Major metabolic pathways and their inadequacy for origin of life proposals

Major metabolic pathways and their inadequacy for origin of life proposals
According to geneticist Michael Denton, the break between the nonliving and the living world ‘represents the most dramatic and fundamental of all the discontinuities of nature.
And John Lennox writes in his book has science buried God ?
It is hard for us to get any kind of picture of the seething, dizzyingly complex activity that occurs inside a living cell, which contains within its lipid membrane maybe 100 million proteins of 20,000 different types and yet the whole cell is so tiny that a couple of hundred could be placed on the dot in this letter ‘i’.
The meaning of the genetic code is also virtually identical in all cells. The size, structure and component design of the protein synthetic machinery is practically the same in all cells. In terms of their basic biochemical design, therefore, no living system can be thought of as being primitive or ancestral with respect to any other system, nor is there the slightest empirical hint of an evolutionary sequence among all the incredibly diverse cells on earth.’
This view is supported by Nobel Prize-winner Jacques Monod, whom Denton cites. ‘We have no idea what the structure of a primitive cell might have been. The simplest living system known to us, the bacterial cell… in its overall chemical plan is the same as that of all other living beings. It employs the same genetic code and the same mechanism of translation as do, for example, human cells. Thus the simplest cells available to us for study have nothing “primitive" about them… no vestiges of truly primitive structures are discernible.’ Thus the cells themselves exhibit a similar kind of ‘stasis’ to that referred to in the previous chapter in connection with the fossil record.
Its interesting to try to figure out what that supposed last universal common ancestor ( LUCA ) was, in order to understand what kind of biochemical mechanisms, metabolism, enzymes, co-factors, proteins and genome information would have to be explained, and its origin.
From a biochemist’s perspective, life at the cellular level can be defined as a network of integrated and carefully regulated metabolic pathways, each contributing to the sum of activities that a cell must carry out. Cellular metabolism is a complex process involving about a thousand chemical reactions catalyzed by globular proteins, enzymes.
In the scientific paper: The Enzymatic and Metabolic Capabilities of Early Life, the author states that several independent studies have used comparative bioinformatics methods to identify taxonomically broad features of genomic sequence data, protein structure data, and metabolic pathway data in order to predict physiological features that were present in early, ancestral life forms. We survey modern metabolic pathways to identify those that maintain the highest frequency of metaconsensus enzymes. Using the full set of modern reactions catalyzed by these metaconsensus enzyme functions, we reconstruct a representative metabolic network that may reflect the core metabolism of early life forms.
Their research revealed the mind blowing complexity of Luca, and its metabolic pathways:
http://reasonandscience.heavenforum.org/t2174-the-enzymatic-and-metabolic-capabilities-of-early-life
According to another research paper : Evolution of the first metabolic cycles, There are two alternatives concerning the origin of life: the origin may be either heterotrophic or autotrophic. The paper : Analysis of the Intermediary Metabolism of a Reductive Chemoautotroph gives a idea of the complexity of it:
http://reasonandscience.heavenforum.org/t2147-the-naturalistic-approach-of-origin-of-life-scenarios
No wonder, do the authors of the paper: How Life Began: The Emergence of Sparse Metabolic Networks , openly admit that: " The process by which the network of extant metabolism emerged is one of the major puzzles in the origin of life field." Another paper admits that " An open question for scientists is when and how cellular metabolism, the network of chemical reactions necessary to produce nucleic acids, amino acids and lipids, the building blocks of life, appeared on the scene." The pathways for synthesis of most of the twenty amino acids used in proteins and the four nucleotides used in RNA are identical or nearly identical in Archaea, bacteria and eukaryotes, suggesting that these pathways were inherited from the LUCA. metabolic network. Thus, it appears that that the LUCA had the ability to synthesize the critical building blocks of life and did not rely on exogenous sources of these compounds. This supposition is supported by bioinformatic reconstructions of the genome of the LUCA. Biosynthetic pathways in extant organisms clearly resemble those in the LUCA. In the scientific paper : In The Ancient Ocean, Did Metabolism Precede The Origin Of Life?
http://reasonandscience.heavenforum.org/t2004-major-metabolic-pathways-and-their-inadequacy-for-origin-of-life-proposals
the author writes :
The observed chemical reactions occurred in the absence of enzymes but were made possible by the chemical molecules found in the Archean sea. Finding a series of reactions that resembles the “core of cellular metabolism” suggests that metabolism predates the origin of life. This implies that, at least initially, metabolism may not have been shaped by evolution but by molecules like RNA formed through the chemical conditions that prevailed in the earliest oceans.
Whether and how the first enzymes adopted the metal-catalyzed reactions described by the scientists remain to be established.
Its easily observable the hudge gap between the just so, almost helpless explanation attempts of the origin and arise of essential metabolic pathways, and their complexity observed even in the simplest cells.
This made the leading Origin of Life researcher Leslie Orgel say following:
The Implausibility of Metabolic Cycles on the Prebiotic Earth
Leslie E Orgel†
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060018
Almost all proposals of hypothetical metabolic cycles have recognized that each of the steps involved must occur rapidly enough for the cycle to be useful in the time available for its operation. It is always assumed that this condition is met, but in no case have persuasive supporting arguments been presented. Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of the reverse citric acid cycle was present anywhere on the primitive Earth, or that the cycle mysteriously organized itself topographically on a metal sulfide surface? The lack of a supporting background in chemistry is even more evident in proposals that metabolic cycles can evolve to “life-like" complexity. The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most nonenzymatic catalysts—has, in general, not been appreciated. If it has, it has been ignored. Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own.

