30 May 2014

Crossing the Line Between Death and Life

In discussing Vitalism and science I mentioned the threshold between living and dead matter. I've already written at some length about the idea of life after death. I've argued that we need to consider Buddhist afterlife beliefs in the context of other afterlife beliefs and to see the structural similarities that make it very similar to other afterlife believes. I've also discussed the problem of transmitting information from one like to another and how pratītyasamutpāda was modified to try to preserve the Buddhist doctrine of karma.

In this essay I want to explore the threshold between death and life, and particularly in this direction, more closely. It seems to me that our perception cannot help but be biased on this subject because of the way we experience life and death. I also want to touch on the state of the field of abiogensis, the study of how living cells might have been created from a combination of non-living components. Of we still don't have all the answers to this question, but we haven't been looking for very long, just a few decades. For most of human history we believed that God, in one form or another, animated dead matter to make living things. Note that the issue of an interim state (antarabhāva) between death and life will be dealt with in a forthcoming essay.

The Quick and the Dead

Our usual perspective on the distinction between living and dead matter arises out of seeing living beings die.  Often if we're with someone who dies and it's calm enough to make observations, we will see that they simply breathe out and never breath in - they expire. Perhaps this is why life is associated with the breath? With no more in-breath the functions of life swiftly stop. I will deal with the issue of the breath and vitalism in a separate essay.

We do not directly witness a "new life" starting in the sense of conception or embryos developing and until very recently did not even know about gendered gametes fusing for form a new zygote. Certainly most of us never see so-called "dead" matter turn into "living" matter since it happens out of sight. We eat food in the form of once living but now dead living things, but we don't see the process of how that "dead" matter is incorporated into our living bodies. We don't see iron being encapsulated in a haem and becoming haemoglobin and transporting oxygen around our bloodstream We might even understand that this does happen, but we never witness it.

Any explanation for life must not only account for large scale beings like humans, but also for microscopic life and even for single celled organisms. The amoeba is clearly a living thing. If matter can enter and leave a living organism continually without ever affecting the status of the organism vis-à-vis' living, then we can explain this in two ways. 

On one hand we might say that as a cell absorbs, say, a molecule of oxygen that has been transported in the blood by haemoglobin, that individual molecule is endowed with jīva, becomes alive, and participates in the collective life of the being. But this sounds a little implausible since oxygen does the same chemistry outside living cells. If every molecule has it's own nano-jīva or some infinitesimal portion of a cosmic jīva then all matter is alive (to some extent). And if all matter is alive then the transition of a living being from alive to dead is just a matter of perspective, since the matter doesn't die when the person dies. The idea of a single life force, splinters into billions of trillions of tiny life forces that add up to a living being. The question is how we would distinguish jīva from ordinary physical energy. Here jīva and energy both do something similar, i.e. animate matter. The argument here is that individual molecules or even subatomic particles must have some animating force. Even so, since matter can appear dead we're still left wondering what is different between a handful of clay and a mouse. We haven't solved the problem of the distinction between life and death at all.

On the other hand we can see life as a property of the cell and see the matter, which comes and goes, as just a building block or a container for a singular jīva. This view is compatible with Vitalism and (more or less) Materialism. But it does mean there is no real distinction between living matter and dead matter; there's just matter and the distinction only applies to larger conglomerations of matter. For the vitalism something non-material (i.e. not made of matter) is added to the cell to make it live whereas to the materialist what is added is energy in various forms particularly heat and stored in chemical bonds.

Either way it seems that matter itself cannot be alive or dead. Matter is just matter. There's no such thing as living matter and dead matter. However there living organisms and dead organisms. So life is not a property of matter per se, but only of organisms. Though of course organisms are complex structures built of matter. 

We used to imagine that something must enter the body at conception in order to make it living. But microscopy has showed that even before conception the zygote is a fully living thing. Sperm are produced as living things in a male's testes. Eggs are living in the ovaries of females from before birth. In the reproductive cycle there is never a time when a cell is produced dead and becomes alive. New living cells are formed from dividing old living cells. All of our cells are from lineages of cell division stretching back at least 3.5 billion years old. So if we never really go from being dead to being alive then what role could a jīva play?

The only time we really need a life force to explain anything is 3.5 billion years ago when the first living organisms came to life. 


Our perspective on the threshold between life and death is almost exclusively focused on the transition from life to death because the transition the other way is invisible to us in every day life. However scientists have been able to "see" into this domain in new ways in the last century so - the field is called abiogensis meaning "originating from the non-living".

image: Duke
The classic experiment that kicked off this field recreated our best guess of the physical and chemical conditions in the earth's atmosphere 3.5 billion years ago. The Miller-Urey Experiment (1953) created a closed system containing a mixture of gases made up of water, methane, ammonia and hydrogen. The gases were subjected to a continuous electrical spark intended to imitate lightening. The experiment ran for a week and at the end it was discovered that a rich variety of organic molecules had been spontaneously synthesised. The products included many molecules essential to life including amino-acids that make up proteins.

