FOCUS: The root of Darwin's evolutionary tree of life is the origin of life; oddly, it is not a part of the theory of evolution. In this unit, the requisites for a cell with metabolism (to draw, transform and use energy and materials from the environment) and code-driven self-replication (to reproduce itself) are examined, followed by the information-processing system that creates the proteins that serve as the cell's molecular work-horses. The challenge such requisites and features pose for evolutionary materialist models for the spontaneous origin of life are examined., including the observed "simple" case of M. pneumoniae. The conclusion is plain: the cell is a complex, coded information-processing system, and there is no mechanism for its spontaneous origin, so the Darwinian tree of life has no well-established root.
--> genes first vs metabolism first scenarios vs evidence
(a) Stumbling across a cell . . .
--> Paley's self-replicating, time-keeping watch
--> The von Neumann Self-Replicator
(b) The cell, biological life and information processing
--> protein synthesis, mRNA, tRNA & the Ribosome
--> Protein transcription animation
(c) The challenge for spontaneous origin of life scenarios
--> Mycoplasma pneumoniae
--> The Flagellum case study
NEXT: Origin of Body-plan level Biodiversity
Originally, the tree of life was viewed as a classification of life, reflecting underlying deep patterns of nature. After Darwin, that pattern has been generally thought to be an evolutionary one. This then leads to the question of the root of the tree; i.e. the origin of life.
Science writer Richard Robinson summed up the current situation as follows:
Every living cell, even the simplest bacterium, teems with molecular contraptions that would be the envy of any nanotechnologist. As they incessantly shake or spin or crawl around the cell, these machines cut, paste and copy genetic molecules, shuttle nutrients around or turn them into energy, build and repair cellular membranes, relay mechanical, chemical or electrical messages—the list goes on and on, and new discoveries add to it all the time.
It is virtually impossible to imagine how a cell’s machines, which are mostly protein-based catalysts called enzymes, could have formed spontaneously as life first arose from nonliving matter around 3.7 billion years ago. To be sure, under the right conditions some building blocks of proteins, the amino acids, form easily from simpler chemicals, as Stanley L. Miller and Harold C. Urey of the University of Chicago discovered in pioneering experiments in the 1950s. But going from there to proteins and enzymes is a different matter . . .
David Berlinsky, in his 2006 Commentary Magazine essay, "On the Origins of Life," gives us a glimpse of why such is so. As he concludes his essay, he writes:
At the conclusion of a long essay, it is customary to summarize what has been learned. In the present case, I suspect it would be more prudent to recall how much has been assumed:
First, that the pre-biotic atmosphere was chemically reductive; second, that nature found a way to synthesize cytosine; third, that nature also found a way to synthesize ribose; fourth, that nature found the means to assemble nucleotides into polynucleotides; fifth, that nature discovered a self-replicating molecule; and sixth, that having done all that, nature promoted a self-replicating molecule into a full system of coded chemistry.
These assumptions are not only vexing but progressively so, ending in a serious impediment to thought. That, indeed, may be why a number of biologists have lately reported a weakening of their commitment to the RNA world altogether, and a desire to look elsewhere for an explanation of the emergence of life on earth. "It's part of a quiet paradigm revolution going on in biology," the biophysicist Harold Morowitz put it in an interview in New Scientist, "in which the radical randomness of Darwinism is being replaced by a much more scientific law-regulated emergence of life."
Morowitz is not a man inclined to wait for the details to accumulate before reorganizing the vista of modern biology. In a series of articles, he has argued for a global vision based on the biochemistry of living systems rather than on their molecular biology or on Darwinian adaptations. His vision treats the living system as more fundamental than its particular species, claiming to represent the "universal and deterministic features of any system of chemical interactions based on a water-covered but rocky planet such as ours."
This view of things - metabolism first, as it is often called - is not only intriguing in itself but is enhanced by a firm commitment to chemistry and to "the model for what science should be." It has been argued with great vigor by Morowitz and others. It represents an alternative to the RNA world. It is a work in progress, and it may well be right. Nonetheless, it suffers from one outstanding defect. There is as yet no evidence that it is true . . .
