Origin of life page

The origin of life

The origin of life in 9 steps

Encyclopaedia Britannica on the Origin of Life
Similar to the phosphor bond in ATP, the peptide bond in polypeptides does not require free energy during dry conditions, but the formation does cost energy in water.
As it has been proposed [ Blac70] that some of the first enzymes could catalyze the reactions of multiple substrates, it is proposed that pF₁, in addition to its phosphorylation reactions, could also condense amino acids or peptides to larger peptides during thermal cycling by synthesis of a peptide bond [ Mull95].
Using PTS, an early pF₁ thus could during repeated thermal cycling synthesize a proteins, and even a library of proteins. In the PTS model for the origin of life a - probably small - part of this library had itself this multiple substrate condensing ability. In this sense pF₁ could therefore propagate, making daughters with identical capability, but not with identical composition.

The pF₁ and PTS concepts permit an origin of life model, with as partials steps:

Small biomolecule synthesis
Large biomolecule synthesis
Protocell formation
Convection
Condensation during thermal cycling
Information formation
Information processing
Information storage
Conversion to isothermy

The origin and function of these hardware components is now treated in more detail:

Step 1: Small biomolecule synthesis

Amino acids

Recent reports mention the synthesis during extraterrestrial conditions of amino acids on ice crystals under UV light [Bern02, Muno02]. They have also been detected in meteorites [Maut95], and have also been found in Miller's classical experiments [ Mill53, 55]. The presence of amino acids on the primitive Earth is therefore plausible.

More generally many small biomolecules have been found in outer space recently as well [Ehre00, Char00].

Step 2: Large biomolecule synthesis

Bernal has proposed the formation of polypeptides from amino acids during the drying of tidal pools at low tide and at mild temperatures (~50°C) [ Bern67].

Proteinoids
Fox has demonstrated condensations of amino acids during dry conditions just above the boiling water of water (~120°C) [ Fox59, 72, 80, 81, 88, 91; Laha78]. Fox called the products proteinoids. Proteinoids can have molecular weight as large as 6000. They should be considered to be proteins, as the amino acids may be linked by other than peptide bonds.

Polypeptides

Other researchers have demonstrated polypeptide formation during heating of amino acids in concentrated salt solutions [ Schw92, Saet93].
Recently a new variation of polypeptide synthesis has been reported by Matsuno. The peptide bonds is formed when water is split off from the -COOH and -NH₂ groups present in two different aminoacids or peptides. Given for instance two amino acids, the peptide bond reaction can occur twice, leading to the formation of a diketopiperazine, which has a ring structure. At first sight diketopiperazine seems a showstopper for peptide elongation. Matsuno has however observed that an amino acid can react with several diketopiperazines: the rings can be broken up, and combined to form a long elongated polypeptide. The reaction would occur during hydrothermal vent conditions [ Futa??].

Step 3: Protocell formation
vesicles Vesicles have been observed in primordial material [Maut95, Dwor01]. Such compartmentalization can help in selection processes, and may offer some protection of larger biomolecules against for instance hydrolysis.

Proteinoid microspheresproteinoid microspheres, with the shape and size of bacteria [ Fox5959, 72, 80, 81, 88, Yana88]. Sidney Fox has proposed a major role for proteinoid microspheres in the origin of life. The microspheres have many interesting properties: they resemble bacteria, their membranes can support an electrical potential difference, they can divide, they are subject to selection. More experimental progress has not been made with these microspheres, though. Fox claimed to have made life with his microspheres, but other origin of life researchers did not follow him in this. Lahav [ Laha99, p 242] gives a rather qualified validation Fox's work. My opinion is that the proteinoid microspheres are a big experimental step forward, a step that may temporarily have fizzled out. What is important is that the microspheres can be obtained with simple means starting with amino acids. Fox's somewhat excessive claims should be separated from his experimental results which I consider as impressive, but which are not as conclusive as Fox claimed them to be.

Step 4: Convection

It follows from the Second law of thermodynamics that the self-organization of life is only possible by invoking a dissipative structure [ Hake78, preface], which as life did not existed yet, must be found in the inanimate world . Few inanimate dissipative structures are known. An interesting one is the maser or microwave laser (for a discussion of the laser as a dissipative structure, see [ Hage78]). In interstellar gas clouds masers form spontaneously [ Elit95], and one may wonder whether such a maser could somehow drive the origin of life. Other dissipative structures can arise from solutions of chemicals that are not in equilibrium: the dissipative structures manifest themselves as chemical oscillations. Such oscillations have been related to oscillations in Ca²⁺ content within organisms.
The most common self-organizing dissipative structure is however the convection cell. Interestingly, Paecht-Horowitz has invoked convection in the origin of life [ Paec84].
Convection is possible in a fluid, that is in a gas as well as a liquid. Several studies ([ Sage94]) have considered primordial reactions in a convecting gas. Aerosol and cloud formation would be the relevant processes.
For the purpose of this study, water is taken as the convecting fluid. A volcanic hot spring does function as the convection cell. The intensity of convection increases with the temperature difference across the cell, and by having an ice cover of the spring a large temperature difference is assured. In the literature there is some discussion on whether life started at a high or at a low temperature. Evidence supporting both temperatures has been given. TS shows that is no necessary contradiction, as a convection cell contains both high and low temperatures. The surface ice means that snowball earth, an early Earth covered with ice, is suited for the cradle of the origin of life.

Woese has already been proposed that the last common ancestor of all living organisms lived in volcanic hot springs [ Woes87].

