Could Life Have Originated Solely Naturalistically?

A Skeptic’s Guide to the Naturalistic Origin of LifeThesis: A naturalistic origin of life account is believed more due to philosophical presuppositions than to any scientific evidence.Allen Homega_sw@yahoo.comwww.OriginsDiscussion.info

Could LifeHave Originated Solely Naturalistically? • Many improbable events were necessary before any potential biological evolution could even start • Origin of the first cell including a membrane • Origin of the information content to support replication • Origin of an information processing system (genetic code) • Origin of metabolic pathways to supply energy to drive necessary chemical reactions • Science provides no plausible naturalistic origin of life • Implausibility has grown over time “To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.” Lynn Margulis

Could Life Originate From Non-Life Apart from a Creator? Most scientists admit no plausible naturalistic scenario exists • “A scenario describing the genesis of life on earth by chance and natural causes which can be accepted on the basis of fact and not faith has not been written.“ Hubert Yockey • “The formation of the first life is viewed as a chance process that occurred in spite of minuscule odds such as 1:10300 and which is accepted only because we are here. “ Christian Schwabe • “No one has an adequate materialistic explanation for how life arose“ Dawkins • Dawkins accepts Schwabe’s odds if applied to the whole universe • 1080 atoms, 4x1017 seconds => <1:10200 chance • U. Arizona study predicts less than 1 in a million chance of even one extra-solar rock • Atheists must appeal to chance to even get evolution started • “Pre-biological natural selection is a contradiction in terms” Dobzhansky • The first evolver cannot itself have evolved • $1,000,000.00 is offered to anyone who can provide a plausible theory • http://www.us.net/life/

Origin of Life Scientist Now Appealsto Multiverse/Anthropic Principle “For biological evolution … to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection.” Eugene Koonin • Yet to get both in first living cell is 1 in 101018 chance “I will argue that I am afraid his answer to this problem might open too broad an avenue to the supporters of intelligent design, as it is currently formulated, and thus does not satisfy me as such as an alternative to the theory to the RNA world.” Eric Bapteste (in reviewing article)

Source: Dr. Fazale Rana Origins of Life

Scientific History of Spontaneous Generation 17th Century • Recipes existed for creating life • Rags + wheat = mice • Francesco Redi disproved that rotting meat generated maggots 19th Century • Spallanzani and Pasteur disproved at microbe level in 1859 • Same year as Darwin’s Origin of Species 20th Century • In 1920s, Oparin/Haldane suggested that lightning sparked life from organic chemicals in a primordial soup

The Myth of the Prebiotic Soup • No evidence an organic soup ever existed • All known carbon deposits from once-living organisms (400 ppm in crust) • Organic compounds tend toward an equilibrium • Continue forming bonds until tar is formed • Definitely could not have been the ocean • “For the salt to dissolve, the organic compounds must precipitate” Thaxton • Any building blocks formed would be too dilute to form life’s long chains • Chemist ArieNissenbaum has studied biomaterials altered to be inedible • Geological depletion prevents accumulation • Primordial soup "well past its sell-by date“ Science Feb 2010 • “The concept of a … ‘primordial broth’ is … most strongly contraindicated by thermodynamic reasoning and by lack of experimental support” Sidney Fox

Natural Formation of Organic Pre-Building Blocks: Miller Urey Experiment In 1953, Miller showed some amino acids form naturally • Assumed unrealistic atmosphere • Experiment fails if oxygen present • “The strongest evidence (for a reducing atmosphere) is provided by conditions for the origin of life. A reducing atmosphere is required.” Walker • Oxygen forms when light splits water in atmosphere • If no oxygen, no ozone to shield from harmful UV rays • Oxygen found in oldest rocks • 46% of earth’s crust is oxygen • Assumed unrealistic spectrum of light • No ultraviolet light allowed • Required a collecting trap to collect amino acids • Energy to drive reactions also destroys products Now acknowledged by most OOL researchers to be irrelevant

Difficulties inCreating Proteins • Cannot connect amino acids in the presence of water • Because water is by-product • Le Chatelier’s Principle: reactions slow considerably in presence of products • “the formation of water in an environment that is full of it is the chemical equivalent of bringing sand to the Sahara.” Shapiro • Water breaks up proteins • UV light rapidly breaks down proteins • Thermodynamics opposes production of life’s molecules • Morowitz: increase in chemical bonding energy in forming 1 E-Coli is equivalent to having your bath water spontaneously increase to 360oC • Same issues apply to forming nucleotides and nucleic acids!

