Hello, my name is Wim Hordijk.
In this lecture,
I will introduce the concept of autocatalytic sets
and why I believe they are relevant to origin of life studies.
But, before I do,
let's review the main hypothesis of how life may have started.
The dominant paradigm in origin of life research
is that of an RNA world.
RNA is a similar kind of molecule as DNA
but mostly exists in single-stranded form.
So, instead of forming a rather inert double helix structure like DNA,
RNA molecules fold into a complicated three-dimensional structure.
This allows them to be chemically active.
In particular, some RNA molecules
are able to catalyze chemical reactions between other RNA molecules.
Initially, the origin of life problem revolved around
the chicken and egg question of -
which came first, DNA or proteins?
DNA molecules store genetic information,
which is translated into proteins that act as catalysts.
But, some of these protein catalysts, in turn,
are necessary to replicate and translate DNA.
Hence, the catch-22.
However, RNA can fulfill both of these roles.
It can store genetic information because of its similarity to DNA,
and it can act as a catalyst because of
its chemically active structure - just like proteins.
This gave rise to the idea of an RNA world:
life starting with a few self-replicating RNA molecules
that were responsible for both the replication
and expression of genetic information.
Such an RNA world would be a selfish world,
where each RNA molecule is responsible for its own replication
and where different RNA molecules would be competing for resources,
such as individual nucleotides.
However, despite the attractiveness and simplicity of this idea,
nobody has been able to show that RNA can indeed catalyze
its own template-directed replication.
What has been shown experimentally though,
is that some RNA molecules can catalyze the formation
of other RNA molecules from shorter fragments.
Moreover, there are experimentally constructed sets of RNA molecules
that mutually catalyze each other's formation.
In other words,
rather than having each RNA molecule catalyze its own replication,
they all help each other's formation from the basic building blocks
in a cooperative molecular network.
The first example of such a mutually catalytic network
was constructed in the lab of Günter von Kiedrowski in Germany.
It consists of a cross-catalytic pair of short nucleotide sequences.
The basic building blocks are trimers A and B
that form each other's base-pair complement.
The hexamers AA and BB now serve as templates
to which the complementary trimers can attach by forming base-pair bonds.
For example, two B trimers can attach to an AA template,
allowing the B trimers to ligate - or chemically join -
into a fully formed BB hexamer.
After strand separation, the original AA template is regained,
plus a new BB template.
In a similar way, such a BB template can facilitate
the ligation of a new AA template from two A trimers.
More recently, an experimental system with up to 16 RNA molecules,
each of around 200 nucleotides long
that mutually catalyzed each other's formation from shorter fragments,
was created in the lab of Niles Lehman at Portland State University.
However, such experimental systems are not restricted to RNA molecules.
A similar set of nine mutually catalytic peptides - or short proteins -
was created and studied in detail by Gonen Ashkenasy and colleagues,
then at the Scripps Research Institute.
What these experimental systems of mutually catalytic molecules
have in common is that they are all instances
of an autocatalytic set.
An autocatalytic set is defined as
a set of reactions and the molecules involved in them,
such that: 1. Each reaction in the set is catalyzed
by at least one of the molecules from the set itself
and, 2. Each molecule in the set
can be produced from a basic food source
through a sequence of reactions from the set itself
The food source consists of basic building blocks,
such as the RNA or peptide fragments in the experimental examples,
or the molecules that were present on the early Earth
in a purely prebiotic setting.
In other words, the food source consists of those elements
that can be assumed to be available in the environment.
Note that this concept of an autocatalytic set
captures two essential properties of living systems.
First, all chemical reactions are facilitated and regulated
by catalysts generated within the network itself.
In other words, the system is catalytically closed.
And, second, it is self-sustaining from resources available in the environment.
This figure shows a simple example of an autocatalytic set
formed by a reaction network where the molecule types -
the black dots - are represented by bit strings,
that is, strings of zeros and ones.
The food source consists of the monomers and dimers,
or bit strings of length one and two.
The longer molecules can be built up through ligation reactions -
the white boxes - between two shorter bit strings.
Solid black arrows indicate reactants going into
and products coming out of a ligation reaction,
and dashed gray arrows indicate which molecules catalyze which reactions.
Given the definition of an autocatalytic set,
it is easy to verify that this reaction network satisfies its two properties.
Note that this simple example
is similar to the experimental systems that have been constructed in the lab.
This concept of autocatalytic sets
was originally... introduced by Stuart Kaufmann,
in descriptive form already back in 1971
and more formally in 1986.
More recently, my colleague Mike Steel and myself
have done more detailed studies of autocatalytic sets,
both mathematically and computationally.
What these detailed studies have shown
is that autocatalytic sets have a high probability of existing
in simple models of chemical reaction networks -
also for chemically plausible levels of catalysis.
For example,
in this simple bit string model where catalysis is assigned randomly,
each molecule only needs to catalyze
between one and two ligation reactions on average
to already have a high probability of autocatalytic sets to exist
in random instances of the model.
Furthermore, it turns out that autocatalytic sets
often consist of a hierarchy of smaller and smaller autocatalytic subsets.
In other words,
a given autocatalytic set often contains several smaller subsets
that themselves also form autocatalytic sets.
For example, this autocatalytic set of five reactions
contains two smaller autocatalytic subsets -
one of two reactions and one of three reactions.
Here is another example from the same bit string model,
which shows an autocatalytic set of eight reactions
containing various smaller autocatalytic subsets,
as indicated by the differently colored shapes.
This hierarchical subset structure
can enable the existence of different types of protocells.
Imagine two compartments formed, for example, by lipid membranes,
which have been shown to form, grow and divide spontaneously
under appropriate circumstances.
Now, assume that
the same chemistry can take place in both of these compartments,
but in one of them
only the red autocatalytic subset is currently present,
and in the other one only the blue autocatalytic subset.
This would form two different types of protocells,
which might compete with each other for food resources -
in this case the monomers and dimers -
and perhaps even give rise to some simple evolutionary dynamics.
Computational studies have shown that autocatalytic sets
are indeed able to evolve and become more complex over time,
exactly because of this existence of multiple autocatalytic subsets.
This is shown here with simulated protocells changing color over time,
depending on which autocatalytic subsets they contain.
These results are mostly based on
computational models of chemical reaction networks
such as the Bitstream model.
However, the formal autocatalytic sets framework
has also been used to study and understand
the existing experimental networks in more detail,
both the RNA one and the peptide one.
Moreover, we have shown that the metabolic network of E.coli
forms a large autocatalytic set.
This supports the original claim
that autocatalytic sets capture essential properties of living systems,
in particular the catalytic closure and self-sustainability.
So, autocatalytic sets are not just abstract mathematical constructs,
but they do exist in real chemical and biological reaction networks
and can be studied formally within those systems.
In conclusion, given that autocatalytic sets are highly likely to exist
in simulated chemical reaction networks,
that they are able to evolve and become more complex,
and that they actually exist
in real chemical and biological networks as well,
an alternative scenario emerges for a possible origin of life.
Perhaps life started with the spontaneous formation
of one or more autocatalytic sets, which then gradually... diversified
and evolved into more and more complex chemical networks,
eventually leading to true metabolic networks.
In other words, life arising as a cooperative effort
among diverse molecule types and catalytically closed
and self-sustaining chemical reaction networks.
I believe there is grandeur in this view of the origin of life.
Of course, there are many details that I have not been able to go into.
But, here are some pointers to further reading.
The first one is a popular science article
that tells the story along similar lines as what I have presented here,
but with more details.
The second one is a more technical review article.
These articles,
and all our other publications on autocatalytic sets,
can be found through my personal website.