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#3 Modified Traits

May 26, 2023 by clarevmerry, posted in The Steps of Creation

Darwin founded his Theory of Descent with Modification through Natural Selection by likening Natural Selection to artificial selection by Man of domesticated animals.

Artificial selection

Charles Darwin knew a lot about artificial selection from his pigeon fancying hobby –which was more of a home-based experiment than a simple hobby. Man has produced many varieties of domesticated animals and cultivated plants, often with quite stunning traits. In Chapter 1 of The Origin of Species Darwin describes artificial selection as nature providing variations in traits and Man adding them up in certain directions useful to him to produce an accumulative selection. The importance consists in the great effect produced by the accumulation in one direction, during successive generations of slight differences (Origin, page 38).

The domestic breeds of pigeon – pouters, fantails, runts, barbs, dragons, carriers and tumblers are all descended from one wild species –the rock pigeon. Darwin thought that the different breeds differed so extraordinarily in length and form of beak that they would have been ranked as distinct genera had they been found in the wild.

The breeder of domesticated animals produces the desired trait over many generations of breeding by selecting offspring that carry the desired trait to some degree and allowing these favoured individuals to survive and breed, while disposing of the remaining offspring.

Adaptation

In the wild, in order to survive, organisms must be adapted to their environment. Darwin showed by careful analysis of many facts that natural populations have many variations in physical traits and individuals carrying advantageous traits that afford them greater adaptation survive and leave more offspring than less adapted individuals. Darwin theorized that the continuing natural selection of slight variations in traits carried by individuals brings about the modification of these traits, and the continuing process leads to speciation.

Species and varieties

In the first two chapters of The Origin of Species Darwin discusses the difficulties that naturalists had of deciding whether closely related forms were distinct species or varieties of the same species. He shows that each naturalist made a different classification with some naturalists ranking forms as distinct species and others ranking the same forms as varieties or geographical races of the same species.

Darwin concluded that no clear line of demarcation can be drawn between species and sub-species. Species can be thought of as strongly marked and permanent varieties (Origin page 59). This leads to the conclusion that species could not have been separately created.

Hybridism

Darwin supports this conclusion by information on hybridism. The degrees of fertility between plants and animals of different varieties, species and genera do not show a definite demarcation.

From the amassing of observations Darwin concludes that allied species are co-descendants from common stocks; species belonging to a genus are descended from one species that has been modified through Natural Selection. He writes that the view that most naturalists at the time entertained and which he formerly entertained – that each species has been independently created – is erroneous.

“I am fully convinced that species are not immutable; but that those belonging to what are called the same genera are lineal descendants of some other and generally extinct species, in the same manner as the acknowledged varieties of any one species are the descendants of that species.” (Origin page 15).

Later in The Origin of Species Darwin expands this view of common descent to families and orders, and finally to class level.

To summarize, Darwin defined Natural Selection as the preservation of favourable variations and the rejection of injurious variations. Darwin established his Theory of Common Descent mainly to class level. Thus, Natural Selection would bring about the modification of structures and other traits such that all the species belonging to one class would have evolved from a common ancestor. (Common descent at class level will be discussed further in Chapter 6).

The modification of traits is the first strand of evolutionary thought in The Origin of Species.

#2 Evolutionary Thought

May 20, 2023 by clarevmerry, posted in The Steps of Creation

During the 17^th and 18^th century classification of the natural world led to the observation that species of plants and animals are found as variations on common themes. It is this observation that impressed many naturalists and in the 19^th century led Charles Darwin to seek an explanation.

A general belief in direct creation by God prevailed in Christian Europe at this time. But by the 19^th century, naturalists generally believed in the continuous special creation of each species of plant and animal, while varieties belonging to species were believed to be produced by secondary causes. The secondary causes included the artificial breeding of animals and cultivation of plants by Man to produce a great diversity of varieties. It was known that extinctions had occurred in past geological eras and that ancient forms of life found as fossils are no longer found living today. It was thought by many that God replenished the Earth with the creation of new species after extinctions had occurred; there was a general belief in Progressive Creationism.

Over the course of the famous five year voyage around the world as naturalist on board HMS Beagle between 1831 and 1836, Charles Darwin became convinced that species are not fixed. Many years later, after much work on barnacles, beetles, orchids and all manner of other natural things including a hobby in pigeon fancying, Darwin wrote On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life published in 1859.

In The Origin of Species Darwin argued against the doctrine of the creation of each separate species. Belief in the design of each species of plant and animal by God was known as the fixity, immutability or permanence of species.

