#17 Against Naturalism to Explain the Origin of Life

Conclusion to this chapter:

Given my belief in God as a real God who acts in a real world, it would not be logical for me to also believe in Naturalism.  Logical and rational thought does not exclude belief in a level of existence beyond the material world.  I believe that God is tangibly present in the universe which He created.  I propose that God created the intrinsic properties of matter with the purpose of bringing forth life in the universe.  Thus, I believe that God created the macromolecules DNA, RNA and proteins as a functioning genetic system within the first living cells which were designed as such.

In this chapter I have described the four types of organic molecule and their subunits; covalent and hydrogen bonding between the elements of molecules; the four layers of protein structure; the stereospecificity of enzymes that function as catalysts in biosynthesis; and the building of monomers into carbon-based polymers. 

There are different levels of order in biochemistry.  The bonding strengths between elements are crucial for the functions that they fulfil as the components of life.  Bonding strengths are determined by the structure of atoms.  Thus, there is a level of order relating to physics.  Simple molecules show chemical affinities for each other and properties such as solubility in water.  Thus, there is a level of order relating to chemistry.  Organic monomers that are themselves relatively complex[1] are joined together to form complex organic macromolecules.  Monomers are reacted together by enzyme catalysts according to stereospecificity rather than natural affinity.  The specificity is dictated by a code carried as DNA.  Thus, there are levels of order in biochemistry that function in accord with rules of assembly.  However, the level of order relating to protein formation in biology embodies information and is specific rather than rule-bound.

The philosophy of Naturalism reposes upon the discovery of natural affinities between elements and molecules and certain observable levels of order.  I contend firstly, that the natural affinities are the result of the original design of the components of living matter, and secondly, that biology exhibits order based on specificity, rather than regularity.

I agree with Creationists and Intelligent Designists that belief in the philosophy of Naturalism has taken over science and is suppressing legitimate avenues of exploration.  The foundations of modern science were not based on a philosophy of Naturalism but on a willingness to explore Nature and ‘think God’s thoughts after Him’.  Naturalism is not delivering the break-throughs in science sort after, especially in the origin of life field.  I believe that recognition of a higher order of reality will produce the insights necessary to a deeper understanding of the universe and the life within it.

[1] Organic monomers are relatively complex, for example, the nucleotide building blocks of nucleic acids contain over 30 atoms, and the average amino acid subunit of proteins is composed of 16 atoms.

#14 Irreducible Complexity

Michael Behe is one of the best Known intelligent design theorists

In his book, Darwin’s Black Box: the Biochemical Challenge to Evolution first published in 1996 (I cite the latest edition of 2006) Behe challenges step-by-step evolution.  Michael Behe rejects NeoDarwinist theories concerning the origin of life through Natural Selection.  He is a Roman Catholic and he believes that God designed and created the first cell.

Behe writes that the advances of science since the 1950s show with piercing clarity that life is based on molecular machines. 

“Molecular machines haul cargo from one place in the cell to another along “highways” made of other molecules, while still others act as cables, ropes, and pulleys to hold the cell in shape.  Machines turn cellular switches on and off, sometimes killing the cell or causing it to grow.  Solar-powered machines capture the energy of photons and store it in chemicals.  Electrical machines allow current to flow through nerves.  Manufacturing machines build other molecular machines, as well as themselves.  Cells swim using machines, copy themselves with machinery, ingest food with machinery.  In short, highly sophisticated molecular machines control every cellular process.  Thus the details of life are finely calibrated, and the machinery of life enormously complex.” (Behe 2006, pages 4-5).

Behe contends that Natural Selection working on variation cannot explain the origin of the systems revealed by biochemistry.  The molecular level is the most fundamental level of life.  Since we have finally reached the ‘bedrock of life’, we are now in a position to make an informed assessment of the mechanism of evolution proposed by Darwin.  Can complex molecular systems be built up by small steps adding components to the system one by one?  The examples of biomolecular systems that Behe (2006) gives include the following:

  • The biochemistry of vision involving rhodopsin.
  • The cilium of eukaryotic cells.
  • The flagellum of bacteria.
  • Blood clotting and fibrinogen.
  • Gated transport of proteins into the lysosome cell organelle for recycling.
  • Antibodies and the immune system.
  • The biosynthesis of the nucleotide AMP (a DNA and RNA subunit).