The meaning of the genetic code is also virtually identical in all cells. The size, structure and component design of the protein synthetic machinery is practically the same in all cells. In terms of their basic biochemical design, therefore, no living system can be thought of as being primitive or ancestral with respect to any other system, nor is there the slightest empirical hint of an evolutionary sequence among all the incredibly diverse cells on earth.’
I'll admit my understanding of all this is pretty kindergarden, yet when I read stuff like you've written up there, it simply does not compute with that background knowledge I possess. Heck I can't even figure out what you are trying to say beyond it's "inadequate to explain the origins of life" (so god did it?) To the best of my knowledge no scientist has claimed to have cracked the nut of "thee origin of life" so calling current explanations inadequate doesn't say a thing. Then to jump from that obvious observation to claiming: "not the slightest empirical hint of an evolutionary sequence" in the development of cells simply doesn't cut it. Current Opinion in Genetics & Development Volume 27, August 2014, Pages 102–108 http://www.sciencedirect.com/science/article/pii/S0959437X14000483 Structural evolution of cell types by step-wise assembly of cellular modules Kaia Achim, Detlev Arendt
No wonder, do the authors of the paper: How Life Began: The Emergence of Sparse Metabolic Networks , openly admit that: " The process by which the network of extant metabolism emerged is one of the major puzzles in the origin of life field." Another paper admits that " An open question for scientists is when and how cellular metabolism, the network of chemical reactions necessary to produce nucleic acids, amino acids and lipids, the building blocks of life, appeared on the scene."
It's no wonder indeed, what's the point here? As for LUCA:
Front Biosci. 2008 May 1;13:5605-13. The genomics of LUCA. Mat WK1, Xue H, Wong JT. Abstract To understand the nature and evolution of LUCA, or Last Universal Common Ancestor, the minimum genome of LUCA has been identified based on the genes common to the eight primitive Euryarchaea and Crenarchaea species Methanopyrus kandleri, Methanothermobacter thermautotrophicum, Methanococcus jannaschii, Pyrococcus abyssi, Pyrococcus furiosus, Pyrococcus horikoshii, Aeropyrum pernix and Pyrobaculum aerophilum, together with the methanogenesis genes of the primitive methanogens. The 424 protein encoding genes in the minimum LUCA genome exceed significantly the 150-340 genes estimated to be present in a minimal proteome compatible with life. Thus LUCA was not a minimal organism but the first modern organism equipped with a DNA genome and the universal genetic code. The hyperthermophilic, Methanopyrus-proximal LUCA is consistent with a Hot Cross Origin of life which proposes that early heterotrophic life forms in the cooler temperature zones invented methanogenesis and a DNA genome upon their adaptation to the hydrothermal vents, where life flourished massively on lithoautotrophy supported by carbon dioxide and hydrogen, thereby leading to the rise of LUCA.
If you really want to have fun what about the evolution of minerals on this here fantastic Earth of ours - who happens to be the mother and creator of us all ;-P

