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

 

 

The Generosity of the Sun

Totality.

Totality.

 An essay dedicated to the Faithless Generation.

For since the creation of the world God’s invisible qualities- his eternal power and divine nature –have been clearly seen, being understood from what has been made, so that people are without excuse. For although they knew God, they neither glorified him as God nor gave thanks to him, but their thinking became futile and their foolish hearts were darkened. Although they claimed to be wise, they became fools..

                                                                                                          Romans 1:20-23

Coincidence is God’s way of remaining anonymous

                                                                      Albert Einstein (from The World As I See It)

When the Moon formed, it was much closer to the Earth, and has been steadily retreating as the energy of its orbital motion has gone into stirring up tides….. Just now the Moon is about 400 times smaller than the Sun, but the Sun is 400 times farther away than the Moon, so that they look the same size on the sky. At the present moment of cosmic time, during an eclipse, the disc of the Moon almost exactly covers the disc of the Sun. In the past the Moon would have looked much bigger and would have completely obscured the Sun during eclipses; in the future, the Moon will look much smaller from Earth and a ring of sunlight will be visible even during an eclipse. Nobody has been able to think of a reason why intelligent beings capable of noticing this oddity should have evolved on Earth just at the time that the coincidence was there to be noticed. It worries me, but most people seem to accept it as just one of those things.

                                                                   John Gribbin (from Alone in the Universe)

The noted science writer and astrophysicist, Dr. John Gribbin, raises an interesting point at the end of the excerpt from his 2011 book, Alone in the Universe, quoted above. He describes the coincidence of a total solar eclipse and the emergence of a global human technical civilization as something that ‘worries’ him. I can well understand that position given the inadequacy of the blind forces of Darwinian evolution to explain why these events are coincident in cosmic time. But that’s only an issue if one assumes biological evolution to be watertight. A more rational, and dare I say, compelling answer to Gribbin’s conundrum is that these events are not mere coincidences but were pre-ordained to occur in a unique window of cosmic history to reveal the attributes of an all powerful Creator; a personal God who, like a great king, wishes to demonstrate His omnipotence to an unbelieving population.

Such a world view, which is currently counter to the prevailing secular corpus of scientific thought, would be strengthened if other attributes of the Sun were found to be odd, peculiar or even unique. Intriguingly, great advances in our knowledge of the Sun over the past 30 years has yielded a solid body of evidence pointing to the possible uniqueness of our Sun, the yellow star that has presided over the extraordinary allegory of events that culminated with a global human technical civilization in the present epoch.

                                                Peculiar formation history

Diligent research over the past century has revealed that stars are not born in isolation but are hatched in their thousands inside enormous clumps of gas and dust. Our Sun was formed from the fragmentation of one such cloud under the auspices of magnetic and gravitational forces that led to the contraction of one cloud fragment, culminating with the ignition of the nuclear fires at the centre of the proto-Sun and the formation of a disc of gas and dust in the plane of the solar equator that would form the elegant planetary system we live in today. Yet the Sun was formed with an unusual assortment of heavy elements that originated in not one but two distinct kinds of supernova events that must have occurred in close proximity to our neonatal solar system to enrich it with those elements. What is more, our solar system was formed during the epoch  when the interstellar medium was maximally enriched with the long-lived radionuclides thorium-232 ( half life 14.1Gyr), uranium-235 (half life 0.704 Gyr) and uranium-238 (half life 4.468 Gyr); elements that provided Earth with the thermal energy to maintain plate tectonics on our planet over geologic time. Without large quantities of these elements, the Earth would have been just another lifeless planet.

But forming the right kind of star and the right kind of planets was still not enough though. Had the Sun and its retinue of planetary bodies remained entangled in the star cluster of its birth for very long, gravitational interactions with nearby stars would have wreaked havoc with our orderly solar system. Moreover, had the Sun formed as part of a binary or multiple star system – as have as many as 70 per cent of sun-like stars in the Galaxy – it would have been game over for a life bearing planet like the Earth, as it would not have able to maintain a stable circular orbit about the Sun over the entire duration of its history. For the Sun and its family of planets to proceed to the next stage of development, it had to be ejected from the cluster of its birth to live in safe isolation from the rest of its stellar siblings.

                                              Peculiar physical properties

In the early 19th century, the German optician, Joseph von Fraunhofer (1787-1826), founded the science of stellar spectroscopy. By attaching a diffraction grating to his achromatic refractor (both of his own design) he was able to demonstrate that stars like Sirius differed significantly from the Sun.

