Friday, December 20, 2013
2001: A Space Odyssey Redux
Hard to believe it has been 45 years since the best science fiction movie ever came out. I remember going with my mother and sister and being utterly dazzled, if perplexed by its meaning (I found out when I read the book some years later). With Apollo mission in full progress (though we hadn't landed a man on the moon yet), it gave me the optimistic vision of the future I retain to this day.
2001: A Space Odyssey is a 1968 British-American science fiction film produced and directed by Stanley Kubrick. The screenplay was written by Kubrick and Arthur C. Clarke, and was partially inspired by Clarke's short story "The Sentinel". Clarke concurrently wrote the novel 2001: A Space Odyssey which was published soon after the film was released. The story deals with a series of encounters between humans and mysterious black monoliths that are apparently affecting human evolution, and a space voyage to Jupiter tracing a signal emitted by one such monolith found on the moon. Keir Dullea and Gary Lockwood star as the two astronauts on this voyage, with Douglas Rain as the voice of the sentient computer HAL 9000 who has full control over their spaceship. The film is frequently described as an "epic film", both for its length and scope, and for its affinity with classical epics.[2][3]
Produced and distributed by the American studio Metro-Goldwyn-Mayer, the film was made almost entirely in England, using both the studio facilities of MGM's subsidiary "MGM British" (among the last movies to be shot there before its closure in 1970)[4] and those of Shepperton Studios, mostly because of the availability of much larger sound stages than in the United States. The film was also co-produced by Kubrick's own "Stanley Kubrick Productions". Kubrick, having already shot his previous two films in England, decided to settle there permanently during the filming of Space Odyssey. Though Space Odyssey was released in the United States over a month before its release in the United Kingdom, and Encyclopædia Britannica calls this an American film,[5] other sources refer to it as an American, British, or American-British production.[6]
Thematically, the film deals with elements of human evolution, technology, artificial intelligence, and extraterrestrial life. It is notable for its scientific accuracy, pioneering special effects, ambiguous imagery, sound in place of traditional narrative techniques, and minimal use of dialogue. The film's memorable soundtrack is the result of the association that Kubrick made between the spinning motion of the satellites and the dancers of waltzes, which led him to use The Blue Danube waltz by Johann Strauss II,[7] and the symphonic poem Also sprach Zarathustra by Richard Strauss, to portray the philosophical concept of the Übermensch in Nietzsche's work of the same name.[8][9]
Despite initially receiving mixed reactions from critics and audiences alike, 2001: A Space Odyssey garnered a cult following and slowly became a box office hit. Some years after its initial release, it eventually became the highest grossing picture from 1968 in North America. Today it is near-universally recognized by critics, filmmakers, and audiences as one of the greatest and most influential films ever made. The 2002 Sight & Sound poll of critics ranked it among the top ten films of all time,[10] placing it #6 behind Tokyo Story. The film retained sixth place on the critics' list in 2012, and was named the second greatest film ever made by the directors' poll of the same magazine.[11] Two years before that, it was ranked the greatest film of all time by The Moving Arts Film Journal.[12] It was nominated for four Academy Awards, and received one for its visual effects. In 1991, it was deemed "culturally, historically, or aesthetically significant" by the United States Library of Congress and selected for preservation in the National Film Registry.[13]
In 1984, a sequel directed by Peter Hyams was released, titled 2010: The Year We Make Contact.
Sirtuins Reverse Aging in Mice; Human Trials to Start Soon
Anthony Loera
Science News (Pop Sci) - 10:07 AM
Sirtuins reverse aging
The scientist that brought us news about Resveratrol, is now going farther and activating all of the sirtuins to reverse aging.
The scientist that brought us news about Resveratrol, is now going farther and activating all of the sirtuins to reverse aging.
New DNA sequence shows that Neanderthals liked incest
Berkeley scientists just generated a pristine genome sequence of Neanderthal DNA—the most complete ever created—and what they found might gross you out. It might also blow your mind.
The DNA sequence came from a 50,000 year old Neanderthal bone, a woman's toe to be exact. The scientists compared it with DNA from modern humans as well as Denisovans, the Neanderthals' contemporaries and often their lovers too. The analysis revealed a new level of complexity in the family tree that connects Neanderthals, Denisovans and a recently discovered mystery human species with modern man.
It also revealed that Neanderthals like to have sex with their siblings. The woman whose toe bone was analyzed, research showed, was the daughter of a very closely related man and woman, likely half siblings. The dataset as a whole suggests that inbreeding was more popular among Neanderthals than modern humans.
We've long known, however, that interbreeding was popular with everybody. The new study, which will be published in Nature on Thursday, says Neanderthals and Denisovans interbred often and are very closely related. Modern humans participated in the interbreeding, too, though they fancied the Neanderthals more than the Denisovans. The researchers estimate 1.5 to 2.1 percent of non-African, modern day genomes can be traced to Neanderthals, while about 0.2 percent can be traced to Denisovans.
Inevitably, we are different, though we're still figuring out exactly how. The new research shows that at least 87 specific genes in the modern day human genome differ from those in Neanderthals and Denisovans. Maybe one of them explains why we won out in the great game of evolution.
Wondering About Ourselves
One of themes of this book is that if we are to satisfy our curiosity about the universe around and within us, we will need to use our imaginations to the best of our abilities, because the universe as we perceive with our physical senses will only take us so far. We saw this first in chapter two, in which our robotic exploration of the solar system revealed worlds which we had not foreseen, at least partly because we had not completely unleashed our imaginations on the possibilities. In chapters three and four we were forced to use our imaginations again to picture how the world of the ultra-tiny, or atoms and electrons, works, by suspending our common-sense ideas and perceptions so that such things could become real and not mere philosophical concepts, tangible things we could get our minds around and acquire a sense of their true nature. My point is that in these journeys we have gained a certain intellectual satisfaction – real questions leading to real answers – but again we are being warned that clinging to the world as modeled by our eyes and visual cortexes is a habit we are going to have to resist, one way or the other, if we expect to keep making progress.
This chapter is on biology, which is why I begin with this emphasis on imagination, for with the possible exception of quantum mechanics, I believe nowhere is imagination more required than on the subject of life. Living things, their origins, their myriad shapes and actions combined with their underlying foundations, and how their marvelous, interdependent, and beautiful adaptivity to all environments they find themselves in, is a series of mysteries that will not yield to the unimaginative mind, however much plodding thought is brought to bear on them. Unconvinced? Then let’s start with the big question, the question even the most renown scientists have been beating their heads against right up to today: What is life? We see it practically everywhere we look (at least on this isolated, tiny planet) and we generally find we have no difficulty in distinguishing it from the world of the non-living.
I think at this point most of us would stop and agree, perhaps after some careful thought, that there is something essential about living things. The impression of this essentialness, this intentionality I will call it, is indeed overwhelming, and easily hits us on the head as the prime divider between life and everything else. All non-living things seem to follow the laws of physics in a dumb, obvious way: a pebble thrown into the air traces out a perfect mathematical parabola as it interacts with the law of gravity, finally striking earth in a completely predictable place at a completely predictable time, given that we know its initial speed and angle with respect to the ground. A pebble thrown into the air … but what about a butterfly? When we watch a butterfly we put away our calculators and measuring instruments, and simply watch in wonder. A butterfly doesn’t blindly follow a parabola, it – well, it seems to do whatever it decides to do, which is why making measurements and calculations are pointless. A butterfly flies away, perhaps never to be seen again. Or maybe it alights on a flower and gazes at us, seemingly as equally puzzled by us as we are of it. We are just certain there’s something going on behind those tiny eyes. Something inexplicable. Something essential. Something that gets down to what makes a pebble just a pebble but a butterfly something ... at the risk of being misunderstood, miraculous.
