QUOTE: "Starting with basic facts about cell biology, Tompa and Rose explain that the parts of cells do not explain the origin of cells. To understand the origin of cells, one must focus on the functional interrelations of those parts, which relations occupy the very tiny space of “alive” in the incomprehensibly larger space of “not alive.”

I’m sorry, but the bold is all we need to know. The rest of the article, including the fact that the parts are interrelated, tells us absolutely nothing about what makes life “vital” or about the origin of cells.

https://evolutionnews.org/2020/04/the-parts-of-cells-dont-explain-the-origin-of-cells/

"Here is a paper that should be in the files of everyone thinking about biological design. It is Peter Tompa and George Rose’s “The Levinthal Paradox of the Interactome” (2011), from the journal Protein Science.

***

"Starting with basic facts about cell biology, Tompa and Rose explain that the parts of cells do not explain the origin of cells. To understand the origin of cells, one must focus on the functional interrelations of those parts, which relations occupy the very tiny space of “alive” in the incomprehensibly larger space of “not alive.”

***

"Any relation or interaction within a cell is not a material object. It is not a part or a thing. The relations that matter to the living state are functions, and, while requiring material parts, the functions cannot be reduced to those parts. Relations are inherently higher-level properties. Tompa and Rose argue that the space of possible interrelations that fail to yield the living state is so much larger than the tiny neighborhood of “alive” that, if the living state is disrupted, the parts of the cell will never find their way back to that state. Instead they embark on a one-way or irreversible random walk out into the universe of not-alive. This is why a bacterium whose membrane or cell wall is disrupted by sonication in a sterile buffer will never come back to life — even though, at that moment, all the molecular parts (DNA, RNA, ribosomes, proteins, lipids, etc.) are co-present in the same microenvironment.

"The essential relations have been lost, irretrievably. The living state, a system of relations, presupposes material things. It is not, however, a material thing itself, and cannot be reduced to materiality. Thus, the bottom-up approach to the origin of life cannot possibly succeed, because it is committed to a category error (i.e., error = the parts of a system are causally primary). Category errors do not yield to further effort. (my bold)

***

"Note carefully: Tompa and Rose do not themselves support a design view of the origin of life. They argue that some unknown, incremental pathway assembled cells: “Presumably, early‐earth life forms originated through an accumulation of changes of ever increasing complexity” (p. 2077). But their interactome analysis does not explain how that pathway would have been traversed, without design – only that (as noted above) having the parts on hand will not yield a cell.

***

"Einstein, in a famous 1918 letter to his friend Michele Besso, put the general epistemological point this way (quoted by Gerald Holton, emphasis added):

…"a theory which wishes to deserve trust must be built upon generalizable facts. Old examples: Chief postulates of thermodynamics [based] on impossibility of perpetuum mobile. Mechanics [based] on grasped [ertasteten] law of inertia. Kinetic gas theory [based] on equivalence of heat and mechanical energy (also historically). Special Relativity on the constancy of light velocity and Maxwell’s equation for the vacuum, which in turn rest on empirical foundations. Relativity with respect to uniform [?] translation is a fact of experience. General [Relativity]: Equivalence of inertial and gravitational mass. Never has a truly useful and deep-going theory really been found purely speculatively."

Comment: Darwinism is purely speculation, although he used some generalizable facts that were true to this day. Darwin was wise not to attempt origin-of-life speculation in view of this definition of life. Tompa and Rose make the full case for design and refuse to follow it to the logical conclusion. I believe this is because religions have contaminated human thinking about the non-human greater power that must exist.

romansh: Ah I got it ... it took mankind to get a scientific education before chemicals first moved through colloids in an electrical field.-Exactly how did this happen on early Earth? In the sea where it is likely life began.-> Romansh: So what is the difference between chance and random?-Is there a difference? I am not well-educated in statistics. I view both as uncontrolled or not prearranged but in a chain of cause and effect.

This is the weirdest response. Electrophoresis is a recent manmade tool. Nuclear fission can be a natural event.
Ah I got it ... it took mankind to get a scientific education before chemicals first moved through colloids in an electrical field.-> As I did.
But I did not accuse you of purposefully omitting relevant data.-> I understand that improbable events occur all the time. I observe them regularly. That doesn't mean my comments were wrong. You didn't answer them directly, which to me is your usual sidestep.
So what is the difference between chance and random?

