organisms you recognize now would reappear; including us. Natural Selection is not goal oriented. It does not direct the future course of change. It only acts on random variations that appear in a population. But those alien life forms would be running virtually identical chemistry. 

The variations on life’s theme are near infinite, but they are just variations. On this planet alone there may have been as many as a billion different variations on that theme. A typical galaxy contains 100 billion suns, and there are over 100 billion galaxies. The number of other worlds is unknown, but our count keeps growing. It seems likely that planetary systems form frequently, very frequently. The actual number of worlds is far greater than any normal human comprehension. As we begin to reach out and explore new worlds, isn’t it possible that we could fly right past a planet with life and not even know it? Not likely.

A drive from coast to coast would surround you with different people, houses, communities, cities, etc. but you would have no trouble recognizing the public park, or the city square, or sports complex. The same holds true for trek through the cells of Earthly life and Alien life. Individual molecules may look different, but you would have no trouble recognizing the genetic storage facility or the molecular machines performing the biological activity. You would instantly recognize activities such as building the machine parts, genetic code replication, cell division and communication. The organism may look weird, but it’s inner workings would be very familiar. Don't expect a planet populated with sentient dinosaurs, or talking cockroaches. Those assemblages of cells are not likely to ever happen again, but do expect to be able to read their DNA.

-End of part 4

Monday, March 04, 2013

A Sample Size Of One and The Search For Life (part 3)

Living things have had it rough. We presently live among a measly 5% of the total number of different types of living things that have ever been. But even at 5% the numbers are staggering --an estimated 8.7 million different species alive, right now --a billion species or more, for all time. And amazingly every one, past and present, is running the same chemical machinery deep down inside. The chemical compounds that stored the genetic code of dinosaurs, also does yours and mine. The basic machinery is so precisely matched that pieces of DNA are completely interchangeable, across species (of even remote ancestry) and function perfectly well. No hiccups, no barriers, no mistakes. Carl Sagan once reflected, “Any tree, could read my DNA”. More to the point, any organism could read any other organism’s DNA. There is no fundamental restriction to this most essential of observations. 

Life is one thing, one event, one instance, playing out over and over again, in “endless forms, most beautiful and most wonderful"1. The fact that life is, at its core, the same for all is not happenstance. As we are quickly learning, the early Universe is (and continues to be) primed for life, our life. The pieces of the molecular machinery that drives our cells is universal –they are found everywhere. It is no coincidence that life is constructed of the same building blocks --they are easily made and in great abundance. They are readily available to be assembled into the larger polymers needed for life to emerge. How does this fact, coupled with our understanding of the characteristics and requirements for life, allow us to make predictions about life elsewhere?

It helps to recognize that there is a very short list of elementary particles that make up everything in the Universe. And those particles come together to form a finite number of elements. And the stability required to make monomers that can assemble into large polymers is further limited to just one atom, carbon. Life is carbon based, not just because it is convenient but because nothing else will do the trick. There are no alternatives (sorry silicon-based life form fans). Large, stable polymers, built on skeletons of carbon, are an essential ingredient for any living systems. There is simply no other way to endow enough complexity into a system to make life emerge without them.

One type of essential carbon compound is protein. Proteins are unique in the world of chemistry. They do something no other molecule is capable of doing. They behave. They move, adjust, act, react, turn, flip, grab, hold, hook, spin, open, close, etc. Every blob in this video, showing the process of DNA replication,  is a protein. It is impossible to watch and not think of them as well rehearsed; coordinating their behavior to achieve a task --as if they were alive. These proteins are performing just a single dance in the larger performance that makes your cells come alive. DNA replication is a universal process; every cell in every organism performs this activity whenever it divides, and the proteins that orchestrate it do so for all life, since day one (or very nearly so).