We still have taken only a few steps in our attempt to define life, however. For the next question is, is our butterfly, and by implication ourselves, truly miraculous?
* * *
Let us try a different tack. Richard Dawkins, in The Blind Watchmaker, proposes a definition of biology that is unusual but which he claims to be perfectly workable: biology is the study of complex things that appear to have been designed for a purpose. I speak of intentionality, but complexity plus the appearance of design provides us with another way of describing it, perhaps an even better way to make progress. Dawkin’s point when applied to our butterfly is threefold; first, like all life forms it is far, far more complex than the pebble, far more complex than our solar system even; second, not only does it act as though it has a mind capable of intentions and a body capable of carrying those intentions out, it gives all the appearance in the world to have been designed that way, designed to fly (as well as many other things); and third, and most significantly, there is an intimate relationship between complexity, intentionality, and design. Flying is not a simple thing, not the way butterflies do it at any rate, so complexity plus design, or as I call it, intentionality, appears to improve our handle on what we mean when we say something is alive.
But is it enough? Or for that matter, is it really true? Living things do not always appear to be complicated. Anyone dissecting a butterfly – no easy task, admittedly – would marvel at its many interlocking intricate parts, but what about the simple amoeba? Or a bacterium? At first sight, such things do not appear to be particularly complex, but we all agree that they are alive; that, like the butterfly, they appear to move under the guidance of some internal intentions, some essence which non-living things, even complex ones like computers, do not possess.
Most of us, I suspect, will find ourselves easily moving along some kind of reasoning like this, perhaps without thinking about it very much. It does seem to handle our common sense objection to calling complex things like computers and airplanes biological while keeping “simple” things like bacteria and amoebas in the same camp as butterflies and human beings. Living things, from the simplest up to the most complex, really do seem to have some special quality or essence that ordinary matter lacks, whatever else that matter has. We almost can feel it there, at the most basic levels, and we are certain that we would never have any difficulty in distinguishing a living thing from the non-living, based on that feeling. Wherever in the universe we might find ourselves, the question of whether we were amongst life or not would appear to be elementary.
* * *
Or would it? To our astonishment, our common sense view of things biological begins to disintegrate the moment we apply curiosity and imagination to it, to dissect it and look into it at the finest levels science allows us to probe. In doing so, try as we might, we never encounter this special essence or quality which seems so obvious at first sight. Instead, what we do find, when we break out our detectors and other scientific instruments, is that living things are composed of atoms and moledcules like everything else, albeit not in the same elemental proportions, yet acting according to the same laws of physics and chemistry as everything else. The mechanical, Newtonian universe of objects and forces, modified by quantum effects on the smallest scales, appear all that is needed to explain why butterflies fly, or mate, or find food, or stare at us with the seeming same curiosity that we feel gazing upon it. All our initial impressions, and all the stories that have been told and retold aside, there appears no miraculous special something that we can affix to or inject matter with to make it come alive; no energy fields, no forces, no protoplasm, no elixir of the living, nothing we can pump into Dr. Frankenstein’s reassembled parts of corpses which will make it groan and open its eyes and have thoughts and feelings and break its bonds to move in accordance with them. There is nothing like that whatsoever. No, whatever it is that characterizes life lies elsewhere.
But the impression of such a force is so strong, so deep, so instinctual that, try as we might, we cannot simply abandon it without at least wondering why it is there, where it comes from, and what it tells us. Something is there, of that there can be no question.
Intentionality. Complexity. Design. Try to put aside your ordinary impressions and perceptions of things, and seed your mind, germinate in your mind, take root and push out of the soil and put forth leaves and vines in your mind, the theme that to satisfy our curiosity we must look at the world from a different perspective, the one that imagination unlocks. Very often, we find that when we look closely, what we thought we were seeing fades away, yet is replaced by something just as amazing – no, more so.
Let us start with the simplest of things that could be called living. Consider the virus. Here is something both considerably smaller and simpler than the smallest, simplest bacterium, all biologists would agree. But on the most microscopic of scales, that of individual atoms and molecules, even the simplest virus turns out to be a machine of remarkable complexity. At the very least it has to be able to recognize a host cell it can parasitize, whether it is a cell in your body or a bacterium (in which case it is called a bactaeriaphage), somehow figure out the molecular locks and other gizmos which cells use to protect themselves from invasion, penetrate the defenses, then usurp the molecular machinery the cell uses to replicate itself, perverting the cell into a factory for producing many more copies of the virus, copies which then have to figure out how to break out of the cell in order to repeat the cycle on other cells or bacteria, all the while avoiding or distracting the many other layers of defenses cells and bodies use to protect themselves from such invasions.
Biologists still debate whether viruses can be legitimately counted among the various kingdoms and domains of life, but there is no doubt that their hosts, whether bacteria or other single celled organisms or multicellular organisms, can be classified in the great Tree of Life, from which all other living things, be they plants, animals, fungi, or you, diverge from. And what dominates this tree, right down to the most primitive beginnings we have yet been able to detect, is a level of complexity that we simply do not encounter among the great many more things than don’t belong on this tree, from rocks to stars to solar systems to galaxies.
So after all this, have we cornered our quarry? We started with the at first sight idea that life possessed some special quality or substance or essence, then realized that we could not find that essence however hard we looked. But what we did find was that living things, even the simplest of them, showed a level of complex organization well beyond the most complex of non-living things.
Life is special. I don’t want to lose sight of that. We are fully justified in our grand division of matter into the non-living – things we explain only by the laws of physics and chemistry at a simple level – and the living, all the things we must also apply whatever biology has to teach us. What I have been trying to show is that, whatever that specialness is, it isn’t as obvious as it appears upon first sight. It is more subtle, involving a number of characters and qualities, one of which is complexity and another the appearance of design or purpose.
* * *
Again, I say that life truly is special. It is early May, and I have just come home from a walk through Pennypack Park, one of the many lovely natural places which skirt the city where I live, Philadelphia, one of several cities along the eastern edge of North America. I would love one day to walk on the moon or on the red soil of the planet Mars, but what I have just experienced would be utterly lacking in those dead, albeit fascinating places. In the spring in this part of the world, as in many other parts of our planet, every sense is roused to life by the call of the wild. Not only are you surrounded by the verdant green of new buds and flowers and grasses, but also by a cacophony of whistles, chirps, tweets, and other rhythmic sounds which reminds you that you that new life is all about, some of it still rustling itself to full wakefulness after winter but much of it already in the air and alit on the many twigs and branches. And even without vision and sound, you can still smell the musty beginnings of stirrings things, the scents of enticing blossoms and irritating pollens, and you can still feel the grass between your toes and the softness of young leaves on your skin as you brush by the undergrowth.
Here I have spoken of complexity and the appearance of purpose and meaning, and perhaps that is exactly what our scientific mission into the heart and soul of biology requires, but this is one place where, I have to submit, we will never really capture the essence of what we are studying. Life is something that has to be experienced, and only living things themselves have the capacity, as far as we know, to experience anything. So, in a sense, our quest to satisfy our curiosity begins with the admission that, at least for the world of the living, we never can completely satisfy it.
Am I going to give up, then? No, because, as I have maintained up to this point, curiosity combined with imagination and the scientific method can undo any knot, unlock any riddle, however baffling and impervious it may seem. I have even suggested a starting place even, this idea of complexity combined with apparent purposefulness, an idea I hope to build upon and demonstrate just how powerful it is. I think we can agree that it is a good starting place. Biological things, even the simplest of them, are highly complex, we now see, and there does seem to be something to this notion of being imbued with purpose, however that comes about. If we can make some progress on this front, then perhaps in the end we will satisfy our intellects after all, as impossible as that seems looking at things from their beginnings.
