Skip to 0 minutes and 27 seconds We have with us professor Juli Peretó of the University of Valencia, and he is also vicedirector the Institute for Integrative Systems Biology (UV-CSIC) He has been working for a long time on the origin of life, on the primitive, -the most basic- biochemical reactions that gave rise to life, and he is here today to answer some of our questions. Can Physics and Chemistry explain life? And what has life added to the physical world?
Skip to 1 minute and 5 seconds Well, it is evident that Physics and Chemistry are necessary for explanations regarding all biological processes, but they are not sufficient in the sense that if you look backwards to the very primitive systems on early Earth, Physics and Chemistry would suffice to explain the diversity and the different molecules that were present in our planet,
Skip to 1 minute and 40 seconds making this kind of prebiotic soup from different origins: from cosmochemistry, from comets and asteroids, from volcanic chemistry or atmospheric chemistry, chemistry associated with the ocean… So, at this moment, we have good schemes for the origin of those molecules, from different energy sources like UV light, or heat, or electricity, organic chemistry in water in general, catalysis by minerals for example…
Skip to 2 minutes and 18 seconds But then, if you go through different levels of complexity, like the emergence of replicative polymers for example, some kind of replicative molecules, ribonucleic acid molecules able to self-replicate with variation, with mutation… So natural selection would emerge and in addition to Chemistry and Physics we must use terms or concepts like adaptation to understand the behaviour and response of those systems to the environment. So in summary, the laws of Physics and Chemistry are necessary for explaining life but are not sufficient. Do we understand the natural emergence of life on Earth? Is it reproducible?
Skip to 3 minutes and 31 seconds As an historical science, Biology will never know the complete details how life emerged on Earth. The scientific research on life origins must consist in formulating hypotheses that are plausible and testable in the laboratory. That mean that everything we can speculate or propose must have an empirical plausibility or, at least, we have to use computational models to test the plausibility of those hypotheses. So, everything must be compatible with all we know about Geology Astronomy, Chemistry or Biology but in addition to that, we have to give support to our hypotheses with empirical tests. If this is the case, we also could try to reproduce, at least in small scale, processes, systems that could be a model for those primitive stages.
Skip to 5 minutes and 1 second For example, we could –in fact we have– experiments of vesicles of a simple character based on fatty acids in water. Those vesicles have a very interesting behaviour in the sense that they are able to grow, to reproduce and even to compete between different populations of vesicles. And it has been also demonstrated that in vesicles incorporating inside nucleic acids, if you induce the replication of the nucleic acids, immediately this process has been related to the growth capacity and reproduction of the vesicle. So, maybe some biological-like processes in which we can observe this pure chemical systems are the fundamentals of properties that we assign to life but have very deep roots in this Physico-Chemical properties. These are problems of all historical sciences…
Skip to 6 minutes and 15 seconds Next would be: was the ancestral life very different from the present? Can present life help to understand the distant origins? Charles Darwin was proposing in a very wide way that all life on Earth has a common ancestor. So today, this conjecture is our best explanation of many communalities that we observe in living beings, for example the universality of the genetic code, the recurrent use of many molecules and metabolic processes… Many different aspects in biochemical and genetic traits of living things that are universally distributed can be assigned to this very old ancestrality.
Skip to 7 minutes and 18 seconds So we talk about the «Last Universal Common Ancestor (LUCA)» that are related to this very last community of cells that were the beginning of the main lineages of life, like bacteria, and arquea. So, scientifically, we can try to reconstruct this last common ancestor using the comparative method in Biology; that means, comparing the different biochemistries that are present in very different and distant lineages or the genomes of the organisms in different branches of the tree of life, trying to deduce this common ancestor.
Skip to 8 minutes and 11 seconds Of course this is very easy to say but very complicated to do in the sense that, for example, we are still developing the proper methods to do that and to manage these big amounts of data But also genomes are kind of incomplete historical documents in the sense that there are many contingencies that we must take into account like horizontal gene transfer or genes that were lost in different lineages. So, the idea is to reconstruct just this minimal denominator of all life but with important methodological difficulties. It is important to remark that trying to reconstruct by phylogeny this ancestor is very different from studying the origins of life.
Skip to 9 minutes and 16 seconds We are talking about two very different things in the sense that we don’t know the time distance between the origins of life and this last common ancestor but we can realize that, from the point of view of complexity, they were very different. We are talking about something similar to extant bacteria with a genetic code, ribosomes, many metabolic pathways well established, but in the origins of life we are talking about very primitive systems. So, we cannot go beyond, in the phylogenetic reconstruction to the origins of ribosomes or proteins. Of course in the origins of life there were no ribosomes or proteins. So, sometimes people are extrapolating the phylogeny to the origins of life but it’s not correct.
Skip to 10 minutes and 21 seconds Is it possible to «predict» the emergence of life? Or, in other words, may life exist in other places in the Universe? Well, I think that it is generally accepted that under a very narrow range of environmental conditions –organic chemistry and water, moderate temperatures…– you have a series of transformations and reactions given rise to the small set of molecules involved in life. So maybe those conditions were not very specific of early Earth but were present in different places of the Universe and in other Solar Systems. So why not?