Improbability of Natural Protein Formation • Assume best-case for a short protein of 100 amino acids • Ignore interfering cross-reactions (amino acids more likely to bind to other organic molecules such as sugars than to each other) • Prebiotic soup consists of only the 20 biologically-relevant amino acids • Probability of getting all left-handed amino acids (1/2 chance per amino acid) • 1 / 2100≈1/1030 • Probability of getting all peptide bonds (1/2 chance bond is peptide) • 1 / 2100≈1/1030 • Probability of getting the right sequence of amino acids • Would be 1 / 20100 but sometimes more than one amino acid allows for functional equivalence • According to MIT evolutionist ≈1/1065 • These probabilities must be simultaneously satisfied • Overall probability ≈ 1/10125 • Account for max amino acids ever randomly formed on earth in time available before first life (* 1045 -> 1/1080 ) • As unlikely as choosing a specific atom out of all atoms in universe

Rarity of Functional Proteins • Bob Sauer (MIT): ratio of functional to non functional sequences was 10-63 for a protein 100 amino acids long • Doug Axe (Cal Tech/Cambridge): ratio was 10-77 for beta-lactamase (150 amino acids long) • Estimated finding any functional protein was 10-74 based on stable folding requirement • Number of atoms in Milky Way is about 1065

Improbability of Natural DNA/RNA Formation“It would be a miracle if a strand of RNA ever appeared on the primitive earth” Leslie Orgel“You have to build straw man upon straw man to get to thepoint where RNA is a viable first biomolecule” Gerald Joyce • Harder to form than proteins and amino acids • No nucleotides from plausible Miller-Urey type experiments • Hard to form the molecule’s backbone due to: • Rareness of phosphates (< 0.08 parts ppm of P in ocean) • Other molecules could easily bond with ribose or phosphates • Inability to produce ribose without hundreds of other sugars • Acceptance of only right-handed ribose • Ribose in solution has half-life of only 1-2 hours • Water breaks down nucleic acids (hydrolysis) • UV rays & metabolism by-products cause lesions • Hard to form nucleotides • 2 bases form only in near freezing temperatures • Other 2 bases form only in near boiling temperatures • Hard to chain together components without other chemicals mixing in

Chirality Problem “All speculation on the origin of life on Earth by chance cannot survive the first criterion of life: proteins are left-handed, sugars in DNA and RNA are right-handed.” Hubert Yockey “I spent 25 years looking for a terrestrial mechanism for homochirality and trying to investigate them and didn't find any supporting evidence. Terrestrial explanations are impotent or nonviable.“Organic chemist William Bonner Right and left-handed versions of amino acids – credit NASA

RNA World - Problems Doesn’t Explain Origin of Information • von Neumann Showed Necessity of Information System in Replicating Systems • Best advance so far is an RNA molecule that can copy 10% of itself (at insufficient fidelity) • Selected out of an engineered pool of 1000 trillion RNA molecules (was 189 nucleotides long) • Szostak, prominent ribozyme engineer, estimates that it may require between 200 and 300 nucleotides of a very specific ordering to perform “proper template binding, fidelity and strand separation.” • Orgel and Joyce have shown that for a single-stranded RNA catalyst to produce an RNA molecule identical to itself, it must find an appropriate RNA molecule nearby to act as a template • RNA template would need to be the exact complement of the replicase • To find matching pair requires 1048 RNA molecules • Vastly exceeds mass of earth • Computations are overly optimistic - based on only a 50 nucleotide RNA

“Many of the experiments designed to explain one or other step in the origin of life are either of tenuous relevance to any believable prebiotic setting or involve an experimental rig in which the hand of the researcher becomes for all intents and purposes the hand of God.” Simon Conway Morris, Life’s Solution

Shapiro:RNA problems • Compared unlikelihood with a golf ball being played below par through an 18-hole course by solely natural forces (i.e. no golfer) • Interferents • Lab examples start off with unrealistically pure reagents • These would disrupt the backbone, cause termination, and lead to side branches (any one of which would likely be fatal to self-replication) • Steve Benner’s borate experiments • “Looking at the same thing, [I] see only the hands of Steve Benner reaching to the shelf of organic chemicals, picking formaldehyde, and from another shelf, picking acidaldehyde, etc. Excluding them carefully. Picking a mineral which occurs only in selective places on the Earth and putting it in in heavy doses. And at the end getting a complex of ribose and borate, which by itself would be of no use for making RNA, because the borate loves to hold onto the ribose, and as long as it holds onto the ribose it can't be used to make RNA. If it lets go of the ribose, then the ribose becomes vulnerable to destruction by all the other environmental agents.