* * *
Actually, I would like to strike out first on a different front than is typical in tomes on biology. I would like to retreat back to simple matter, of the kind we started to explore in chapter four, and work up to what I see as an essential question: can the laws of physics and chemistry, as we have come to know them, even provide a platform for the vast complexity of living things? In other words, do atoms, those basic building blocks of all things material, even allow for the enormous intricacies let alone purposefulness of the biological world?
This is a very good question for it turns out, at least for the great majority of atoms that we investigate toward this end, the answer is a clear and resounding No. Try as hard as we can, we find that when we begin assembling most atoms into more and more complicated molecules or other structures, they aren’t very cooperative in this process. No, things fall apart, often violently, even if we can figure out a way of putting them together. For the great majority of the kinds of atoms to be found in nature, constructing an edifice of complexity sufficient for life is a hopeless task. They simply will not stay put and do as they are told.
All that is with one, yes really only one, fortuitous exception, and one that we began to explore in the previous chapter. The carbon atom. Atomic number six on our periodic chart, a chart which now runs to over a hundred if we include the extremely short-lived ones humans have made in laboratories, is truly special. Carbon is what makes it all possible, to the point where we can confidently say that if that if this one lone atom out of the dozens had proved impossible for the universe to produce in any significant quantities, neither you nor I nor any of the myriad millions of species of life we share this planet – on perhaps any planet – with would have any chance at existing. Carbon alone is not sufficient for life, but it is absolutely necessary. Of all the other elements in the biological stew, perhaps substitutes could have been found, but no element, under any conditions imaginable, appears a likely alternative to carbon. This is because no other element yet discovered or made could take its place as the backbone of the sizes and varieties of the molecular components needed to make life, even the simplest forms of life, possible. I will even go as far to say that if an alternative form of life is ever found, if carbon isn’t at its roots than neither is chemistry.
Carbon, indeed, is so important that it is the only element whose existence was predicted by the fact that living things do exist. All of the naturally occurring elements in the universe today come from one of two sources: either they were made in the first few minutes of the universe’s existence, in the Big Bang which we will come to in a later chapter, or they were made in the cores of the many trillions of massive stars that have come and gone since the beginning. The reasons for both is the same: larger, more complex atomic nuclei – the core of protons and neutrons which make up the center of atoms and ultimately determine their respective element’s properties – have to be made from the simpler ones, ultimately from the simplest of them all: hydrogen, atomic number one, a single proton (sometimes combined with one or even two neutrons). This is done by smashing two smaller nuclei together to make the larger one, a process which requires extremely high pressures and temperatures because all nuclei are positively electrically charged and ordinarily repel each other unless they can be brought close enough together to be captured by something called the strong nuclear force. Such conditions existed naturally only in the moments after the Big Bang and today in the hearts of stars, particularly the larger, hotter stars. Essentially, to create a carbon atomic nucleus of six protons and six neutrons, what must happen is that three helium four nuclei, each consisting of two protons and two neutrons apiece, must be welded together in exceedingly short order, within a millionth of a millionth of a second, and then held together until they can relax and become stable. This so-called “triple-alpha” process (an alpha particle is a helium four nucleus) would itself seem to be an insurmountable barrier to carbon and all the elements beyond, but surprisingly that turns out to be not so: the pressures and temperatures which come to exist in large stars – stars large enough to explode or somehow spew their core substances into intergalactic space, making all those large atomic nuclei available to new generations of stars and planets such as our own, not to mention our own existence – are sufficient to guarantee this process will happen enough to account for all the carbon we are going to need.
With one problem. This problem lies in the fact that our newborn carbon nucleus is ringing and pulsing with so much energy that it should almost instantly fragment into smaller pieces. What we need is some kind of stable “resonance” at such high energies, which will allow the newly born nucleus to hang together just long enough to relax by a variety of processes into a lower, energetically stable state. But when the details of Big Bang and stellar nucleosynthesis were being worked out in the 1940’s and 50’s, no such resonance state was known, nor was there any theoretical reason – theoretical from the standpoint of physics at that time that is – to think one should exist.
The problem was solved by the single and to this day to my knowledge lone instance of the so-called Anthropic Principle being used to successfully explain an actual physical fact. If you are not familiar with it, the Anthropic Principle, in its most basic, common-sense form, is simply the statement that since we exist in this universe, the laws governing it must be compatible with our existence (this seems obvious, but there are other versions of the Anthropic Principle which are more controversial). In this case, what the principle insists is straightforward and simple: it insists that since the element carbon does exist in sufficient quantities for our existence, there must be a resonance energy level available for the newly bred nuclei. The Anthropic Principle is not an argument physicists are usually enamored of, but one group was sufficiently impressed by the line of reasoning to take an actual look and see if the resonance level really did exist. Lo and behold, they found that it did. In fact the discovery not only explained the existence of carbon in sufficient quantities in the universe, but also of the many elements that are in turn built up from it: oxygen, neon, silicon, indeed basically the entire periodic zoo of elements we find, to varying degrees of magnitude, present in the universe today.
* * *
So, carbon exists. It isn’t a very common element, and the fraction of it that does reside in our universe in conditions where life can form, is relatively small. But it is enough to account for, not just you and I, but all of the manifestations of biology all about us, almost anywhere you go on this planet, and probably what other worlds or places we may one day find life. The next question is, what is it about carbon that gives it its uniqueness, its specialness, its ability to construct the large and complex and seemingly purposeful phenomena that we call living things? What does carbon have that no other atom seems to possess, however hard we play with them and build castles in the air from them? Why do these carbon-based organisms which are found with such fecundity on Earth and hopefully on at least some other planets or moons or asteroids or places we’ve yet to think of, exist, continue to exist, and have existed for so long? Yes, carbon is special, but special in what ways, so many ways that no other atom has a prayer of filling its role?
The answer to this question is answered by a combination of chemistry and physics, some of which I have already explored in the last chapter. It involves two separate characteristics of carbon, chemical as well as physical characteristics, characteristics which carbon and carbon alone possesses, characteristics which we can never even mock up in any other element, however hard we try.
One of those characteristics is smallness. It is not coincidence that the great majority of the atoms which constitute life are to be found at the top of the periodic table, where the smallest and simplest of atoms resides. One reason for that no doubt is that small atoms are, due to the processes which forge them, simply more common than large ones. But another reason, the key reason, is that smallness means that these atoms can come much closer to each other in the bond-forming process, resulting in bonds that are much stronger and stabler than larger atoms can form. It is, in fact, well accepted, that the small sizes of the first and second rows of the periodic table account for much of the uniqueness of their chemistry, especially in the ways they differ from their heavier cousins, even in the same column. To give an example, sulfur, selenium, and tellurium are much more similar to each other than the first member of their column, oxygen. This is a statement which could be made for nitrogen and boron as well, and even, although to a lesser extent, lithium and fluorine. Small atoms make for short, strong bonds, something necessary if we are to build up to the size and complexity of living things and have them remain stable. Even a structure as small as a bacterium demands a level of complexity which only carbon and other small atoms can provide.
So smallness is important, but it is not sufficient. The reason for this can be found by examining the other elements in the first row, for example hydrogen, which can bond with one and only one other atom; usually another hydrogen atom, making the molecule H2, which is almost entirely what we are dealing with when working with hydrogen on the scale of pressures and temperatures we are accustomed to. Likewise, nitrogen and oxygen, also essential to life, appear to form stable binary molecules, N2 and O2, which do not spontaneously join together into longer, more complicated structures but make up the most common constituents of this planet’s air we breathe, which is about 78% N2 and 21% O2.