Just how do proteins perform these incredible feats? Their trick is in their shape. Proteins are build as strings of amino acids and after they are made, then fold and twist into 3D shapes, looking a little like a tangled extension cord. From their shape emerges their function, their behavior. Protein strings can fold into an infinite number of shapes. Most have no interesting biological function (at least, for life here on this planet), but some do. Their shapes are the result of the interactions of the different amino acids and their position in the chain. Change the sequence and you change the shape. Since the proteins of Earthly life uses 20 different amino acids, there are more possible sequences, and therefore shapes and functions, than there are total number of atoms in the Universe! DNA replication only uses about a dozen.

As remarkable are proteins are, surely there must be another way to build molecules of sufficient complexity and variability get life going. Is there any reason to suspect that all life, everywhere, would use the same building blocks?

The ubiquity of the building blocks themselves is compellingly suggestive of the likely use  of proteins in life throughout the Universe. Amino acids are everywhere. If life needs molecules like proteins, why not simply use proteins. The probability of another prebiotic system stumbling upon a novel chemistry to substitute the molecular complexity of proteins, while simultaneously missing the available building blocks to make proteins, must be incalculably low. Prebiotic chemistry is simple chemistry. The first “living” chemical pathways would have appropriated the material that was on hand, or could be easily synthesized. In a Universe filled with amino acid precursors, it is highly unlikely that anything else would have won. Life everywhere must have co-opted what was available.

Encoding protein information to ensure persistence across generations while simultaneously allowing for variations in amino acid sequences for selection to take hold, requires a molecule that works like DNA works. This line of reasoning is entirely anthropocentric (or should it be DNApocentric?), but considering that, like amino acids, nucleic acids are everywhere, the arguments for their incorporation into the machinery of life are equivalent as for proteins. In this case some flexibility is allowed. We know, for example, that proteins can perform double duty, encoding their own sequences or directing their own replication. We also know that nucleic acids can catalyze their own replication without the need for proteins to orchestrate it. Either way, these molecules work alone or in concert, but they are the ones that work. There is nothing else available.

Once you establish the common chemistry of life throughout the Universe, the next steps are to establish the common characteristics that chemistry produces and to then establish the range at which those characteristics can exist and persist. This is the where and what to look for.

-End of part 3 (part 4)

1 Darwin, Charles (1859), On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (Full image view 1st ed.), London: John Murray, pp. 502, retrieved 2013-03-04

Friday, March 01, 2013

A Sample Size Of One and The Search For Life (part 2)

“The study of a single instance of extraterrestrial life, no matter how humble, will deprovincialize biology. For the first time, the biologists will know what other kinds of life are possible.” When Carl Sagan spoke these words over 30 years ago, he was arguing for caution against our human tendencies to over-emphasize our own significance. He wanted to allow for the possibility of life forms, however different from us to inhabit worlds equally as unimaginable. However, he was not advocating for a “no-holds-barred” free-for-all of ideas. Sagan was very much a rationalist and understood the limits of chemistry and physics. He knew that any instance of life, anywhere, would have to play by the rules. And he knew, very well, what those rules are. He was, as he put it, a carbon chauvinist and a water chauvinist when it came to musings on alien life. (He was also very much a nucleic acid and amino acid chauvinist, although less vocally so.) But how could he know? How could any of us really know what another example of life might be like? We only know of one example of life. Aren’t we hopelessly biased? Isn’t every speculation, by our very circumstance, provincial?

As it turns out, we can know quite a lot from our limited sampling. “Follow the water” is a grade school prerequisite, but it speaks volumes to our present understanding and expectations for life on other worlds. It says that we fully expect life to be chemically based, as it is here. Atoms and molecules need to collide into each other to react, and those collision take place best in water. Water is a good solvent for organic molecules and is liquid over a wide range of temperatures. Plus, water is everywhere. All of our water is extraterrestrial in origin. There is water on the moon and Mars, and in the atmospheres of the gas giants, the moons of Jupiter, and even on our Sun’s closest planet, Mercury. It’s everywhere. Throughout the Universe, the watery stage is easily set for life to make its appearance. 