The theory that these examples illustrate involves the notion of Irreducible Complexity.  A system that is irreducibly complex cannot be formed by numerous, successive, slight modifications.  (William Dembski has introduced the concept of Specified Complexity – see footnote[1]).  Behe writes,

“By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.”  (Behe 2006, page 39).

An irreducibly complex system cannot be produced by continuously improving the initial function of a precursor system because any precursor that is missing a part is by definition non-functional.  Behe declares that irreducibly complex biological systems present a powerful challenge to Darwinian evolution since Natural Selection can only choose systems that are already working.  “In order to be a candidate for natural selection a system must have minimal function: the ability to accomplish a task in physically realistic circumstances.” (Behe 2006, page 45).  If a biological system cannot be produced gradually, it would have to arise as an integrated unit for Natural Selection to have anything to act on.

He asks, “How can we recognize an irreducibly complex biological system?”  And answers, “One must specify both the function of the system and all the system components.  An irreducibly complex object will be composed of several parts, all of which contribute to the function”.  This is one example:

“The function of the cilium is to be a motorized paddle.  In order to achieve this function microtubules, nexin linkers, and motor proteins all have to be ordered in a precise fashion.  They have to recognize each other intimately, and interact exactly.  The function is not present if any of the components is missing.  Furthermore, many more factors besides those listed are required to make the system useful for a living cell: the cilium has to be positioned in the right place, oriented correctly, and turned on or off according to the needs of the cell.” (Behe 2006, page 204).

He states that the laws of chemistry work strongly against the undirected development of the biochemical systems that make molecules such as AMP.  The nucleotide AMP which is a component of DNA and RNA is synthesized in 13 steps involving 12 different enzymes (Behe 2006, page 149).  If only the end product is used by the cell while the intermediates are not useful on their own, why would the intermediates evolve one by one?

Behe believes that the universe is the billions of years old that physicists say it is.  He also believes in microevolution, and states that Darwinism explains microevolution very nicely.  Microevolution is defined as the differences between different populations in different geographic areas or ecological niches.  Populations are divisions within a single species.  Behe rejects macroevolution referred to as “large jumps”.  Macroevolution is defined as evolution above the species level.

Behe claims that he finds the idea of common descent –that all organisms share a common ancestor –convincing (Behe 2006, page 5).  This appears to contradict his rejection of ‘macroevolution’.  However, he finally explains his theory of design as follows:

According to Behe, the simplest possible design scenario posits a single cell –formed billions of years ago –that already contained all the information necessary to produce descendant organisms (Behe 2006, page 231).  Thus, four billion years ago, the designer made the first cell, already containing all of the irreducibly complex biochemical systems discussed in the book and many others.  The designs for systems to be used later, such as blood clotting, were present, but not ‘turned on’ in this original cell (Behe 2006, pages 227-228).

My Comment

Behe claims that biochemical ‘machines’ defeat Darwinism and the Theory of Natural Selection.  “Yet for the Darwinian theory of evolution to be true, it has to account for the molecular structure of life.  It is the purpose of this book to show that it does not.” (Behe 2006, page 25).  However, Behe’s opposition to “Darwinian evolution” on the basis that biochemical pathways cannot be built up step by step polarizes positions.

In The Origin of Species Darwin made no claims about biochemical pathways, indeed he made no mention of microscopic cells or unicellular life whose existence was hardly known before the time of Louis Pasteur in the 1860s.  Darwin’s starting point was created multicellular plant and animal archetypes, no doubt complete with biochemical pathways.  Contrary to the statements of Behe, (for example on page 173), Darwin did not claim a natural origin to life via Natural Selection, or address the origin of vision itself.  (The multicellular animals Darwin proposed as archetypes presumably had eyes). 