Following this line of argument, shouldn’t stable C2 molecules exist also, thereby undermining this theme of small atoms making large, structurally stable molecules, and once again pulling the rug out from underneath our feet in our quest to make the large, complex yet stable molecules and molecular edifices that biological things demand? Here is the interesting part, however; the neat trick by which nature refuses to be obvious but instead manages to provide us with exactly what we were looking for. For it turns out that C2 does not (or only rarely) exist, indeed is not normally stable, and once again we are allowed to proceed in the directions biology calls upon us to follow.
O2 and N2 are stable due to the smallness of oxygen and nitrogen atoms, but there are limits to how large you can build these small, compact molecules. These limits are inherit in the kinds of bonds that atoms can form with one another. In chapter four, I introduced the idea of the molecular orbital as the bond between two atoms created by the combination of the atoms’ atomic orbitals. The strength of the resulting bond depends on how well the atomic orbitals can overlap in space. This is where smallness comes into play. The bond between two hydrogen atoms is very strong because these atoms are very small and can approach each other quite closely, allowing for maximum overlap.
A picture being worth a thousand words, let me recapitulate some of the material for the preceding chapter about molecular bonds. If you’ll remember the case of the H2 molecule, we explained the bond as the overlap of s orbitals, in which two new orbitals came into existence:
one bonding one between the atoms, which strengthens the bond, and one antibonding orbital, which weakens it:
The bonding MO in this case has a name: it is called a sigma, or σ, bond, as chemists call them. This sigma bond, to reemphasize, is formed by the overlap of the s orbitals in the two hydrogen atoms, but more broadly, sigma orbitals / bonds are at highest density between the two orbitals. There is another type of σ bond, however, which can be formed by the overlap of p bonds. If you’ll recall, these bonds have the general shape
Here, the lines drawn represent the y (vertical) and z (horizontal) axes, while the x axis orbital would point at straight angles through the page. This is why I say that there are three p orbitals, all perpendicular to each other. Now, if you imagine the pz orbitals of two atoms, lying along the horizontal line above, the z axis, you can see how they too can overlap to form sigma orbitals, just as the s orbitals did. Very nice, and exactly what happens for many elements in the first row of the periodic chart. But now, remembering that there are three p type orbitals, you can see that in the case of two atoms the pz and the py don’t directly overlap, but appear to be parallel to each other. Hang in here. For I think I can make this clear with a few more diagrams and words. The orbital above, which I called py because the lobes are oriented in the y direction along the axis, cannot form σ (sigma) molecular bonding orbitals, because they don’t directly overlap between the atoms. But there are other kinds of bonds, bonds in which the overlap of the atomic orbitals is not so direct and obvious. The py and pz type orbitals possessed by the above atom are a perfect example of this. Still, using our imaginations, we can see that, although these orbitals do not combine headlong, there is nevertheless an overlap, an oblique or sideways overlap, between the lobes of the orbitals, for both the px and pz orbitals, if the atoms involved approach each other closely enough. The overlap is not as strong as with the pz orbitals, which directly overlap in the plane of the paper to form σ bonds, just like the s orbitals do, but it is there nevertheless. It is strong enough that we can construct new molecular orbitals, or bonding orbitals, using these oblique or sideways oriented atomic orbitals. Chemists have a name for these kinds of bonding orbitals as well; they are called π orbitals or pi bonds, again applying our habit of using Greek letters, in this case the letter π which we call pi. An example of this sideways, pi type bond is given below:
The nucleus of each atom lying at the center of the two py lobes is shown by the intersection of the x and z axes, while the py orbitals are the areas “smeared out” above and around them. Can you see that there can be sufficient overlap, and hence bond formation, between the two atoms using their py orbitals, shown by the grey regions, provided that they can be brought close enough together? Also, is it clear to the eye that the π bonds are not as strong as sigma (or σ) bonds, composed of either s or px orbitals, which occupy the space directly between the atomic nuclei, and that to have any strength at all the respective atoms must be able to approach each other very closely, which in turn means that only small atoms form stable π bonds? I think yes, just by looking at them, we can see that π bonds will be weaker and easier to break than σ bonds, a disparity that can only increase as we look at larger and larger atoms.
So. What has all this got to do with living things and their chemical makeup? As it turns out, plenty. The molecules N2 and O2 are stable only because of the smallness of their atomic sizes, and so can have as many as two (as in N2 or O2) π bonds, in addition to their σ bonds – this, by the way, is why we call them triply-bonded or doubly-bonded molecules.
Still, they would prefer for energetic reasons to exchange these π bonds and create or join in with molecules where all the bonding is of σ character; that is why we find how easily they combine with, for example, hydrogen atoms to make the simple molecules of water (H2O) and ammonia (NH3). Even carbon, which we are reserving as the basis of many manifestations of life, is often found bound up with hydrogen too, in this case to yield the simple molecule of methane (CH4) as seen in the last chapter. I should also mention to make this clearer that this is the same reason why third level elements, even those in the same family of nitrogen and oxygen – phosphorus and sulfur – do not easily form π bonds, as the larger size of these atoms do not allow them to approach each other closely enough; thus, we do no see p2 or s2 molecules, but more complex structures (this is also because these atoms have available 3d orbitals for additional bond forming, but we will not go there).
As we alluded to in chapter 4 carbon’s versatility comes forth even in these most basic of molecules. Using sp3 (again, you may have to refer to the last chapter to refamiliarlize yourself with them) hybrid orbitals, carbon can form as many as four strong, sigma bonds with other atoms, a feat no other atom can boast of. Since up to four of those atoms it can combine with is another carbon, we can imagine a vast network of sigma-bonded carbon atoms, a network that can grow virtually as large, and as complicated, as it likes. Such networks in fact do exist, and as already mentioned we call them diamonds, allegedly the hardest substance in the universe. What is more important for this discussion is that if the simple atom of carbon can yield the hardest of materials in the universe, then the creation of living things would appear to be a natural outflow of this process of bonding one carbon atom to another. Moreover, with each carbon atom having four “hands” or valence electrons to offer any other atoms it may encounter, we should be able to come up with just about any large, complex, stable molecular structure we can imagine.
Indeed we can, and have, and the subject even has been given a special name: organic chemistry. That’s right; carbon is so unique in its abilities to build complex structures and edifices – meaning large, complicated molecules – that it and it alone is awarded the very special prestige of having an entire branch of chemistry constructed around it. As a matter of fact, go to any university’s web site and start checking out the chemistry courses and you will see that the very subject appears to have two major branches: organic and all the rest, some of the rest actually being called inorganic chemistry. No other element even comes close to commanding such respect. So we finally see carbon’s commanding role being due to its unique ability to form the backbone of an almost infinite variety of molecular sculptures. And it is exactly that kind of versatility we are going to need if we are to make any sense of the fantastically complex, seemingly purposeful assemblages of atoms and molecules which comprise the roots and foundations of the vast panoply of biology spread before us. When it comes to satisfying our curiosities, that is one nail we can pound in completely and begin our explorations around. We can now say that basic, straightforward physics and chemistry do allow for biology, though, again this must be stressed, they are nowhere close to explaining it by themselves. The explanation requires something else, something that we have been edging toward, a grand idea or set of ideas that provide the gratification we have been seeking. It is time to fully enmesh ourselves in these ideas, and bask in the glory of what we have been seeking.
