The Tree of Life

Remembering Lucretius Caro and Jay Stephen Gould

The Tree of Life
The Tree of Life
23 FEB 2017

Usually Charles Darwin is represented as an old man with a copious white beard, see below (figure 5) – which is not so fair, as he was famous already in his young age (figure 6), and when his famous book came out, in 1859, he was only fifty years old. It is not fair because this conveys the idea that he arrived at his theory of evolution in his mature age. And not many know that he sketched the first tree of life in his notebook (see figure 4), in 1837, when he was not yet thirty years old. He had come back from his famous trip around the world with the Beagle – which he started 1831, as a simple 22-years old paying passenger, and which lasted almost five years.

Note in that sketched page the first letters: “I think…”. The two little words were destined to produce the most terrific revolution in biology and all life sciences. It can be said, without fear of exaggeration, that after Darwin’ work, the world was not the same. He kept his book for many years in his drawer, not finding the courage to print it, as his theory was against the Christian religious view, actually it would have been seen by many, including his devotee wife, as a blasphemy: the main idea of the book was in fact that the living species were not created by God once and for all – but that they were the product of evolution from primordial forms, and all were coming from a common ancestor – a unique, ancestral form of life, having perhaps a natural origin, and not a divine one. A pristine original form from which life had being evolving spontaneously in many directions without any predetermined aim. This story has been told many times, and here I will limit myself to a few side considerations about the tree of life.

Let us begin by looking at a modern version of the tree of life, although in a very simplified version. Figure 3 shows the three life kingdoms, (the bacteria, the eukarya and the archaea) from which all living organisms on our planet have originated. The figure is oversimplified mostly among the eukarya (our domain): the term “animals” should branch out in many different directions, one of these should be “mammals”, and this should also branch out in very many different species. And so should be for “plants” or “fungi”.

All these lineages of descent have been determined by analysing and comparing the nucleic acid structures of the various organisms, with the basic idea that the species with a more similar genome were closer in the evolutionary scale, while those which had very different genomes were more distant from each other in the evolution. A complete tree of life should encompass all species present in our planet, around one million or so. And the importance of this statement should not be underestimated.

Thus, imagine an Alien who comes to study what is life on our planet. He would be amazed by the observation that each living species is a historical product, and in fact, starting from, say, the genome of homo sapiens for as many as ten million years back, he would arrive down to the first primates, and from this, he would go back to the first mammals, arriving than to the multicellular forms of life, and from those to an original unicellular organism LUCA, last universal common ancestor. But our Alien would arrive to the same final point also starting from a fish, from a pelican, or from a daisy, finding several inter-crossing nodes. He would then conclude that all forms of life on Earth are historically and causally linked to each other, where causally here means here that each species is a descendant from a preceding one.

The tree of life is in fact the most beautiful expression of the systems view of life – a gigantic web of organisms which are interconnected from the historical point of view and which presently are linked to each other by an incessant flow of common molecules (for a more complete understanding of the systems view of life, see the recent books by Capra and Luisi). Indulging a little in rhetoric, we can say that the tree of life is the most spiritual rendering of biology on Earth, as it shows that all living creatures are linked with each other, and indulging a little bit more in rhetoric, we can then say that we are all brother and sisters – with all animals and plants.

The creativity of contingency

Having said that, we can now pass to what for many people, particularly for believers, is one of the bitter pills of Darwinian evolution. This is the statement, already made above, that evolution proceeds without a predetermined plan. There was no predetermined plan to make bananas, or swans or sharks. So, how did they come out?

By chance? This word would not be completely correct. In fact, in order to answer this important question in the terms accepted by the largest majority of biologists, such as Ernst Mayr, or Stephen Jay Gould, or Christian de Duve, we have to introduce the notion of contingency – the major driving force of evolution. Contingency is the set of independent environmental and chemical parameters which happen to be operating in that certain place in that certain time thus affecting the structure of the growing unit. Gould, looking at the Cambrian revolution, which signed the major development of multicellular organisms after the hegemony for two billions years of unicellular life, wrote that famous sentence: “run the tape again… ” meaning that by repeating the time course of evolution at that point but under different environmental conditions, the passage from uni- to multicellular life might have taken twelve instead of two billions years. Or, it might never have taken place. This implies, by the way, that mankind might have not come out then, or ever.

Why contingency is not chance? To understand this point, consider figure 1, (from my recent book on the origin of life) which may represent a peptide structure p which is growing in evolution. In the pathway, p comes to interact with five shorter peptides, indicated as a, b, c, d, e. If pure chance would be at work, p would react randomly with one of those, or with all of them. But in fact, given the structural determinism of p (for example, because it is positively charged) and because of the contingent conditions of the environment (like acidity, pressure, temperature, concentration… ), p will react only with, say, b. And the formed, pb, proceeding in its zig-zagging, would encounter other reaction partners (indicated as u, v, w, x, z) and because of the particular conditions operating there in that moment (by contingency) we would arrive at pbz.

Now, those compounds a, b, c, d, e and eventually u, v, w, x, z are there by chance – but the way of growing of p and eventually pb is not determined by chance, is not a random event, is due to contingency. If the environmental conditions would have been different, then the reaction course and the final product would have been different. Thus, our banana could have come out black instead of yellow – or might have not come out at all. And so for mankind.

All the above can be expressed in a different way, by affirming the primacy of structure over the function. Nature, evolution, constructs structures with the driving force of contingency. The structure may – or may not – display a function. The main point is, that the function is secondary to the structure. This is another “hard pill”: there was no plan to make a beating heart, or a photosynthetic machinery, or the enzyme alcohol dehydrogenase. They came out as the result of the erratic zig-zagging of contingency. First came the structure, eventually the function. Difficult to comprehend, difficult to accept?

Well, let’s go back in time two thousand years, and listen at what Lucretius in his De Rerum Natura, from the verse 833, was writing (obviously in Latin):

… nothing is part of our body
To be used in a very precise manner.
It is the use that originates from the organ:
"sed quod natum est id procreat usum"
Nobody has ever seen before having the eyes
And nobody spoke before having the tongue
But the tongue existed before the spoken language
And the ear arrived to us before we heard the sound
Therefore, one should say
The organs all existed before the function:
Therefore, they did not develop at the aim of giving us a service …
The habit to give rest to the body when the body is tired
Is much older than the invention of the bed
And everybody was able to drink
When there were no cups around…
Other things existed out of a spontaneous creation
And only later they could be of some use
Among those things, certainly
The reason, and the arms.
We need therefore to reject the false theory
According to which all this was given
To serve to us.

It is simply astonishing that a man, a poet, should write a page which could have been written by Jay Stephen Gould two thousand years later. And something that our Creationists today cannot yet see and comprehend.

S. J. Gould, Wonderful Life, Norton, New York, 1989.
F. Capra and P. L. Luisi, The Systems View of Life - a Unitarian Vision, Cambridge Univ. Press, 2014.
P. L. Luisi, The Emergence of Life, 2nd edition, Cambridge Univ. Press, 2016.
T. Pievani, La Vita Inaspettata, Cortina, Milano, 2011.
E. Mayr, Towards a New Philosophy of Biology, Harvard Univ. Press, Cambridge, 1988.