There had already been some attempts at an evolutionary understanding of the world, the most famous of which was proposed by the French naturalist Chevalier de Lamarck in Zoological Philosophy (1809). Lamarck’s evolutionary ideas were quickly rejected, although the term ‘biology’, which he coined, became widely used. Darwin’s own grandfather, Erasmus Darwin (1731-1802) also held evolutionary views. Erasmus Darwin was a free thinker and political radical, who founded a philosophical society in Derby. He had an unusual talent for writing scientific treatises in rhyming verse. Erasmus Darwin wrote Zoonomia or the Laws of Organic Life in 1794-1796 in which he expressed the notion that species modify themselves by adapting to their environment with purpose residing in the desires of the animal itself. Lamarckism was similar to this view.

Vestiges of the Natural History of Creation (1844) published anonymously by the Scottish autodidact and publisher Robert Chambers also had some influence at the time. The case for evolution in Vestiges rested upon the observation that fossils found from the most ancient to the most recent geological strata demonstrate a gradual ‘ascent’. It was proposed that new species could arise by sudden mutations in the course of reproduction. These ‘hopeful monsters’ met with much ridicule from other naturalists and professors such as Adam Sedgwick. However, Sedgwick argued against Vestiges on the grounds of theology, rather than science. (The geological collection of Adam Sedgwick is kept at Cambridge University and is open to the public).

Evolution was ‘in the air’, especially among families with progressive ideas such as the Darwins, but Charles Darwin went much further. He hit upon a new idea and followed it up with detailed scientific arguments. Darwin proposed what he described as a principle of evolution and laws of variation in organic beings; he named the principle Natural Selection. Natural Selection, as conceived by Darwin, is a natural process which is not guided towards any defined purpose or preconceived goal. Even so, Darwin believed that the principle would have been set up by God in the beginning with the creation of the first forms of life.

In how Natural Selection stands in relation to the Creator, Charles Darwin suggests that the Creator created the laws of science. Darwin states emphatically in letters such as in a letter written to Asa Gray dated 22^nd May 1860, that he never had the intention to write “atheistically” (Francis Darwin 2000, page 249). Darwin writes in this letter, “I am inclined to look at everything as resulting from designed laws, with the details, whether good or bad, left to the working out of what we may call chance.” Further down Darwin concludes, “I can see no reason why a man, or other animal, may not have been aboriginally produced by other laws, and that all these laws may have been expressly designed by an omniscient Creator, who foresaw every future event and consequence.”

Within Darwin’s concept of Natural Selection described in The Origin of Species there are three main strands of evolutionary thought. I will explore the three strands of evolutionary thought under the subtitles Modified traits, Highly perfected organs and Replacement of less-improved forms.

#1 Natural Selection: Strands of Evolutionary Thought

May 13, 2023 by clarevmerry, posted in The Steps of Creation

The Theory of Entropic Evolution includes the concept of Natural Selection. But what is this concept? In fact, as Charles Darwin presented it, the concept of Natural Selection is more than one single concept – it is a concept composed of several strands of thought. The objective of this chapter is to untie those strands and examine them.

The Origin of Species is one of my favourite books and very enjoyable to read. I first read it when I was at University studying biology (in my first year) and its influence has stayed with me ever since. Although I do not reach the same conclusions as Darwin, I have always felt complete oneness with his thought processes and the mode of his reasoning.

Due to the importance of Natural Selection and associated concepts for the Theory of Nanocreation and Entropic Evolution, I am going to give a detailed description and analysis of the ideas contained in The Origin of Species in this chapter / series of posts.

I will also take this opportunity to discuss the relationship between belief in Evolution and faith, and types of Creationism.

Ref. THE STEPS OF CREATION PART I: LIFE (2016) Chapter 5

#17 Against Naturalism to Explain the Origin of Life

April 28, 2023 by clarevmerry, posted in The Steps of Creation

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.

#16 Origin of the First Cells

April 14, 2023 by clarevmerry, posted in The Steps of Creation

Darwinism and the warm little pond

A natural origin to life was not an original tenet of Darwinism. The position of Charles Darwin in The Origin of Species was that the Creator breathed life into a few forms or into one (Origin, pages 421-422), and Natural Selection worked upon these or this multicellular life form to produce the many species found in the world today.