Professor John Walton's lecture on the origin of life here [[HT: VJT of UD] is also well worth watching, to set the context:
The Origin of Life from Phil Holden on Vimeo.
The key challenge, then, is accounting for the origin of the information-rich functionally specific complexity of the cell (multiplied by the challenges of an information-based self-replicator joined to a metabolic system -- and what Berlinski hints at bears underscoring: such is the only Carbon-chemistry life we have empirical evidence for):
Now, William Paley famously contrasted stumbling across a stone in a field with finding a watch in the same field; inferring design from the characteristics of a watch that are distinct from those of a stone. Especially, that “. . . its several parts are framed and put together for a [[functionally specific] purpose, e.g., that they are so formed and adjusted as to produce motion, and that motion so regulated as to point out the hour of the day.”
Also, going beyond what Paley could have known, it uses coded symbolic information, has digital storage of this information, and also reading and guiding mechanisms that direct the replicating machinery and process. So, it is reasonable to consider whether “. . . its several parts are framed and put together for a [[functionally specific] purpose.”
In fact, the observed cell -- which is what we need to explain the origin of -- joins together (i) a metabolising entity that draws in energy and materials from its surroundings and processes them, ejecting wastes, to (ii) a symbol-based coded system that allows it to replicate itself.
That is, we are looking at a molecular scale von Neumann self-replicating, metabolising automaton, functionally similar to that in Fig G.2 as was presented with a more elaborate description than the following, above:
Fig. G.2, copied: A schematic, 3-D/“kinematic” von Neumann-style self-replicating machine. [[NB: von Neumann viewed self-replication as a special case of universal construction; “mak[[ing] anything” under programmed control.] (Adapted, Tempesti.)
Fig. G.2 (b), copied: Mignea's schematic of the requisites of kinematic self-replication, showing duplication and arrangement then separation into daughter automata. This requires stored algorithmic procedures, descriptions sufficient to construct components, means to execute instructions, materials handling, controlled energy flows, wastes disposal and more. (Source: Mignea, 2012, slide show; fair use. Presentation speech is here.)
Now, following von Neumann generally (and as previously noted), such a machine uses . . .
That is, we see here an irreducibly complex set of core components that must all be present in a properly organised fashion for a successful self-replicating machine to exist. [[Take just one core part out, and self-replicating functionality ceases: the self-replicating machine is irreducibly complex (IC).]
This irreducible complexity is compounded by the requirement (i) for codes, requiring organised symbols and rules to specify both steps to take and formats for storing information, and (v) for appropriate material resources and energy sources.
Immediately, we are looking at islands of organised function for both the machinery and the information in the wider sea of possible (but mostly non-functional) configurations.
In short, outside such functionally specific -- thus, isolated -- information-rich hot (or, "target") zones, want of correct components and/or of proper organisation and/or co-ordination will block function from emerging or being sustained across time from generation to generation. So, once the set of possible configurations is large enough and the islands of function are credibly sufficiently specific/isolated, it is unreasonable to expect such function to arise from chance, or from chance circumstances driving blind natural forces under the known laws of nature.
The significance of this becomes immediately apparent once we examine:
- organisation based on functional cells
- homeostatic regulation of the resulting internal environment
- metabolic processing of energy and materials (with elimination of waste)
- growth and development across the life cycle
- individual and collective adaptive responses to environmental circumstances
- responsiveness to stimuli
The above definition underscores just how central the cell is to biological life, and just how difficult the challenge to propose an empirically credible spontaneous origin model for the cell is.
Key to that challenge is how central programmed, digital information processing is to the cell's functional organisation and ability to replicate itself. This can best be seen from the process of protein synthesis, which creates the workhorse molecules of the cell through a regulated process:
Fig. G.8 (a): Overview of Protein Synthesis: [[Courtesy Wikimedia, under GNU. (Also, cf a medically oriented survey here.)]
Fig. G.8 (b): The gene regulatory network that controls the protein transcription and translation process. (Source: Wiki, public domain. Cf. similar diagram and explanatory discussion here.)
Fig. G.8(c): The gene regulatory network (GRN) for part of the embryonic development of a Sea Urchin, showing how genes are activated on a phased, controlled step by step basis to implement the body plan. (Original here, with explanatory discussion. Under fair use.)
