Life Originally Arose via. Abiogenesis
This debate challenge is the arranged debate made with Joepalscak. I would like to make a late apology for a previous debate we held which I forfeited all my rounds.[http://www.debate.org...] The same will most certainly not be occurring again.
"Biological life on Earth originally arose via. abiogenesis"
In this debate I will be proposing that an organism that would have been capable of evolving through evolution via. natural selection would have arisen from purely chemical origins, and indeed is the explanation existing in the first place on Earth.
Abiogenesis: The hypothesis of life arising from abiotic chemical origins
Life: Systems that can self-replicate and evolve via. natural selection
Round 1: Acceptance, Definitions
Round 2: Opening arguments & rebuttals
Round 3: Arguments & Rebuttals
Round 4: Rebuttals & Conclusion (No new arguments)
Message me if you wish for any changes in the format, definitions etc.
A system of symbolic communication that manifests code, syntax, and semantics (note: such a system will invariably also manifest pragmatics. I have chosen to leave pragmatics out of the relevant terminology here simply to maintain sharper clarity and focus).
1. A general theory of signs and symbolism, usually divided into the branches of pragmatics, semantics, and syntax.
2. A general philosophical theory of signs and symbols that deals especially with their function in languages and comprises syntax, semantics and pragmatics.
A system of signals or symbols for communication.
The study of the rules for the formation of grammatical sentences in a language.
the study of the meaning of words and phrases.
The idea that is represented by a word, phrase, etc.
Notice the abstract, immaterial nature of every single component of semiotic language.
A NOTE ON PRO'S DEFINITION OF LIFE
There is no single agreed upon definition of what life is. Pro's definition, while straightforward, ignores many features which distinguish life from non-life. It is critical that I note here in the definition section that every entity that can unambiguously said to be (or have been at one time) "alive" has a genome. A genome is critical and indispensable to life.
What is life
i. The ‘food’ sources are of low entropy
ii. Total entropy of the environment increases at each stage via. heat release & mitosis
iii. The system is autocatalytic, as the product itself can particulate in each cycle
Because the system is autocatalytic, if all other factors are irrelevant then the system will continue to multiply at an exponential rate. This repeats itself over and over until you have 4,8,16,32 etc.. So long as there is food in the system, the cells will replicate indefinitely, and it is partially for this reason why life is so stubborn, since it constantly replaces itself at an exponential rate. Moreover life has the ability to evolve over generations which allows life to achieve versatility over a variety of conditions.
In this debate, pro has assumed the burden of persuading us that the evidence establishes natural causation; to wit, "abiogenesis happened." It is up to me to establish that his conclusion is not warranted, given the evidence. Indeed, I will show that the evidence decisively renders natural causation as an unreasonable conclusion, and, though it is not strictly necessary according to the terms of this debate, that the evidence does establish deliberate action (intelligent agency) as the only reasonable cause.
My case will focus on, but not be limited to, two primary lines of evidence:
1). The semiotic information systems that undergird all life
2). The mathematical realities against natural causation
Each of these lines of evidence is, by itself, powerful testimony in favor of intelligent causation and against natural causation. Taken together, they constitute a case that is as strong as any historical conclusion can possibly be.
In this opening statement, I provide a brief overview of the evidence:
1). THE SEMIOTIC INFORMATION SYSTEMS THAT UNDERGIRD ALL LIFE
Francis Crick, who with James Watson first elucidated the DNA double helix structure, recognized that the three dimensional proteins which do the jobs of keeping all living systems alive, are prescribed by a semiotic information system - the DNA/RNA protein synthesis system. Crick's insight became know as the "Sequence Hypothesis," . As Crick puts it, his hypothesis, "in its simplest form assumes that the specificity of a nucleic acid is expressed solely by the sequence of its bases, and that this sequence is a code for the amino acid sequence of a particular protein." 
The explanatory power of the sequence hypothesis has played a major role in unlocking our understanding of the genome (to the extent that we understand it) and of the pivotal role of information in all living systems.
