Origins of Life: A Closer Look Part II

Imitation is the sincerest form of flattery!

 

 

Continuing a critical analysis of Professor Jack Szostak’s Origin of Life scenario proposed here.

See Part I for comments on earlier sections of the video

The goal: to critically appraise each of the steps Dr. Szostak presents in light of the latest research findings that show that any such scheme of events is physio-chemically untenable from a purely naturalistic perspective.

Video Clock Time 10-30 mins

Dr.Szostak’s RNA chains contain homochiral ribose (D ribose) though he has not disclosed how this D ribose originated. This is a crucially important point that the reader must gain an appreciation of. This will be discussed on this page.

No D ribose, no nucleotides, and no oligonucleotide chains.

                                                            Imago

Dr. Szostak completely avoids another intractable problem for his chemical synthesis scenario; that of the homochirality of sugars and amino acids. As shall be outlined in the next section, this is a very exciting and fast moving arena of research (owing to the pressing nature of the underlying problem), but as I shall demonstrate, it is still a mystery.

One of the key molecular features of life is that its major polymers are built up from chiral molecules. Chiral molecules exhibit handedness. All celllular life on Earth utilises left handed amino acids ( L amino acids) and right handed sugars ( D sugars). The L and D forms of the same molecules are called enantiomers and can be distinguished by how they rotate the plane of plane-polarised light in aqueous solution (either to the left or right) Because amino acids and sugars in all life on Earth exclusively incorporate L and D enantiomers, respectively, they are said to be homochiral.

The problem begins when scientists set out to explore synthetic means of producing molecules such as ribose, which almost invariably produce a 50:50 mixture of both enantiomers. Such a condition is said to be racemic.

To maintain biochemical viability, the ribose must be 100 percent in the D enantiomeric form; mixtures will soon grind any synthetic scheme to a halt.

Reference: Biochemistry Voet, D. & Voet J.D, (2011) Wiley pp 74-75.

Looking for solutions: what the latest research (as of 2015) has revealed

Scientists have been searching for many decades for a solution to the homochirality problem. One source was shown to occur via the production of 100 per cent circularly polarised light derived from the vicinity of black holes and neutron stars. This light selectively destroys one enantiomer over the other, with the result that one chiral form is selected for. The problem with this astrophysical source is that it only generates 20% enantiomeric enrichment, not enough to allow life processes to proceed or to explain the homochirlality problem.

Reference: Hazen, R.M., Life’s Rocky Start, Scientific American (April 2001)  77-85.

Molecules are not the only entities that exhibit mirror images of each other. In physics, the parity principle states that physical processes that display symmetry about a central plane operate as mirror images. According to this principle, nature shows no preference for either left- or right-handedness. In the 1950s however, physicists discovered an exception to this rule, referring to this interesting idea as a parity breaking. Chinese physicists demonstrated that the electro-weak force displays a slight preference for left-handed  amino acid enantiomers . When a radioactive nucleus undergoes decay, it emits polarised light with a slight left-handed bias. Some physicists have suggested that this parity breaking could have led to homochirality. But since the energy difference between enantiomers is only of the order of 10 J Mol^-1 it would have no appreciable effect on chemical reactions, a situation endorsed by leading astrobiologists.

Reference: Rikken, G. L. J. A. Rikken & Raupach, E., Enantioselective Magnetochiral Photochemistry, Nature, 405 ( 2000), 932-35.

The inconvenient truth about homochirality in biochemical systems has led some more zealous scientists to uncover chemical means to surmount the problem. The most promising of these will be discussed here.

One way to create some chiral excess is a process called oligomerisation. Biological polymers are built up of subunits called monomers. By chemically linking up these monomers a polymer is created. An oligomer is an intermediate state between a monomer and a polymer, usually having several tens of monomer units. Some laboratory studies have shown that oligomerisation reactions are inhibited  when a racemic mixture of monomers is incorporated into the reaction.Specifically, if the researchers add the opposite enantiomer of a nucleotide during the oligomerisation of RNA nucleotides, the addition inhibits the reaction. This, some researchers have suggested, provides a way of producing homochiral polymers.

Reference:Joyce et al, RNA Evolution, pp 217-24.

