Researchers propose computer model of protein that may have existed when life began

Hopefully PaV was just kidding about redox and rust- I mean yes it does produce rust but that isn't the extent of redox reactions ET

Yes, apicomplexans use redox metabolism- well it is an important pathway in all apicomplexans. But metabolism is more than redox reactions. ET

PaV

Are you saying, then, that forming rust is not a redox reaction? Did life begin when things began to rust? Is this your logic?

What Ambli said. R J Sawyer

OK, great. What they need to do next is see if their protein will form without their intervention even given all of the chemical precursors and some energy input. ET

what is the dividing line between living and non-living

Howard Pattee answered that question decades ago, the answer is semiosis. The ideology and biases of materialists have prevented this unique distinction from getting any traction (after all, the logical entailments are not only extremely high, but also very clear and deeply fixed in the history of discovery) but the distinction is entirely valid all the same. Upright BiPed

redox reactions are ubiquitous and necessary in living organisms

What role do redox reactions (or any other aspects of this research) play in the establishment of the discontinuous (non-integrable) associations that are necessary to specify objects and organize biology? Upright BiPed

Well, of course!! What are the ‘odds’ of it ’emerging spontaneously’? The ‘odds’ are 1 in 2^ 12, or 1 in 4096!! What a low threshold!!

This is the odds of drawing a specific sequence of 12 amino acids, assuming there are two possibilities which are each equally likely. I can't see any way you could argue this is related the odds of a peptide emerging. (Though it's very similar to Hoyle's ridiculed arguments).

Are you saying, then, that forming rust is not a redox reaction?

I think what they are saying is that rusting is a redox reaction, but there is much more to redox than rust. Like, the entire basis of metabolism... (if you did high school biology you might remember the citric acid cycle, glycolosis and oxidative phosphorylation?) Amblyrhynchus

R J Sawyer:

But by far the biggest question is, what is the dividing line between living and non-living?

All of those poor biologists don't know what they are supposed to be studying. Or is what RJ said just a crock? Is there any evidence for a more simple life-form than the most simple life-form today? Nope. There is just a need for such a thing. ET

R J Sawyer: Are you saying, then, that forming rust is not a redox reaction? Did life begin when things began to rust? Is this your logic? PaV

Latemarch, thanks for the heads up on the dead link. I searched and the article has disappeared as far as I can tell. So to further back up the claim, from the missing paper, that Entanglement and Coherence are two sides of the same coin, I reference the following paper:

Physicists find quantum coherence and quantum entanglement are two sides of the same coin - June 25, 2015 by Lisa Zyga Excerpt: Quantum coherence and quantum entanglement are two landmark features of quantum physics, and now physicists have demonstrated that the two phenomena are "operationally equivalent"—that is, equivalent for all practical purposes, though still conceptually distinct. This finding allows physicists to apply decades of research on entanglement to the more fundamental but less-well-researched concept of coherence, offering the possibility of advancing a wide range of quantum technologies. It's well-known that quantum coherence and quantum entanglement are both rooted in the superposition principle—the phenomenon in which a single quantum state simultaneously consists of multiple states—but in different ways. Quantum coherence deals with the idea that all objects have wave-like properties.,,, The second phenomenon, quantum entanglement, also involves superposition. But in this case, the states in a superposition are the shared states of two entangled particles,,, The physicists arrived at this result by showing that, in general, any nonzero amount of coherence in a system can be converted into an equal amount of entanglement between that system and another initially incoherent one. This discovery of the conversion between coherence and entanglement has several important implications. For one, it means that quantum coherence can be measured through entanglement. Consequently, all of the comprehensive knowledge that researchers have obtained about entanglement can now be directly applied to coherence, which in general is not nearly as well-researched (outside of the area of quantum optics). https://phys.org/news/2015-06-physicists-quantum-coherence-entanglement-sides.html

bornagain77

PaV

I stand by my statement.