Certainly, Darwin had a minimalist position concerning religion, and it may be said that Darwin never firmly nor fully defined his position regarding the origin of life, but Darwin did not adhere to a philosophy of Naturalism. Thus, NeoDarwinism extends the scope of Evolution and natural processes involving Natural Selection far beyond the original claim.

Origin of life theorists are keen to link themselves to Darwin by citing a letter Darwin wrote in 1871 in which he wrote that life may have emerged in a warm little pond. Whether this was as some bacterial slime or as a Mudskipper is open to all interpretations.

Creation of the first cells

I propose with the Theory of Nanocreation that the first living cells were created as such. There are three basic types of single cell organisms; they are the Archaea, Eubacteria and eukaryotic Protista.

Archaean cells have DNA, RNA and proteins. Archaea have different components to their plasma membranes and cell walls than Eubacteria, and their ribosomal RNA has different base sequences. Archaea are very small cells that are adapted to very extreme environments.

Eubacteria are prokaryotic cells like Archaea, often somewhat bigger. They have cell walls composed of peptidoglycan. They reproduce asexually like Archaea and have many forms of nutrition with metabolic functions taking place in the cytoplasm of the cell.

The first eukaryotic single cell organisms belonged to the Protista kingdom. They are much bigger cells than bacteria with DNA in a nucleus surrounded by a nucleus membrane. The metabolic functions of the cell take place in membrane-bound cell organelles found within the cytoplasm. Later eukaryotes became multicellular.

The creation of whole unicellular organisms means that DNA, RNA and proteins, as well as other macromolecules such as lipids that form membranes were created together and designed as living cells. Support for the idea that DNA, RNA and proteins came into existence simultaneously in a living cell is that the genetic system does not function at all without all three components being present.

#15 Naturalism

April 7, 2023 by clarevmerry, posted in The Steps of Creation

Today science is dominated by a commitment to Naturalism whose main tenet is that everything that exists in the universe can be explained by natural processes. The guiding principle behind all these processes would be Evolution written large with Natural Selection acting as a type of (creative) force.

We are all agreed that science should be an enterprise based on rational thought and logic, and free from superstitions and various forms of pseudoscience. Many, if not, most things in science, once demonstrated empirically come to form a basis of understanding about the universe that is widely accepted and shared among the members of our society.

Evolution, however, is a different case from other areas of science, indeed it is a guiding principle that may be applied to all areas of science. Evolution is in various ways theory, fact and philosophy.

Scientists have theories and hypotheses, work on projects, make observations, discover facts, but they also have a culture embodying a philosophy that may be unspoken. The whole collection of ways of thinking by scientists at a given time is known, in the words of Thomas Kuhn (1962), as the scientific paradigm. A paradigm is an all-encompassing world view. ‘Paradigm shifts’ may occur, but they require nothing short of a revolution. Today’s scientific paradigm links Evolution with Naturalism.

Naturalism is a definition of reality which excludes God. Definitions of reality are philosophical positions.

Theistic Evolutionists who are also NeoDarwinists have adopted what they call Methodological Naturalism. Theistic Evolutionists have no argument with non-religious scientists on any major point. They believe that evolution involving secondary, natural causes accomplishes everything in the universe without the direct intervention of God. However, the Theists say that the existence of God gives reality and science meaning. For these Theists, as far as science is concerned, meaning and purpose are metaphysical categories while as far as the individual is concerned the Revealed God gives meaning and purpose in real terms.

In general, Theistic Evolutionists do not offer a religious alternative to the currently held conception of the world by the scientific community. Theistic Evolutionists give, in their publications, a meaningful interpretation of scientific findings from a religious point of view. This does not change the scientific investigation or conclusions reached in any way.

One of the people who have challenged the NeoDarwinian philosophy of science is Phillip Johnson (1991) in his book Darwin on Trial. Phillip Johnson is one of the founders of the Intelligent Design movement. I.D. followers believe that God created and designed living organisms. Johnson does not offer an alternative to “Darwinian natural selection”, but he strongly opposes the philosophy of Naturalism in science. Johnson claims that Naturalism limits scientific inquiry and he has this to say about it:

“If the purpose of Darwinism is to persuade the public to believe that there is no purposeful intelligence that transcends the natural world, then this purpose implies two important limitations upon scientific inquiry. First, scientists may not consider all the possibilities, but must restrict themselves to those which are consistent with a strict philosophical naturalism. For example, they may not study genetic information on the assumption that it may be the product of intelligent communication. Second, scientists may not falsify an element of Darwinism, such as the creative power of natural selection, until and unless they can provide an acceptable substitute. This rule is necessary because advocates of naturalism must at all times have a complete theory at their disposal to prevent any rival philosophy from establishing a foothold.” (Johnson 1991, page 154).