The main problem with this model resides with the probability of assembling sufficiently long RNA oligomers for it to allow the process to occur in a realistic prebiotic setting. To get anything viable, at least 50 subunits must be routinely produced and preferably much longer chains. As a result, most researchers in the field now consider the probability of this mechanism favouring homochirality to be too remote to be a viable option. Others have suggested that enantiomers with the same handedness could react preferentially to form the oligomer chain. However, no such selectivity  has thus far been observed in laboratory experiments.

Theoretical work first conducted in the 1950s by the chemist F.C. Frank showed another way forward; Asymmetric Autocatalysis.

A chemical reaction in which one or more products serve as a catalyst is called autocatalysis. In this process, the enantiometric products selectively exert  their catalytic activity driving the production of one or more compounds of the same molecular handedness. In exact racemic mixtures, asymmetric autocatalysis would lead to no chiral excess. In reality however, chemical reactions are never an exact 50:50 mixture. Statistical fluctuations cause nearly imperceptible imbalances of enantiomers. This slight excess, created by statistical fluctuations- can be amplified. One demonstration of this mechanism is called the Soai Process, after the Japanese chemist, Kenso Soai, how first  elucidated it in the 1990s.

Reference:Blackmond, D.G,  Asymmetric Autocatalysis and its Implications for the Origins of Homochirality, Proceedings of the National Academy of Sciences (PNAS),101, (April 2004) 5732-36.

The Soai process involves the alkylation of pyrimidyl aldehydes by dialylzincs. The product of this reaction is a pyrimidyl alcohol that can exist in left- or right-handed enantiomers. Soai discovered that the alcohol products catalyses this transformation. As the pyrimidyl alcohol products are produced, statistical fluctuations cause these compounds to display a slight excess of one of the enantiomers over the other. This minor imbalance sets up asymmetric autocatalysis i.e. the more abundant enantiomer selectively catalyses the production of its corresponding chiral counterpart Over time, chiral excesses on the order of nearly 99 per cent can be achieved.

Soai’s discovery may sound like a plausible breakthrough to creating homochirality but significant problems remain. For one thing, the Soai reaction has no relevance in biological systems as none of the reactants and products have been documented in bona fide biological systems.In addition to this, this reaction is the only real-life example of asymmetric autocatalysis discovered to date.

Further theoretical studies of asymmetric autocatalysis reveal that the chiral excess produced by this reaction is short-lived; because it rapidly decays from near 99 per cent chiral enrichment back to the racemic condition (50 per cent) caused by the activity of the other enantiomer, which also acts as an autocatalyst, competing with its mirror image. Curiously, this does not occur in the Soai reaction because the enantiomer that achieves an excess not only acts catalytically but also acts as its own anticatalyst. The oddity of the Soai process is more a reflection of the scientist’s genius in recognising the underlying mechanism  and pursuing it experimentally and not a general chemical principle.

Other chemists and astrobiologists have looked for other autocatalytic mechanisms that are relevant to studies of prebiotic chemistry. In particular, chemist Sandra Pizzarello and Arthur Weber have shown that the amino acids alanine and isovaline (which show slight chiral enrichment in the Murchison meteorite) can catalyse the formose reaction leading to ribose.

Specifically, when amino acids that catalyse the formose reaction harbour a chiral  exess, the sugar products generated also display a chiral excess. In other words, the amino acids are able to transfer this chiral excess  to the sugar products. Researchers observed that when the amino acid catalysts were enantiomerically pure, the sugar products displayed a chiral enrichment of up to 10 per cent. Yet, as the enantiomeric purity of the amino acid declined, the chiral excess of the sugar products also decreased. Of particular note is that when the enantiomeric imbalance of the amino acid catalyst reached 10 per cent, the chiral excess in the sugar products became imperceptible.

Further research by the same scientists showed chiral enrichment when homochiral dipeptides were used as catalysts.

Reference: Pizzarello, S., Weber, A.L., Prebiotic Amino Acids as Asymmetric Catalysts, Science 303 ( February 20, 2004), 1151.