Fig. G.8(d): A GRN for the formation of flowers in a plant, with explanation of symbols used: "Gene regulatory network controlling early Arabidopsis [[rockcress] flower development. Regulatory genes and their known interactions are shown. Upstream inputs and downstream targets are indicated for each gene. Activators are connected to their targets by arrows, repressors by blunted lines [[i.e. with short bars]. Blue dots underneath gene symbols indicate that direct binding to these genes has been demonstrated. Note their small number in the diagram, indicating the limited knowledge of transcription factor binding sites. White circles represent protein complexes. Dashed lines indicate that gene products do not function as transcriptional regulators." (Source: Smurfit Institute , fair use.)
Fig. G.9: Protein translation using mRNA and tRNA -- an expansion of the Ribosome at (c) in Fig G.8(a). [[Courtesy Wikimedia under GNU.]
Cells use hundreds or more proteins to carry out their work, embedding many thousands of bits of functionally specific digitally coded information.
The required protein synthesis system also exhibits irreducible complexity, and uses algorithmic processing. Thus, the “analogy” between the cell and electronic information processing systems is sufficiently close to again raise questions of purposeful design of codes, storage systems, readers, and effecting machinery.
(Indeed, since the actual essential nature of digital, flexible, code-based algorithmic processing systems is a mathematical one, it is also reasonable to say that the protein synthesis system instantiates such a digital information system. And if that is at all a reasonable inference, then all objections that pivot on dismissing "analogies" collapse -- even, if we for the moment ignore the key role analogy plays in inductive reasoning.)
Further to this, Tokuriki and Tawfik note how islands of function for proteins are strongly constrained, thermodynamically and kinetically:
The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability--the ability of proteins to acquire changes in sequence and function. [["Stability effects of mutations and protein evolvability," Curr Opin Struct Biol. 2009 Oct; 19(5):596-604. Epub 2009 Sep 16. Emphasis added.]
Moreover, the expression of such stability constrained functional proteins and the development of body plans are based on a complex regulated process as shown. As this may be summarised:
A gene regulatory network or genetic regulatory network (GRN) is a collection of DNA segments in a cell which interact with each other (indirectly through their RNA and protein expression products) and with other substances in the cell, thereby governing the rates at which genes in the network are transcribed into mRNA.
In general, each mRNA molecule goes on to make a specific protein (or set of proteins).Immediately, we see that complex regulatory networks (with duly complex "wiring plans") are intimately involved in the development of a body plan from embryonic stages onwards, and in the responsiveness of life forms to their environment.
In some cases this protein will be structural, and will accumulate at the cell-wall or within the cell to give it particular structural properties. In other cases the protein will be an enzyme; a micro-machine that catalyses a certain reaction, such as the breakdown of a food source or toxin.
Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in regulatory networks or cascades. By binding to the promoter region at the start of other genes they turn them on, initiating the production of another protein, and so on. Some transcription factors are inhibitory.
In single-celled organisms regulatory networks respond to the external environment, optimising the cell at a given time for survival in this environment. Thus a yeast cell, finding itself in a sugar solution, will turn on genes to make enzymes that process the sugar to alcohol. This process, which we associate with wine-making, is how the yeast cell makes its living, gaining energy to multiply, which under normal circumstances would enhance its survival prospects.
In multicellular animals the same principle has been put in the service of gene cascades that control body-shape. Each time a cell divides, two cells result which, although they contain the same genome in full, can differ in which genes are turned on and making proteins. Sometimes a 'self-sustaining feedback loop' ensures that a cell maintains its identity and passes it on . . . [[.]
A major feature of multicellular animals is the use of morphogen gradients, which in effect provide a positioning system that tells a cell where in the body it is, and hence what sort of cell to become. A gene that is turned on in one cell may make a product that leaves the cell and diffuses through adjacent cells, entering them and turning on genes only when it is present above a certain threshold level. These cells are thus induced into a new fate, and may even generate other morphogens that signal back to the original cell.
