Life's Ratchet: How Molecular Machines Extract Order from Chaos (43 page)

Quotation from Lynn Margulis and Dorion Sagan,
What Is Life?
© 2000 by the Regents of the University of California. Published by the University of California Press.

W
E HAVE COME A LONG WAY—FROM THE VITAL FORCES of the ancients to the molecules of molecular biologists and biophysicists. If we were seeking the “life force,” the force that animates life, then our search has been successful. This animating force is the random force of atoms, the jittering afterglow of the creation of the universe. The molecular machines, which take this undirected force and give it direction, embody the tight embrace of chance and necessity and are themselves the product of this embrace. Sculpted by evolution, the molecular machines of our bodies tame the molecular storm and turn it into the dance of life.

The universe is the child of chance and necessity. Every star and galaxy, planet and mountain, microbe and elephant is a testament to the interaction between these two basic tendencies of nature. Should this view of the universe, as informed by modern science, influence how we think about ourselves? On one hand, maybe not. Life happens on many levels, from colliding atoms to the mind of a genius. The molecular machines are part of who we are, but they do not determine who we are. We are intelligent, creative beings, a natural extension of the creativity of the universe, but we are not determined by nature. While based on machines, we are not machines ourselves.

On the other hand, science has allowed us to learn something very profound about ourselves. Life is a wonderful molecular mechanism. This should make us admire life even at its most “primitive.” Even a virus is a
miracle of nature. Humans are part of that same nature—and moreover, we are the most miraculous part of it. We are all the same, and at the same time, we are very different. By
necessity
, we are all bound to the unity of life, but by
chance
, we are all unique. We are supposed to be here—in one shape or another.

If there is life elsewhere in the universe, it will be based on molecular machines. As far as we can determine, the laws of physics are the same everywhere. Everywhere, the nanoscale is the special scale where energies can be easily transformed, providing the potential for autonomous nanoscale machines. Even the humblest living organism is incredibly complex. To attain such complexity, the organism must consist of many interacting parts. These parts must be small, active, varied and complex—only molecules can fit the bill.

To understand the world as a whole, we need to abandon our linear, deterministic thinking. The complexity of life, of our minds, of human society, is the result of adding a dash of randomness to the rules of the game—a game that is played on a network of complex relationships, a game full of emergent properties. I believe (but I cannot prove) that life was inevitable in our large and ancient universe. Consider that life on Earth contains only a tiny fraction of all the matter in the universe. Even if there were millions of inhabited worlds in every galaxy in the universe, the total amount of matter contained in all living beings would still only be a miniscule fraction of all the matter in the universe.

The universe is not a victim of the second law of thermodynamics. If this were so, the universe would just contain diffuse nebulae of hydrogen and helium. But this is not the case. Before life appeared, gravity acted to concentrate atoms. Stars cooked up heavier elements. Planets provided a surface where atoms could be concentrated further, which enabled the creation of complex molecules. The universe is 13.75 billion years old. It had plenty of time and plenty of matter to come up with life
somewhere
. Considering the inherent drive of matter to form ever more complex structures, life seems inevitable.

Of course, there are many who refuse these findings of modern science. They would like to maintain a view of themselves that puts them apart from nature and apart from the universe. In a memorable passage from his 1925 essay “What I Believe,” the philosopher Bertrand Russell
contrasted such a view with the vision that science has provided: “Even if the open windows of science at first make us shiver after the cozy indoor warmth of traditional humanizing myths, in the end the fresh air brings vigor, and the great spaces have a splendor all their own.” To which I would add that once we learn more about science, we find that this shiver is the shiver of excitement—excitement over the grandeur of our universe and our astounding ability to understand a small, but growing corner of it.

Many people express incredulity that something like a human could be the result of the “blind forces” of chance and necessity. They want to believe that the creation of complex structures requires the planning mind of a designer. But how does a mind invent? How do new ideas arise? Are new ideas not chance events, popping into our heads like uninvited houseguests? Could not the same molecular storm that animates our cells sometimes shake our thoughts and create sudden insights? Such random thoughts may cause us to create new connections between seemingly unconnected experiences, leading us to think outside the box. This model of human thought makes sense to me. How could new ideas come about any other way? Where would they come from? From the outside? No, we know that ideas are generated by brains, which are complex networks of biological cells, communicating via chemical and electrical signals. The only way to generate new ideas is by involving some degree of randomness. Even if we invoke an all-powerful mind to explain the origin of the universe or of life, we are thrown back to the same basic forces of chance and necessity. Even this all-powerful mind would have to depend on them.