That’s fine. But given that redox reactions are ubiquitous and necessary in living organisms, forgive me if I don’t take your “So, this “peptide” makes things “rust”! statement seriously. R J Sawyer

BREAKING: Researchers have determined that the vast quantities of silicon in the deserts, beaches and rocks of the world mindlessly and accidentally led to electronic circuitry, and then to calculators and eventually to computers. Here is current state of the theory:

The fossil record indicates that there were handheld calculators with at least 240 kilobytes of stored programs in existence almost as soon as the earth cooled. Possibly, handheld calculators originated when special conditions allowed the formation of silicon chips and circuit boards (primitive genes). Heat, perhaps generated by radioactivity, volcanoes or meteor impacts, melted some sand to form a silicon flake. Random splashing of molten metal caused metal filaments to form a circuit board on the flake. Oily film on ponds dried into the hard plastic material needed for the shell. Lightning provided the first source of electrical power. Prototypes in seawater, at just the right distance from the strike, received sufficient voltage without being destroyed. Batteries (allowing independent metabolism) came later. The first batteries were iron acid batteries, formed in mud pockets. Lithium batteries were a very late development. This primitive protocalculator somehow acquired ten to 25 bytes of stored programs (40 to 100 nucleotides) that enabled it to have some function that made it useful. Now we find evidence for only the fully evolved handheld calculators similar to the ones used today, with function keys and lengthy installed programs, because the fossil record is incomplete.

(I shamelessly stole that parody from panspermia.org) harry

BA Thanks for the reply. I actually read the articles and watched the videos.....a lot to absorb. I now appreciate that life itself is significantly involved with quantum effects. Not unexpected as life has always seemed to be more than the sum of its material parts. Of side note. This link http://www.nonlocal.com/hbar/n.....rence.htmlin your #7 is dead. Latemarch

RJ Sawyer: I stand by my statement. PaV

PaV

So, this “peptide” makes things “rust”!

Actually a redox catalyst is any catalyst that facilitates the gain or loss of electrons in a molecule. Given the billions of chemical reactions that involve the gain or loss of electrons, I think that “makes things rust” greatly underestimated the importance of redox catalysts. R J Sawyer

From the linked article:

The scientists used computers to model a short, 12-amino acid protein and tested it in the laboratory. This peptide has several impressive and important features. It contains only two types of amino acids (rather than the estimated 20 amino acids that synthesize millions of different proteins needed for specific body functions), it is very short and it could have emerged spontaneously on the early Earth in the right conditions. The metal cluster at the core of this peptide resembles the structure and chemistry of iron-sulfur minerals that were abundant in early Earth oceans. The peptide can also charge and discharge electrons repeatedly without falling apart, according to Nanda, a resident faculty member at the Center for Advanced Technology and Medicine.

[I]t could have emerged spontaneously on the early Earth . . . Well, of course!! What are the 'odds' of it 'emerging spontaneously'? The 'odds' are 1 in 2^ 12, or 1 in 4096!! What a low threshold!! /////////////////////////////////////// Well, what's the title of their paper: Minimal Heterochiral de Novo Designed 4Fe–4S Binding Peptide Capable of Robust Electron Transfer Interesting! It was 'design' at work, then. /////////////////////////////////////////////// From the linked article:

“Modern proteins called ferredoxins do this, shuttling electrons around the cell to promote metabolism,” said senior author Professor Paul G. Falkowski, who leads Rutgers’ Environmental Biophysics and Molecular Ecology Laboratory. “A primordial peptide like the one we studied may have served a similar function in the origins of life.”

Consider the logic of the quote in bold: . . . . . This "peptide" isn't a fore-runner of life because the absence of life makes this "peptide" completely useless. IOW, having this "peptide" present in the early ocean waters of no utility whatsoever UNLESS all the ingredients for life are already present. That is, this "peptide" performs a function between ALREADY existing components of a living cell. So, this is a completely illogical point of view. It's like saying the presence of oil in the deep oceans laid the foundation for drilling rigs. //////////////////////////////////////////////////////// And what does this "peptide" do? Well, it's a "redox catalyst." That is, it carries out a 'redox' reaction. So, knowing what I would find, I googled 'redox.' Here's part of the response I found:

An everyday example of a redox reaction that we are all familiar with is the process of rusting. Rust is the flaky brown substance that forms on iron objects left exposed to the elements for too long, especially if the objects get wet. Rust doesn’t just form on the iron object, the iron actually turns into rust (rust is actually a form of oxidized iron).