Skip to 11 minutes and 12 seconds I mean, if you consider that given a set of molecules and a set of conditions, then the increasing complexity and the appearing of complex systems behaving with reproduction or replication and other properties we can recognize in very simple biological systems, it could be that life is present in many other places of our Universe.
Skip to 11 minutes and 45 seconds Is it possible to predict the direction of the evolution of life? In Evolutionary Biology we have many examples of similar solutions to similar problems. I mean, evolutionary convergence and analogous solutions are present in the evolutionary history. But we (scientist) are very skeptical about the prediction of any evolutionary pathway in the sense that always for all biological processes you have a fraction of historical contingency. So the greater the contingency, the weaker our capacity to predict [becomes]. So, for sure we can predict things that we are completely convinced that will happen, for example extinction. We know every single species that has lived on Earth will disappear.
Skip to 12 minutes and 47 seconds Of course existent species will disappear and in the ultimate extinction, even those species that are very resistant and very reluctant to any aggression like bacteria, will also be extinct in 4.5 billion (4500 million) years, when the Sun will explode and collapse all the inner planets. That’s the very last thing that will happen on Earth. Thank you very much.
Conversation with Juli Peretó
Juli Peretó, Professor of Molecular Biology at the Valencia University and Vice-director of the Institute for Systems Biology (UV-CSIC).
Has been working on many aspects of the basic origins of life, helping to understand that the biological meaning of natural selection can also be applied to the pre-biotic systems.
He is also working on the evolution of simple models, like the microbial ecosystems or the relationship of host-parasite interactions.
Important concepts from the conversation
1. Prebiotic soup (1’.47’’)
This is a classical term to explain the abiogenesis (natural process by which life arises from non-living matter, such as simple organic compounds) proposed by Oparin in 1924. In its modern form, it may be summarized by:
- The early Earth had a chemically reducing atmosphere.
- This atmosphere, exposed to energy in various forms, produced simple organic compounds ("monomers").
- These compounds accumulated in a "soup" that may have concentrated at various locations (shorelines, oceanic vents etc.).
- By further transformation, more complex organic polymers – and ultimately life – developed in the soup.
2. Catalysis (2’.20’’)
This is the increase in the rate of a chemical reaction due to the participation of an additional substance called a catalyst, which is not consumed in the catalyzed reaction and can continue to act repeatedly. In biology, many proteins act as catalysts and are called enzymes; they are essential for making the reactions that sustains life, that without them would happen at an extremely low rate, incompatible with life.
3. Replicative polymers (2’.30’’)
Life is a self-replicating machine that has to have self-replicating elements. There are several polymers (large molecules, or macromolecules, composed of many repeated subunits) that have this property of being able to make copies of itself. Among them the best known are the nucleic acids, RNA (ribonucleic acid) and DNA (deoxyribonucleic acid), that are essential parts of present life. In early life, there may have been many other replicative polymers.
4. Empirical (4’.43’’)
Empirical evidence is the knowledge acquired by means of the senses, particularly by observation and experimentation. It is at the base of scientific knowledge.
5. Vesicle (5’.12’’)
In cell biology, a vesicle is a small structure within a cell, consisting of fluid enclosed by a lipid bilayer, that is, a double layer of fatty acids. Vesicles form naturally during the processes of secretion, uptake and transport of materials within the cell. Alternatively, they may be prepared artificially.
6. Universality of the genetic code (6’.58’’)
The genetic code is the set of rules by which the information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells. This set of rules (equivalence of groups of three nucleotides of the nucleic acid for each aminoacid of the sequence of the protein) is universal among all form of life, a fact not due to physicochemical constraints but to a common origin of all living beings.
7. Last Universal Common Ancestor (LUCA) (7’.29’’)
The LUCA is the most recent population of organisms from which all organisms now living on Earth have a common descent; thus it is the most recent common ancestor of all current life on Earth. LUCA should not be assumed to be the first living organism on Earth. The LUCA is estimated to have lived some 3.5 to 3.8 billion years ago. The composition of the LUCA is not directly accessible as a fossil, but can be studied by comparing the genomes of its descendants, the organisms living today.
8. Phylogeny (9’.12’’)
A phylogeny is the evolutionary relationship among a set of species. In general it is represented in the form of a phylogenetic (or evolutionary) tree with a branching diagram or "tree" showing the inferred evolutionary relationships among the species based upon similarities and differences in their physical or genetic characteristics. The tree shows the ordered set of common ancestors between pairs of species. It is not just a classification, but a reconstruction of the evolutionary process among the species considered; in this reconstruction, it is important to use characteristics for which the tempo and mode of change is known.
9. Ribosome (9’.46’’)
The ribosome is a complex molecular machine, found within all living cells, that serves as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules, which comes from the sequence of the DNA (transcription).
10. Evolutionary convergence (12’.06’’)
Convergent evolution is the independent evolution of similar features in species of different lineages. Convergent evolution creates structures that have similar form or function but were not present in the last common ancestor of those groups. The recurrent evolution of flight is a classic example, as flying insects, birds, and bats have independently evolved the useful capacity of flight.
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