A dipeptide consists of two amino acids that have undergone a condensation reaction, linked by a peptide bond. Curiously, the dipeptide catalysts yielded an 80 per cent chiral enrichment, raising hopes that this could have been the breakthrough origin of life researchers were looking for. But, yet again, there are problems with this scheme of events. As shown in Part I, it is not at all clear where such homochiral dipeptides might have originated from. Carbonaceous chondrites have been suggested as a possible source. In addition, relatively high concentrations of these dipeptide catalysts were required in laboratory experiments to generate this chiral enrichment, so much so that stretches credulity that the concentrations required were ever attained on the primordial Earth. But there are more sonorous reasons why either asymmetric or symmetric autocatalysis could ever have been a viable option; which derives from the properties of chiral molecules themselves.

Firstly, the dipeptide catalyts require extremely exacting pH and temperature regulation if they are to act out their roles. In other words, this phenomenon only works within very narrow temperature and pH regimes, something very unlikely to occur on the primordial Earth. A chemical process that does not have geological relevance creates a further problem for chemical evolutionary models for the origin of homochirality. Worst still, the examples explored above which generate homochiral excess are transitory at best. The reasons are due to the fact that enantiomers establish a dynamic equilibrium with each other that cause them to flip flop between enantiomeric states; a process called racemisation. This process causes enantiomerically pure compounds to transform over time back to their racemic form through structural inversion. Laboratory studies estimate that a set of homochiral amino acids would become completely racemic in one thousand years at 50 C and in one million years at O C under dry conditions, but much faster under aqueous conditions.

References:

Bada, J., Origins of Homochirality, Nature 374, (April 13, 1995), 594

Irion, R., Did Twisty Starlight Set Stage for Life, Science, 281 (July 31, 1998), 627.

The consequences of racemisation are troubling for chemical evolutionary scenarios, because even if homochiral excess could be achieved, it could not be realistically maintained  on the primitive Earth. The important point to remember here is that all such studies ignore, or fail to account for, the transitory nature of achieving chiral excess. This means that because the researchers have to stop and start their experiments as soon as they achieve some enrichment, they unconsciously cultivate a false sense of success.This is intelligent design through and through!

                                              A Closer Look at Hydrothermal Vents

Dr Szostak has emphasised prebiotic molecule synthesis at hydrothemal vents. The origin of these ideas come from a team of Japanese researchers who had searched for ways that homochirality could be produced at such sites. In their simulation studies, designed to mimic hydrothermal vents, these investigators noticed that both left-handed and right-handed versions of the amino acid alanine undergo racemisation from a pure state at 230 C in a matter of 30 to 40 minutes. To their surprise however, the left handed enantiomer is racemised to a slightly lesser extent than the right-handed counterpart. This effect was concentration dependent however, occurring when there was only unrealistically high concentrations of alanine present.

Reference:

Atsushi Nemoto et al, Enantiomeric Excess of Amino Acids in Hydrothermal Vents, Origins of Life and Evolution of Biospheres 35 (April 2005), 167-74.

                                                       PNAs and that…...

These studies prompted the late Stanley Miller to formerly acknowledge the intractability of the problem of homochirality’s origin. As a consequence, he proposed that the first replicating molecules were achiral peptide nucleic acids (PNA).

Reference:

Nelson, K.E., et al, Peptide Nucleic Acids Rather Than RNA May Have Been the First Genetic Material,  PNAS, 97 (April 11, 2000): 3368-71.

Miller was drawn to these models because he knew no meaningful progress could be made using sugar- or dipeptide-based catalysts, as discussed above. PNA chemistry is simpler, because neither does it contain sugar or phosphates and because they can form base pairs as well as helical structures. The nucleobases of PNA are joined together through a molecule of acetic acid and a chiral amino acid of non biological origin; 2-aminoethyl glycine (AEG). For a PNA origin-of-life scenario to be viable, a plentiful source of acetic acid, nucleobases and AEG had to identified. To date, only acetic acid synthesis has been achieved and AEG has not been detected either terrestrially or extraterrestrially.

Miller’s PNA molecules  have other problems however; they are stable; too stable.They bond very strongly to any daughter molecules they may have replicated but could only do so very slowly, too slowly to be relevant to realistic origin-of-life scenarios.