So, this "peptide" makes things "rust"! Wonderful! We're off to a flying start in our quest for the origin of life! PaV

Thus, since 'non-local' quantum correlations are now shown to be completely independent of any time and space constraints, and cannot possibly be explained by reference to the particles themselves, then one is forced to appeal to a cause that is itself not limited to time and space in order to explain quantum correlations! For the Christian Theist this should not be surprising. The bible has always held that God 'holds all things together'.

Colossians 1:17 He is before all things, and in Him all things hold together.

It is also interesting to note that quantum information is 'conserved'

Quantum no-hiding theorem experimentally confirmed for first time - 2011 Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. - per physorg

Besides providing direct empirical falsification of neo-Darwinian claims that say information is emergent from a material basis, the implication of finding 'non-local', beyond space and time, and ‘conserved’, quantum information in molecular biology on such a massive scale, in every DNA and protein molecule, is fairly, and pleasantly, obvious. That pleasant implication, or course, being the fact that we now have strong physical evidence suggesting that we do indeed have an eternal soul that is capable of living beyond the death of our material bodies. In the following video, entitled Quantum Entangled Consciousness, Stuart Hameroff states that 'But the quantum information,,,, isn’t destroyed. It can’t be destroyed.,,, it's possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul'.

“Let’s say the heart stops beating. The blood stops flowing. The microtubules lose their quantum state. But the quantum information, which is in the microtubules, isn’t destroyed. It can’t be destroyed. It just distributes and dissipates to the universe at large. If a patient is resuscitated, revived, this quantum information can go back into the microtubules and the patient says, “I had a near death experience. I saw a white light. I saw a tunnel. I saw my dead relatives.,,” Now if they’re not revived and the patient dies, then it's possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.” - Stuart Hameroff - Quantum Entangled Consciousness - Life After Death - video (5:00 minute mark) https://youtu.be/jjpEc98o_Oo?t=300

Verse:

Mark 8:37 Is anything worth more than your soul? Psalm 139:13 For you created my inmost being; you knit me together in my mother's womb. Matthew 22:37 Jesus replied: "'Love the Lord your God with all your heart and with all your soul and with all your mind.'

bornagain77

At 5 Latemarch asks:

"Forgive me for turning the comments in a different direction. Eight or so years ago there was much speculation that there was quantum entanglement going on in the process of photosynthesis. Figuring that you will know. Did anything come of that? If so that would layer in a whole new level of functional complexity that random mutation and natural selection can’t explain."

Yes there has been quite a bit of progress. To the point of extending the spooky 'non-local' aspect of quantum entanglement, beyond photosynthesis, to DNA and proteins themselves: In the following article entitled "Quantum coherent-like state observed in a biological protein for the first time, it was found that protein molecules act like inanimate matter cooled down to near absolute zero.

Quantum coherent-like state observed in a biological protein for the first time - October 13, 2015 Excerpt: If you take certain atoms and make them almost as cold as they possibly can be, the atoms will fuse into a collective low-energy quantum state called a Bose-Einstein condensate. In 1968 physicist Herbert Fröhlich predicted that a similar process at a much higher temperature could concentrate all of the vibrational energy in a biological protein into its lowest-frequency vibrational mode. Now scientists in Sweden and Germany have the first experimental evidence of such so-called Fröhlich condensation (in proteins).,,, The real-world support for Fröhlich's theory took so long to obtain because of the technical challenges of the experiment, Katona said. https://phys.org/news/2015-10-quantum-coherent-like-state-biological-protein.html

This finding is confirmation of Schrödinger's claim, and also falsifies the Darwinian belief in pervasive 'random thermodynamic jostling' within life. Specifically, “To paraphrase, (Erwin Schrödinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate matter cooled down to near absolute zero. Where quantum effects play a very important role."