Are we getting closer to understanding all there is to understand? One hundred and fifty years ago, Charles Darwin threw up his hands and exclaimed, “I feel most deeply that this whole question of Creation is too profound for human intellect. A dog might as well speculate on the mind of Newton! Let each man hope and believe what he can
.
” I understand the sentiment. We are
still
far away from penetrating the mystery of mysteries. But we have come much, much closer.

If we do not yet completely understand life, it is because life is incredibly complex. How does one combine the fundamental parts of life—DNA, enzymes, molecular machines—to create a Shakespeare or an Einstein?
Faced with such mysteries, many people want to throw up their hands like Darwin and declare that it is not possible to explain life after all. Yet, as we have seen throughout this book, science can turn darkness into light and can reveal deep secrets of life. We have seen that life is governed by chance and necessity.

actin
A long, fibrous protein that is part of the “skeleton” of a cell. Also acts as track for myosin and forms the fibers on which myosin II pulls in muscles.

activation barrier
Energy barrier that molecules have to overcome when they change shape or react with one another.

ADP (adenosine diphosphate)
Product of removal of one phosphate group from ATP, an energy-carrying molecule that is used in cells to move chemical energy around. ADP consists of a nucleotide (adenine) with two phosphate groups attached.

allostery
The ability of some enzymes to change shape and functionality in response to binding a control molecule. Allostery constitutes the basis of regulation in cells.

amino acid
Smallest unit of a protein. Proteins consist of a various combinations of the twenty amino acids that are used in nature.

amphiphilic
A molecule that has both hydrophilic and hydrophobic characteristics.

animism
The belief that everything has a soul and is alive.

atomic force microscopy (AFM)
Type of scanning probe microscopy, which measures small forces between a sharp tip and a surface. AFM can provide high-resolution images or can be used to measure forces between molecules.

atomism
The belief that everything is made of small, indivisible, and perpetually moving particles.

atoms
Smallest chemical units, composed of a nucleus (made of protons and neutrons) and a cloud of electrons. Electrons are responsible for chemical bonding.

ATP (adenosine triphosphate)
Energy-carrying molecule, used in cells to move chemical energy around. Consists of a nucleotide (adenine) with three phosphate groups attached.

ATP hydrolysis
Reaction of ATP with water, which detaches one of its phosphate groups and liberates a large amount of energy. End product: ADP (adenosine diphosphate).

ATP synthase
Sophisticated rotary molecular machine located in mitochondria. Uses a proton gradient to recharge ATP.

ATPase
Enzyme that breaks down ATP. Part of almost all molecular machines.

bit
Minimum quantity of information; information contained in a “yes” or “no” answer (or “1” and “0”).

Brownian motion
The random motion of small particles as the result of many collisions with molecules in the air or in a liquid.

Brownian ratchet
A molecular machine that moves in a specific direction via a directed diffusion process. Does not violate the second law of thermodynamics because in order to work, energy is supplied to the ratchet to periodically detach the machine from the track on which it moves. This energy is then dissipated.

chance and necessity
The basic principles responsible for everything there is. Chance arises from quantum mechanics and the molecular storm, while necessity is due to physical laws.

chaperonin
Proteins that help other proteins fold into the correct shape.

chromosome
A bundle of DNA in the cell nucleus.

codon
A “word” in the genetic code; consists of three nucleotide letters. Each codon encodes one amino acid according to the genetic code.

collagen
Fibrous proteins. Part of the extracellular matrix, giving structure to animal bodies.

complexity
Attribute of a system that is composed of many interacting parts and that exhibits emergent properties.

cooperativity
The property of some processes wherein several parts must act together simultaneously for the process to occur.

diffusion
Random motion of molecules or atoms. On average, diffusion leads to the movement of particles from a region of high concentration to a region of low concentration.

dissipation
Degradation of usable (free) energy into unusable energy (heat).

DNA (deoxyribonucleic acid)
A long, double-helical molecule located in the cell nucleus; stores the sequences to make proteins and directs the development of the cell.

domain
Part of a large molecule.

dynein
Family of molecular motors that move on microtubules.

emergence
Arising of properties resulting from the interaction of many parts; the emergent properties are not properties of the parts by themselves.

energy
A propensity to perform work. The unit of energy is the joule (J).

energy landscape
Conceptual idea of a multidimensional landscape representing how the energy of a protein changes as it changes shape. Each location in the landscape corresponds to a specific protein shape, while the height of the landscape represents the energy associated with the shape.

energy transformation
The change of energy from one type into another, for example, from chemical to kinetic energy, as in a car.

entropic forces
Forces that are not due to the reduction in energy, but are due to an increase in entropy. Examples are depletion forces and hydrophobic forces.

entropy
The degree to which energy is dispersed. Often equated with “disorder.”