                                                             Mineral Surfaces

Another possibility for the origin of homochirality is via mineral surfaces, discussed by Dr. Szostak in his video. Some mineral surfaces can indeed generate chiral excess, which has given rise to some optimism in the prebiotic chemistry community.

Reference:

Hazen, R., et al, Selective Absorption of L-and D-Amino Acids On Calcite: Implications For Biochemical Homochirality, PNAS 98 (May 1, 2001) 5487-90.

This proposal involves clays and mineral surfaces with highly specific chemical and spatial orientations – like quartz and calcite – that can selectively absorb either left- or right-handed enantiomeric substrates. Curiously, it was discovered that when these surfaces were exposed to dilute solutions of amino acids, they will differentially become absorbed onto these surfaces creating a chiral excess.

Reference: Ibid

But let’s take a closer look at this process. For one thing the mineral surfaces must be ultra clean. The actual laboratory protocol for creating these surfaces involves successive washings in this order; deionised water, ultra-pure methanol, methylene chloride, more ultra-pure methanol and finally another soaking in deionised water. No contamination can be tolerated to even get the process started.

This in and of itself raises serious doubts as to the validity of using clay surfaces as loci for the naturalistic generation of chiral excess, as no real life site could be expected to offer such ultra clean surfaces. What is more, such crystal structures actually occur in two forms – opposite in their chiral specificity. This would produce only very small and geographically dispersed opportunities for any absorption to take place, preventing the build up of high enough concentrations of prebiotically relevant reservoirs of such molecules.

References:

Hazen, R., et al, Selective Absorption of L-and D-Amino Acids On Calcite: Implications For Biochemical Homochirality, PNAS 98 (May 1, 2001) 5487-90.

Thomas, J.A & Rana. F, The Influence of Environmental Conditions , Lipid Composition, and Phase Behavior on the Origin of Cell Membranes, Origins of Life and Evolution of Biospheres, 37( June 2007): 267-85

                                    Crystallisaton-induced Homochirality Studies

One more mechanism of achieving chiral excess has been recently explored; crystallisation. The great French chemist and microbiologist, Louis Pasteur was one of the earliest investigators of homochirality, when he was able to distinguish between L tartaric acid and D tartaric acid using a microscope. This chiral preference occurs with other substances too and leads to the formation of enantiomerically pure crystalline forms. This curious phenomenon has encouraged researchers to investigate whether this differential ‘sifting’ of prebiotic molecules on the primitive Earth could have led to homochirality.

When evaporated to dryness in the presence of a porous material, the amino acids, aspartate and glutamate will form crystals that are enantiomerically pure. But this is the exception rather than the rule because, under, normal circumstances the crystals usually form racemic arrays. However, in the presence of some porous materials, they can form supersaturated solutions during evaporation, and, as a result, produce chirally pure crystals.

Researchers led by Ronald Breslow (whose names also makes an appearance in Szostak’s presentation) of Columbia University suggested that it was in fact the material that was left behind in the solution during the crystallisation  event that was the source of the homochirality and went on to show this was indeed the case for the amino acid phenylalanine. While the crystal contained a racemic mixture of the amino acid, the aqueous phase became enriched with the enantiomer that initially showed a slight statistical excess. Furthermore, Breslow and colleagues showed that a chiral excess of about 1 per cent can be amplified to about 90 per cent after just two successive rounds of crystallisation. They envision a scenario on the early Earth, where carbonaceous chondrites might have seeded the oceans with amino acids. Tides would then wash these amino acids onto ancient beaches and, after evaporation, crystals would form and a slight chiral excess of the other enantiomer. This, they claim, would have slowly caused the build up of one enantiomer over the other, leading the way to homochirality.

Reference:Science Daily, Meteorites Delivered the Seeds of Earth’s Left-Hand Life, Experts Argue, (April 7 2008).

But this reasoning is flawed. Dr. Fazale Rana, in his recent book on the matter, Creating Life in the Lab, presented the reason why; amino acids tend to stay single in aqueous solutions and not form higher order structures like peptides. This is thermodynamically the most stable state for them in this environment. The Columbia University researchers have tried to counter this argument by suggesting that condensation reactions would begin during the drying out phase in this scheme of events.. But as Dr. Rana has pointed out, these amino acids would be a racemic mixture with little or no chiral excess. Thus, the mechanism proposed as the origin of homochirality would in fact inhibit the process! In addition to this, any dipeptide exposed to the fierce UV flux from the Sun (remember there was no ozone layer) would quickly degrade them. One need only look at how biotechnology companies recommend they be stored to verify this (personal communication). See here and here for examples.