Behe builds up “Darwinian evolution” far beyond the original claims of Darwin, and then knocks it down.  It is to his contemporary NeoDarwinists that Behe should be addressing himself since it is NeoDarwinian theory that has taken a path directly opposing it to design.  I also oppose NeoDarwinism, but I am a Darwinist since I believe in modification by Natural Selection. 

“Design is simply the purposeful arrangement of parts.” (Behe 2006, page 193).  Design is the ordering of separate components in a system to achieve an identifiable function that is beyond any of the components themselves.  I agree with Behe that many biochemical systems were designed and came into existence as integrated units by the activity of an intelligent Being.  I also agree that “The conclusion of intelligent design flows naturally from the data itself –not from sacred books or sectarian beliefs.”  (Behe 2006, page 193). 

I think, however, that Behe’s idea of common descent involving the creation of one primordial cell that contained the genetic blueprint for all subsequent organisms on Earth in switched-off form is not practicable.  Quite apart from any other considerations, the bacterial cell that would have been the first cell has a genome that does not contain genes.  The single copy DNA of bacteria has operons that are transcribed and translated in a much simpler way to the genes of multicellular organisms.  I conclude that Behe provides no sensible framework in which to hang the details he has so painstakingly described.

[1] Specified Complexity is a mathematical concept belonging to Information Theory.  Irreducible Complexity is a special case of Specified Complexity.  Complex specified information is viewed by Dembski as an empirical marker of purpose, intelligence or design.  This is presented as a mode of scientific explanation since naturalistic explanations are incomplete.  In the Theory of Intelligent Design, an intelligence originated the complexity and specificity found in the cosmos and especially in biological systems.  Dembski writes that “Persons with theological commitments can co-opt this designer and identify this designer with the object of their worship.” (Dembski 2002, page xv).  Dembski (2002, page 318) explains that “specified complexity is not a free lunch in the sense that natural causes cannot generate it.  Nevertheless, natural causes can take already existing specified complexity and shift it around” 

Dembski, William A.  (2002)  No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence Rowman & Littlefield Publishers, Inc.

#11 Origin of biochemistry

Origin of life is about the origin of biochemistry.  Biochemistry is the chemistry of carbon-based molecules, the organic molecules of life.  Carbon is unique in its ability to form stable bonds with other carbon atoms and to form long chains or rings.  The carbon atom forms four bonds, so a carbon atom in a chain is bonded to other carbon atoms on either side, and can still form bonds with other types of atom or with carbon side-chains. 

The types of atoms or elements of life are mainly six: carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorous (P) and sulphur (S).

The simplest types of cells –bacterial cells – contain some 5000 different organic molecules.  However, organic molecules fall into only four major categories: carbohydrates, lipids, proteins and nucleic acids.

Carbohydrates, lipids, proteins and nucleic acids are macromolecules.  The largest are polymers synthesized by linking together large numbers of subunits called monomers by dehydration reactions.  Lipids are not polymers, but they can associate to form membranes. 

The subunits of carbohydrates are monosaccharide sugars.  The subunits of lipids are glycerol and fatty acids consisting of long hydrocarbon chains.  The subunits of proteins are amino acids joined to form polypeptides.  A protein may be composed of several polypeptide chains.  The subunits of nucleic acids are nucleotides.  A nucleic acid polymer has a sugar-phosphate backbone with different nitrogen-containing bases attached.  In DNA the four bases are adenine (A), cytosine (C), guanine (G) and thymine (T).  In RNA thymine is replaced by uracil (U).  ATP (adenosine triphosphate) is a nucleotide with three phosphate groups.  The last two phosphate bonds are unstable which means that they can be broken to release energy.

Biochemistry involves two types of chemical bond: covalent bonds which are strong and hydrogen bonds which are weak.  Covalent bonds can be single, double or triple with the double or triple being stronger than the single.

The peptide bonds joining amino acids in a polypeptide chain are covalent bonds.  Proteins may be strengthened by bonding between sulphur atoms to form cross-links between polypeptides.  The folding of proteins involves the formation of many weak hydrogen bonds. 