DNA employs four specific chemical bases, abbreviated A,C,G,T (When translated to RNA, T is swapped out for U). These bases comprise the code of biological information. It is the specificity of the sequence of the bases, as Crick noted, which prescribes specific AA sequences. Just as specific sequences of English letters prescribe specific words, constituting the semantics of our language, so too, the specificity of base sequences prescribing specific AA sequences constitutes the semantics of biological information. These sequences must be read as a contiguous string of "codons," or "triplets" (groups of three bases); the rules of biological grammar - the syntax.
The nucleotide and codon syntax of DNA language has no physical explanation. All nucleotides are bound with the same 3'5' phosphodiester bonds. The codon table is arbitrary and formal, not determined by physics and chemistry. As I noted in round 1, every aspect of semiotic language is abstract and immaterial. So it is with biological information. Material symbols are employed, whether they are nucleotide bases, alphabetical characters, 0's and 1's (as in machine code), or semaphore flags, but they are employed to convey abstract messages. Abstract realities are only produced by minds with the express intention of producing those abstract realities. Natural processes have never been observed to deal in symbolic meaning. Natural processes are governed by deterministic laws, not arbitrary rules. Pro has the unenviable task of demonstrating that the rule based abstract semiotic information which makes all life possible has arisen via strictly natural processes. I wish him luck!
2.) THE MATHEMATICAL REALITIES AGAINST NATURAL CAUSATION
Clearly, any coherent causal account for the origin of life must explain the origin of the semiotic information systems that make life possible. Most, if not all proposed abiogenesis scenarios provide no such explanation. Rather, these scenarios seek purely physical pathways to the highly specified chemical arrangements of life. Setting aside the information requirements for the moment, let us closely examine just what the champions of abiogenesis are up against:
*Sir Fred Hoyle calculated the chance chemical formation of a single cell bacterium to be 1 in 10^40,000.
*a single protein of average length (300 AAs) represents one sequence among 10^390.
*there are only 10^65 atoms in our galaxy and only 10^80 elementary particles in the known universe.
Given only the above information, the mathematical odds against a specific linear chain of AAs capable of folding into a functional three dimensional protein forming purely by chance is many orders of magnitude smaller than the odds of randomly selecting a specific atom from our galaxy. In other words, the chance occurrence of such an event is so wildly improbable that it cannot be seriously entertained as a scientific possibility.
Of course, this is not the entire story. There are other factors. For example, it is crucial to get a handle on the ratio of functional sequences to non functional sequences. If every chain of 300 AAs will yield a functional protein, the problem of finding a functional chain at random completely disappears. A few decades ago, Robert Sauer conducted experiments which led to the estimate that for a short protein of 92 AAs, the ratio of functional sequences to non-functional sequences was 1 in 10^63 . This estimate was roughly in agreement with the work of information scientist Hubert Yockey's estimates of 1 in 10^90 for a protein 100 AAs long. Later work by Douglas Axe (1 in 10^77 for a protein 150 AA long) reveals similar improbabilities.
All of these estimates fall orders of magnitude below any reasonable level this side of "essentially impossible." Thus, it appears that the chance formation of a string of AAs that could produce a chain capable of folding into even a single modest protein has such a vanishingly small probability of occurring that it is far more reasonable to assume that it never happened. Life - even the simplest single cell organism - requires many proteins.
But there is more: While there are only 20 biologically relevant AAs, there are many more non-biologically relevant AAs. AAs in protein chains must be bound by peptide bonds, but other bonds are every bit as likely. Moreover, every amino acid can assume one of two forms. In nature, both forms are roughly equally represented. This is know as a "racemic," or, right-handed and left-handed mixture, but biologically relevant AAs must be completely homochiral (the left-handed form). A single non biologically relevant AA (or any other chemical for that matter), or a single right-handed AA, or a single bond other than a peptide bond, renders a chain of any length biologically worthless. The realities of interfering cross reactions, correct bonding, and the homochiral requirement, pile orders of magnitudes upon orders of magnitudes against the already infinitesimal chance formation of any biologically relevant chain.
Without even considering the informational requirements of life, the math alone provides decisive testimony against abiogenesis. It is incumbent upon pro to give us good evidential reason to believe that the probability of abiogenesis rises far, far above the level of operationally impossible.