Joseph von Fraunhofer demsonstrating the spectroscope.

Joseph von Fraunhofer demsonstrating the spectroscope.

Today, we follow in the great optician’s footsteps, employing diffraction gratings to obtain high resolution spectra of a multitude of stars, allowing astronomers to perform a so-called differential element analysis on a large stellar population.These and other techniques have revealed a curious truth about our star, the Sun. While it is easy to find twins of almost any other star, an exact solar twin has yet to be found. And though quite a few stars can be matched to the Sun with respect to its basic parameters like mass, age and luminosity (G2V spectral class), the Sun stands out like a sore thumb with respect to these solar analogues, showing a 20 per cent depletion in certain refractory (non-volatile) elements such as calcium, aluminium, magnesium and silicon; the elements that wound up inside the rocky terrestrial planets of our solar system.

 The Sun, though widely reported to be an ‘ordinary star’ is actually more massive than 95 per cent of all other stars in the Galaxy. The vast majority of stars, the teeming multitudes of red and brown dwarves, are too cool to hold planets at a safe distance from their fiery surfaces in order that liquid water could be profitably maintained on their surfaces over the aeons. Such stars would need to spawn planets very close in – typically an order of magnitude closer than Mercury is to our Sun – causing them to become tidally locked. This means that they would keep the same face to their parent stars in much the same way our Moon does while orbiting the Earth. This scenario would render life incredibly difficult on such planets. After all, the permanently illuminated hemisphere would be incinerated while the other would be in a perpetual frigid darkness. Lower mass stars, by their nature, emit less ultraviolet (UV) radiation too – a plus you might think – until you learn of how important UV radiation is for generating and sustaining the ozone layer. And no ozone layer would make life very difficult indeed on the landmasses of any putative world orbiting these low mass stars.

But there are yet other perils that attend stars with lower masses than the Sun. In the summer months, I use my 3 inch classical refractor to project an image of the Sun on a piece of white cardboard or by using a full-aperture solar filter. More often than not, I can make out small sunspots – regions of intense magnetic activity that correspond to cooler regions of the solar photosphere – that make an otherwise bland solar disc all the more interesting to observe. Sunspots though, are also strongly correlated with flare activity and it is not an inconsiderable fact that stars even a little lower in mass than the Sun have significantly higher activity in this regard. Ongoing solar research suggests that during sunspot maximum (which follows a roughly 11 year cycle) our Sun already has the ability to inflict potentially serious damage to living cells, as well as hampering human telecommunication  systems, so that any significantly greater activity would prove disastrous for life on Earth in general and human civilization in particular.

Sol, as it appeared at appeared on the sunny afternoon of May 7, 2013.

Sol, as it appeared through the author’s 3-inch Fraunhofer refractor  on the sunny afternoon of May 7, 2013.

The tiny fraction of stars in the Galaxy larger than the Sun have very short lifetimes (scaling with mass as M^-2), insufficiently long to allow even microbial life (if it exists at all) to start the process of heavy metal concentration – which include the so-called ‘vital poisons,’ as well as the heavy metal deposits needed to sustain a high-technology society – in their planet’s crust.

                                                           Peculiar stability

How does flare activity correlate with stellar age? It turns out that solar flaring has continued to decline over time, reaching a minimum in the present epoch, roughly half way through the life of our star and dovetailing nicely with the emergence of humanity in the solar system. What’s more, sensitive measurements reveal that our star varies less in luminosity (typically by less than 0.1 per cent) than any known star.

                                                       Peculiar kinematics

In 2008, a team of astronomers led by Charles Lineweaver based at the Australian National University, conducted a study on a large body of stars taken from the Hipparcos archive and discovered that the Sun has a more circular orbit than 93 per cent of other stars in the distribution. Safely tucked away between spiral arms near the co-rotation axis of our Galaxy (a peculiarly stable place to be!), some 27,000 light years from its centre, we live on a planet spared the deadly effects of short wave radiation that have surely sterilised the down town regions of the Milky Way. Out here, in Galactic suburbia, we move around the centre of the Galaxy once every 0.25Gyr, enjoying transparent, dark skies that allow us to look all the way back in time to the earliest epochs in cosmic history, so enabling humans to elucidate the physical events that shaped the unfolding cosmos in which we find ourselves in.

