Molecular Dance

Photo credit – https://www.flickr.com/photos/michaelpaul/

Life is a molecular dance that exists between the stillness of cold and the randomness of heat

Life’s intricate structure has a vulnerable existence in the midst of molecular storm of heat. Cells can survive, function, and replicate only within a narrow range of temperatures. They die if exposed to high temperatures and would slow down or even stop functioning at low temperatures.

Wood frog dies in winter and returns back to life in spring

Wood frogs are seen in the forests of Alaska and north eastern United States. It is the only species of frog that can survive in cold regions beyond Arctic circle. It does a fascinating trick to survive in sub zero temperatures of winter by freezing itself into an ‘Ice frog’. It stops breathing and the heart beat also ceases. Cells quit all forms of metabolism and water between the cells freezes. It lays dead on the forest floor. There is no pain, no motion, no life and in that moment it is no different from a ball of ice. Once the weather changes and sun warms up air and earth, ice melts. Heat enters the frog and slowly the heart beat returns. The frog gets back to life, roams around in forest, feeding and mating.

If we can pull the same trick then our body could be frozen lifeless into a non aging solid block and then thawed back to life once our society has advanced enough to migrate to Mars. A person with an incurable metastatic cancer can be frozen before natural death could happen and then brought back to life once a cure is identified. There will be instances in which people will take a couple of months of frozen lifeless vacation in hopes to rejuvenate ‘soul’.

Fortunately we are far away in terms of knowledge gap to achieve such alien desires. At present if you freeze a human body, water inside our cells would turn into ice crystals that will rip through complex cellular structures. When the body is thawed back, all we would have is a bag of water. No force of nature could ever bring back the life that formlessly dissolved into that water.

How does the frog stay intact without breathing for months? Our cells begin to die within seconds after heart beat stops due to lack of oxygen and energy. Thirty minutes without heart beat most of the cells are dead. If death is defined as a state from which traces of ‘life’ are irreversible lost, then there exist a state called ‘lifelessness’ between life and death. The frog actually does not ‘die’ during the winter, it just becomes lifeless once heat is taken out. The key difference between all these ‘states’ of biology is preservation of complex three dimensional structure. In death, both flow of energy and structure are irreversibly lost. But a ‘Lifeless body’ has a preserved structure with no flow of energy. When energy flow begins, the structure comes back to life. A seed is another example of a structure that is neither alive nor dead, it just waits in a state of lifelessness until it hits a fertile ground where it comes to life once energy flow begins. To gain good insight into these biological entities, we must review some fundamental concepts of thermal physics in simple terms.

Temperature, heat and absolute zero

Temperature is the easiest property of matter to get an intuitive understanding as we can directly feel it with our senses. Further inquiry into this concept reveals that it is related to the average kinetic energy of atoms and molecules within the substance. As the temperature of body increases, atoms move, vibrate, rotate and collide chaotically. It is this random chaotic movement of atoms that is measured as the temperature of a body. At room temperature, an oxygen molecule in the air we breathe moves at a speed of 1000 miles per hour. The apparent stillness that we see even in the quietest of the room is just an illusion. They all have atoms moving chaotically at the speed of bullets.

Absolute zero corresponds to the lowest temperature that is theoretically possible. It is equivalent to -273.15 degrees Celsius. At this point, all atoms and molecules are completely still and have no energy for motion. No events can happen in that substance and flow of time stops until the body interacts with another substance that has temperature or motion.

Heat is a form of energy that spontaneously flows from one body to another due to differences in temperature. Heat is not a property of a particular state of matter. It is a term to only describe the energy that flows between two systems in different temperatures. Once the heat energy is transferred to an object, it becomes a part of the internal energy of the system. How this energy will subsequently be distributed among the atoms depends on the underlying structure of the system. Let’s imagine a thought experiment in which a block of ice is placed inside a room with air at 25 degrees Celsius temperature. Here we have two systems, the ice and the air inside the room, that have dissimilar physical properties in contact with each other.

What events will unfold naturally and spontaneously with time?

Heat energy will flow into the ice from the air particles in the room. It will raise the kinetic energy(temperature) of the water molecules and allow it to have chaotic movement. With flow of time, this will break down the orderly crystal structure of ice. The heat will flow spontaneously from air into the ice until it’s temperature becomes 25 degrees Celsius. At this temperature, ice can no longer maintain its order and turns into liquid water with molecules in chaos.