In science it is the origin of things that causes philosophical argument, not the working of things. Adherence to the philosophy of Naturalism makes imperative the origin of life by some unknown natural law from some form of reducing atmosphere, primordial soup, lipid-bounded vesicles, RNA genome, and autocatalytic proto-metabolism in a protocell.

Naturalism mythologizes Natural Selection by making Natural Selection an all-powerful entity that can produce life, and almost anything in the universe. To be sure, life exists, but Natural Selection is used as a rationalization of its existence, rather than an explanation. When it is said that the molecules in the prebiotic soup were ‘selectionally optimized’ or underwent ‘selective competition’ or ‘selective bias’ that caused them to become macromolecules and form a protometabolism because polymers (long molecules) are better than monomers (short molecules) for survival –why is this not an explanation? It is not an explanation because it ‘explains’ anything and everything.

Karl Popper analysed the theories of Marxism and Freudianism and concluded that they are pseudoscience because a theory that appears to explain everything actually explains nothing. According to Popper (1963) a theory with genuine explanatory power makes risky predictions, which exclude most possible outcomes. Success in prediction is impressive only to the extent that failure was a real possibility. Popper placed the condition that for a theory to be scientific, it must be possible to refute it.

In the origin of life field, the NeoDarwinist philosophical argument is that life obviously exists, and if a naturalistic process is the only conceivable explanation for its existence, then the difficulties must not be as insuperable as they appear. Over fifty years of experiments have not produced life, and the many models of early Earth have not produced the key to understanding. A natural origin of life is proving as elusive as the gold sort by the alchemists of former times.

#14 Irreducible Complexity

April 1, 2023 by clarevmerry, posted in The Steps of Creation

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.

#13 Protocells without Enzymes?

March 24, 2023 by clarevmerry, posted in The Steps of Creation

An article by Leslie Orgel (2008) entitled “The Implausibility of Metabolic Cycles on the Prebiotic Earth” investigates whether biochemical pathways could have occurred in simplified ways without the catalysing function of complex enzymes. Could autocatalytic cycles have occurred in protocells on the primitive Earth?

Biochemical research on reactions has shown that although mineral catalysts can catalyse biochemical pathways, they are not specific enough to avoid disruptive side reactions. (Side reactions produce the wrong product). Orgel writes,

“While enzymes discriminate readily between very similar substrates, such discrimination is rare, but not impossible, in reactions catalyzed by small molecules or mineral surfaces.” (Orgel 2008, page 4 of 10)

“Lack of specificity rather than inadequate efficiency may be the predominant barrier to the existence of complex autocatalytic cycles of almost any kind.” (Orgel 2008, page 5 of 10)

Experimental evidence shows that a very important aspect of enzymes in the building of the organic molecules of life is their ability to discriminate between very similar substrates. The highly specific catalytic activity of enzymes is due to their stable three-dimensional structure. This ensures that only the correct ligations are made in the joining of peptide monomers.

Orgel gives an analysis of a paper presented by Kauffman entitled “Autocatalytic Sets of Proteins”[1]. Kauffman presents a theory of peptide self-organization in which he assumes that a mixture of monomer (short) peptides will condense spontaneously into a mixture of long peptides. Orgel shows that Kauffman has misunderstood the initial conditions that would give any chance of this happening.

Orgel, who has dedicated much of his life to investigating how cells and biochemistry could have originated by natural means, concludes that molecular evolution involving prebiotic amino acids and hypothetical complex nonenzymatic metabolic cycles must show chemical plausibility. He states that one autocatalytic cycle – the core of the formose reaction is understood reasonably well, and one or two other simple cycles may exist. However, three decades after Orgel’s original work his tone seems generally pessimistic; he ends the article with the comment,

“However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help.” (Orgel 2008, page 9 of 10).

The conclusion that we may draw is that a natural origin to biochemistry has not been found despite large amounts of effort and imagination.

[1] Kauffman, S. A. (1986) Journal of Theoretical Biology Vol. 119, pages 1-24.

#12 Stereospecific Properties

March 18, 2023 by clarevmerry, posted in The Steps of Creation

It was the French biochemists François Jacob and Jacques Monod working in the 1960s who recognized the significance of the shape-recognition properties of protein enzymes with their substrates, and protein transcription factors with DNA.