Stars not only move within the plane of the Milky Way’s thin disc but oscillate up and down as they orbit the Galactic centre. Many years of kinematic studies conducted by astronomers show that its amplitude of oscillation is smaller than many stars in the solar neighbourhood which makes the solar system less susceptible to gravitational perturbations that could potentially destabilise established planetary orbits. Indeed, according to the stellar astronomer, Dr. Guillermo Gonzalez, the Sun’s kinematic attributes are more reminiscent of a young star than one that is 4.57 billion years old!

                                                            Not forever!

As I have attempted to outline thus far, it seems patently clear that the Sun is a very unusual star enjoying a rather unusually stable phase in its life. Over billions of years since its birth, the Sun has grown steadily brighter and life on Earth, particularly the green plants, have worked to compensate for the Sun’s increasing luminosity by removing more of the greenhouse gases (particularly carbon dioxide and water vapour) from the Earth’s atmosphere. But the unchanging laws of physics that govern the Sun’s evolution are the same yesterday, today and tomorrow. This means that the Sun is going to continue to brighten and heat the Earth’s surface. But the levels (currently 392ppm) of carbon dioxide needed to conduct photosynthesis are already close to the minimum necessary (~150ppm) to sustain vigorous plant growth. Clearly, the current situation cannot be maintained indefinitely. Likewise, as it continues to evolve (and stars really do evolve because there is a robust physical theory underpinning that process), flare activity will increase to a point where large animal life cannot be sustained. Clearly therefore, we are living in the best of times.

                                               Just one of those things….

Sol Invictus!

Sol Invictus!

 

 

I suppose one could always shrug one’s shoulders and say something like, “that’s a strange coincidence,” or “it’s mere chance.” But, these answers are not very satisfying to a curious intellect; an intellect hard wired to spot patterns. Cast your mind back once more to the exquisite geometry of a total solar eclipse. A few million years ago, the Moon’s apparent diameter was larger than the Sun’s and the non-human primates – Homo Erectus or some such – that inhabited the Earth at that time, lacked the sophistication – both mentally and spiritually – to appreciate the event. In a few million years hence, the Moon will be smaller than the Sun’s face and the Earth will be unfit for human habitation. Only at a time sandwiched neatly between these epochs did creatures with the necessary cognitive capacities emerge on the scene to understand the significance of this alignment, allowing them to deduce both the geometry and scale of the solar system. Even the mind-boggling logic of Einstein’s theory of general relativity was confirmed during a solar eclipse.

Do you really think these solar peculiarities are just coincidences? How many coincidences and peculiarities does one need to convince one of a greater, underlying truth about the Sun and our relationship with it? And where does Darwinian evolution – the ‘blind watchmaker’ – fit into all of this?

Thank goodness for small mercies!

If you’d like to hear more amazing coincidences about the Universe we inhabit, you might be interested in my new book, Grab ‘n’ Go Astronomy, due out this Summer.

 

De fideli

This essay was inspired by the continuing work of Dr. Hugh Ross, Founder & President of Reasons to Believe and colleagues; truly a candle shining in an ever growing sea of darkness.

Some References for Further Study.

Barrow J.D. & Tippler, F.J. (1988), The Anthropic Cosmological Principle, Cambridge University Press.

Ross, H. (2008), Why the Universe is the Way it is, Baker Books.

Ward, P.D, & Brownlee, D, (2000) Rare Earth: Why Complex Life Is Uncommon in the Universe, Copernicus.

Gribbin, J, (2011), Alone in the Universe, Wiley.

Philips, A.C. (2001), The Physics of Stars, Wiley.

Want to explore More? Follow me on Facetube & Twatter.

 

Pause for Thought: Mars, Barnard and his Byrne.

Young Edward

Edward Emerson Barnard (1857-1923) needs no introduction in the world of amateur astronomy. Emerging from abject poverty, his natural curiosity, regal humility and diligence for his work, set him on a path that would lead to his becoming arguably the greatest visual observer of all time. In this short presentation, the author recounts Barnard’s earliest forays into telescopic astronomy, and in particular, the acquisition of his ‘pet’; a 5-inch achromatic refractor by the relatively obscure New York optician, John Byrne. His devotion to that instrument established his reputation as a gifted telescopist.

While Mars mania was quickly turning the world’s pre-eminent planetologists into imbeciles, this young man, endowed with wisdom far beyond his years, eschewed the unbridled imaginations of his contemporaries, and quietly watched the Red Planet with his ‘large telescope’.

De Fideli.