WHERE WE STAND TODAY
The reality is that we have no idea how life first arose from aimless, inanimate matter. We can only infer what happened from the clues available to us. Before the Sequence Hypothesis, all of the available relevant clues seemed to be of a physical nature. But from the SH forward, we have come to realize that not only is DNA biological information, it is the most efficient[5 ] and advanced[6 ] information storage and processing system we have ever encountered. This constitutes evidence. Hard evidence which must be dealt with.
Pro is committed to insisting that natural processes are responsible for the origin of life. This is fine, but pro must deal with the hard evidence of the information of life as well as the mathematical evidence against abiogenesis. Pro's opening argument presents scenarios which attempt to mitigate the mathematical problem. In my rebuttal round, when I examine his arguments in detail, I will reveal why theses attempts fail. Finally, I will note that pro's opening argument completely ignores biological information.
 "On Protein Synthesis," Crick, 1958
 "Functionally accepted substitutions in Two Alpha Helical Regions of Lambda Repressor," Reidaar-Olson and Sauer
 "On the Information Content of Cytochrome C," Yockey
 "Estimating the Prevalence of Protein Sequences Adapting Functional Enzyme Folds," Axe
 a single line of genetic text can contain multiple independent messages. Bill Gates has noted that DNA is like computer software, but far more advanced than anything we have created
Con probably has his own formulation of this, but this is essentially contains all the content of Con’s opening round and his desired conclusion. I will tackle these assumptions independantly.
*Pro offers us several possible abiogenesis scenarios. It cannot be stressed enough that as origin of life proposals, these scenarios are hypothetical. They are not emperical. In other words, these scenarios are speculation. Pure speculation.
*Furthermore, pro's scenarios all rely on the primary assumption that life can emerge from simpler precursors.
To be sure, pro does bring an element of scientific fact into his various scenarios. Nonetheless, his speculations go well beyond the facts and his primary assumption has no basis beyond a desire that it be so. Indeed, that life has arisen from simpler precursors is the very thing that pro needs to convince us of. To simply assume it, reduces his argument to pure tautology: Life has arisen from simpler precursors because life has arisen from simpler precursors!
Mixing some scientific fact with a heavy dose of speculation and wishful assumptions can be the stuff of good science fiction. It can even suggest fruitful avenues of research. But pro must separate speculation from evidence. The place to look for evidence concerning the origin of life is life itself. Pro postulates that life used to be something other than life and immediately sets out to discover what that "something" might be. He does not consider the evidence from life.
Pro claims that life is thermodynamically inevitable, stating that the prebiotic earth,
" was under significant thermodynamic stress and this is where life comes in. Life is very good at relieving this thermodynamic stress."
But it does not ipso facto follow that therefore life "inevitably" arose. I have a relative who is under constant economic stress and money is very good at relieving economic stress. It does not follow that therefore money will inevitably arise in my relative's life to relieve that stress. And money is already in existence!
Living systems are themselves highly organized and therefore represent low entropy states, so why is life so good at relieving thermodynamic stress? Because of the work that living systems accomplish. And how is this work accomplished? It is accomplished by a myriad of molecular machines which in turn are made up of proteins and protein complexes, which are prescribed by biological information! Without machines to do the work, living systems do not relieve thermodynamic stress, and unless information to build those machines is already present, no machines emerge. The fundamental question remains: where did the information come from?
Pro suggests that so-called self organization (autocatalysis) provides a natural pathway to life. But biological information is possible specifically because the sequences of bases - the very sequences which prescribe the proteins - are not affected by (indeed, are free from) so-called self organization . Pro declares that natural autocatalytic processes are rather life like, but as he himself notes,
" Life takes in raw materials in the form of food, which the cell uses to create additional imperfect copies of itself."
Indeed life takes in raw materials and processes those materials for a myriad of functions which include reproduction. But again, this processing requires a vast ensemble of molecular machines; molecular machines which, incidentally, work with each other in a coordinated fashion. No molecular machinery exists in any non-biological autocatalytic process.
The cell is the indivisible unit of life. Theoretical and experimental work on the minimal complexity required to sustain the simplest possible living organism suggests a lower bound of 250-400 genes with their associated proteins [8,9].