Reference:

Rana, F., Creating Life in the Lab, (2011) Baker Books.

Summary:This section discussed at length the concept of homochirality, the handedness of life’s sugars and amino acids. Szostak’s RNA chains were all produced with pre-primed nucleotides, replete with ready made D-ribose. The work illustrated shows that producing D ribose under credible prebiotic conditions (and indeed the L amino acids) has not been satisfactorily achieved and that any process that attains significant chiral excess is actually the result of careful  adjustment of the experimental conditions and artificial selection of specified outcomes; again the manifestation of intelligent design. As we have seen, the inherent tendency for an enantiomeric excess to rapidly return to its thermodynamically most stable state, that is, racemic, would severely curtail or completely halt any realistic abiogenic scheme. The probability of achieving true homochirality via naturalistic mechanisms is very highly unlikely, if indeed well nigh impossible.

I leave you with a quote from Francis Crick and Leslie Orgel’s book: Life Itself

An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going.

Video Clock Time: 30-54 minutes

On Vesicles:

One of the basic properties of living cells is their ability to maintain a chemical environment distinct from the space surrounding it. Life exists in the world and despite of the world, but is not of the world. This is achieved by creating a membrane which separates internal chemistry from external chemistry. Researchers have known for many years that under laboratory conditions certain kinds of molecules – what Dr. Szostak calls amphiphiles – made from fatty acids and phospholipids, which can form spherical structures called vesicles. An amphiphile is a molecule which has has both hydrophobic and hydrophilic natures. We are all familiar with the old adage; oil and water don’t mix. That’s because oil does not have chemical groups that can stably interact with water, blending with it, to create a solution. They are said to be hydrophobic because their chemistry does not permit them to dissolve in water. Molecules that have the right chemical groups to stably interact with water are said to be hydrophilic. Sugars are good examples of hydrophilic molecules. An amphiphile, as its name implies, has both hydrophilic and hydrophobic properties, allowing them to form unstable suspensions in water, usually in the form of single-layered micelles. Phospholipids – the components of real cells – and fatty acids (discussed by Szostak) possess such amphiphilic properties. When shaken up in an aqueous environment, they arrange themselves in such a way that their hydrophobic ends huddle together, like oil, and their hydrophilic end points outwards to form stronger interactions with water. The most stable (read lowest energy) arrangements are spherical structures – the vesicles that Szostak describes in his video.

Superficially, these vesicles look like cells and have served as a starting point to create the protocells he describes. As Dr Szostak explains, these membrane-bound vesicles can segregate materials located inside them from their surrounding environment.

As well as providing a physical barrier from the outside world, membranes harbour proteins that act as channels and transporters of molecules both into and out of the cell . They also act as sensors of the environment, as well as energy transducers. Synthetic biologists such as Dr. Szostak have to figure out not only how to form vesicles but also enable them with a means of transporting substances across their boundaries. One way forward is to try to manipulate the chemical structure of these amphiphiles in such a way that they can incorporate proteins both inside and on the membrane in order to serve as pores, environmental sensors and energy transducers.

As most any high school student of biology will tell you, reproduction is one of the basic characteristics of all living cells and this ability fundamentally resides in its DNA, which is replicated and then partitioned into two daughter nuclei before the cell fissures. Scientists must thus find ways to encapsulate DNA (or in this case RNA) molecules within the vesicle. When supplied with the right mix of chemicals, the encapsulated genetic material can then be used to synthesise proteins, which in turn could at least set the stage for the replication of the ‘protocell.’ The trick is to find a way to get the vesicle to divide in two, and in such a way that ensures that each new daughter vesicle has a copy of the genetic material.