Chicken-Egg Problems Numerous inter-dependent systems exist within every cell • DNA provides blueprints for building proteins • Numerous highly specialized proteins needed for DNA replication • To unwind and uncoil DNA, split the strands, etc. • RNA and proteins required to make proteins • Amino acids required to proteins • RNA and proteins required to make amino acids How does all this randomly form in first cell and within a membrane? And we cannot plausibly prebiotically form any of these!

Boeing 747: 5 million parts Humpty-Dumpty Experiments • A punctured cell always dies • It has all the fully assembled chemicals but never revives • Despite extensive restoration efforts 1 cell: billions of parts

Life’s Minimum Complexity “Of all the problems with the hypothesis that life started as nude replicating RNA molecules, the one I find most insurmountable is the one most rarely talked about: all living things seem to have a minimal complexity below which it is impossible to go.” Stuart Kauffman • Life must harness energy, grow and reproduce • All life is cellular: no evidence for other life forms • Even simplest cell more complex than ever envisioned • Simplest organisms: Non-parasitic (~1500 genes), Parasitic (~470 genes) • A minimum set of cell features is irreducibly complex • Replication System • Translation System (Manufacture proteins) • Cell membrane - critical to selectively allow in nutrients, protect cell • Without any of these the cell dies

The minimal gene complement (“parts list”)of Mycoplasma genitalium(Fraser et al., 1995) 470 genes, 580,070 base DNA pairs for a parasite

High-Level Diagram: Mycoplasma genitalium

Biology’s Worst Problem in Irreducible Complexity:Protein Translation System “For biological evolution that is governed primarily by natural selection to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection.” Koonin Koonindescribes a “dreary vicious circle: what would be the selective force behind the evolution of the extremely complex translation system before there were functional proteins? And, of course, there could be no proteins without a sufficiently effective translation system.” • Can’t rely on evolution to evolve the first protein-based evolver! Minimal Complexity of Protein Translation System (based on E-Coli) • Ribosome has 52 proteins (7459 amino acids), 4566 RNA nucleotides • 90K atoms in large subunit alone • Craig Venter’s team unsuccessful in making synthetic ribosomes: “Nobody knows how to get ones that can actually do protein synthesis…. And you can’t have life without it.” • 106 proteins, 31 tRNA’s, & 20 aaRS’s (to establish genetic code) • Available amino acids, ATP for energy to drive reactions • mRNA information content to direct protein synthesis and via genetic code • How do you evolve an integrated code-driven system for making proteins before proteins even exist? • Natural selection can only favor some organisms over others not by itself innovate!

Features of Genetic Code • DNA used solely for informational purpose • No connection between chemical properties and information content • All other examples of codes originate from intelligence • Optimal choice of bases to form a parity code • Built-in ability to detect errors via nucleotide choice • Hamming error-coding theory “anticipated by nature” • Optimized to minimize errors in mapping to amino acids • Accounts for increased likelihood of certain types of mistakes • Supplies similar or exact amino acid when error occurs • Minimizes effects of frameshift mutations • Carries “arbitrary parallel codes better than the vast majority of other possible genetic codes.” Genome Research

Error Minimization of Genetic Code • Genetic code has “eerie perfection”, “startling evidence of optimization” Samuel Conway Morris • Genetic Code is “One in a Trillion” • Or “it appears at or very close to a global optimum for error minimization: the best of all possible codes.” Study by Univ. of Bath

Universal Genetic Code Argues for Design Why genetic code cannot appreciably evolve: “Any mutation in the genetic code itself … would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation...this would spell disaster.” Dawkins Selection pressure is negative • Effect on all proteins is detrimental • Relative optimization benefits are tiny • Minor variance in codes occurs • All are less optimal than canonical code Even if it could evolve, is there time? • Yockey: natural selection would have to explore 1.4x1070 codes in 6.3 x 1015secs • Age of genetic code seems to coincide with life