Sophisticated machines, such as are found in all living systems do not arise spontaneously in nature, nor do the proteins which comprise these machines. Needless to say, complex networks of machines integrated into sophisticated holistic networks responding to and coordinated with one another by extensive communication systems do not arise spontaneously in nature either. Yet such networks characterize every single living cell. Nothing simpler than a single cell has ever been demonstrated to be alive. In his opening statement, pro claims that,
"the elements of a genome which I will argue to be accessible via. abiogenesis will be one that possesses memory capability, template, and imperfect replication ability."
Well yes, but there is also the fundamental matter of the cybernetic reality of life's organization and information properties. How are these realities accessible via abiogenesis? On this crucial question, pro is absolutely silent. Pro goes on to concede:
"Note, this system is unlike even the simplest of cell systems that are extant today, and abiogenesis in this debate will not address their formation. However, such a system must necessarily be capable of producing life we have today."
Pro is correct to point out that his hypothetical system is nothing like life today, or for that matter, any life we know of. As I have pointed out, the simplest known life manifests advanced cybernetic properties; indeed, even single cell life represents the most advanced cybernetic system we have ever encountered . To understand just how far removed pro's hypothetical system is from what a living system is, watch these fascinating animated videos:
In a perfect world I would have have been able to present a video on a single cell organism, and perhaps such a video exists, but I was unable to find one. Nonetheless, each of the above three videos serve to bring home the high levels of purpose, function, bona fide organization and cybernetic properties that characterize every living cell. Yockey's observation hits the nail on the head:
"More than any other characteristic, computational linear digital algorithms distinguish life from non-life".
Even the simplest known life will:
*delineate itself from its environment; realize the production and maintenance of membrane equivalent for selective absorption of nutrients, excretion of wastes, and overcoming osmotic and toxic gradients.
*store and pass along to its progeny Prescriptive Information needed for organization; provide steering, control, regulation and management for usable energy derivation and for needed metabolite production and function; operate a semiotic material symbol system using messenger molecules.
*capture, transduce, store, call up when needed, and carefully utilize energy for formal, useful work.
*actively self-replicate and eventually reproduce, not just passively polymerize or crystallize; pass along the know-how for homeostatic metabolism and reproduction into progeny.
*self monitor and self repair its constantly deteriorating matrix of bioinstruction, retention/transmission, and its architecture.
*productively react to environmental stimuli in an efficacious manner that is supportive of survival, development, growth, and reproduction.
*possess relative phenotypic stability, yet sufficient genetic variability to allow for adaptation.
*be capable of dying.
Even if we generously grant pro his prebiotic "system," there is a huge gulf between it and anything that can be classified as life. If pro want to convince us that life has arisen by abiogenesis, he is going to have bridge that gulf for us.
ABIOTIC SYNTHESIS OF RNA
here pro glowing cites work by Sutherland et al. Let's take a peek behind the curtain: To achieve their results, the team used pH manipulation, phosphate buffers and irradiation all at the correct times and amounts; they exercised careful selection of the precursors, control of competing reactions by pH selection, and a phenomenally high phosphate concentration.
What is on display here but massive infusions of intelligent design?!
The same is true when it comes to rybozyme engineering and many other origin of life efforts: it is often the case that the extent to which positive results can be claimed is very close to the extent of deliberate experimenter manipulation (in other words, intelligent design) required to achieve those results. Origin of Life research never delivers any purely naturalistic pathway to life. To the contrary, these efforts constantly reaffirm the necessity for the deliberate, active hand of intelligence.
Pro is content to seek natural processes which might produce randomly ordered amino acid chains. But proteins are formed by specifically ordered, not randomly ordered chains. In my opening round, I pointed to several studies which estimate the ratio of functional AA sequences to non-functional sequences (I note that Pro has challenged this and will respond to his challenges in my next round). The dominance of non functional sequences in sequence space clearly points to the inadequacy of random sequences and the absolute necessity of specific sequences.
Throughout his presentation, pro fails to address the origin of the information of life, but this is exactly what needs to be addressed.