So the process can best be seen as a series of steps which include;
1. The membrane has to be assembled.
2. Development of an energy transducing capability by the boundary membrane.
3. Genetic material must be encapsulated into the vesicle.
4. Pore proteins must be added that can funnel material into and out of the vesicle.
5. Generation of membrane bound systems that allow complex molecules to grow.
6. Generation of catalysts to speed up any given chemical process within the vesicle e.g DNA/ RNA replication.
7. Introduction of information-rich molecules that can direct the synthesis of other molecules of benefit to the developing chemical environment within the vesicle
8. Development of mechanisms that cause the boundary membrane to subdivide into smaller systems that can demonstrate ‘growth’.
9. Development of a means to pass information containing molecules into the daughter vesicles.

As you imagine, this is an incredibly complex process, effortlessly achieved by even the simplest living cells, but the list serves to illustrate one approach to the creation of artificial life; the so-called ‘ground up’ approach. This is the approach adopted by Szostak and his team.

Starting in the 1990s, he and his colleagues have exerted great effort into getting vesicles to grow and divide, getting genetic material to replicate and evolve within these vesicles and the creation of artificial proteins by either synthesising them under laboratory conditions or utilising pre-existing proteins that have been genetically engineered. Szostak coordinates several teams of scientists who bring as many of these steps together to create states that indeed show some of the characteristics that we would recognise as ‘alive’.

Like all scientists, Szostak builds his work on the shoulder of others who have pioneered methods to produce vesicles from purified phospholipids, trap molecules of interest within them and then incorporate purified proteins into the vesicle walls. Synthetic biologists like Szostak strive to capitalise on the vesicle forming properties of amphiphiles in order to construct protocells. The first such experiments began with the pioneering work of membrane biophysicist Pier Luigi Luisi, who encapsulated ribosomes (the molecular machines which carry out protein synthesis and other chemical components within phospholipid vesicles and, in so doing, managed to create an artificial protein – polyphenylalanine – within the vesicle.

Reference:

Oberholzer, T., Nierhuas, K.H. & Luisi, P.L., Protein Expression in Liposomes, BBRC, 261, (August 1999) 238-41

This work was followed up by other researchers who investigated ways of designing protocells consisting of vesicles made from simpler amphiphiles such as fatty acids, because they were considered more versatile than phospholipids (which are actually found in real cell membranes). Luisi and his collaborator Dr. David Deamer (cited on Szostak’s slides). By the early 2000s, Deamer‘s group showed that fatty acids can indeed assemble into bilayers ( just like real cell membranes) but under highly specific conditions, of concentration, pH, temperature and salt concentration. Furthermore, all of these conditions vary considerably between fatty acid species.

Reference:

Hanczyc, M.M., Fujikawa, S.M.,Szostak, J., Experimental Models of Primitive Cellular Compartments, Science 302 (October 2003): 618-22.

Luisi’s team showed that certain kinds of these vesicles can ‘grow’ if supplied with more fatty acids. This causes the vesicles to enlarge, become unstable, before dividing into two daughter vesicles. The same researchers have used fatty acid vesicles to encapsulate interesting enzymes such as polynucleotide phosphorylase, which uses adenosine diphosphate (ADP) as a substrate to build the DNA analog called polyadenylic acid.

Reference:

Thomas, J.A & Rana. F, The Influence of Environmental Conditions , Lipid Composition, and Phase Behavior on the Origin of Cell Membranes, Origins of Life and Evolution of Biospheres, 37( June 2007): 267-85

This was widely cited in the origin-of-life community as a sort of ‘proof of concept’ that genetic material could indeed replicate inside vesicles and hence a demonstration of the first step towards the generation of self-replicating protocells.

Szostak’s group built on all these successes to attempt to create more life-like protocells. Specifically, they allowed fatty acids to interact with mineral surfaces (discussed above) and showed that this improves the efficiency of vesicle formation.

Reference:

Ibid

But vesicles constructed from fatty acid substrates have marginal long-term stability. Another show stopper is that even small amounts of salts (ionic substances) completely inhibit vesicle formation, a point completely avoided by Dr. Szostak. What’s more, the consensus opinion is that primordial oceans would have had a higher salinity than those existing today. What is more, real cell membranes are not symmetrically arranged but are assymetric, providing much greater compexity than anything utlised by Szostak’s team. See here for a commentray on membrane biochemistry. Yet again, without the maintenance of exacting conditions of pH, temperature, salinity, etc, these vesicles would fall apart. Indeed, no method has been demonstrated that can maintain stable, long-lasting vesicles. Such stability is a necessary pre-condition to the creation of artificial life.

