What is Life?:How chemistry becomes biology

by Pross, Addy

  In fact, it is intriguing to point out that those biologists who have argued against the concept of teleonomy, have, without realizing it, demonstrated their total faith in the principle by their everyday actions. Those scientists, like us all, actually stake their lives on its validity. Every time we get into a motor car, for example, we are betting our lives on teleonomy! Our purpose in getting into our car is to get to some destination, and to do so safely. On the roads we have to manoeuvre through an endless stream of vehicular metal—the other cars—careering about hither and yon, a real threat to life and limb. The consequences of a collision between any two metal hunks can be personally disastrous, yet we happily accept that risk day by day. Why? Because of teleonomy. We know that within every other metal hunk careering about, there is a driver whose purpose is identical to our own—to get to his destination in one piece! Though one occasionally comes across an erratic driver who seems to prove the exception to the teleonomic rule, for most of us, on most days, that teleonomic principle operates reliably and, as anticipated, we arrive at our destination safely. So those so-called disbelievers in teleonomy are actually silent and committed believers. The world we have to navigate our way through on a daily basis is composed of both biological and non-biological systems. When dealing with the non-biological world we intuitively apply the laws of physics and chemistry. But, consciously or unconsciously, no person would be able to get through a single day without continuous application of the teleonomic principle. No doubt whatever, in the living world, teleonomy, as a predictive and explanatory principle, is the way to go.

  The fact that multicellular animals, like us, behave in a purposeful manner may not appear that surprising. After all, as already noted, we animals are highly complex—we possess a brain and nervous system so it might be argued that in us animals the teleonomic character is just a reflection of significant neural complexity. But here’s the surprise. It is not just multicellular cognitive beings—humans, monkeys, camels, and the like, with a brain and central nervous system that manifest this teleonomic character. That character is also clearly manifest at the level of the single cell! Put a bacterium in a glucose solution in which the glucose concentration is variable and the bacterium ‘swims’ toward the high concentration region. That phenomenon is called chemotaxis. The bacterium, which utilizes the glucose’s chemical energy to power its metabolic processes, is effectively going out for dinner, much like the crouching lion about to pounce on a zebra.

  Of course a bacterial cell cannot swim in the conventional sense of the word. A simple bacterium such as E. Coli is powered by several flagella, which, depending on the direction of flagella rotation, enable the bacterium to direct its motion within the solution. If the solution contains nutrition, then the bacterium rotates the flagella in one direction such that its motion is toward the nutrition. However, if the solution contains toxins, then it rotates the flagella in the opposite direction causing the bacterium to tumble, thereby changing its direction away from those toxins. The directed swimming action of the bacterium is unambiguous: without a brain or in fact any neural activity whatever, that clump of chemical aggregates within a membrane (which is itself a chemical aggregate) that we call a living bacterium follows its agenda of seeking out its next meal, keeping out of trouble, and getting on with its life. The fundamental behavioural patterns of bacteria and humans are not as different as one might initially conceive.

  We have focused on the teleonomic behaviour of the living cell but in point of fact it’s not just the actions of the bacterium that reflect its teleonomic character. The highly complex cell structure that we have already discussed is the most explicit and profound expression of that teleonomic character. Pretty well every element within that bacterium can be associated with a particular cell function, in much the same way that the individual components of a clock—pendulum, cogs and wheels, springs, hands, cabinet, etc.—can also be associated with a particular function, except that within the cell the structural complexity and intricacy is orders of magnitude greater. The long string of Nobel prizes awarded to the pioneers of cell structure and function, beginning with Watson and Crick’s 1953 structure elucidation of DNA, the molecule of heredity, attests to the importance that the scientific community has attributed to these landmark discoveries. The simplest cell is a marvel of teleonomic design, breathtaking in its intricacy and efficiency. Bottom line: teleonomy is as evident at the single-cell level as at the multicell level. The living world screams out teleonomy no matter where you look.

  Our confident recognition that teleonomy is an undeniable and legitimate concept does raise a problem. We believe in a material world, we no longer believe in a vital force, we now know living things are made up of the same ‘dead’ molecules as non-living ones, so what is going on here? How can any organization of inert matter come to life? How can any natural organization of matter act on its own behalf? How is it that a small crystal of sugar, say, about the same size as that bacterial cell that we’ve been discussing, behaves so differently from the bacterial cell? It is true that the sugar crystal is composed of just one single organic compound, sucrose, whereas the bacterial cell is made up of thousands of different organic molecules and molecular aggregates enclosed within a membrane. But how can this complex mixture of organic materials behave so differently from the single organic compound, sucrose? Just mixing together a thousand different organic materials in any and every combination certainly does not create a living system.