Step 5: Condensation during thermal cycling

The properties of the proposed pF₁ have already been mentioned. pF₁ can perform PTS, i.e., it can condense several substrates resulting in phosphorylation or peptide bond formation while it is being thermally cycled. The mechanism involves the establishment of a local dehydrated environment within the enzyme, which helps the product to form. The product can only be released by a thermal unfolding of the enzyme. The mechanism thus is a thermal variation of the binding change mechanism for F₁ as described by Boyer and Penefsky.
The library of products synthesized by pF₁ contains itself some molecules with pF₁ capabilities.
The plausibility of the TS model for the origin of life depends crucially on the probability of the chance that a molecule in the library is a pF₁ synthesis. Orgel has claimed that such a process is highly unlikely [ Orge87]. The use of randomly constituted protein libraries is now standard practice in the commercial search for enzymes. By adding thermal cycling the chance of pF₁ formation could be experimentally determined. The chance is expected to increase with the salt concentration, as the decrease of water activity associated with the latter must decrease the free energy for a condensation reaction.
PTS capability may selects microspheres, as membranes are stabilized by phosphorylation of the membrane components [ Davi58, West87].

At the end of step 5 thus a very inefficiently propagating pF₁ has been obtained that has a metabolism, condensing substrates, that uses thermal cycling.

Step 6: Information formation

Generalising an idea of Dyson on the origin of RNA [ Dyso82, 85], it is proposed that the first information carrying molecules did not give a selective advantage to its parent, and that they were like parasites. They are present in that large part of the library of pF₁ products that does not have pF₁ capabilities. Some pF₁ is assumed to have been able to duplicate or replicate these information carrying molecules, which we give the name of pRNA.

Note the similarity with the PCR method for nucleic acid duplication, which also makes use of thermal cycling.

How pRNA was replaced by RNA cannot be modelled at this moment. The origin of the required ribose remains a major problem [ Shap86, 88].

Alternatives for RNA have been found such as peptide nucleic acids, which even can hybridize with DNA [ Niel91]. The author is not aware of alternatives that have all the capabilities of present day RNA, including its ribozyme activity.

So an assumption is made in step 6, the emergence of RNA. PTS is the energy source for its replication.

Step 7: Information procession

UNDER REVISION:
see preprint (2005): "Thermosynthesis as energy source of the RNA World: a new model for the origin of life"

The emergence of the genetic system
RNA perform three functions:
ribosomal RNA (rRNA) constitutes the major part of the ribosome, the place where proteins are synthesized, transfer RNA (tRNA) activates amino acids, and messenger RNA (mRNA), which contains the information for the peptide composition.
In the TS theory the ribosome enhanced the fidelity of pF₁ propagation. In a gradual process the precision increased, until a system making use of the genetic code had appeared [Hart75, 78, Eige71, 77, 81, Woes65, 77, 80a, 80b, Woes87, Dyso85]. Many reactions are assumed to have involved pF₁, other reactions may have involved ribozyme-like reactions.
By defining a simple function for the protein product, the plausibility of its synthesis is enhanced: the synthesis of a complex enzyme is not that probable.

Step 8: Information storage

Upon the acquisition of reverse transcriptase it has become possible to synthesize DNA. Appropriate thermozymes are obtained derived from present thermozymes for DNA transcription.

The genetic apparatus completed
After the emergence of the genetic system the rest of evolution can follow its Darwinian path. Gene duplication, enzyme diversification and enzyme specialization make the evolution of life simple.

Step 9: Conversion to isothermy

It would give an organims a selective advantage to have its enzymes being able to work during at a constant temperature instead of having a thermal cycling requirement. During evolution thermozymes are therefore expected to have lost this requirement. The loss may have been effected by making use of protein phosphorylation, which can be considered as a method to mimic thermal cycling of a protein, and, for membranes, by making use of Ca²⁺, which can increase the thermotropic phase transition of a membrane.
Some proteins may however have kept the thermal cycling requirement. Thermal cycling still is a requirement for many physiological processes: germination, vcell division, flowering, budding. Many organisms still are subject to thermal cycling, for instance our daily body temperature varies cyclicly, in women a monthly cycle exists; many organisms perform daily vertical migrations in natural waters, which because of a thermocline must often result in thermal cycling.

Discussion

The model for the origin of life is of interest for several reasons.
(1) It is often claimed that no comprehensive origin of life model is possible. TS shows that this is not true. TS is however not the only theory on the origin of life that claims to be comprehensive, there are others, see [ Laha01].
(2) Second, many organisms show a thermal cycling requirement for cell division or germination. In TS this requirement is interpreted as a possible relic of PTS.
(3) The origin of life must support a simple metabolism. Dyson has proposed that biogenesis comprised two steps, a first biogenesis and a second biogenesis [ Dyso82,85]. The first biogenesis would involve a primitive metabolism, and is identified with PTS. The emergence of the genetic machinery code constituted the second biogenesis; this occurs during the gradual increase in accuracy of pF₁ synthesis under the influence of information carrying molecules. Other models for the origin of life postulate large networks of enzymes (Kaufman, Lahav)[ Kauf93, Laha01]; the many required enzymes, and the large genome, make the proposed emergence of the genetic machinery however implausible.

(4) In the model proteins come first, and nucleic acids come later. Proteins take care of the required energy, information transfer capability is acquired later. It is often assumed that nucleic acids must have come present before proteins during the origin of life. But energy is required for information transfer - the computer has to be switched on before it can copy a file. Therefore, the chicken must have come before the egg.
(5) Since thermal cycling occurs on the surface of almost all celestial objects, and will also occur in convection currents underneath surface ice when this covers these objects, the origin of life could have happened almost everywhere in the Solar System.

The next page gives the details of a second mechanism for thermosynthesis, a mechanism that makes use of biomembrane: Membrane-associated Thermosynthesis.