* * *
So, the chemistry of carbon, along with a handful of other atoms like oxygen, nitrogen, hydrogen, sulfur, phosphorus, and a smattering of other trace elements gives us all the building blocks we need to create human beings, elm trees, barnacles, tyrannosaurs, and paramecia, but that doesn’t explain how or why the blocks manage to come together in the right ways. Brachiosaurs, which were very large, plant eating dinosaurs, may be built from the same carbon and nitrogen and all the other atoms in our own biological grab-bag of goodies, but no amount of blending, whipping, hurling around, or piling one thing on top of another will never give us that Jurassic eating machine, or anything else that could be even remotely construed as alive in any sense of the word.
Here we are in our quandary, because we know the answer provided by thousands of years of folk-wisdom, occasionally dressed up in full theological garb. God, or some pantheon of gods, or something supernatural and miraculous, conjured up all the millions of species that creep, run, swim, fly, fester, or patiently await for the comings and goings of seasons and suns, so goes the wisdom of the ancients. Most people who have ever lived, and probably most of those alive at this moment, find this answer satisfactory. But if we are to truly gratify our curiosity, we have to accept that this is no answer at all. It is just another waving of the wand of the miraculous, with results unexplained and unexplainable. Or to put it another, yet more devastating, way: if God or some set of gods explains the complexity plus appearance of purpose we find in biology, then what explains Its / their equally perplexing purposeful complexities? It’s an infinite regress, which leads nowhere and satisfies nothing in the end. The only possible way this “explanation” can work is if we can come up with something that is intelligent, intentional, creative, and yet somehow simple. My suspicion is that is exactly the kind of reasoning, at a largely sub-conscious level, the theological inclined are actually all about. To which all I can say is, I cannot dismiss it completely out of hand, because imagination might someday find just such a joker in the deck. My suspicion, however, is that there really are limits on what reality can present us with. Intelligence and intention must be built upon an edifice of complexity, along with the law of physics and chemistry, any way we cut the cards. Five hundred years of science, and five thousand of philosophy, have yet to sniff out any alternatives, and seem unlikely ever to do so.
So the supernatural is a non-starter, at least if we intend to stay true to the themes of this book: curiosity, imagination, and the scientific approach to explaining things. We have to find something, or things, in what we already know, or can reasonably speculate about, if life is to be laid out, dissected, elucidated in some manner that satisfies us. What I experienced during my walk through Pennypack Park begs for explanation as much as, if not more, than anything else one might experience. But where does one begin this journey towards enlightenment? How do we even start to think about it?
* * *
Fortunately, there is a place to start; not a place that makes everything that follows easy or simple, but one that I believe at least parses the subject of life into two separate, somewhat more manageable sub-topics. One sub-topic is the question of the origin: how the atoms and molecules that in early Earth were in arrangements almost entirely non or pre-biological came to be re-assembled – or super-assembled is perhaps the better term – into the most primitive versions of our complexity plus (appearance of) purpose life forms that appear first on this planet between three and a half and four billion years ago.
Is this a separate question? Yes, it clearly is, and for the following reasons: first, all things biological, however large or small, or ephemeral or long-loved, or whatever their form or function, or however they eke out their livings, rely upon a common basis of biochemistry which can be clearly seen in all of them, if you examine them at the level of atoms and molecules. That in itself suggests a common origin, and provides the platform for the other reason: this platform, this origin aside, is what accounts for the overwhelming diversity in livings things that we witness today, billions of years after the beginnings, in the various shapes, colors, sizes, and behaviors of the tens of millions of plants, animals, fungi, and other species which have crawled, flown, walked, swam, or in whatever manner reached practically every corner and niche of remotely inhabitable space that can be found on Earth.
Here, in the early twenty-first century, this cleavage of the problem of life into these two daughter problems is supported by so much evidence that there can be no doubt that it is the proper way to initiate our quest. The chemical evidence from DNA, RNA, proteins, carbohydrates, and other biomolecules has demonstrated their common origin beyond any reasonable doubt. As an example, the viruses which I have mentioned, so tiny that they cannot be seen by any optical microscope however powerful, and whose relative simplicity makes their place in the bower of biology still a disputed issue, can feast upon hosts as disparate as bacteria and human beings and redwood trees only because the molecular machinery underpinning all of these things, including the viruses themselves, is almost identical. The same could be said about the relationship between virulent bacteria and their animal / plant / fungus hosts; for that matter, about the plain, ordinary fact that most living things on this planet make their living by somehow consuming other living things. This is something that couldn’t happen if we weren’t all made up of the same basic, chemical, stuff, underneath all our appearances of diversity.
Of course, it may still prove possible that the same kinds of processes explain both phenomena, the origin of life, and its subsequent diversification. But there is no reason to assume, a priori, that this is true, and in fact it is the position of almost all scientists who tackle these two problems that it is almost certainly not true, or at least not true for the most part though there may be some overlap in some places.
What is true, however, is that we are given a choice, right here and now, at the start of our trek toward understanding. As in Robert Frost’s poem, we are presented a choice of two roads to walk upon, both of which seem equally enticing:
Two roads diverged in a yellow wood,
And sorry I could not travel both
And be one traveler, long I stood
And looked down one as far as I could
To where it bent in the undergrowth;
Then took the other, as just as fair,
And having perhaps the better claim,
Because it was grassy and wanted wear;
Though as for that the passing there
Had worn them really about the same,
And both that morning equally lay
In leaves no step had trodden black.
Oh, I kept the first for another day!
Yet knowing how way leads on to way,
I doubted if I should ever come back.
I shall be telling this with a sigh
Somewhere ages and ages hence:
Two roads diverged in a wood, and I—
I took the one less traveled by
And that has made all the difference.
Unlike Frost’s poem, the two roads we are faced with look very unequal even before we take the first step on either of them. Again, beginning with our vantage point at the start of the twenty-first century, we can say that one of these roads really is well-worn, although there do remain many thickets and tangles and vines and thorns to be waded through; while the other, superficially the more straightforward of the two, is actually much more mired in undergrowth and mystery, one on which many faltering first steps have been made or attempted still with no clear path in sight. That seemingly-clearer road is the problem of the origins of life; a surprise only as long as we overlook the one, real, overwhelming obstacle in our path: which is that, however it happened, it did so either billions of years ago on this planet, or trillions of miles away on other possible worlds as discussed in chapter two, and then transported here; either of which leaves us exceedingly short of useful data upon which we can build testable theories. Both of which leave us prey to the purveyors of miracles, a shortage of which is seemingly never found; as long as, however, we forget that if miracles are answers, then science would never have explained anything, and curiosity and imagination would be pointless. Even if we do never solve some particular problem, this is no cause for capitulation; we are, after all, mere human beings with human abilities, and it shouldn’t surprise anyone that some questions remain forever unanswered, no matter how much of those abilities are applied to them for how long. It is quite possible that the origin of life, or its different possible origins, remains a nut we never quite crack. Disappointing as that would be, it is no cause for dismay or futility or some kind of existential malaise; besides which, we will no doubt discover many amazing things in our endeavors to solve this problem. Indeed, this has already happened, with examples of amazing self-organizing complexity in various chemical systems being the most obvious examples. This is actually one of the most amazing things about science, at least as I have experienced it: that our attempts to hammer out a solution to one problem ends up leading us completely unexpected paths, stumbling upon unknown veins of gold.
* * *
The problem of the origin(s) of life is a fascinating and of course commanding one, one in which many books can and have been written on and which careers have been dedicated to. However, I have deliberately chosen to leave it out of this book because meandering down so long a path with so many thickets and brambles is likely to end up with ourselves just scratching ourselves all over, and mending and binding the many wounds which we will receive, with no clear end in sight as our reward. Actually, even Darwin himself knew this. In all his tomes on evolution, he persistently avoids and evades the question of life’s origins, leaving it in backwaters to be treaded by the minds that were to come after him. If possible, he doesn’t even mention or allude to it. He had the foresight and, in our hindsight, the wisdom, to know that mucking around in those waters would only muddy the tale he was bent on weaving, a tale with enough problems of its own. Fittingly, it is a problem he only alights upon to let us know that he too will have nothing of the supernatural in solving it. Just as Newton was wise enough to know to let the cause of the gravity he so deftly described be a problem left to his successors, so Darwin also avoids this slippery trap and leaves the question of origins to minds to come after him.