Morphogenesis is microscopic. Monod anticipated that,

“…. the construction of a tissue or the differentiation of an organ – macroscopic phenomena – must be viewed as integrated results of multiple microscopic interactions due to proteins, and as deriving from the stereospecific recognition properties of those proteins, by way of the spontaneous forming of noncovalent complexes.” (Monod 1970, page 88).

The fundamental principle of associative stereospecificity accounts for the discriminative properties of proteins (Monod, 1970, page 104). It also accounts for the complementarity of the DNA strands which allows replication to occur. “In a very real sense it is at this level of chemical organization that the secret of life (if there is one) is to be found.” (Monod 1970, page 94).

Monod writes that proteins have complex foldings that determine the molecule’s three-dimensional structure, including the exact shape of the stereospecific binding sites by which the molecule performs its recognition activity. It is the sum of the noncovalent interactions that stabilizes the functional structure of the protein. It interacts through noncovalent bonds with other molecules. The precision of structure of proteins encoded in the amino acid sequence is indispensable to their specific binding properties (Monod 1970, page 90-91).

It emerges that two things are very important to the functioning of the genetic system: firstly that subunits associate in predictable ways as units (rather than amorphous masses that disintegrate), and secondly that the subunits are associated by noncovalent bonds that can be broken by relatively mild treatment.

For example, the noncovalent hydrogen bonds between complementary base pairs can be broken and the two DNA strands unzipped for replication to occur without the covalent bonds holding the DNA backbone together in each strand being affected.

Another more recently investigated example is that the mediator (or molecular bridge) involved in the transcription of DNA has 20 subunits united by noncovalent bonds whose energy equals one covalent bond. This is possibly just enough force to allow the DNA to be released from one covalently bonded methyl group so that transcription can occur. The weakness in the bonds between the mediator subunits also allows them to disassemble when transcription is completed (Allison 2007, pages 336, 337, 340).

It is important to understand that organic ingredients act as units of complex molecules that do not combine in a random fashion, but according to their chemical preferences for bond formation. The units have some properties of self-assembly and spontaneous association. Properties of self-assembly are not to be confused with stereospecificity. Monod (1970, pages 104-105) points out that the DNA structure can accommodate any sequence of DNA bases. The sequence of DNA bases is entirely ‘free’; it is not determined by chemistry. This is what makes DNA an information carrier. The DNA sequence specifies the stereospecific properties of the protein products.

The structure of DNA is achieved by complementary base pairing. The nucleotide bases A and G are purines which means that they are composed of two fused rings. The nucleotide bases C and T are pyramidines which means they only have one ring. Base pairing occurs such that A and T form two hydrogen bonds with each other, while C and G form three hydrogen bonds with each other. Thus, in double helix DNA where there is A in one strand there is T in the other, and where there is C in one strand there is G in the other. The two strands of DNA are complementary to each other. The pairing of nucleotide bases is stereospecific – it is always the same, but the order of nucleotide bases along the DNA strands is entirely free and not dictated by bonding properties. The structure of genes is therefore not stereospecific.

Monod (1970, pages 78-79) calls this the concept of gratuity –that the function of allosteric enzymes is not determined by chemistry. The specificity of the interactions is due to the structure of the protein in the various states it is able to adopt, a structure freely and arbitrarily dictated by the structure of a gene.

“An allosteric protein should be seen as a specialized product of molecular ‘engineering’, enabling an interaction, positive or negative, to take place between compounds without chemical affinity, and thereby eventually subordinating any reaction to the intervention of compounds that are chemically foreign and indifferent to this reaction.” (Monod 1970, pages 78-79).

We may conclude that the functioning of the living cell is not determined by the laws of chemistry. Life transcends the laws of chemistry and the laws of physics. Chemistry, and especially the properties of different types of bonds do, however, impose some order on the genetic system. No system would continue to function without various levels of order.

In the minds of some people, the discovery of levels of order that may be produced by the spontaneous association of organic molecules is interpreted as meaning that there need be no rational intention or design behind nature. They believe that nature functions according to laws naturally and spontaneously with no other input being necessary. Some people have confused the stereospecificity of protein enzymes and the nucleotide structure of DNA with the totally free ordering of nucleotide bases in the structure of genes; they believe that genes are specified by natural rules of assembly. Thus, they have not understood that although information is carried by an ordered molecule called DNA, the information DNA carries has another source.

#11 Origin of biochemistry

March 10, 2023 by clarevmerry, posted in The Steps of Creation

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.