  What then is the nature and source of life’s apparent élan vital, that teleonomic character already evident in a bacterial cell? How is it possible for the living world to be seemingly governed by different laws from those that are operational in the inanimate world? If we wish to understand life, we will need to provide a rationale for life’s teleonomic character in the same chemical terms we use to explain the global characteristics of inanimate systems. Simply sweeping the issue of teleonomy under the complexity carpet with a shallow explanation of ‘emergent properties of complex systems’ will not suffice. Such a response is little more than dressing up the discredited élan vital concept in scientifically more acceptable attire. As we will discuss in chapter 2, Jacques Monod, the French biologist, who won the Nobel Prize for his contribution to the understanding of DNA replication and its role in protein synthesis, and who had a deep appreciation of the complex chemical behaviour of the living cell, was confounded by this apparent paradox. No wonder then that the great physicists of the twentieth century were both fascinated and troubled by this duality in material behaviour. The question of teleonomy is one with profound scientific and philosophical implications. If we ultimately believe in the material nature of living things, then life’s teleonomic character should somehow be a manifestation of the material that produces that teleonomic character, just as the hardness of a crystal of salt or the softness of a rubber ball are understandable characteristics of the materials from which these objects are made. We won’t understand life till we understand teleonomy. Indeed, as part of our goal of understanding life, in chapter 8, I will propose a physicochemical characterization of teleonomy, as well as a mechanism for its emergence.

  We have noted that biological systems are purposeful both in form and action. But what exactly is the purpose? Can it be specified? Ask a number of different people what their goal or purpose in life is, and you’ll get a variety of answers. One person might say their goal is to travel the world, another to make a lot of money, yet another to make the national Olympic team, to get married and have ten kids, yet another to write a book on the nature of life. The list is endless. Of course any one person might have a number of different goals in mind. We humans are a restless species, never entirely satisfied. But if we want to get to the very essence of biological purpose, we need to get away from multicellular complex beings and look at the simplest life form, that simple cell, the prokaryotic (without a nucleus) bacterium. As we have seen, everything that the single bacterial cell does, every aspect of its hi
ghly complex internal structure, is teleonomic, and the entire teleonomic apparatus associated with that bacterial cell is directed toward one goal—cell division. In recognizing that fact for single-cell creatures, one can discern that in multicellular creatures that replicating drive is also immensely powerful. Ultimately many of the life goals of living creatures, if not explicitly related to reproduction, can be understood as indirectly related to reproduction, as a means to that end. Living things, even the very simplest ones, are strange, yes, very strange.

  One final comment concerning the reality of teleonomy and whether it can serve as a totally legitimate scientific concept. The argument might be put that teleonomy is only conceptual, merely in our minds, not real like physical forces, such as gravity. However, this distinction is not as valid as it might initially seem. True, teleonomy is conceptual, it is just in our minds. Teleonomy is indeed a construct, intangible in a physical sense, one that enables us to better understand the biological world. But now think about the Newtonian concept of gravity for a moment. That’s a real force, right? But what does ‘real’ actually mean? Have you ever seen, heard, or touched a gravitational field? Is there some sophisticated scientific instrument that will reveal such a field, say by capturing its image? The answer is no. A gravitational field is not directly observable in any way—it also is a concept, just like the teleonomic principle. It is useful to talk about gravitational fields because the concept enables us to explain the behaviour of matter—falling apples, for example. Metaphysically speaking, however, both gravity and teleonomy are mental constructs that assist us in organizing the world around us. Inductive reasoning, which we will discuss in chapter 3, is, in its very essence, conceptual. All inferred patterns are conceptual and are nowhere to be found except within our minds. True, the concept of gravity can be quantified, while the teleonomic concept cannot, and quantifiable concepts, quite rightly, have a preferred status in science compared to non-quantifiable ones. But the fact that a concept is not quantifiable does not make it any less real than one that is. If we are all willing on a daily basis to get into our cars and stake our lives on the validity of the teleonomic principle, then, despite it not being quantifiable, we must all be quite convinced of its reality.

  Life’s dynamic character

  We have discussed in some detail the fact that the living cell is a highly organized entity and compared it to a familiar mechanical entity, a clock. Both are organized in the sense that all of the component parts contribute to the operation of the holistic entity. The parts of the clock enable it to fulfil its function of telling the time, the parts of the cell enable it to fulfil its function and become two cells. Of course the clock is an organized entity that has been constructed to fulfil its particular function—it is man-made, whereas the bacterial cell has somehow come about of its own accord. Nevertheless, the machine metaphor for understanding living systems has been useful and allowed us to continue to probe cell function, to discover in ever greater detail the precise workings of this remarkable ‘machine’. Closer examination of the two ‘machines’, however, reveals an extraordinary distinction between the machine-like characteristics of the clock and the cell. Within the clock the components remain in place and continue to operate until one or other of them wears out and the system ceases to function. But within the living cell the situation is spectacularly different. Whereas a clock is a static system, whose parts are permanent and unchanged, every living system is dynamic. Its parts are continually being turned over. Let me explain.