There is one last point I would like to make here. It was well accepted by the late eighteen hundreds that one of the most important characteristics of livings things today is that all of them had parents, of one form or another. That fact, so obvious to us now, was finally nailed down by Louis Pasteur in a series of famous experiments, thereby separating the problem of biology into its two great sub-problems, its origins and its subsequent evolution. What Pasteur showed was that wherever even the simplest of living things came from, whether they be mice or maggots, they didn’t just burst into existence out of inorganic or simple organic beginnings. No, all of them, without exception, were begat in some manner; moms and dads, or at least a parent of some sort, were involved, even if no one knew in any detail how the begetting was done. You could breed billions of bacteria from one bacterium, but not a one from zero, however hard you tried. That clear and indisputable truth was a beginning into everything the twentieth century contributed about the fundamentals of biology: Everything comes from something, nothing comes from nothing. At least not on this planet, at this point in its history.
* * *
It would appear that we at least have a beginning here in our wonderings about ourselves, about life, that we can summarize. A quartet of beginnings, actually. First is that it displays levels of complexity, organization, and seeming purpose which would appear to defy explanation. Second, at its most fundamental level, life and its origins are based on nothing more than physics and chemistry, most crucially on the amazing properties of that amazing element carbon, although a plethora of other elements play essential roles as well. In addition, we and our ancestors all share a common biochemistry, a biochemistry built on DNA, proteins, and so forth, and have certainly done so going back a good three billion plus years in Earth’s history.
The third beginning is an inevitable consequence of the first two, that of procreation being the only way nature has now of producing new organisms, from bacteria to human beings, that living things are simply too complicated and organized to assemble by chance. Not only that, but offspring resemble their parent(s) (although, of course this is not always immediately obvious, as we all know from the example of a caterpillar hatching from a butterfly’s egg), a resemblance which will be passed on to future generations, albeit with occasional mutations.
As for the fourth beginning, evolution, that it occurs and has been occurring for a vastly long time, that it explains the many forms and functions and niches life has found on our world, and that, most importantly, we possess the fundamental understanding of how and why it occurs, underlays biology just as physics underlays chemistry and mathematics underlays physics. Furthermore, just as our third beginning derived from its predecessors, the fourth emerges inevitably from the third. It is the beginning that took two English naturalists, Charles Darwin and Alfred Russell Wallace, and these Victorian gentlemen’s elegant and brilliant reasoning which derive from the observation of two natural phenomena: the inheritance of physical and behavioral traits from parent to offspring, and competition for scarce resources among those offspring to survive and repeat the process: natural selection. What to me makes their accomplishments all the more remarkable is that how heredity works was something neither man had a clear concept of (even though this was the same time that Gregor Mendel was doing his experiments with peas which would have helped both of them immensely – experiments which remained in obscurity until the early 1900s); indeed, some of Darwin’s concepts in this field actually made his theory harder to defend. Still, they convinced the scientific establishment of their day within a short period of time.
* * *
It is natural selection and random mutation that have conspired together over millions of years to wire our brains into the relentless curious, pattern hunting, story weaving machines I spoke of in chapter one. This unconscious conspiracy has been so successful that we imagine that we see people and animals among the stars and, if like most of us who have ever lived do not know better, believe tales of how they came to be there. It is also of course one of the main wellsprings of all art and literature, from the Mona Lisa and War and Peace to the Campbell’s soup label and idle gossip. It is, ironically, the reason that I used the word conspiracy and all it implies without a second thought, and probably the reason you may not have questioned my doing so.
The obvious downside to this marvelous, compelling faculty of our brains is that the patterns and stories are often unsuspicious products of it. When this happens, then they, like magic, only sidetrack and mislead us too, perhaps disastrously so. In fact, neither our brains nor the rest of our bodies are the culmination of any kind of conspiracy, but only one of many possible, logical outcomes of nature’s blind laws.
So we tread carefully when we look at the universe about and within us and try to make sense of its workings and history. Each step has the potential to take us either into deeper understanding or shallower error. If we place too much trust in this part of what nature has wired into us, we seriously risk the latter. We must always be prepared to pull back to reexamine what we think we see, to be skeptical, to consider other possibilities, and to use another gift we have been given by those same blind laws, that of our ability to reason. If we tread the path carefully enough, our prospects for success, I believe, are promising.
Why do I begin a discussion of evolution this way? The best answer I can offer is to return to the beginning of this chapter: “One of themes of this book is that if we are to satisfy our curiosity about the universe around us, we will need to use our imaginations, because the universe as we perceive it simply doesn’t get us very far.”
Yet imagination stripped of pattern seeking and story telling would be a moribund faculty of our minds, if indeed our minds could have it at all. It surely would be nowhere close to the task of fleshing out and filling in our understanding of things. Not that it would it matter though for our curiosity would be almost severely crippled as well, probably to no more than an animal instinct serving few goals greater than finding food and mates and avoiding predators.
Nowhere is this shown better than in the work on the structure and workings of the DNA molecule, the beating heart of heredity, a heart that, perhaps more than anything else science has discovered before or since, would never have been found without that combination of imagination, pattern seeking and story telling, skepticism, and reason which make us such unique organisms that we may indeed be alone (although I hope not) in the universe.
As with so many other parts of my scientific education, I was first exposed to DNA and its workings one of the Time-Life books (or maybe it was one of Isaac Asimov’s many books on science). I was then too young to understand it in much detail, but I do recall being profoundly impressed with how important it was to all life on this planet, and at least the rudiments of why. The deeper comprehension was something that has taken a fair part of my life to even begin to grasp, and even today I know that comprehension is nowhere near as deep as it could be – not that I feel embarrassed or ashamed about that for even the most brilliant minds in the world have spent both this and a large part of the last century yet still have many mysteries arrayed against them.
* * *
I cannot resist a recapitulation here. It has been almost six months since I took the stroll through Pennypack Park I described earlier in this chapter, but right now, thinking of these issues, I find myself irresistibly drawn back to that day. Doing so, I find that my senses are as enthralled now as they were then. Once again I see and hear and smell the many living things surrounding me, almost making me feel as though I have been transported to some kind of paradise. For here I am, surrounded by the oaks and the maples and the sycamores and occasional pine trees, and admittedly many others I do not recognize. The branches and twigs of bushes, both low and high, brush against my body, and my shoes swish over the uncut grass. Birds circle in the air, dart between the trees, then settle on their branches and study the world around them. If I close my eyes, not only do I hear their many languages, I am greeted by a cacophony of other noises: insects of all kinds, the rustling of just opening leaves in the spring breeze, the splashing of fish breaking the surface of the still cold water, the dabbling and occasional quacking of ducks, the distant, patient calls of bull frogs toward potential mates, the scratching of squirrels racing up and down the trees, and others which I cannot with any certainty place or, to be honest, remember now. I am also of course aware of the humans around me and their myriad tongues with their myriad emotions and hopes, not to mention the clopping of those fortunate enough to be riding horses. Dogs bark from time to time, also reminding me of our presence. Opening my eyes again, I look for the other, more silent or better concealed creatures I know to be about, from mice and ground hogs and snakes, to ones like skunks, raccoons, opossums, and others that only come out at night. I see no deer, but don’t doubt they are about, that it is only a matter of time and attention. Stroking my fingers on a stone wall I feel the velvet of new moss against my fingertips. It is too early for mushrooms and most other fungi, but they too hide in dark places, waiting for warmer weather and longer days to coax them out. The insects I heard swirl around me now, and spiders lurk in cracks in the stone walls or hang from fresh webs, waiting for victims. Taking it all in, it is difficult to imagine how nature could have been more creative in her choice of forms and functions for her productions. Humans have nowhere near such power, and perhaps never will.