Szostak’s team has explored ways to get vesicles to grow and divide like real cells. By the addition of fresh fatty acids to the medium and studying their behaviour, his team has developed a deeper understanding of how this process works.
Reference:

Chen, I.A., Szostak, J., A Kinetic Study of the Growth of Fatty Acid Vesicles, Biophysical Journal 87, (August 1 2004) 988-98.

While Luisi’s team produced vesicle fissuring, they do so unstably. Szostak’s team have addressed this issue by developing ways to sustain vesicle division after a period of growth. This is achieved by pushing the expanded vesicles through pores (extrusion). In so doing, Dr. Szostak has shown that the process can be repeated indefinitely to create multiple ‘generations’ of protocells.

Reference: Hanczyc, M.M.& Szostak, J., Replicating Vesicles as Models of Primitive cell Growth and Division, Current Opinion in Chemical Biology 8 (December 2004) 600-64

When Szostak et al encapsulated RNA molecules inside such vesicles, they actually promote growth because they produce osmotic pressure on the vesicle walls, increasing membrane stress, which in turn allows fresh fatty acids to become incorporated into the bilayer membrane. He further showed that the RNA molecules are retained inside the vesicle after filter extrusion. Researchers have also encapsulated clay minerals inside vesicles, along with RNA, and demonstrated that the clay is also retained by the vesicles during the growth and division process.

Reference:

Ibid

The next phase in this ‘bottom up’ approach is to provide an energy source for more sophisticated protocell activities. Cells use pH gradients as a way to harvest energy. Indeed this is the fundamental way in which all real cells synthesise the universal energy currency of life: adenosine triphosphate (ATP).

To this end, some researchers have incorporated special molecules which can absorb light into phospholipid membranes to create such pH gradients. Then by adding the pre-existing enzyme complex F0F1 ATP synthase (a remarkable molecular machine in its own right!), they were able to use these pH gradients to synthesise ATP.

Reference:Steinberg,-Yfrach, G. et al, Light-Driven Production of ATP  Catalysed by F0F1 ATP Synthase in Artificial Photosynthetic Membrane, Nature 392 ( April 2, 1998) 479-82.

Szostak’s team has simplified this process. Specifically, they found that the growth of vesicles made from fatty acids naturally generates pH gradients. So, the growth and division of vesicles can provide an energy source.

Reference:Chen, I.A, Szostak, J, Membrane Growth can Generate a Trans-membrane pH Gradient in Fatty Acid Vesicles, PNAS 101( May 25, 2004) 7965-70.

The fatty acid vesicles created by Szostak’s team delivered another advantage over their phospholipid based counterparts; they were more permeable, allowing easier transport of molecules both into and out of the vesicle. Activated (pre-made) nucleotides, which serve as the building blocks for DNA and RNA, were able to move into the vesicles more easily. This led the team to develop systems that could incorporate these activated nucleotides and, using a pre-encapsulated strand of DNA, demonstrated replication capabilities. In addition, his laboratories began experimenting with different types of amphiphiles (including unsaturated fatty acids, alcohols and monoglycerides), mixing them up to try to optimise their stability between the freezing and boiling point of water.

Reference: Mansy, S. & Szostak, J. Thermostability of Model Protocell Membranes,  PNAS 105 (September 9, 2008) 13351-55.

These are important advances, because they have steadily improved the robustness of their protocells and allow scientists to chemically replicate genetic material within the interior of the vesicle.Szostak’s group at Harvard hope to learn how to coordinate the replication of the genetic material encapsulated within these vesicles with the process of vesicle fission. By engineering more and more properties into these vesicles, Szostak and his collaborators hope to create systems tailor made to carry out specific functions.Their ultimate goal is to create synthetic cells that can carry out novel biochemical processes in order to make new biomedical advances and novel pharmaceuticals that will greatly enrich biotechnology. Some foresee that, at the current rate of advancement, these will be a reality as early as a decade from now.