The highly complex shape of proteins involves four layers of structure.  The primary structure of a protein is the linear sequence of amino acids.  The secondary structure of a protein involves folds held by hydrogen bonds.  The tertiary structure involves packing to form a compact structure by some side chains being hydrophobic and others hydrophilic.  Hydrophobic side chains form a water-free zone in the interior of the protein with hydrogen bonding stabilizing the structure.  The quaternary structure, if present, consists of several polypeptides assembling together to form a protein which functions as a single three-dimensional structure.

Organic macromolecules are synthesized by cells using enzymes as catalysts.  Reactions do not occur haphazardly, but as metabolic pathways where one reaction leads to the next reaction in a highly structured manner to produce the end product.

Enzymes function by forming a complex with their substrate by binding on at the active site.  The enzyme orientates monomers such that a bond can be formed between them.  A polymer made from bonded monomers is thus formed.  ATP is used as a source of energy for the formation of each bond.

For more detailed information on biochemistry see the appendix for this chapter.  This basic understanding of biochemistry serves as an introduction to the discussion on the stereospecific properties of proteins discussed in the next section.

#8 Ribozymes?

Let us look in detail at the catalytic properties of RNA.  The single intron of the large ribosomal RNA of Tetrahymena thermophila (a ciliated protozoan) has self-splicing activity in vitro.  This RNA was named a ribozyme because it is an RNA that acts like an enzyme.   However, most, if not all other RNA-based catalytic reactions are thought to take place in conjunction with proteins.  Spliceosome and ribosomal RNAs have the ability to catalyse peptide bond formation, but they are better described as catalytic ribonucleoproteins than ribozymes since they do not make the role of proteins unnecessary.

Large ribozymes mostly include members of the group I and group II intron family found in algae, fungi and plants.  These are self-splicing introns.  Group I ribozymes use an external guanosine (G) nucleotide as a cofactor and group II ribozymes require an active site containing Mg2+ ions for catalysis.  Group I and group II introns self-splice under certain conditions in vitro, but require proteins to fold the intron RNA into the catalytically active structure in vivo.  The proteins are either encoded by the introns themselves or encoded by other genes (Allison 2007, pages 69-73 and 455-457).

Small ribozymes found in viruses and viroids act as riboswitches involved in gene regulation.  The other small ribozymes are involved in self-replication of the circular RNA of viruses (Allison 2007, page 75).

From this detailed account it can be seen that ribozymes represent a limited case found in a few organisms.  Intron-splicing by a ribozyme is catalytic and leads to modification of the RNA itself.  This characteristic contradicts the classic definition of an enzyme as being a substance that increases the rate of a chemical reaction, but is not itself changed in the process.  Therefore, a ribozyme does not simply act as an enzyme made of RNA rather than protein.

The autocatalytic nature of RNAs cited as ribozymes is highly questionable when one pays attention to detail.  It emerges that in vivo none of these RNAs act alone – their catalytic properties are dependent on proteins to initiate folding that makes the RNA structure catalytically active.  Therefore, RNA ribozymes do not act alone, but in conjunction with proteins.  It looks like proteins won’t go away.

I have not used the word hypothesis in connection with RNA World because it is untestable.  It is a speculation upheld by an almost mystical view of Natural Selection in which Natural Selection acts in a world of personified molecules that ‘want’ to replicate.  Shapiro accuses the adherents of these origin of life theories as creating a mythology whose truth cannot be challenged even in the face of adverse evidence (Shapiro, 1986, page 32).

“In the origin-of-life field, a particular theory or point of view is frequently elevated to the status of a myth.  It is then treated only as a doctrine to be validated, and not one to be challenged.”  (Shapiro 1986, page 33).

#5 Metabolism without Enzymes and Cell Membranes?

Clay Catalysts

Metabolic processes within cells are catalysed by protein enzymes.  It was realized that the formation of macromolecules had to be catalysed by something, and unless life pulled itself up by its own bootstraps these catalysts could not be enzymes.  So, it was proposed by A.G. Caines-Smith in 1985 that clay composed of silicates was the catalyst of protometabolism (see footnote[1]). 