Over longer distances morphogens may use the active process of signal transduction. Such signalling controls embryogenesis, the building of a body plan from scratch through a series of sequential steps. They also control maintain adult bodies through feedback processes, and the loss of such feedback because of a mutation can be responsible for the cell proliferation that is seen in cancer.
In parallel with this process of building structure, the gene cascade turns on genes that make structural proteins that give each cell the physical properties it needs . . . .
[[B]iological cells can be thought of as "partially-mixed bags" of biological chemicals . . . mRNA and proteins interact with each other with various degrees of specificity. Some diffuse around the cell. Others are bound to cell membranes, interacting with molecules in the environment. Still others pass through cell membranes and mediate long range signals to other cells in a multi-cellular organism.
These molecules and their interactions comprise a gene regulatory network. A typical gene regulatory network looks something like this: The nodes of this network are proteins, their corresponding mRNAs, and protein/protein complexes. Nodes that are depicted as lying along vertical lines are associated with the cell/environment interfaces, while the others are free-floating and diffusible. Implied are genes, the DNA sequences which are transcribed into the mRNAs that translate into proteins.
Edges between nodes represent individual molecular reactions, the protein/protein and protein/mRNA interactions through which the products of one gene affect those of another, though the lack of experimentally obtained information often implies that some reactions are not modeled at such a fine level of detail.
These interactions can be inductive (the arrowheads), with an increase in the concentration of one leading to an increase in the other, or inhibitory (the filled circles), with an increase in one leading to a decrease in the other. A series of edges indicates a chain of such dependencies, with cycles corresponding to feedback loops.
Abiogenesis is the study of how life could have spontaneously emerged, by some combination of chance circumstances and chemical and physical forces, in a pre-biotic world. The just linked generic source provides a helpful short summary of the current state of the discussion, but unfortunately stacks the deck a bit, requiring a parenthetical note or two. Highlights will help us observe the gaps and suppositions in the chain of reasoning:
There is no truly "standard model" of the origin of life. Most currently accepted models draw at least some elements from the framework laid out by the Oparin-Haldane hypothesis. Under that umbrella, however, are a wide array of disparate discoveries and conjectures such as the following, listed in a rough order of postulated emergence:So, point 4 is the key issue, and leads to the two main alternative abiogenesis models : “genes/ nucleic acids first” models (especially RNA world models), and “metabolism/ proteins first” ones (currently a minority view among OOL researchers).
- Some theorists suggest that the atmosphere of the early Earth may have been chemically reducing in nature [[NB: a fairly controversial claim, as others argue that the geological evidence points to an oxidising or neutral composition, which is much less friendly to Miller-Urey-type syntheses] , composed primarily of methane (CH4), ammonia (NH3), water (H2O), hydrogen sulfide (H2S), carbon dioxide (CO2) or carbon monoxide (CO), and phosphate (PO43-), with molecular oxygen (O2) and ozone (O3) either rare or absent.
- In such a reducing atmosphere [[notice the critical dependence on a debatable assumption], electrical activity can catalyze the creation of certain basic small molecules (monomers) of life, such as amino acids. [[Mostly, the very simplest ones, which had to be rapidly trapped out lest hey be destroyed by the same process that created them] This was demonstrated in the Miller–Urey experiment by Stanley L. Miller and Harold C. Urey in 1953.
- Phospholipids (of an appropriate length) can spontaneously form lipid bilayers, a basic component of the cell membrane.
- A fundamental question is about the nature of the first self-replicating molecule. Since replication is accomplished in modern cells through the cooperative action of proteins and nucleic acids, the major schools of thought about how the process originated can be broadly classified as "proteins first" and "nucleic acids first".
- The principal thrust of the "nucleic acids first" argument is as follows:
- The polymerization of nucleotides into random RNA molecules might have resulted in self-replicating ribozymes (RNA world hypothesis) [[Does not account for the highly specific nature of observed self-replicating chains, nor the problem of hydrolysis by which ever-present water molecules could relatively easily break chains]
- Selection pressures for catalytic efficiency and diversity might have resulted in ribozymes which catalyse peptidyl transfer (hence formation of small proteins), since oligopeptides complex with RNA to form better catalysts. The first ribosome might have been created by such a process, resulting in more prevalent protein synthesis.