Jim Al-Khalili, at the 2:30 minute mark of the following video states, ",,and Physicists and Chemists have had a long time to try and get use to it (Quantum Mechanics). Biologists, on the other hand have got off lightly in my view. They are very happy with their balls and sticks models of molecules. The balls are the atoms. The sticks are the bonds between the atoms. And when they can't build them physically in the lab nowadays they have very powerful computers that will simulate a huge molecule.,, It doesn't really require much in the way of quantum mechanics in the way to explain it." At the 6:52 minute mark of the video, Jim Al-Khalili goes on to state: “To paraphrase, (Erwin Schrödinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate matter cooled down to near absolute zero. Where quantum effects play a very important role. There is something special about the structure, about the order, inside a living cell. So Schrodinger speculated that maybe quantum mechanics plays a role in life”. Jim Al-Khalili – Quantum biology – video https://www.youtube.com/watch?v=zOzCkeTPR3Q

Here is a video that goes into a bit more detail on the particular "quantum" falsification of the 'random thermodynamic jostling' "prediction" of Darwinian theory:

Darwinian Materialism vs. Quantum Biology - video https://youtu.be/LHdD2Am1g5Y

The following paper also confirmed Erwin Schrödinger's contention that life, and proteins in particular, are based on quantum mechanical principles:

Proteins ‘ring like bells’ - June 2014 Excerpt: As far back as 1948, Erwin Schrödinger—the inventor of modern quantum mechanics—published the book “What is life?” In it, he suggested that quantum mechanics and coherent ringing might be at the basis of all biochemical reactions. At the time, this idea never found wide acceptance because it was generally assumed that vibrations in protein molecules would be too rapidly damped. Now, scientists at the University of Glasgow have proven he was on the right track after all. Using modern laser spectroscopy, the scientists have been able to measure the vibrational spectrum of the enzyme lysozyme, ,,, The experiments show that the ringing motion lasts for only a picosecond or one millionth of a millionth of a second. Biochemical reactions take place on a picosecond timescale and,,, (are) optimised enzymes to ring for just the right amount of time. Any shorter, and biochemical reactions would become inefficient as energy is drained from the system too quickly. Any longer and the enzyme would simple oscillate forever: react, unreact, react, unreact, etc. The picosecond ringing time is just perfect for the most efficient reaction.,,, Klaas Wynne, Chair in Chemical Physics at the University of Glasgow said: “This research shows us that proteins have mechanical properties that are highly unexpected and geared towards maximising efficiency.”,,, http://www.gla.ac.uk/news/headline_334344_en.html

And as if the probability of finding a functional protein from random sequences of amino acids was not already an insurmountable difficulty for random Darwinian processes to explain, “Quantum Proteins” make this insurmountable difficulty for Darwinian processes of finding a functional protein that much worse. ,,, In the following paper entitled, “Quantum criticality in a wide range of important biomolecules”, it was found that the possibility of finding even one (biomolecule) that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,

Quantum criticality in a wide range of important biomolecules – Mar. 6, 2015 Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say. That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.” The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one (biomolecule) that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,, “what exactly is the advantage that criticality confers?” https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552

One reason this exasperates the insurmountable search problem for Darwinists is because, instead of amino acids being treated as if they are independent of all other amino acid sites (as is usually assumed in the probability calculations), quantum proteins, (due to the quantum coherence of the entire protein molecule), act as a single unified whole and therefore the amino acids in any given functional protein sequence are actually shown to be mutually interdependent of one another. To quote Durstin, "These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well."

(A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics - 2012 Excerpt (Page 4): The Probabilities Get Worse This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent, (i.e. context dependent), with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search. http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions-Durston-or-Myers_.pdf

More devastating than that fact is the fact that quantum entanglement and quantum coherence are, by definition, "non-local" effects that refuse to be reduced to any possible Darwinian, i.e. reductive materialistic, explanation.