David: Then used electrophoresis:
> 
> Romansh:Are you suggesting the phenomena of electrophoresis did not exist about 4 billion years ago? If you are that would be vey foolish of you, David. Now there are other phenomena that might "select" unintelligently. This argument is like saying self sustaining nuclear fission reactors exist today on Earth because of intelligent design, they could not possibly have existed 1.8 billion years ago on Earth because of chance.-This is the weirdest response. Electrophoresis is a recent manmade tool. Nuclear fission can be a natural event.
> 
> > David: You left this out purposefully. Was such an apparatus present 3.6 billion years ago?
> Romansh: I left the link for people to evaluate the context for themselves.-As I did.
> 
> Romansh: My personal conclusion is that intelligent design theists don't really understand the issues surrounding chance and selection.
> 
> They conflate chance and random and see selection being impossible without a designer. I will admit disbelievers don't help by using random and chance interchangeably.-I understand that improbable events occur all the time. I observe them regularly. That doesn't mean my comments were wrong. You didn't answer them directly, which to me is your usual sidestep.

Then used electrophoresis:-Are you suggesting the phenomena of electrophoresis did not exist about 4 billion years ago? If you are that would be vey foolish of you, David. Now there are other phenomena that might "select" unintelligently. This argument is like saying self sustaining nuclear fission reactors exist today on Earth because of intelligent design, they could not possibly have existed 1.8 billion years ago on Earth because of chance.
 
> You left this out purposefully. Was such an apparatus present 3.6 billion years ago?
I left the link for people to evaluate the context for themselves.
Oklo - https://en.wikipedia.org/wiki/Natural_nuclear_fission_reactor
 
> Conclusion for wishful thinking atheists: What is described is intelligent design in laboratories, nothing more. Where do all the nucleotides and polymerizing enzymes on early Earth come from? And so far from the lab research done to date, no ribozyme developed in a lab can reproduce with the accuracy of life on Earth today. and without that accuracy there is no life!-My personal conclusion is that intelligent design theists don't really understand the issues surrounding chance and selection.-They conflate chance and random and see selection being impossible without a designer. I will admit disbelievers don't help by using random and chance interchangeably.

Romansh: http://www.science20.com/stars_planets_life/calculating_odds_life_could_begin_chance&am... 
> > The results were amazing. After only 4 rounds of selection and amplification they began to see an increase in catalytic activity, and after 10 rounds the rate was 7 million times faster than the uncatalyzed rate. It was even possible to watch the RNA evolve.-Nice try. You've picked out a line from an article I know well and have used in my books. I'm referring to this study in the column you presented:-"Now I will recall a classic experiment by David Bartel and Jack Szostak, published in Science in 1993. Their goal was to see if a completely random system of molecules could undergo selection in such a way that defined species of molecules emerged with specific properties. They began by synthesizing many trillions of different RNA molecules about 300 nucleotides long, but the nucleotides were all random nucleotide sequences."-Started with trillions of possibilities!!!-Then used electrophoresis:-"Nucleic acids can be separated and visualized by a technique called gel electrophoresis. The mixture is put in at the top of a gel held between two glass plates and a voltage is applied. Small molecules travel fastest through the gel, and larger molecules move more slowly, so they are separated."-You left this out purposefully. Was such an apparatus present 3.6 billion years ago?-From the article:-"Bartel and Szostak's results have been repeated and extended by other researchers, and they demonstrate a fundamental principle of evolution at the molecular level. At the start of the experiment, every molecule of RNA was different from all the rest because they were assembled by a chance process. There were no species, just a mixture of trillions of different molecules. But then a selective hurdle was imposed, a ligation reaction that allowed only certain molecules to survive and reproduce enzymatically."-Conclusion for wishful thinking atheists: What is described is intelligent design in laboratories, nothing more. Where do all the nucleotides and polymerizing enzymes on early Earth come from? And so far from the lab research done to date, no ribozyme developed in a lab can reproduce with the accuracy of life on Earth today. and without that accuracy there is no life!

Romansh: Life comes from star dust-Of course the necessary elements come from star dust, but no one in the origin of life lab industry can do much without pieces of the genome.