- Synthesized proteins might then outcompete ribozymes in catalytic ability, and therefore become the dominant biopolymer, relegating nucleic acids to their modern use, predominantly as a carrier of genomic information. [[Does not account for the origin of codes, the information in the codes, the algorithms to put it to use, or the co-ordinated machines to physically execute the algorithms.]
As of 2010, no one has yet synthesized a "protocell" using basic components which would have the necessary properties of life (the so-called "bottom-up-approach"). Without such a proof-of-principle, explanations have tended to be short on specifics. [[Acc.: Aug 5, 2010, coloured emphases and parentheses added.]
The basic reason why neither is sufficiently robust to be decisively dominant can be seen from the following exchange between champions of the two models:
A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . .
To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . .
Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . .
It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . few would believe that any assembly of minerals on the primitive Earth is likely to have promoted these syntheses in significant yield . . . . Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of [[for instance] the reverse citric acid cycle was present anywhere on the primitive Earth [, or that the cycle mysteriously organized itself topographically on a metal sulfide surface [? . . . Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . .
The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help. [[Emphases added.]
● M. pneumoniae’s transcribed [[DNA] is much more similar to that of eukaryotes. As in eukaryotes, a large proportion of the transcripts produced from M. pneumoniae's DNA are not translated into proteins.
● M. pneumoniae’s gene expression is more complex than expected.
● M. pneumoniae is incredibly flexible and readily adjusts its metabolism to drastic changes in environmental conditions. This adaptability and its underlying regulatory mechanisms mean M. pneumoniae has the potential to adapt quickly.
The case of the bacterial flagellum underscores this, as Scott Minnich explains:
Bacterial Flagella: A Paradigm for Design from The Veritas Forum on Vimeo.
No wonder, then that we see the self-contradictory stance by prof Richard Dawkins that was recently highlighted by Rabbi. As he summarises:
In Dawkins' own words:
What Science has now achieved is an emancipation from that impulse to attribute these things [[origin of life and/or its major forms] to a creator... It was a supreme achievement of the human intellect to realize there is a better explanation ... that these things can come about by purely natural causes ... we understand essentially how life came into being.20 (from the Dawkins-Lennox debate)"We understand essentially how life came into being"?! – Who understands? Who is "we"? Is it Dr. Stuart Kauffman? "Anyone who tells you that he or she knows how life started ... is a fool or a knave." 21
Is it Dr. Robert Shapiro? "The weakest point is our lack of understanding of the origin of life. No evidence remains that we know of to explain the steps that started life here, billions of years ago." 22
Is it Dr. George Whitesides? "Most chemists believe as I do that life emerged spontaneously from mixtures of chemicals in the prebiotic earth. How? I have no idea... On the basis of all chemistry I know, it seems astonishingly improbable."
Is it Dr. G. Cairns-Smith? "Is it any wonder that [many scientists] find the origin of life to be utterly perplexing?" 23
Is it Dr. Paul Davies? "Many investigators feel uneasy about stating in public that the origin of life is a mystery, even though behind closed doors they freely admit they are baffled ... the problem of how and where life began is one of the great out-standing mysteries of science."
Is it Dr. Richard Dawkins? Here is how Dawkins responded to questions about the Origin of Life during an interview with Ben Stein in the film Expelled: No Intelligence Allowed:
Stein: How did it start?
Dawkins: Nobody knows how it started, we know the kind of event that it must have been, we know the sort of event that must have happened for the origin of life.
Stein: What was that?
Dawkins: It was the origin of the first self replicating molecule.
Stein: How did that happen?
Dawkins: I told you I don't know.
Stein: So you have no idea how it started?
Dawkins: No, No, NOR DOES ANYONE ELSE. 24
“Nobody understands the origin of life, if they say they do, they are probably trying to fool you.” (Dr. Ken Nealson, microbiologist and co-chairman of the Committee on the Origin and Evolution of Life for the National Academy of Sciences)
Nobody, including Professor Dawkins, has any idea "how life came into being!" [[The Design Argument: Answers to Atheists' Objections, online at Aish.com here. (Especially note Dawkins' "must have been . . . " deductions from his a priori evolutionary materialism, as highlighted.)]