Yet I have only just brushed up against the most amazing thing about all this splendor. Which is that, were we to take samples of all of it, and place it under an instrument powerful enough to see that deeply into the structure of life, they would all reveal the spirals of DNA at the very core of their beings, spirals which account for that amazing creativity. In no case would the spirals be exactly the same – they would differ in their lengths and, in most places, their specific nucleotide sequences – but the similarities would vastly outweigh the differences in even the most distantly related organisms. Walking through the park, we are inescapably aware of the diversity which infinitely impresses us, yet it is only when we look closer, much closer, do we see – probably the most profound paradox of life on this world – the foundation which is shared by all of it.
Which is why of course I began by speaking of patterns and stories, and the double-edged sword in our minds which compels us to see and create them. If you will recall the beginning of this chapter, I dared the reader to define what life actually is, and gave some examples of how our forebears answered it. The important point about our forebears is that the answers they did come up, as persuasive as they were to them, could not have been more mistaken. The patterns they perceived in life, and the stories they told to explain them and their origins, however compelling and reasonable they seemed at the time, have turned out to be wrong, dead wrong, in retrospect absurdly wrong. What accounts for all living things is the laws of physics and chemistry, working within the forces of evolution by natural selection.
But if we stop there we fail to appreciate the power of the other edge of the sword. The discovery of DNA and the other molecules of heredity, the probing into and teasing out how they work, would not have been possible without our ability and willingness to use this edge as well as all the other facets of imagination, in combination with the hardest of scientific acumen. For what pattern in nature could be more arresting than the DNA spiral? And what story could be more captivating than the story that led to its discovery and unraveling – except, perhaps, the story that DNA, and the millions of years it has been evolving in so many directions, itself tells?
* * *
We take it as common knowledge today that DNA (or, in some cases, its brother molecule RNA) forms the hereditary basis for almost all living things on this planet, but Darwin and Wallace died long before it was discovered. Yet neither man could have failed to grasp the power of this one molecule to fulfill its dual responsibilities as the instruction set for both developing biological things and maintaining so many of their essential functions. They would no doubt have been equally impressed – no, elated – with its additional ability to create new information via mutation, information to be tested in the living, breathing, real world of life and death. Natural selection could not have a greater ally.
I have been emphasizing the almost incomprehensible complexity of living things, but in describing DNA we are surprisingly impressed, at least at first sight, by its simplicity. The simplicity is such that Crick and Watson, who revealed its structure to the world a little over fifty years ago (without, alas, giving Rosalind Franklin her due credit), were able to deduce how it replicates itself – something it must do every time a cell divides – without a single additional observation or experiment to back their deduction up (although they were rather cagey in how they mentioned it in their paper). And although there are still much research to be done, we have since that time been able to elucidate what DNA does and how it does it with impressive detail.
Simplicity does not mean lack of sophistication, however. DNA, comprised of two strands of sugar phosphate backbones, twirled together and held that way by pairs of small, interlocking “base pair” molecules, may not sound promising as genetic material; it would probably not even be the first choice of an engineer looking for an efficient molecule for storing information. But remember the discussion earlier of the power of the carbon atom to assemble stable molecules of very large size. As large as, for example, the Hope diamond. The DNA contained in chromosome one of the forty-six chromosomes of a single cell of your body would, if teased out to its full length, be approximately three inches long and contain over two hundred million base pairs (I can’t resist the calculation that if all the DNA in all our cells were laid end to end, they would stretch from here to the moon and back some twelve thousand times!). Given that the four bases can have any potential sequence, yielding 4200000000 or over 10100000000 possible arrangements in just that one chromosome, perhaps our engineer should take a second look. Incidentally, don’t try: that is a number no amount of imagination will make real in your mind; even all the atoms in the entire known universe only sum up to less than a paltry 1080.
Actually, on third thought, if anything we seem to be dealing with such an overkill of information storage capacity that we wonder why nature chose to employ DNA at all. Would wonder, that is, if nature truly were an intelligent engineer that could choose anything.
So DNA, its deceptive initial simplicity aside, is easily – way easily – more than up to the task of encoding all the information needed to create and maintain not only ourselves, but also any living organism we can conceive of, however strange and wondrous; more than all the organisms that have ever lived on this planet, or might live in the future. Or that might have or will live anywhere else in our universe, assuming they use DNA as their genetic code. Or in a billion billion universes (if they exist) spanning a billion billion years.
Information … but of what nature? And how is it encoded in the DNA spiral? And how does our biological machinery and processes extract it, and turn it into the raw material of our beings? And how has it allowed the combination of random mutation and natural selection to drive life from its simplest beginnings over three billion years ago to the incredible diversity of much more complex forms, including ourselves, that we see today – a diversity my walk through Pennypack Park only revealed only the tiniest fraction of?
It is time to talk about protein.
* * *
Here is a subject we are all at least somewhat familiar with. Who doesn’t remember as a child being cajoled, coaxed, and badgered into making sure we ate enough protein to grow strong and tall? Go into any health food store and you will find rows of large containers of protein supplements, each promising to build stronger muscles in absurdly short times.
Proteins are large organic molecules (though nowhere near as large as DNA) which, when we consume them, are broken down by digestive processes into small molecular units called amino acids. There are some twenty kinds of amino acids in living things, and different combinations and numbers of them link together to make all the proteins nature produces. Having broken down the proteins we eat, we then reassemble the freed amino acids to construct the many new different proteins our own bodies need. And our bodies need them for many different purposes.
What makes proteins so important and so versatile is the fact that they are not merely random strings of amino acids, like glass beads on a thread. Instead, because of the intramolecular forces in them, they coil, wrap around each other, form plate-like structures, and then fold up into specific, detailed shapes which are determined by their specific sequences. That is why the glutinous, translucent “white” of an egg becomes firm and truly white when we cook it, for heat, as well as other physical and chemical assaults, unravels the globular shape of the albumin proteins and make them lay flat against each other.
The myriad sizes and shapes of proteins are employed by bodies to perform all kinds of functions. For example, proteins studding the surface of a cell control the rate at which water and other molecules and ions (electrically charged atoms and molecules) enter and leave. They are employed in such diverse roles as construction material for hair and nails and cartilage, and as essential components of important biological molecules such as the hemoglobin in your blood, which carries oxygen from your lungs to every cell in your body and carries away the carbon dioxide waste to be exhaled. Numerous different types are critical to cell metabolism, in particular those that serve as enzymes, which catalyze chemical reactions in your cells to produce other important molecules. The elasticity of proteins in muscle cells allow those cells to expand and contract, allowing your heart to beat and you to use your arms and legs. They are also important in cell signaling and the proper functioning of your immune system. Your parents were indeed wise to exhort you to get enough of them in your diet, even if they did not know why.
Curiosity ought to be provoking a question in your mind right about now. Digestion breaks down the proteins we eat into their component amino acids. The amino acids are then transported by the blood to all the cells in the body. It is in our cells that all the proteins we need are constructed. Yet proteins contain from hundreds to tens of thousands of amino acids, all joined together in the specified orders they require to perform their functions. The greatest engineer in the world would be running out of his factory screaming if handed a task this monumental. How do our cells handle it with such aplomb?