Proto-cell Membranes

It was soon realized that since the entire sea could not function as a metabolism, it had to be compartmentalized.  It was observed that cell membranes are composed of phospholipids that naturally form spheres when placed in water.  So, it was proposed that the protocell was bounded by a very simple lipid membrane that formed spontaneously.  The problem with this simple model is that the protocell would be isolated from its environment.  The phospholipid membrane of the hypothetical protocell would not allow molecules that fuel metabolism to enter the protocell, nor would it allow toxic waste products out.  Isolation from the environment spells non-viability for cells.

The cells we know have a phospholipid bilayer plasma membrane with both embedded and peripheral proteins that regulate the entry and exit of substances into and out of the cytoplasm.  The selectively permeable cell membrane maintains a steady internal environment within the cell.  Water and some small molecules can cross the phospholipid membrane and follow their concentration gradient, but larger molecules such as glucose and amino acids, and also ions are assisted across the membrane by carrier proteins that are specific to each molecule or ion.  Transmembrane proteins include channel proteins, carrier proteins, cell recognition proteins, receptor proteins and enzymatic proteins and transport may be active requiring the expenditure of energy donated by ATP.

The conclusion to this short section is that simple membranes would isolate a cell, making it unable to function as a cell, and complex membranes containing channels and carrier proteins that allow the cell to interact with its environment are complex.

[1] Cairns-Smith A.G.  (1985)  Seven Clues to the Origin of Life  Cambridge University Press; Cairns-Smith A.G. (1993) Genetic Takeover: And the Mineral Origins of Life Cambridge University Press

#4 Primeval Soup Theory

The Primeval Soup Theory for the origin of life on Earth was first proposed by J. B. S. Haldane (1892-1964), a British Marxist biologist who lived in the USA and Britain, and Alexander Oparin (1894-1980) of the USSR.  It is the idea that life arose from inorganic matter under conditions proposed as having existed on the early Earth, but not existing now.

There are various versions of the Primeval Soup Theory differing in some details.  All must include a reducing atmosphere since organic macromolecules will not form naturally without it.  Hence it is proposed that the atmosphere of the early Earth was composed of methane, ammonia and hydrogen.  There was a sea of water formed from condensed water vapour.  The energy which would trigger the emergence of life came from flashes of lightning, ultraviolet radiation or even meteorite impact.  The effect of the light or heat energy on the atmosphere of strange gases would be the formation of organic, carbon-based molecules that would accumulate in the water which thus became a prebiotic soup.

It is now known that if the early atmosphere was so reducing that it did not contain any carbon dioxide, then the Earth would have been covered with ice.  The discovery of the exotic world of hydrothermal vents then led to the hypothesis that life emerged in one of the places on Earth that had reducing conditions in a limited location.

The primeval soup would contain carbohydrates the components of sugars; amino acids the components of proteins; and nucleotides the components of DNA and RNA.  Thus, it is proposed in the Primeval Soup Theory that all the ingredients of life were present as building blocks on early Earth.  It has been observed that the building blocks of life do combine with each other in predictable ways.  At this point the Natural Selection argument is used to explain that little organic molecules (monomers) have an advantage if they become big organic molecules (polymers) and if they learn to self-replicate.  The survival of the fittest idea is applied to molecules, which form themselves into a protometabolism whose function is to form new types of molecules.  The idea of the evolution of macromolecules was proposed by Francis Crick and Leslie E. Orgel in 1973.

Robert Shapiro points out that the proposed compositions of the atmosphere of early Earth and the ‘soup’ are hypothetical, and may never have existed at all.  He also points out that the water of this ocean would prevent the formation of biological macromolecules since water prises nucleotides apart from each other by breaking sugar-phosphate bonds and severing bases from sugars (Shapiro 1986, pages 173-174).  Thus, DNA and RNA macromolecules in water become nucleotide small molecules.  Also, in the presence of water peptide polymers and proteins slowly break down into their amino acid components.

It seems that, whereas in the world of speculation, ‘Natural Selection’ as the driver builds up complex molecules, in the real world thermodynamics breaks down complex molecules into simpler ones.