Many subsequent variations of this experiment have been conducted and showed that by fine tuning the conditions almost all the molecules required for life might have spontaneously occurred on early Earth. New theories about the conditions on early earth have provided new avenues of exploration. In addition, analysis of meteorites has shown that they frequently contain organic compounds as well and may have seeded some of the important molecules to the "primordial soup". 

It's no longer beyond the scope of imagination for all of the required elements of life to have assembled spontaneously. Enclosed membranes made of lipids form under the right conditions; RNA molecules self-replicate and even noticeably evolve; amino acids occur in asteroids and meteors. It's only the last step that remains unknown. Just as quantum mechanics has broken down the barriers between physics and chemistry, the study of molecular biology is breaking down the distinction between chemistry and biology.

Life as a New Kind of Stability.

We've known for a long time that high energy systems are unstable and tend to find ways to shed energy and achieve greater stability. We understand this process as increasing the entropy in the system. Entropy can also be understood in terms of order: a highly ordered state has less entropy. With no external inputs systems tend to lower energy, less order, i.e. higher entropy states. So a drop of coloured dye in a container of water will diffuse until it is randomly distributed through out. A hot object will radiate heat until it matches the ambient temperature around it. If we add energy to a solid it will become a liquid then a gas (decreasing order) and vice versa.

Addy Pross, Professor of Chemistry at Ben-Gurion University, Israel, has suggested that living systems attain a new kind of stability that is different to the thermodynamic stability of minimal entropy states (Aeon Magazine). Over time the entropy of the universe increases. But living organisms bucks this trend. Living things at the molecular level is both high energy and highly ordered, indeed living things continually absorb energy rather than shedding it. In terms of thermodynamics living things ought to be unstable and short-lived. But living things are remarkably stable in thermodynamic terms. Pross calls this dynamic kinetic stability.

Pross argues that this dynamic kinetic stability is a feature of self-replicating molecular systems. For example, given the right conditions RNA molecules spontaneously self-replicate. But not always perfectly. All self-replicators will tend to exponential growth, but some variations replicate faster than others. The faster variants will come to dominate a system. A system of two RNA replicators which catalyse each other is even more stable.

Thus there seem to be two kinds of system stability: "one based on probabilities and energy, the other on exponentially driven self-replication." Mathematical of both kinds of system are relatively simple. Pross concludes: 
"This distinction does not trace the dividing line between living and dead matter precisely – but it does explain it, and many of the other riddles of life into the bargain."
The approach is explored in more depth and the state of the field of systems chemistry is reviewed in Ruiz-Mirazo et al. (2014) - see below. 


In trying to think about the distinction between life and death most of us are hampered by only having access to knowledge of the transition in one direction: living to dead. I would argue that even the conception process which involves the joining of two already living gamete-cells is rather abstract for most people. The bio-chemistry which describes the movement of matter into and out of living systems is opaque to non-scientists. Thus most of us are ill-equipped to understand the distinctions between living and dead organisms. Certainly many Vitalists still seek to frame the discussion in terms of living and dead matter despite this being anachronistic and inapplicable.

The science of abiogensis is far from providing a complete description of the systems that might have existed as precursors to living cells. The first serious attempts to recreate the conditions for living systems date only from the 1950s. It's easy to forget that it's only a few decades since such investigations began. It is relatively early days for this field and some significant progress has been made and there is no reason to believe that at some point a plausible set of starting conditions and pathways will not emerge. As Ruiz-Mirazo et al. conclude:
"Although chemistry operating on the prebiotic Earth must have been extraordinarily complex and heterogeneous, we believe it is not impossible to understand. A number of concepts and methodologies, developed over the past 30 years, are now mature enough to ensure a brilliant future for such an old and challenging endeavor of human beings: getting to know about their ancient origins from inert chemical matter."
The most important conclusion however is that there is no need to posit a life force which animates "dead matter". This aspect of Vitalism is entirely discredited. 


See also (updated 23 Apr 2015)
Attwater, James & Holliger, Philipp. 'A synthetic approach to abiogenesis.' Nature Methods 11, 495–498 (2014) doi:10.1038/nmeth.2893
Pross, Addy. 'Life’s restlessness.' Aeon Magazine
Ruiz-Mirazo, Kepa; Briones, Carlos; and Escosura, Andrés de la. 'Prebiotic Systems Chemistry: New Perspectives for the Origins of Life.' Chemical Reviews. 
Singer, Emily. How Structure Arose in the Primordial SoupQuanta Magazine. (16 April 2015)
Wolchover, Natalie. A New Physics Theory of LifeQuanta Magazine. (January 22, 2014)

25 Feb 2016.
A very interesting view on the origins of life is the Alkaline Hydrothermal Vents Origin Theory. One of the leading proponents of this theory is Nick Lane (who was interviewed this week by Jim Al-khalili on his Life Scientific radio show). A full length (71 min) description of this theory can be found on YouTube. I highly recommend this lecture. This is the most plausible theory of the origin of life that I know of. It also critiques the Miller-Urey approach, which never got beyond creating amino acids, and shows how to improve upon it. 

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