Entropy, equilibrium and steady state

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If left alone the two systems will continue to undergo further changes spontaneously. These changes are not entirely random and there is a direction in which it always ‘naturally’ walks. Block of ice becomes a puddle of water. Then water molecules gradually leave the puddle and mix with air molecules. Changes continue to happen until all the water molecules have turned into vapor and become air. Eventually, the water molecules that were present in the ice at the beginning will be evenly distributed in the room full of air. At this point in time, all samples of air taken from the room will have the same temperature and concentration of molecules. This is called the state of thermodynamic equilibrium. The flow of time stops when the system reaches equilibrium. There will be no new events in this system between now and million years later. It will remain exactly the same. This is the definition of equilibrium. Time ceases to exist at two states of system, absolute zero and at equilibrium. At absolute zero, atoms have no kinetic energy and they exhibit no motion and hence no changes can happen. All dance and music exist between these two states when changes come to life. When heat enters a body that is at absolute zero, it makes the atoms to vibrate, rotate, bounce and collide. The ability to know the position and the energy of individual atoms will gradually be lost to randomness as it’s temperature increases.

Entropy is a fundamental property of matter that quantifies the degree of randomness in the distribution of energy within the system among its atoms and molecules. It is a physical property with a numerical quantity like temperature. My whole body at this point in time has a certain entropy value like it has mass and surface area. At a low temperature, the water molecules in ice has some degree of order and predictability. Once heat enters the system, the random motion increases. It becomes hard to know how the water molecules and it’s energy are distributed at 25 degrees Celsius. Once all the water molecules are evenly distributed among the air molecules, the entropy increases to the maximum and it becomes even harder to know the details of the molecular system. This spontaneous tendency of all natural system to progress to a state of more and more random distribution of matter and energy with time is an inescapable property of the universe. Everything in nature evolves to a state of equilibrium with maximum entropy over time. This is the second law of thermodynamics, an unassailable essence of nature.

Nothing is certain in life except death, taxes and second law of thermodynamics

Seth Lloyd

Before we go to biological systems, I want to simplify one other concept. In the same thought experiment, let’s replace the block of ice with a carat of diamond.

What kind of evolution will happen between the diamond and the air at room temperature?

What will happen to the orderliness of diamond’s crystal structure over time?

Diamond will remain still inside that room for millions of years. No perceptible change will occur. Room temperature of 25 degrees Celsius is equivalent to absolute zero for the tightly bonded carbon atoms in diamond. The chaos due to thermal motion is not strong enough to disturb the stability. However if the air in the room is heated to 763 degrees Celsius, the oxygen in the room will begin to interact with the diamond rock. Events will begin to happen, time will unwind and the rock will slowly be chipped away. Eventually with time all of the diamond will turn into carbon dioxide vapor and ultimately it will lose all the orderliness at that temperature. The system will come to a new equilibrium with maximum entropy in which all the carbon atoms that were meticulously arranged by millions of years of gravitational pressure are now thrown everywhere in the room randomly by the heat of 763 celsius. This example is to show that all systems are in a state of stillness at absolute zero. But the motion begins at different temperatures for different systems depending on the sturdiness of the underlying structure.

In the same thought experiment imagine a situation where something that has a freewill decides to preserve the puddle of water in the same state forever while the universe is trying to pull it towards equilibrium. The freewill must design a device that can measure the number of water molecules that escapes from the puddle into the air and replace it promptly and constantly. Here as long as this device works successfully, the water puddle remains exactly the same for an outside observer. This is defined as a steady state. In this state of system, there is a constant flow of matter and energy from system to the environment due to the natural tendency to decay. However homeostatic mechanisms that are built inside the system can constantly measure and correct in order to maintain the system at a steady state and prevent it from decaying to the uniformity of equilibrium.

Absolute zero – Temperature at which no atomic motion exist and hence there can be no time and no change

Equilibrium – State at which the system is at maximum entropy with complete randomness. The atoms in this system are all uniformly distributed and there is no net flow of matter or energy within the system. Macroscopically the system has no detectable change and time ceases to exist.

Steady state – A state of the system that exist at some point between absolute zero and complete equilibrium. In this state the system continuously exchanges matter and energy with the environment but still it remains intact due to the compensatory mechanisms. Systems naturally decay. But continuous and organized work and energy input prevents the progressive increase in entropy.