Water is only the beginning. An examination of life reveals a remarkable pattern; one that reverberates throughout the Universe. The living machinery of life, the chemistry, is composed of a relatively small number of simple compounds. The tens of thousands (perhaps hundreds of thousands) of unique proteins and many millions (maybe infinite) versions of DNA, belies the simplicity of their construction. Just a few dozen monomers comprise virtually all of the chemical parts of cells. These building blocks include the 20 or so amino acids used to build all proteins, the 5 nucleotides found in all nucleic acids (DNA and RNA), and some odd and ends in the form of sugars and lipids. Notice the qualifier “all” in the previous sentence. There are no exceptions. The rich diversity of living things, past and present (and future), is the result of the near infinite ways in which these building block can be put together. Individually, these monomers are quite boring, but collectively the polymers they form can make everything from butterfly scales, to pollen grains, to tooth enamel. 

Perhaps most amazingly is the fact that these few dozen monomers are not unique to Earth. They, like water, are found throughout the Universe. Life is built from these monomers because (but not solely “because”) these monomers are everywhere we look. From the tails of comets, to the pools of dark between the Stars, the Universe is littered with the stuff of life.

We can interpret the close match between the chemistry of life and the chemistry of the Universe as extreme coincidence. Or we can propose a simpler alternative --as direct cause and effect; as the inevitable outcome of a Universe primed for life. But, to do so requires more evidence.

-End of part 2   (part 3)

Copyright 2013 theBIOguy

Thursday, February 28, 2013

A Sample Size Of One and The Search For Life (part 1)

We can never know everything about anything. No matter how narrow our focus or determined our effort, there will always remain unknowns. Our information is never complete; the gaps in our knowledge stubbornly persist. It is this fact that drives us to conduct experiments; to ask questions of the Universe and compare the answers with our best predictions, to see how close we are for now.

But the Universe is vast, and our reach comparatively minute. How do we know if we have asked the right question? Or gathered enough data? How do we know when we have observed a sufficient number of meteors, for example, before we can say anything about them, with confidence? Perhaps all of our observations on meteors are peculiar to this remote location of our solar system, or local group, or galaxy. How do we quantify our confidence? How can we ever know for sure?

What if we only had one example of a thing? Found just one meteor, or experienced just one hurricane? What can we learn from a sample size of one?

Before we answer we need to consider exactly what it is we are trying to learn, and the nature of the thing to be sampled. For example, if we are trying to learn the best time to pick and eat a newly discovered fruit, a sample size of one is inadequate. Even if our fruit tasted good (or bad), we wouldn’t know if it’s flavor improves or worsens given more time. The inherent variation in fruit flavor, ripening time, etc., makes it impossible to determine the optimum time to pick from a sample of just one. Now consider trying to determine if our soup is properly salted. We only need a single taste to find out. Why? The principle of diffusion, and the properties of dissolved salt, guarantees that every sample will have nearly the same amount, so a sample size of one is all we need.

Considerations like these are not trivial, they are essential when we consider bigger questions such as “What will life on other worlds be like?” Science fiction has offered up numerous hypothetical life forms spanning a range from bipedal, bilaterally symmetrical, hominids (complete with two eyes, a single nose, a mouth and ear, and all in the right place) to life as a formless, boundless “pure energy” capable of traveling back and forth through time. Given this apparent “the-sky’s-the-limit” attitude, how can we know what we are looking for? Couldn’t life easily escape our notice? If not for their clever camouflage but for our own inadequate means of detection? Couldn’t a time-traveling organism of pure energy be sitting right behind me, looking over my shoulder as I type these words, and go unnoticed? Doesn’t our sample size of one (one planet, one life1) fundamentally handicap our attempts at finding life elsewhere in the Cosmos? How do we build a “life-detector” if we don’t know what we are looking for?

You may be surprised to learn that we do have an idea of what to look for, as well as when and where. Our “life-detector” is fined tuned to look for life within very narrowly defined limits. And it’s not likely to miss the invisible, time-travelling, pure energy aliens, because there aren’t any.