Some Prominent Evolutionists Now Believe in Multiple Independent Origin of Life Events “...there is no more reason to imagine only a single kind of cell as the progenitor of all contemporary life than there is to imagine only Adam and Eve as the progenitors of the human race.” W. Ford Doolittle “I don't necessarily buy that there is a single ancestor. It’s counterintuitive to me. I think we may have thousands of recent common ancestors and they are not necessarily so common.” Craig Venter “The time has come for Biology to go beyond the Doctrine of Common Descent” Carl Woese Why this makes things much worse: “The odds of the same dictionary of arbitrary ‘meanings’ arising twice are almost unimaginably small.” Dawkins 24 January 2009 issue

What is actual record from early Earth? “We are now thinking, in geochemical terms, of instant life.“ Ponnamperuma “Presence of .. stromatolites, microfossils, chemical fossils … in early Precambrian rocks suggests that life originated virtually simultaneously with the formation of the crust of the earth.” Walton • Sterilizing Late Heavy Bombardment ended when life first appears Earliest geochemical evidence and microfossils include: • Highly complex sulfate-reducing bacteria • Mats of bacterial ecosystems called stromatolites • Including Cyanobacteria • Utilized complicated, plant-like photosynthesis to harness solar energy • “Resemblance to moderns forms of cyanobacteria is occasionally uncanny” Margulis Fossils and current examples found in Shark Bay, Australia (background)

Why aren’t Origin of Life problems widely known? “Many investigators feel uneasy about stating in public that the origin of life is a mystery, even though behind closed doors they freely admit that they are baffled. There are two reasons for their unease. First they feel it opens the door to religious fundamentalists… Second, they worry that a frank admission of ignorance will undermine funding…” Paul Davies, The Fifth Miracle: The Search for the Origin and Meaning of Life

If a naturalistic origin of life were not presupposed, it would not be considered a viable scientific theory. “Spontaneous generation was scientifically disproved 120 years ago by Louis Pasteur and others, but that leaves us with only one other possibility . . . that life came as a supernatural act of creation by God, but I can't accept that philosophically because I do not want to believe in God. Therefore I choose to believe in that which I know is scientifically impossible, spontaneous generation leading to evolution.” George Wald, Harvard Nobel Laureate

Why we should be skeptical that a plausible naturalistic explanation will ever be found? “Chance and necessity do not explain the origin of life” Article by Trevors and Abel • “No natural mechanism … can explain the high information content of genomes. This is a mathematical truism, not a matter subject to overturning by future empirical data.” • “Natural processes have never been observed to write conceptual instructions, to symbolize such algorithmic meaning, or to translate it using code” • “No physical mechanism has been suggested for the source of abstract genetic instructions themselves.” • “Random walks … will never provide an adequate explanation for the generation of such a highly refined translative coding system.” (nor does it explain the operating system and information processing programs) • “It is difficult to envision how the laws of physics and chemistry could explain encryption/decryption.” • “Cause-and-effect physicality has no ability to anticipate or devise a conceptual system that employs symbolic representationalism.” • “The four known forces of physics know nothing of the phenomenon of linguistic translation.” Eugene Koonin appeals to multiple universes • “Any conceivable scenario of life's evolution necessarily requires combinations of highly unlikely conditions and events prior to the onset of biological evolution, including the abiogenic synthesis of fairly complex and not particularly stable organic molecules, such as nucleotides, the concentration of these molecules within appropriate compartments, and their polymerization yielding polynucleotides of sufficient size and diversity. Thus, anthropic selection appears to be an inevitable aspect of life's evolution.” • “The statistical probability that organic structures and the most precisely harmonized reactions that typify living organisms would be generated by accident is zero.” Prigogine

Questions

What about Metabolism First? • Orgel “In my opinion, there is no basis in known chemistry for the belief that long sequences of reactions can organize spontaneously – and every reason to believe that they cannot.” • Orgel’s last paper – the “solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help.”

Which takes more faith to believe? Life originated by purely unguided natural causes: • The universe came into existence uncaused out of nothing before space and time existed and overcame statistically miraculous odds to be life-supporting • Specified complexity arose from randomness • Information arose from random, undirected processes • Through numerous unknown chance events, a highly optimal genetic code arose • Luck overcome ridiculous odds against formation of first cell Life was created by God • Science is not tricking us – the universe & life look designed because they were!