Looking beyond space and time to cope with quantum theory – 29 October 2012 Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” http://www.quantumlah.org/highlight/121029_hidden_influences.php Coherence and nonlocality Usually quantum nonlocality is discussed in terms of correlated multiparticle systems such as those discussed by John Bell in his famous 1964 theorem and then later clarified by GHZ, David Mermin and others. But more striking and significant is the qualitative nonlocal phenomena associated with coherent states,,,, In fact, theoretically these two kinds of nonlocality have precisely the same basis: the unmeasured singlet state uncovered by EPR is a coherent 'pure state' despite its spatial extension, and when the parts are realized in a measurement (a la Bell) this coherence is harvested or cashed in. Whereas the "EPR" connections are ephemeral and fragile, some forms of nonlocal coherence are robust. http://www.nonlocal.com/hbar/nonlocalcoherence.html

Moreover,, in the following paper it was found that 'the greater the number of particles in a quantum hypergraph state, (such as what we see with quantum biology), the more strongly it violates local realism, with the strength increasing exponentially with the number of particles.'

Physicists find extreme violation of local realism in quantum hypergraph states - Lisa Zyga - March 4, 2016 Excerpt: Many quantum technologies rely on quantum states that violate local realism, which means that they either violate locality (such as when entangled particles influence each other from far away) or realism (the assumption that quantum states have well-defined properties, independent of measurement), or possibly both. Violation of local realism is one of the many counterintuitive, yet experimentally supported, characteristics of the quantum world. Determining whether or not multiparticle quantum states violate local realism can be challenging. Now in a new paper, physicists have shown that a large family of multiparticle quantum states called hypergraph states violates local realism in many ways. The results suggest that these states may serve as useful resources for quantum technologies, such as quantum computers and detecting gravitational waves.,,, The physicists also showed that the greater the number of particles in a quantum hypergraph state, the more strongly it violates local realism, with the strength increasing exponentially with the number of particles. In addition, even if a quantum hypergraph state loses one of its particles, it continues to violate local realism. This robustness to particle loss is in stark contrast to other types of quantum states, which no longer violate local realism if they lose a particle. This property is particularly appealing for applications, since it might allow for more noise in experiments. http://phys.org/news/2016-03-physicists-extreme-violation-local-realism.html

bornagain77

If life arose naturally, we know what the first lifeform didn’t look like. It didn’t look like a modern bacterial cell with DNA. Nobody disputes that. The hard question is, what could it have looked like? Was it organic or inorganic? Was it membrane bound? Did it reside in shallow pools, in the surface layer of the ocean or in the deep sea? Were it’s primitive catalysts simple proteins or inorganic metal complexes? These, and hundreds of other questions, are very interesting and can be tested to some extent, but we will never know with absolute certainty. Even in the very unlikely event that life somehow arises during one of these experiments, we will never know if this was how the first life formed. But by far the biggest question is, what is the dividing line between living and non-living? We can’t even agree on whether viruses are alive. R J Sawyer

BA@3 Thanks for that compilation. I particularly liked the fitness testing of the ancient bacteria and yeast. Thanks also for pointing out the obvious that the molecule is in fact designed. Good overview of designed metaloproteins here. The article is 9 years old and much progress has been made since then in structural biology. Tellingly, all of these articles are filled with "purpose", "design", and other teleological vocabulary. The design of a minimal molecule is no longer that difficult so to pop one out and then make the unsubstantiated (ludicrous) claim that this could be a precursor to life gives a whole new depth to the word hubris. Forgive me for turning the comments in a different direction. Eight or so years ago there was much speculation that there was quantum entanglement going on in the process of photosynthesis. Figuring that you will know. Did anything come of that? If so that would layer in a whole new level of functional complexity that random mutation and natural selection can't explain. Mount Improbable has become so high and its backside so long that no one arrives at the peak when all of the probabilistic resources of the universe are used. Latemarch