 "Calculation of the Probability of Spontaneous Biogenesis by Information Theory," Yockey, Journal of Theoretical Biology, 1977
 "Seeking Life's Bare Genetic Necessities," E. Pennisi, Science, 1996
 "Gene Set for Cellular Life Derived by Comparison of Complete Bacterial Genomes," A. Mushegian and E. Koonin, Proceedings of the National Academy of the Sciences, 1996
 Note that a single emperical example of molecular machines or even a single protein arising by purely natural processes would defeat my case.
 "What is ProtoBioCybernetics?," Abel, 2011
 "Origin of Life on Earth and Shannon's Theory of Communication," Yockey, 2000
 "The Birth of Protocells," Abel 2011
Envisage forfeited this round.
"You absolutely need a code"
My thanks to pro for a spirited debate on a crucial topic. By prior agreement, I will not be addressing pro's final round.
There is no kind way to put this: we see on display in pro's rebuttal round a toxic blend of blind faith mixed with misinformation and demonstrable falsehood. I cannot possibly address everything, so I have selected a few examples. I use the abbreviation, "P:" to denote "pro said."
P: "there is no reason to expect that the existing codon mechanism is irreducible"
Let us analyze the audacity of this claim:
*there is not a shred of evidence that doublet or singlet codons have ever existed.
*by pro's own admission, a doublet codon would dramatically reduce the pool of existing amino acids by 25% (from 20 to 15 with one necessary stop codon).
*allowing for maximum AA retention requires the complete elimination of redundancy. T the more we learn, the more critical and prominent the role of redundancy becomes[15,16].
*Given that most proteins require AA chains of several hundred, consider the catastrophic effect on the number of proteins that would be lost by a doublet codon system. By way of analogy, remove any 6 letters from the english alphabet and consider how many paragraphs would be lost.
*all living systems employ the standard triplet codon, nothing less.
*The laws of information theory make it absolute that any pre-existing code has to have been at least as complex as the current code . Codes are not and cannot be built bottom up.
Here and elsewhere, pro relies on a prebiotic natural selection, but NS presupposes self replication systems. Von Neumann has shown that any system capable of self replication would require subsystems functionally equivalent to the processing systems of extant cells . Prior to function, there is nothing to select. As Dobzhansky noted, 'Prebiotic NS is a contradiction in terms"
P: "I don't know how Con can make the claim "AAs in protein chains must be bound by peptide bonds, but other bonds are every bit as likely." Since peptide bonds (-CONH-) are essentially the only covalent bonds that can form between amines & carboxylic acids at ambient conditions."
Pro is confused here. He is really talking about amide bonds. Peptide bonds are a kind of amide bond, but they are not the only kind. However, they are the only biologically relevant kind. All kinds of amide bonds - peptide and non-peptide - are equally possible. My point stands.
P: " a cursory search of one of the most highly conserved proteins ubiquitous in life, the cytochrome C protein is 100 AA long, and has a massive ~40 amino acid variation (40%)"
Pro wants us to be impressed by 40%, but this figure can only be the product of either pure ignorance or pure deceit. With 20 AAs possible at each of 100 positions, allowing for 40 substitutions means that only 1 in 10^128 (rounded down) sequences will result in cytochrome C! There's still plenty of room for all the functional chains an organism could want and Yockey's functional chain estimate of 1 in 10^90 remains safe. Ironically, Yockey derived his estimate directly from his studies of cytochrome C!
P: "Con makes numerous claims about amino acids. First we can rule most of these irrelevant as they are evolutionary issues"
Obviously false. Amino acids are indispensable to life.
P: " Moreover homochirality has a thermodynamic drive to arise in systems"
homochirality in natural processes remains purely hypothetical.
P: " We are not limited to "chance".
But pro offers chains of random polymers as a starting point. This does indeed return him to a "chance" search!
P: "Con"s entire set of arguments here is based on the "prosecutor"s fallacy"
Noting that highly improbable events happen all the time, pro offers 3 examples: a SS#, a phone #, and me (resulting from pregnancy), he adds:
However nobody makes the claim your social security number, or Joepalscak"s existence is anything but the result of chance, simply because we are not "privileging the result".