Summary

What Professor Szostak and his colleagues have achieved is truly remarkable! By divesting many millions of dollars from public and private donors, recruiting a very large team of the finest biochemists and molecular biologists, and  utilising the most advanced equipment ever assembled, real progress can be made and his success is bound to continue over the coming years. But, as I have indicated previously, this progress has not come about through Darwinian means, far from it! What Szostak’s work has demonstrated is that by deliberate effort and the harnessing of extraordinary human ingenuity, the era of synthetic biology is well and truly upon us. Their work empirically shows that even the simplest life-form ( which are orders of magnitude more complex than the ‘protocells’ discussed) cannot arise without the involvement of an intelligent agent.

Fatty acids do not  form bilayered membranes when added to ordinary water. On the contrary, their work shows that it is possible to coax stable vesicles to form only by making conscious choices about the kinds of fatty acids (in Szostak’s case the monounsaturated variety) and other amphiphiles that constitute them. If the wrong choice is made, the vesicles cannot even form. What is more, vesicle formation and stability depend critically on fine-tuning the optimal concentration of the amphiphiles in an aqueous environment carefully controlled for pH (buffers), salinity and temperature. Those clays and minerals must be scrupulously clean. The melting point of the fatty acids employed in the vesicles must also be considered. In a real life laboratory environment, the vesicles must, in some cases, be repeatedly frozen and thawed and, as highlighted above, their physical extrusion through pores must be carried out. Even then, vesicles of only the desired size are selected to optimise the process. Creating the vesicles from scratch requires advanced knowledge of the chemical properties of the amphiphiles making them up. After all, the mantra of the biochemist is ‘structure dictates function.’ Furthermore, Szostak’s progress depends upon the prior work of thousands of intelligent minds across the human world, and from many generations.

Sic transit gloria mundi!

This analysis shows that it is unreasonable to expect life to have arisen without an intelligent agency.

I believe this agency to be a personal being, infinitely good, infinitely powerful and infinitely well funded; the God uniquely revealed in the Bible.

                                                           Imago Dei

I believe in one God, the Father, the Almighty

Maker of Heaven and Earth.

Of all that is seen and unseen.

Through Him all things were made.

For us men and for our salvation, He came down from Heaven.

By the power of the Holy Spirit He became incarnate with the virgin Mary and was made man.

For our sake He was crucified under Pontius Pilate.

He suffered death and was buried.

On the third day, He rose again, in accordance with the Scriptures, and is seated at the right-hand of power.

He will come again to judge the living and the dead.

And His Kingdom shall have no end.

Neil English holds a PhD in Biochemistry from the University of Dundee and has carried out post doctoral work in the field of Cytochrome P450 mediated fatty acid hydroxylation and associated gene expression.

De Fideli

 

 

6 thoughts on “Origins of Life: A Closer Look Part II

  1. I don’t think so, Neil. I noticed, maybe one typo. What I liked is that you wrote in clear sentences. Further, it seemed like you were being attentive to how the interested amateur (i.e. me) would best understand things, by taking the time to unfold one piece, a bit at a time and then move on.

    It reminded me, in fact, of our local bishop who is bilingual (spanish/english) and for us anglos who don’t know Spanish, what he did is speak a bit in Spanish and then repeated that bit in English; say five sentences or so.

    Which brings me to a really funny joke told me by a Canadian teacher with whom I worked;

    Canadian: Otto, what do they call a person who speaks three or more languages?

    Otto: Multi-lingual.

    Canadian: Very good, Otto. What do they call a person who speaks two languages fluently?

    Otto: Bi-lingual.

    Canadian: Correct again. What do they call a person who speaks only one language.

    Otto: (pause) (hem and haw). (Finally) I don’t know.

    Canadian: An American.

  2. Hi Otto and Neil,
    Well now, being an American, having been brought up a Catholic and having spent all but two High School years in Parochial Schools, does Latin count?
    Ten years shy of being an octogenarian and I can still recite the Lords Prayer among a few others in Latin, that just has to count for something don’t you think?

    It still surprises me………… and my sweet wife!
    Ray

  3. Sure Latin counts!

    Sometimes I’ve wondered in Fortran counts as well (yes, I’m that old).

    Otto

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