Moreover, in terms of morphology, billion year old bacteria "surprisingly looked exactly like modern species," and the similarity in morphology is widespread among fossils of [varying] times,”

Static evolution: is pond scum the same now as billions of years ago? Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found; http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330

Here are a few more references to drive this point home:

AMBER: THE LOOKING GLASS INTO THE PAST: Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms. http://bcb705.blogspot.com/2007/03/amber-looking-glass-into-past_23.html Scientists find signs of life in Australia dating back 3.48 billion years - Thu November 14, 2013 Excerpt: “We conclude that the MISS in the Dresser Formation record a complex microbial ecosystem, hitherto unknown, and represent one of the most ancient signs of life on Earth.”... “this MISS displays the same associations that are known from modern as well as fossil” finds. The MISS also shows microbes that act like “modern cyanobacteria,” http://www.cnn.com/2013/11/13/world/asia/australia-ancient-life/ Geobiologist Noffke Reports Signs of Life that Are 3.48 Billion Years Old - 11/11/13 Excerpt: the mats woven of tiny microbes we see today covering tidal flats were also present as life was beginning on Earth. The mats, which are colonies of cyanobacteria, can cause unusual textures and formations in the sand beneath them. Noffke has identified 17 main groups of such textures caused by present-day microbial mats, and has found corresponding structures in geological formations dating back through the ages. http://www.odu.edu/about/odu-publications/insideodu/2013/11/11/topstory1

Bottom line, studies of microbes consistently falsify Darwinian presuppositions:

Darwin vs. Microbes - video https://youtu.be/ntxc4X9Zt-I

Here is a more honest assessment of the situation for proteins at the origin of life, "The appearance of early protein families, he has remarked, is “something like close to a miracle.”"

Dan S. Tawfik Group - The New View of Proteins - Tyler Hampton - 2016 Excerpt: one of the most favorable and liberal estimates is by Jack Szostak: 1 in 10^11. 42 He ascertained this figure by looking to see how random sequences—about eighty amino acids in length, long enough to fold—could cling to the biologically crucial molecule adenosine triphosphate, or ATP. At first glance, this is an improvement over Salisbury’s calculations by 489 powers of ten. But while an issue has been addressed, the problem has only been deferred. ,,, ,,, nucleotide synthesis, requires several steps. If five enzyme functions were needed (ten are needed in modern adenine synthesis), 43 then the probability would be 1 in (10^11)5, or 1 in 10^55. If all the operations needed for a small autonomous biology were ten functions—this is before evolution can even start to help—the probability is 1 in (10^11)10, or 1 in 10^110. This is more than the number of seconds since the Big Bang, more protons than there are in the universe. In considering a similar figure derived in a different context, Tawfik concedes that if true, this would make “the emergence of sequences with function a highly improbable event, despite considerable redundancy (many sequences giving the same structure and function).”44 In other words, these odds are impossible.,,, Tawfik soberly recognizes the problem. The appearance of early protein families, he has remarked, is “something like close to a miracle.”45,,, “In fact, to our knowledge,” Tawfik and Tóth-Petróczy write, “no macromutations ... that gave birth to novel proteins have yet been identified.”69 The emerging picture, once luminous, has settled to gray. It is not clear how natural selection can operate in the origin of folds or active site architecture (of proteins). It is equally unclear how either micromutations or macromutations could repeatedly and reliably lead to large evolutionary transitions. What remains is a deep, tantalizing, perhaps immovable mystery. http://inference-review.com/article/the-new-view-of-proteins

A bit more honesty for the Origin of Life in particular is found here:

“We have no idea how the molecules that compose living systems could have been devised such that they would work in concert to fulfill biology’s functions. We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids, and proteins, were made and how they could have coupled into the proper sequences, and then transformed into the ordered assemblies until there was the construction of a complex biological system, and eventually to that first cell. Nobody has any idea how this was done when using our commonly understood mechanisms of chemical science. Those that say they understand are generally wholly uninformed regarding chemical synthesis. Those that say “Oh, this is well worked out,” they know nothing, nothing about chemical synthesis – Nothing! Further cluelessness – From a synthetic chemical perspective, neither I nor any of my colleagues can fathom a prebiotic molecular route to construction of a complex system. We cannot figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids, and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks let alone their assembly into a complex system. That’s how clueless we are. I’ve asked all of my colleagues – National Academy members, Nobel Prize winners -I sit with them in offices; nobody understands this. So if your professors say it’s all worked out, your teachers say it’s all worked out, they don’t know what they’re talking about. It is not worked out. You cannot just refer this to somebody else; they don’t know what they’re talking about.” James Tour – one of the top ten leading chemists in the world The Origin of Life: An Inside Story - March 2016 Lecture with James Tour https://www.youtube.com/watch?v=_zQXgJ-dXM4 An Open Letter to My Colleagues - James Tour - 2017 Excerpt: We synthetic chemists should state the obvious. The appearance of life on earth is a mystery. We are nowhere near solving this problem. The proposals offered thus far to explain life’s origin make no scientific sense. Beyond our planet, all the others that have been probed are lifeless, a result in accord with our chemical expectations. The laws of physics and chemistry’s Periodic Table are universal, suggesting that life based upon amino acids, nucleotides, saccharides and lipids is an anomaly. Life should not exist anywhere in our universe. Life should not even exist on the surface of the earth.17 http://inference-review.com/article/an-open-letter-to-my-colleagues James Tour is one of the synthetic organic chemists in the world Origin of Life: An Inside Story - Professor James Tour – May 1, 2016 Excerpt: “All right, now let’s assemble the Dream Team. We’ve got good professors here, so let’s assemble the Dream Team. Let’s further assume that the world’s top 100 synthetic chemists, top 100 biochemists and top 100 evolutionary biologists combined forces into a limitlessly funded Dream Team. The Dream Team has all the carbohydrates, lipids, amino acids and nucleic acids stored in freezers in their laboratories… All of them are in 100% enantiomer purity. [Let’s] even give the team all the reagents they wish, the most advanced laboratories, and the analytical facilities, and complete scientific literature, and synthetic and natural non-living coupling agents. Mobilize the Dream Team to assemble the building blocks into a living system – nothing complex, just a single cell. The members scratch their heads and walk away, frustrated… So let’s help the Dream Team out by providing the polymerized forms: polypeptides, all the enzymes they desire, the polysaccharides, DNA and RNA in any sequence they desire, cleanly assembled. The level of sophistication in even the simplest of possible living cells is so chemically complex that we are even more clueless now than with anything discussed regarding prebiotic chemistry or macroevolution. The Dream Team will not know where to start. Moving all this off Earth does not solve the problem, because our physical laws are universal. You see the problem for the chemists? Welcome to my world. This is what I’m confronted with, every day.“ James Tour – leading Chemist https://uncommondesc.wpengine.com/intelligent-design/origin-of-life-professor-james-tour-points-the-way-forward-for-intelligent-design/

Verse:

John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind.

bornagain77

From the peer review article we find that this supposed protein precusor is 'designed':

"Ambidoxin is a designed, minimal dodecapeptide consisting of alternating L and D amino acids that binds a 4Fe–4S cluster through ligand–metal interactions and an extensive network of second-shell hydrogen bonds. https://pubs.acs.org/doi/10.1021/jacs.8b07553

Yet in the public release they claim that this 'perhaps only hard evidence',,, "could have emerged spontaneously".

Rutgers researchers have found among the first and perhaps only hard evidence,,, "it could have emerged spontaneously on the early Earth in the right conditions. https://news.rutgers.edu/rutgers-scientists-identify-protein-may-have-existed-when-life-began/20180829#.W5OTDh-YWiv

And even they themselves admitted that this "designed" protein. that 'could have emerged spontaneously' is far different than what is found in life,

Human DNA consists of genes that code for proteins that are a few hundred to a few thousand amino acids long.