-End of part 1   (Part 2)

1One look at the diversity of life on this planet gives the false impression that we are surrounded with millions of samples of life. We are not. All living things, past and present, are modifications on a single theme of life. The essential living machinery –the hardware, appeared only one. But the software of the genetic code has been repeatedly modified. Just as there can be many different types of guitars, each playing many different tunes, there is only one type of instrument called “guitar”. If we wish to enumerate the instances of “life” on this planet, the total is just one.

Copyright 2013 by theBIOguy

Friday, June 15, 2012

Our Humanity

The last 150 years have not been a good for Homo sapiens. We are a proud (if insecure) bunch. We relish in highlighting distinctions that separate us from the rest of the animal kingdom. We are especially sensitive to features that we believe distinguish us from closely related primates, both extant and extinct. When the first hominid fossils were discovered in the mid 1800’s, they revealed an organism with a brain the same size, or bigger, than ours. These fossils (later identified as Neanderthals) were first thought to be us; to be human. What else could we think? Our large brains clearly distinguish us from the great apes. Our brains were responsible for those uniquely human qualities such as language or art. It was the seat of our intellect, our morality. It made us human. So, that first hominid fossil had to be a human, albeit slightly deformed with a protruding face and large brow.

Over the last 150 years we’ve come to discover a lot about our origins, and even more about Neanderthals. And, our discoveries have systematically knocked down each and every feature and characteristic we cherished as uniquely human. Neanderthals actually had larger brains, used language, wore clothes, manufactured and used complex tools, controlled fire, coordinated and hunted in groups, built shelters, and ritually buried their dead. But they are not us. They are not Homo sapiens. They are not even our ancestors. We did not come from Neanderthals.

This was a relief for some; a problem for many. How could a non-human hominid embody so many human characteristics? How could anything, other than human, speak to each other, plan for the future, live in complex social hierarchies, and hope for an afterlife? There had to be something that was all ours. There had to be something that clearly distinguished our humanity. We thought there was.

Neanderthals never made art.

Thursday, May 10, 2012

Hero Dog

When I was 12 years old, my parents got me a pet snake. I use to pick it up and let it snake over my arms and hands. It didn’t take long to recognize that it had a preference for my neck and would often stop moving and remain coiled there. It also didn’t take long for me to explain that behavior by anthropomorphosis. The snake was coiled, motionless around my neck as a sign of affection. It had grown comfortable with me, in a trusting sort-of-way, and found a place to snuggle. We were friends.

At 12, this explanation was the best I could come up with. Now I understand the better explanation is that my neck is warm and snakes move towards warmth.

So, what are we to make of a dog that apparently sacrifices itsown safety, maybe its own life, to save the life of its owner? Well, we could say just that, it was a “sacrifice”, and bring into the dog's world the notion of the lesser value of its life relative to the greater value of its owners. We can call the dog a “hero”, a title given to few humans (in fact, we are so guarded against use of the word “hero” for humans that we have created an entirely new category of “true hero” just for clarity).

But, is the dog a hero? Did it sacrifice? Dose it understand the concepts of force and momentum to perceive the train as a threat? Does it understand the human condition of “loss of consciousness” to realize that its owner wasn’t going to move on her own? Probably not. So, how do we explain such behavior? By remembering that dogs are predators and scavengers. After a kill or a find, many predator/scavengers will drag the kill to a safe location before eating; a “drag away” behavior. This is done to minimize the chance of losing your hard-earned kill to another predator/scavenger. It’s a behavior molded over millennia of natural selection; If you ate in the open, you were more likely to fight to keep your kill, if you dragged it away, you got more to eat. The “drag away” predator/scavengers left behind lots of “drag away” offspring, from which dogs are descended.

Lilly was probably exhibiting a simple behavior pattern, similar to the patterns that make them chase and return a stick, tug on a rope, or burry a bone. Lilly probably thought her lifeless owner was food, and was simply trying to drag her away, to eat in relative safety, but was too slow.

So, cheers to you Lilly, for exhibiting typical predator/scavenger behavior. You are a role model for dogs everywhere and a worthy ambassador of your rich and long ancestry. Oh, and thanks for trying to drag that hunk of food to a safer eating place. Good dog.

Copyright 2012 theBIOguy