Note that in all three of his examples, the context demands an inevitable result. So why do we "privilege" the result of a particular AA chain? It is true that sheer complexity by itself does not demand privilege, but specified complexity does! Consider pro's telephone # analogy. Most telephone numbers are randomly assigned. However, businesses will typically request and receive a deliberately customized number. I am a caterer. If my phone number were C-A-T-E-R-E-R-J-O-E, would you have excellent reason to believe that this number is a "privileged" result as opposed to a chance result? Similarly, the probability of any random chain several hundred AAs in length ever emerging in nature is by itself vanishingly small. Unlike pro's examples, the context of nature does not guarantee the emergence of a single instance. But when we further consider that each of the AAs in the chain must all come from a defined subset comprising less than 10% of all AAs, that they must all exhibit left handed chirality, that they all must be bound exclusively by peptide bonds, and that a primary protein structure results, specified complexity is on clear display.
Pro's confessed aim in this debate is to propose a possible "proto life." His entire presentation comes from the realm of the hypothetical. He confidently assures us that "cumulative, sophisticated systems" can emerge in nature, that autocatalytic processes are "rather life like," that ribozymes are ribozomes waiting to happen and so forth. He assures us that these kinds of things are favored by nature. But if this is true, we surely should have discovered at least one unambiguous example of a "proto life" by now. An empirical example would go a long way to elevating pro's case. He does not provide us with any and it is glaringly obvious why not.
Pro consistently offers simple deterministic redundant processes as explanations for the most advanced cybernetic systems we have ever encountered. It simply does not add up. It simply does not work.
Most origin of life research is grounded in a belief in abiogenesis, dedicated to proposing how it might have happened. To date, abiogenesis remains elusive. Indeed, the only consistent result that has arisen out the extensive OOL enterprise is that time and again even the most modest triumphs that show any promise towards life require extensive steering of events, careful selection of conditions, establishing and arranging the actualization of targets, repeated purifying processes; in short, massive infusions of intelligent design! Certainly not the stuff of natural processes.
OOL researchers are free to speculate all they wish, but their speculation is rooted in an entirely unproven assumption. Empirical reality points in the opposite direction.
Life has never been shown to be the result of a seamless process of successive, "inevitable" natural states. Rather, life is clearly distinguished from the natural world, and it is distinguished specifically by its cybernetic and information properties. Pro has never touched either of these distinguishing characteristics. There are good reasons for this. For cybernetic systems and information systems to come into existence, certain attributes are required: planning, problem solving, bona fide organization (as opposed to mere self-ordering), deliberate steering of events toward functional target results, to name a few. None of these attributes are available to nature. They are exclusive to intelligent agents.
The information of life is objectively real. It has led us into levels of understanding not possible before the sequence hypothesis. It is enshrined in textbooks. It is the stuff of college degrees. It drives exciting new fields of research. It is axiomatic in today's scientific literature that information lies at the foundation of life.
In this debate I have presented peer reviewed citations to support the following:
*the information of life is semiotic
*life is cybernetic
*any pre existing genetic code has to have been at least as complex as the current one
*any system capable of self replication must contain subsystems comparable to those of living systems today.
*even the simplest life form likely requires at least 250-400 genes with their associated proteins and systems.
Pro, on the other hand, has steadfastly refused to deal with this fundamental reality of life. He has exhibited a failure to understand his own citations, as I have documented in the cases of peptide bonds and cytochrome C. Indeed, upon examination, virtually all of his citations unabashedly employ the same language of speculation that runs throughout his presentation here.
Pro is free to believe what he wishes, but the hypothetical "things" he proposes fall well short of the simplest possible life form. Based on everything we know to be true, the only cause capable of producing what life really is - cybernetic information based systems - is intelligent agency. No known natural processes are capable of producing anything we can describe as being alive.
 Shannon's Channel Capacity Theorem
 "Theory of Self-reproducing Automata," Von Neumann, 1966.
 a term first coined by Leslie Orgel, rigorously and extensively developed by mathematician Bill Dembski
 excerpt from the standard college textbook, Molecular Biology of the Cell: "Living Cells, like computers, deal in information...All living cells on earth, without any known exception, store their hereditary information in the form of...DNA"
 many schools now offer degrees in bioinformatics
 the research field of bioinformatics is actually a mature field by now, being almost as old as the Sequence Hypothesis
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