Their solution to this problem?

These complex proteins – needed to make all living-things function properly – are the result of billions of years of evolution. When life began, proteins were likely much simpler, perhaps just 10 to 20 amino acids long.

This is pure unsubstantiated conjecture and unrestrained imagination on their part. They have no empirical evidence whatsoever that proteins were much simpler billions of years ago. Period! The empirical evidence that we do have shows that the simplest cells have, in direct contradiction to Darwinian claims, remained persistently the same for tens of millions, hundreds of millions, even billions of years. Ancient bacteria spores recovered from amber crystals and salt crystals, which are tens to hundreds of millions of years old, have been 'revived',,,

Ancient Bacteria - 2008 Excerpt: “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.” http://www.physicsforums.com/showthread.php?t=281961 “After the onslaught of publicity and worldwide attention (and scrutiny) after the publication of our discovery in Science, there have been, as expected, a considerable number of challenges to our claims, but in this case, the scientific method has smiled on us. There have been at least three independent verifications of the isolation of a living microorganism from amber." - R. Cano http://www.asmscience.org/content/book/10.1128/9781555818128.chap37

,, have been revived, and have now been compared to their living descendants of today. ,,, To the disbelieving shock of Darwinists, “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.”

The Paradox of the "Ancient" (250 Million Year Old) Bacterium Which Contains "Modern" Protein-Coding Genes: Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; - 2002 “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637

I wrote an e-mail to Dr. Cano and asked him if he had performed a 'fitness test' on the ancient bacteria he had revived to see if they were more fit than their modern day descendants. He wrote back and said that he had done such a test and that 'we surmised that the putative "ancient",,, isolate was capable of utilizing a broader scope of substrates” than the modern strain

"We performed such a (fitness) test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative "ancient" B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the (ancient) amber isolate." RJ Cano and MK Borucki - Fitness test which compared ancient amber sealed bacteria to its modern day descendants

Moreover, the ancient yeast that Dr. Cano had also isolated from the amber was also found to be more resilient than modern day yeast in terms of making beer:

Amber Ale: Brewing Beer From 45-Million-Year-Old Yeast - July 20, 2009 Excerpt: Cano,,,brought back to life something that had been trapped in amber for more than 25 million years.,,, Cano identified it as a bacterial spore,,, Ambergene's board of directors decided to confirm Cano's claims of reanimation. "I was very skeptical," says Chip Lambert, a microbiologist tapped by Ambergene to try to duplicate Cano's results. The company provided him with amber and all of Cano's sterilization and extraction protocols. Lambert doubled all of the cleaning processes and added some of his own. He was still able to duplicate Cano's discovery.,,, In April 1995, during his amber-cracking spree, Cano made another important discovery. A piece of fossilized resin from Burma yielded,, brewer's or baker's yeast. Normally, Hackett ends the primary fermentation process by "crashing the tank"—lowering the temperature to shock the yeast into dormancy. But that didn't work on Cano's yeast. "It was just sitting on the bottom and nibbling on the sugar like a couch potato," Hackett says. A strain that had survived 45 million years in suspended animation was not about to go quietly. https://www.wired.com/2009/07/ff-primordial-yeast/

Thus, these ancient bacteria are actually more resilient than their modern day descendents. This is exactly the opposite finding one would have expected from a Darwinian perspective. bornagain77

Good point Latemarch! OLV

Look at this and then look at gpuccio's post and realize that there are light years of difference. Where is the science that shows how one morphs "naturally" into the other? Why would anyone think that this is the starting point? Quote from article...bolding mine.

With computer modeling, Rutgers scientists have been exploring what early peptides may. have looked like and their possible chemical functions, according to Nanda.

It's made of both D and L amino acids. How do we get from there to life that only uses L? Why is there no organism that still uses this? How long will you have to wait for the random protein that can use the electron that this only briefly stores? Can you say "grasping at straws"? I knew you could! Latemarch