Histone-Binding Code

Parity Codes Even Parity Bit Odd Parity Bit 000000000 100000000 011111111 111111111 110100001 010100001

Parity Code in DNA • Only A, G, C, and T yield an even parity code in DNA H-Bond donor = 1 H-Bond acceptor = 0 Ring structure is the parity bit purine =0 pyrimidine =1

Craig Venter Creates Synthetic Life Form Craig Venter and his team have built the genome of a bacterium from scratch and incorporated it into a cell to make what they call the world's first synthetic life formThe Guardian, May 20, 2010Ian Samples, Science Correspondent

Synthetic Biology Practical Applications: • Biomedicine • Biotechnology

Synthetic Biology and the Origin of Life Synthetic Biology • Create artificial life • Build life in the lab starting with simple chemicals • Free to use any means available Origin of Life • Understand how life originated on Earth • Recapitulate origin of life in lab starting with simple chemicals • Constrained by condition of early Earth

Trends/Notes • CD disbelieved by Woese and Doolittle and other experts studying genomics etc. and trying to build trees • Would require multiple origins • But then how do we get a universal genetic code (nearly univ.) • Also need common nucleotides, amino acids, aminoacyl t-rna synthetases etc. • Journal articles document how multiple of each of these could have been chosen other than what is actually used in life • Prob then is that we are close to a LUCA but not close enough • How would one explain 5 independent origins of the same blueprint for life?

Add quote from Orgel about bridging the gap between prim life and DNA/protein world • Note how science uses the Principle of Continuity to assess theories • If there is no gradual set of plausible steps in a proposed pathway from A->B then the theory is not considered plausible • If we apply this to OOL we see that none are!

Venter • The lay press likes to talk about creating life from scratch. But while we can create and develop new species, we're not creating life from scratch. We talked about the ribosome; we tried to make synthetic ribosomes, starting with the genetic code and building them — the ribosome is such an incredibly beautiful complex entity, you can make synthetic ribosomes, but they don't function totally yet. Nobody knows how to get ones that can actually do protein synthesis. But starting with an intact ribosome is cheating anyway right? That is not building life from scratch but relying on billions of years of evolution. When starting with an existing protein synthesis machinery we can create new life forms, we can create a synthetic chromosome that we can now do transplants of, and develop new species with very unique properties — so we can create human-made species — but we're not really creating life from scratch. You can boot up a system but right now all life derives from other living entities. What we're doing is really no different, because we're just putting a new operating system into a living cell.

Church • The ribosome, both looking at the past and at the future, is a very significant structure — it's the most complicated thing that is present in all organisms. Craig does comparative genomics, and you find that almost the only thing that's in common across all organisms is the ribosome. And it's recognizable; it's highly conserved. So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that's what I would focus on; how did the ribosome come to be? The only way we're going to become good scientists and prove that it could come into being spontaneously is to develop a much better in vitro system where you can make smaller versions of the ribosome that still work, and make all kinds of variations on it to do really useful things but that are really wildly different, and so forth, and get real familiarity with this really complicated machine. Because it does a really great thing: it does this mutual information trick, but not from changing something kind of trivial, from DNA to RNA; that's really easy. It can change from DNA three nucleotides into one amino acid. That's really marvelous. We need to understand that better. • VENTER: And you can't have life without it. • … • CHURCH: But isn't it the case that, if we take all the life forms we have so far, isn't the minimum for the ribosome about 53 proteins and 3 polynucleotides? And hasn't that kind of already reached a plateau where adding more genomes doesn‘t reduce that number of proteins?

Nelson • Excellent arguments/quotes etc. from Doolittle etc. and concerning growing number of experts in cladistics and systematics who question CD (thus need multiple origins) but then … • How could there be so much similarity between types? • Nucleotides, sugars in DNA, amino acids in proteins • Experiments have shown these could have been different • Same Ribosome arose mult times

Shapiro on Miller-Urey • Agrees that assumption of early earth’s atmosphere was unrealistic • Points out problems of dilution, mix-ins, trap to isolate reactants form energy source

Could Life Have Originated Solely Naturalistically?