John Lennox : There is no publication in the scientific literature – in prestigious journals, specialty journals, or books – that describes how molecular evolution of any real, complex, biochemical system either did occur, or even might have occurred. There are assertions that such evolution occurred, but absolutely none is supported by pertinent experiments or calculations… despite comparing sequences and mathematical modelling, molecular evolution has never addressed the question of how complex structures came to be.
James Shapiro, a biochemist at the University of Chicago, also admits that there are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system; only a variety of wishful speculations. Even the highly critical review of Behe by Cavalier-Smith concedes Behe’s point that no detailed biochemical models exist.

I would need to know what he means by “molecular evolution”, because that certainly occurs all the time and is quite well documented. Does this page help? ]
Here’s another page that tallies the number of articles on the subject and references the Cavalier-Smith article. Have you read that article?]
And it just keeps getting better.]

You’ve never heard of this paper from the ID guys? Not surprising, they’ve never cited it. Cavalier-Smith pointed this out way back in his 1997 review of Darwin’s Black Box in TREE (see Cavalier-Smith, 1997, “The Blind Biochemist," Trends in Ecology and Evolution 12(4), 162-163, April 1997), and I’ve never seen any IDer acknowledge the oversight. Stumbling on this review while looking up this other book review is literally what got me into this whole ID thing in the first place. I had originally thought, “Hmm, Behe might have a point about the lack of literature on the evolution of complex systems." Then I read Cavalier-Smith’s review and realized I’d been snookered. The rest is history.

This will always be a very difficult question to answer for several reasons.