  You meet an old friend that you haven’t seen in a few years and you greet him with the comment: ‘Hi Bill, great to see you again, you haven’t changed a bit!’ You make that comment because Bill looks very much as you remember him from your last encounter. But here is an extraordinary fact. The person standing in front of you, who looks like Bill, talks like Bill, and is called Bill, is, materially speaking, effectively a totally different person from the Bill you saw some time back. Just about every molecule in Bill’s body has been replaced since you last saw him. Almost all the stuff of which Bill (and you and me) is made has been turned over. For some parts of us, our hair and fingernails, for example, that turnover is obvious. But for the rest of what makes you, you, the turnover is hidden from view. It takes place surreptitiously. Like all human beings you are primarily composed of the some 10 thousand billion (10,000,000,000,000) cells that make up your body. (We actually also contain within our bodies some 100 thousand billion foreign cells, bacteria, but we’ll get to the significance of that later in the book.) And each of those cells is itself composed of an array of biomolecules—lipids, proteins, nucleic acids, and so on.

  Consider proteins, as they are the archetypal molecules of life. Much of life’s infrastructure is based on the huge array of different proteins in our body. Muscle is protein, cartilage is protein, enzymes are proteins, indeed much of the internal workings of the cell chemistry involve protein molecules. And now to the key point: due to the critical importance of proteins in governing life’s functions, protein structure must be strictly regulated and controlled to ensure no damaging mutations have taken place in their structure over time. The consequences of such mutations could well be catastrophic—even cell death. Protein integrity is crucial for life’s successful function. Several years ago a key mechanism for maintaining the proteins’ structural integrity was discovered by Avram Hershko, Aaron Ciechanover, two researchers at the Technion in Israel, and Irwin Rose, at the University of California at Irvine, for which they received the Nobel Prize in chemistry in 2004. What they discovered was that intracellular protein is continually being turned over—cellular protein is constantly being degraded and resynthesized in a tightly regulated process.

  At least one of the reasons for that dynamic process is to ensure that the proteins’ structural integrity is maintained. The mechanism of that process need not concern us here, but the net effect of this protein regulation and control mechanism is that even within a few hours much of the cellular protein in our bodies has been degraded and reconstituted. And if that dynamic molecular character isn’t enough to get you wondering, let’s also point out that at the cellular level the degree of turnover is no less impressive. Your blood cells, billions of them, are replaced daily, your skin cells continually turn over. In fact in an adult human being hundreds of billions of new cells are created daily and these new cells are created in order to replace a similar number that die, many by design, through what is termed programmed cell death.

  The bottom line: essentially all of the stuff that makes you, you, and Bill, Bill, is being constantly turned over so that over a period of weeks you are in a strictly material sense a totally different person. The ‘life as a machine’ analogy, though of value, offers no hint of life’s underlying dynamic character. Yes, life is very strange. Answering the ‘what is life’ question will have to come up with a good explanation for life’s dynamic and ephemeral nature.

  Life’s diversity

  As we have already commented, life is spectacularly diverse. True, there is considerable diversity in the non-living world, but the diversity of the living world is quite different in character. Non-living diversity is arbitrary, while living diversity seems deliberate, coherent. Look at the plant kingdom, look at the animal kingdom—literally millions of different species, each perfectly adapted to function and survive in its particular ecological niche. Life’s staggering and very special diversity in all its grandeur is out there, everywhere, all around us.

  But the macroscopic diversity that we see around us is just the tip of the diversity iceberg. The largely invisible microbial world is where the concept of diversity takes on new meaning. Microbes are effectively everywhere. An early estimate of the earth’s bacterial biomass puts it at 2 × 1014 tons.3 That’s sufficient to cover the earth’s land surface to a depth of 1.5 metres! More recently it has been discovered that a litre of sea water can contain as many as one billion bacteria4 emphasizing how little we know about that invisible wor
ld. Indeed, estimating bacterial diversity is still in its infancy due to the difficulties in culturing and sequencing diverse microbial populations. By some estimates the number of bacterial species in a gram of soil could be in the order of a million and a common estimate of the number of all bacterial species on earth range between 10 million and one billion. Let me be clear here—we are speaking of the number of bacterial species, not the number of bacteria! In fact the diversity is so overwhelming that microbial genomicists have started to think in terms of ‘species genomes’ or pangenomes that possess a common core of shared genes. Individual genomes are too diverse to allow meaningful characterization. What is clear and beyond dispute is that the diversity in the microbial world is one of staggering proportions.

  What is remarkable, however, is that the underlying basis for life’s diversity continues to trouble biologists, beginning with Charles Darwin and through to the present day. In his Origin of Species text, Darwin proposed a Principle of Divergence, though from that monumental work it is not entirely clear whether the Principle of Divergence derives from his primary principle, the Principle of Natural Selection, or should be considered as an independent principle. Darwin himself seemed ambivalent on this point. The source of the conflict is clear: divergence means that many are derived from few, whereas selection (of any kind, natural or otherwise) means many are reduced to few. The two are inherently contradictory and no amount of verbal gymnastics can get around that. No wonder then that attempts to reconcile the apparently irreconcilable continues to torment modern biologists.5,6 What is clear is that the source of life’s diversity does begin with reproductive variation, though the detailed manner in which that variation leads to speciation and diversity remains controversial. In chapter 8, we will propose a physical approach to the problem of diversity in the living world and the cooperative nature of biological interaction that has accompanied that diversity.