The molecular machinery which assembles proteins in the cell is a subject which, if I were an expert on it, I could easily fill the rest of this chapter and more describing. Fortunately, I’m not an expert on that particular topic, which means I can segue back to DNA without further ado. The point in this discussion on proteins is that DNA is the template which is used to build them. A gene is a section of DNA serving as the template for a specific protein. More specifically, the sequence of DNA bases determine the sequence of amino acids, the correspondence between base and amino acid being three to one: each amino acid corresponds to, is encoded by, three nucleotide bases in succession. As there are four such bases, this gives us 4 × 4 × 4 = 64 possible amino acids we could code for, well more than the twenty that are actually used in nature.
Actually, this is worth elaborating on to some detail, due to another digression I feel is worth making. If we represent the four nucleotide bases in DNA, adenine, thymine, guanine, and cytosine, by their initial letters, A, T, G, and C, we find that we have an excellent “quaternary” coding system to work with. I use the word quaternary here in the same way the word “binary” is used when discussing computer code. When you run your favorite computer program, or even much less than favorite program, the code your computer is executing is essentially nothing more than a series of (electronic) 0s and 1s. This series of 0s and 1s tell the computer’s processing chip(s) and all the associated electronics and other gizmos what to do (some of which you saw in chapter two); bear in mind that with enough 0s and 1s we can create a computer program as sophisticated as we like; if my understanding of computer science is correct, given enough 0s and 1s we could create a program that simulated the entire universe and its history, though whether this universe includes the program and the computer it is running on is still unclear to me.
The three to one correspondence between bases and amino acids modifies the coding system of DNA but does not alter the analogy with computer programming code, an analogy I would like to continue with. It means that if we were to read the amino acid sequence of a section of DNA by “unzipping” it and looking at the base sequence, instead of looking at it one base at a time we would have to read it in groups of three: e. g., TTA, CAG, CTG, GCA, and so on, each group of three coding for one acid. As noted, that is well more than enough for the twenty amino acids nature uses in living things.
Computer programming. Like one of the individuals who have inspired this book, I too have had considerable experience in the field and so too am drawn to the comparison of DNA to programming code. It is a powerful and compelling comparison – the idea of DNA as digital information, to be molded in any direction the blind but non-random forces of evolution wield – has, for me at least, as much appeal to imagination and useful insight as any other idea in biology over the last quarter century or so. Now, with the digital age fully upon us, the comparison, or analogy, is even more forceful to the mind. Personally, as a (very) part-time science fiction writer it conjures up images of artificial living beings, of synthetic organs and tissues to prolong our lives, perhaps indefinitely, of expanding the already impressive capacities of our brains with biochips, and even such cybernetic ideas as an Internet composed of human minds directly connected to and communicating with each other and with sentient computers. Given that I honestly expect to see some of this happen at least in my lifetime not to mention my children’s, the digital view of biology is perhaps too seductive.
* * *
After everything I have said about imagination and our need to use it to answer our questions about ourselves and our universe, the word seductive alone ought to suggest I am about to pull back, at least somewhat. So I am. Not that I don’t truly believe that many if not all of the above mentioned wonders of coming technology will happen someday. But the emphasis on the digital nature of DNA can potentially mislead us as well as inform.
The reason for this is that our digital DNA codes, serves as a template for, the highly analog proteins that are the actual machinery of our bodies. By analog I simply mean the opposite of digital: continuous in change as opposed to changing in discrete steps. (A hopefully not too outdated example of the difference would be the analog dial on old radio sets which, as you turned it, changed the tuning of the receiver continuously from one frequency to another, as opposed to digital push-button radios today which jump instantly to a specific frequency.) In calling proteins analog, I do not mean the sequence of amino acids which comprise them; that is still as digital as DNA in that an amino acid change in the sequence is discrete – you can’t continuously change between one acid and another.
Hang on, for I am getting to the reason for this digression. It is true that the amino acid sequence in a protein is digital, but what matters for proteins, what they do and how they work, is largely their specific size and shape, qualities that usually can be varied more or less continuously by changes in the amino acid sequence which comprises them. That is, if we replace one amino acid in a protein consisting of hundreds or thousands with another, the most likely outcome is a small, perhaps even insignificant, change in its shape – resulting in a proportionately tiny change in how the protein does its job. For example, if the protein is an enzyme, a slight change in its shape would cause the rate at which it catalyzes its specific reaction to be somewhat faster or slower. Or if the protein controls the rate at which a certain molecule or ion enters or leaves cells, that could be modified slightly. Furthermore, additional amino acid changes are likely to lead to similar small, cumulative changes in the protein’s function.
Small, cumulative changes. We are practically talking about the heart and soul of Darwinian evolution. But what would cause these single amino acid changes in a protein’s make-up? Recall that it is a particular sequence of three consecutive nucleotide bases on DNA which correspond to the amino acid at a particular location in a protein. Any number of agents have the potential to alter, or “mutate” a base in DNA: radiation and various kinds of chemical assaults. Such mutations (there are others) even has a name: point mutations. Point mutations are surprisingly common. Most are caught and corrected by molecular machinery in the cell designed for the purpose, but they occasionally slip through the defenses. In doing so they can lead to the amino acid changes in proteins which often (not always: sickle-cell anemia is caused by just such a single change on one of the globin proteins in hemoglobin) cause those proteins’ functioning to alter slightly, causing somewhat higher or lower production of another chemical or modifying cell membrane permeability to a molecule / ion, leading to … well, for example, if the protein is involved in embryological development, a modest change in the physiology or behavior of the organism. The point is, when talking about natural selection, modest changes, such as those that lead to slightly longer or shorter legs, have a better chance of being advantageous than large changes, which are almost certain to be disastrous. And given that changes can accumulate over geological time, constantly being molded and “directed” by natural selection, I hope it is by now clear that the entire edifice of DNA / proteins / form and function, though completely unknown in Darwin’s and Wallace’s time, could hardly have been better tailored to the revolutionary ideas they unleashed upon the world.
* * *
Wondering about ourselves is, of course, an endeavor that never ends, and no such pretense will be made here. On the contrary, the territory covered in this chapter is only a tiny fraction of the vast subject of life, what it is and how it has come to be. Alas, curiosity demands more, far more much more, than I could hope to deliver even in an entire book, assuming I was well versed enough in the subject for such an undertaking. But I do hope that certain basics about life, in general, have been laid down: its utterly improbable complexity, seeming design and purposefulness (what I have called intentionality); the underlying chemistry, particularly of carbon, that makes it possible (on our planet); the continuity, in that all living organisms are in some way descended from a parent or parents, going back to the beginnings of life on Earth some three and a half or more billion years ago; the basics of Darwinian / Wallician evolution, which explains how life today came from its much simpler beginnings; and the interworkings of the tapestry of DNA with the working machinery of proteins which are essential to both life’s functioning and its evolution. I hope you feel that we have not made a bad start.
But there is another aspect to our self exploration, one that can’t be, and won’t be, ignored. That is our wondering about ourselves as individuals. How is it, each of us asks at least from time to time, that I came to be; what and why am I; what is my place and destiny, if any, in the scheme of things, whatever that scheme is assuming; what does it mean to be human and what else could I have been? The reason I have excluded this aspect from this chapter is that the sciences that answer it, if any, are necessarily more speculative, to the point where it is questionable in many cases to call them sciences at all. But that doesn’t stop our asking the questions. It doesn’t quench our curiosity, or make it go away. And we can still use our imaginations – gingerly, for we tread on unknown territories – in our quest to come up with answers that just might make some degree of sense. Or so we hope.
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