  1. The chemical processes themselves which eventually lead to the first autonomously reproducing organism do not leave a fossil record.
  2. The processes that lead to life occurred in a lab of enormous proportions (earth)
  3. The natural experiment that lead to life ran 24/7 for hundreds of millions of years.
  4. #2 and #3 create a situation where so many reactions were taking place over such a huge expanse of time that even if an exceedingly rare sequence of events needed to occur in sequence to give rise to life it could have easily occurred someplace at sometime.
    It may then be very difficult to replicate or even imagine how life began given these obstacles but its always fun to try and especially entertaining to listen to people who say that a particular set of circumstances is so unlikely as to be impossible.
    I suspect we may only start to get answers to this when we begin to find examples of exobiology on planets where life has only just begun to gain a foot hold.
"its always ... especially entertaining to listen to people who say that a particular set of circumstances is so unlikely as to be impossible"
Buying just one Powerball ticket twice a week for a year and getting all the numbers right on each of those 104 tickets is "so unlikely as to be impossible" [as regards any meaningful sense of possible].
The infinite monkey theorem states that a monkey hitting keys at random on a typewriter keyboard for an infinite amount of time will almost surely type a given text, such as the complete works of William Shakespeare. In this context, "almost surely" is a mathematical term with a precise meaning, and the "monkey" is not an actual monkey, but a metaphor for an abstract device that produces an endless random sequence of letters and symbols. ... The relevance of the theorem is questionable—the probability of a universe full of monkeys typing a complete work such as Shakespeare's Hamlet is so tiny that the chance of it occurring during a period of time hundreds of thousands of orders of magnitude longer than the age of the universe is extremely low (but technically not zero).
https://en.wikipedia.org/wiki/Infinite_monkey_theorem
"its always ... especially entertaining to listen to people who say that a particular set of circumstances is so unlikely as to be impossible"
Buying just one Powerball ticket twice a week for a year and getting all the numbers right on each of those 104 tickets is "so unlikely as to be impossible" [as regards any meaningful sense of possible]. Ha. The noob proved you wrong, Mac. This is not always entertaining.
Major metabolic pathways and their inadequacy for origin of life proposals According to geneticist Michael Denton, the break between the nonliving and the living world ‘represents the most dramatic and fundamental of all the discontinuities of nature. And John Lennox writes in his book has science buried God ?
This view creates it's own glaring break, that between the billions of years evidence of evolution which requires no intercession and the sudden appearance of an unknown agency to initiate the appearance of life. What's more likely, that we simply lack the necessary details of what exact conditions were in existence a little less than 4 billion years ago that allowed the initiation of a very long chain of biological adaptation. Or there is an unidentified intelligent presence that intercedes in the natural world at its own will when and where it wants.
It is hard for us to get any kind of picture of the seething, dizzyingly complex activity that occurs inside a living cell, which contains within its lipid membrane maybe 100 million proteins of 20,000 different types and yet the whole cell is so tiny that a couple of hundred could be placed on the dot in this letter ‘i’. The meaning of the genetic code is also virtually identical in all cells. The size, structure and component design of the protein synthetic machinery is practically the same in all cells. In terms of their basic biochemical design, therefore, no living system can be thought of as being primitive or ancestral with respect to any other system, nor is there the slightest empirical hint of an evolutionary sequence among all the incredibly diverse cells on earth.’
Evolution is a continuous variation of an original theme, it doesn't rewrite the song book from scratch every epoch. Which means that eventually all life is related to all other life on the planet if you back far enough. And molecular biology backs this up as we can see that species that appear on the surface to be closely related often share very close genetic make-up. Such as Bonobos and Homo Sapiens Sapiens. This could all be a huge coincidence or an indication that all life shares a common root that only requires the necessary physical conditions to begin.
This will always be a very difficult question to answer for several reasons. 1) The chemical processes themselves which eventually lead to the first autonomously reproducing organism do not leave a fossil record. 2) The processes that lead to life occurred in a lab of enormous proportions (earth) 3) The natural experiment that lead to life ran 24/7 for hundreds of millions of years. 4) #2 and #3 create a situation where so many reactions were taking place over such a huge expanse of time that even if an exceedingly rare sequence of events needed to occur in sequence to give rise to life it could have easily occurred someplace at sometime. It may then be very difficult to replicate or even imagine how life began given these obstacles but its always fun to try and especially entertaining to listen to people who say that a particular set of circumstances is so unlikely as to be impossible. I suspect we may only start to get answers to this when we begin to find examples of exobiology on planets where life has only just begun to gain a foot hold.
Which sums it up very well I think. The early Earth was a massive chemical lab who's exact conditions we can't even determine beyond any general details. It was constantly being bombarded from space by all sorts of material that would have introduced a very wide variety of complex molecules into the lab and there would have been a wide variety of possible energy sources to power reactions. Who knows what catalysts were involved. And all this would have played out over millions of years with an untold number of chemical reactions. It's possible there is more than one pathway to a self sustaining chemical process that we now refer to as biology but all that's required is that one becomes established after which point biological evolution takes over to produce the huge variety of life we see today. Pinning down the exact sequence of chemical reactions that result in abiotic genesis is a very daunting challenge. The fact that no one has yet worked out the details is the result of this almost certainly. Not that fact that abiotic genesis isn't possible.
**lots and lots of complicated sciency words** Wow, that is complicated! I do not understand it. Therefore goddidit!!
When so many of your posts have that format, it's difficult to not write you off as someone who can't get past the argument from ignorance. I don't know if you're aware of the fact that science has reduced the number of phenomenon that Western civilization uses the 'god argument' to answer from 100% a few hundred years ago down to the few cutting-edge science questions you focus on. That is a pattern that can't be ignored by a rational person.