I suppose in the end, the whole of life becomes an act of letting go, but what hurts the most is not taking a moment to say goodbye

Life of Pi

In biology, equilibrium means death

The structure and motion of life exist in the midst of molecular storm of heat. Living system has a highly complex and orderly organization of trillions and trillions of molecules. This is a very low entropy state and at body temperature of 37 degrees Celsius, all these molecules would have enough energy to slowly consume this order with time. If unattended, it will crumble into equilibrium. These structures stay alive in a steady state by constantly exchanging material and energy with environment.

Cells maintain a steady state with tiny water spaces between the cells(interstitium)

Organs maintain a steady state with blood.

The whole body maintains a steady state with the outside environment.

If a cell is kept outside in air. It will instantly dry out and crumble. If put in water, in seconds the water will burst it open. If an organ is kept outside the body at room temperature, it will become featureless in an hour. All of this is due to the effect of molecular motion due to temperature. All systems decay into a state of equilibrium. In biology, equilibrium means death. Steady state is life and homeostasis is maintained by performing work by utilizing energy.

No other part of science has contributed as much to the liberation of the human spirit as the second law of thermodynamics

Peter Atkins

Steady state in a cell

Cell is a very tiny unit of life. Its structure has fascinated physicists. Erwin Schrodinger in his influential book, What is life? eloquently expressed his awe on how such an immense degree of order could exist in a very tiny space in the midst of the storm without crumbling into chaos. Cell is actually a very tiny drop of water with millions of molecular machines inside it. These machines perform the work of maintaining the order inside the cell and the functions that contribute to the stability of the superstructure of the organism. It is in contact with water outside of the cell called interstitium. There exist a chemical and electrical disequilibrium between the inside and the outside of the cell. This disequilibrium is extremely important for the cell to stay in a steady state. At body temperature, this disequilibrium continuously tends to dissipate. There are molecular pumps on the surface of the cell that constantly perform the work to correct the dissipation. This is similar to our device that we saw in the thought experiment that was trying to maintain the puddle of water. These pumps require constant energy supply to perform its work. A brain cell spends about 50% of its energy to support these pumps(Na+/K+ -ATPase). This is precisely why we need oxygen and energy continuously. Once you cut off the blood supply to brain, these pumps instantly fail to do the corrective work and the cell will unavoidably begin its march from steady state towards equilibrium and surrender itself to the second law of thermodynamics by dissolving into chaos.

If the same brain cell is kept at a very low temperature, the kinetic energy of all the molecules within the cell will drop. At this point the disintegration may stop and the cell wont need any energy for preservation. However in this state, with no flow of energy, the cell will be ‘lifeless’ but not dead. Once heat is transferred, both life and decay will begin simultaneously. Heat behaves both as a creator and a destroyer once it walks into the cell. It drives disintegration, but it is the same molecular motion of heat that also kick starts the tiny machines or enzymes inside the cell. The function of the pumps and enzymes in the cell depends on heat and temperature. Even the most fundamental process of life, oxygen transport to cells from air, is driven by thermal motion and it is called as diffusion. Every species of life has a range of temperature within which the forces of dissipation and the constructive work of enzymes can stay in a homeostatic balance. Life is a molecular dance that exists between the stillness of cold and the randomness of heat.

Photo credit – https://www.flickr.com/photos/djou/

Going back to the wood frog…

Now it is bit easier to understand the mystery behind the wood frog’s resurrection. Winter takes the heat out of the frog’s body. This will reduce the random molecular motion and the tendency to dissipate towards thermodynamic equilibrium(death). The requirement for oxygen, food and energy stops as the work needed to maintain the biological organization ceases. This will allow the frog to enter the lifeless state. Evolution has armored the frog’s cell with the capacity to prevent the water from freezing even at sub zero temperatures. As the temperature falls, the cell produces copious amounts of sugar and other solutes that dissolves into cell’s water. This results in freezing point depression and allows water to stay without turning into piercing ice crystals. Once the air warms up in spring, heat spreads throughout the body and agitate the molecules again. Motion and destruction will begin simultaneously to indulge in a mortal dance until one consumes the other in the path of time’s arrow.

அந்த தெய்வ ரகசியம் புரிகிறதே

இங்கு எதுவும் நிலை இல்லை கரைகிறதே

Na. Muthukumar

3 thoughts on “Molecular Dance

  1. Excellent read with good analogies. I haven’t heard about wood frog before. Its survival or adaptation is amazing. While humans have used his knowledge to control the energy flow and invented various HVAC(heating, ventillation and Airconditioning) techniques to adapt in cold areas, these little creatures(wood frogs) have gone miles ahead to adapt themselves in these harsh environments. The survival technique is phenomenal.

    Liked by 1 person

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