#3 Origin of Life: Theory and Politics

As far as the history of ideas is concerned, the notion that life can arise from non-life was linked to the rise of Communism during the 20th century and its atheistic underpinning.  It was a necessary corollary to belief in Dialectical Materialism that Soviet scientists find an origin to life that did not involve God.  Thus, origin of life theories of the 20th century stepped forward hand in hand with the political ideals of the day.

Soviet scientists claimed that just as Marxism shows that history must drive itself forward towards the triumph of Communism, the beginnings of life drove itself forward towards the colonization of Earth by an imperative logic.  Soviet scientists believed that the cytoplasm of the cell contained the means of running the metabolism of the cell (just as the worker’s collectives supposedly ran the Soviet Union).  They hotly denied that the genetic material found in the nucleus of the cell contained the program for running the cell.  They claimed that the idea that the nucleus runs the cell was part of elitist ideology.  DNA had been discovered by scientists in Western Europe and was therefore denounced as a capitalist hypothesis. 

It seems that history had the last word, since genes did not go away and Communism fell.  However, the idea that life arose by chance or by some natural means that did not involve God remained in circulation and became part of the official dogma of NeoDarwinism. 

#2 Spontaneous Generation?

Historically nobody was much troubled by the origin of life.  The origin of life – where life came from – did not in the past really formulate itself as a question.  Quite apart from believing that the world has always been the way it is, and that God made it that way, it was commonly held that small forms of life simply came into existence spontaneously under certain conditions.

Spontaneous Generation is the belief that some living creatures arise suddenly by chance from matter independently of any parents.  Spontaneous Generation was accepted without dissent since ancient times until the second half of the 19th century.  It was thought that rotten meat turned into maggots, household dirt took on the form of Silverfish, while mould and bacterial colonies arise from damp corners.  Life simply appeared everywhere, all the time.  Nobody thought that the origin of life was a problem; it was only its persistent manifestation that was a problem.

The man who changed this situation was Louis Pasteur (1822-1895), French scientist and devout Roman Catholic.  He discovered that disease is caused by unseen germs and that the fermentation of wine and beer is caused by yeast.  His discoveries had many practical applications for improved public health, but he also applied himself to the investigation of Spontaneous Generation.  During the 1860s his experiments showed that spores of living organisms are carried on dust in the air, thus the organisms found growing on broth do not come from nowhere and will not grow in the absence of dust.  The French Academy of Sciences awarded him a prize for this discovery in 1862.

During the course of the 20th century science has revealed to a greater and greater extent the complexity of even the simplest life, and the difficulty in explaining its origin.  The simplest living organism, a unicellular bacterium, is immensely complex.  As the resolving power of microscopes has advanced, the living cell has revealed itself as a microcosm replete with cell organelles performing the tasks of living with astonishing precision and orderliness.

#1 Origin of Life – Chance, Unknown Law or Design?

The Steps of Creation Part I Chapter 9 – a series of posts taken from the book on the theme of evolution: what it can achieve and what it cannot achieve.


The investigation into the origin of life is one of the most speculative areas of science, but it is of the utmost importance to NeoDarwinism.  The NeoDarwinist project does not exist without the proposition that life arose by natural means.  As we will see, there are enormous difficulties in explaining and demonstrating how this could have been.  As scientists enter deeper and deeper into the secrets of life, the gulf between the simplest forms of life and no life manifests itself with greater and greater clarity. Attempts to find a natural explanation for the origin of life have gone on for over half a century now.  Some believe that there will be a break-through, and others believe that the problems are insurmountable.  And there we have it: it is a question of belief.  There is no known law for life to emerge from non-life.

“Was the start of life an accident, or the inevitable outcome of natural laws, or perhaps the deliberate act of a powerful supernatural being?”  (Shapiro 1986, page 30).

Did life evolve by chance as a happy one-off accident on a planet called Earth in an immense universe?  Is the evolution of life inevitable on inhabitable planets due to some unknown law that causes a rise in the complexity and interconnection of organic molecules?  Did God use natural processes to cause life to emerge from matter in the universe?  Did God create life by carefully designing its organic components such that they perform functions of amazing intricacy?  It is all a matter of belief.