> dhw:you don't seem to have fully understood my own point that science can explain the machinery by which thought is transmuted into action, but it cannot explain thought. That is why your attempts to automatize cells by describing their machinery seem to me to “miss the mark”.-I know that science can tell us how thoughts are made by cells, and I know that certain motor areas of the brain control muscular action. In my version of free will my conscious mind tells my brain to move my arm and it does. My brain automatically responds to my wishes. What is your point? I'm right on the mark.-> 
> dhw: You don't care about the illogicality of the argument that life and thought can only be created by a mind, but the mind that created them did not have to be created. You try to balance your theism by closing your eyes to the fact that belief in chance and belief in God BOTH run counter to reason. That is why we use the word “faith”.-You are using faith in my case in the wrong way. I see no other logical explanation for the universe and life than a planning mind. That is my logical conclusion. I have 'faith' in my reasoning that I am right. Then secondarily I accept faith in God. Just as I try not to interpret God's personality, I keep Him at a slight distance compared to reverential religious folk.
> 
> dhw: If other organisms behave as if they are intelligent, and many researchers tell us they are, why insist they are not? Why not keep an open mind? -Because the odds are 50/50 I am right, and I've reached this conclusion and will stick to it. Bacteria act intelligently because they follow intelligent instructions. I quote from Shapiro:-"The contemporary view of cell information processing...makes the point that DNA cannot do anything or direct anything by itself; it must interact with other cell molecules. So all genomic action is subject to the inputs and information-processing networks we know operate in living cells."- These networks are all molecular interactions. Nowhere in his book does he have a subject called cell thinking. Instead:-"The best we can do right now is to recognize that cells use many kinds of molecular interactions to process information and execute appropriate decisions." I haven't met a thinking protein molecule yet. They are thousands of atoms strung together to make a functional molecule. Those functional molecules interplay with DNA to achieve results, some of which are epigenetic changes in DNA, the thrust of his research. His thoughts and mine are NOT in opposition.-> 
> dhw: When people say consciousness “emerges”, they usually mean that it is produced by the interplay between the neurons. If consciousness exists independently and the brain is a receiver and not a transmitter, the progressive complexity of the nervous system and of brains is the RESULT of increasingly complex consciousness, not the producer. Is that what you mean?-The concept of receiving consciousness arises from the discovery that NDE's demonstrate consciousness independent of a living brain. The theory is really a form of dualism. I am sure the extreme complexity of our brain, as compared to lower animals, results in a much more complex form of consciousness, which we certainly have. Under this thought, there is a universal consciousness 'out there' with lower and higher levels that can be 'received' by the brain at its current level of complexity (or "receivingness"). Since I believe as God, the universal consciousness, it all fits with my way of looking at things.


> Dhw:... but it takes consciousness to perceive, name, analyse and use it. You are trying to restrict the term “information” to instructions, so that you can ask who gave the instructions (answer: God). But information does not consist only of instructions.-True enough, but I'm trying to point out two types of information: descriptive and instructive. DNA has both but only the instructive runs life.-> dhw: An atheist can say that all the information needed for life was contained in unconscious materials which luckily assembled themselves into a life-giving form, and that, through time and experience, evolved its own increasingly complex "instructional information" - a hypothesis no less miraculous than that of a universal, eternal, self-aware, unified form of energy inexplicably possessed of all the “instructional information” needed to create life and the universe. You see the improbability of the one and refuse to see that of the other.-I don't care what atheists can conjure up as an excuse for life. Only mentation can create the instructions. You constantly refuse to allow for that as the prime consideration, and try to balance your agnosticism by bringing up chance. 
> 
> dhw; But if you insist that “instructional information” requires a mind, then the instructional cooperation, communication and decision-making carried out by bacteria show that they have “minds”! You can't have it both ways.-Yes I can. No one can distinguish, from the outside of bacteria, between automatism run by complete instructions or some type of mental process without neurons to process it. There is no avoiding that observation. You know what side I take
> 
> DAVID: Much of our body works in a materialistic way. I've described that with my reference to the kidney and liver. My response is graded by the complexity of the evolutionary ladder. Bacteria do not think. Cambrian animals had a degree of mentation, primates more so, and humans a huge jump beyond. Progressive complexity of the nervous system and of brains.
> 
> dhw: Agreed, apart from your dogmatic refusal to acknowledge the possibility that bacteria do think. But if you attribute thought to progressive material complexity, what happened to your dualism?-I'm not avoiding dualism at all. It takes neuronal complexity to allow consciousness to emerge as the brain acts as a receiver.


> dhw: Tony began by saying he thought you had missed the mark, and the argument that life begets life still doesn't explain life, any more than the union of sperm and egg explains life. I would like to highlight what Tony says, because it is so important: “It is not that they can't explain the machinery, it's that they can't explain the spark.” And I would apply that both to life and to thought, with emphasis on the fact that scientists can explain the machinery by which organisms operate, but they cannot explain the cognitive, decision-making, communicative skills of those organisms, ranging from the simplest to the most complex.-I fully understand the point. That is why I said life is a continuum. Once it appeared with all of its magical properties it has continued to make life in different forms. The 'spark', as were the instructions (information), were given in a miraculous beginning. As long as life can maintain itself by reproducing itself it will continue. If that continuum is stopped, it will take another miracle to start it again. This is why I am a believer.

tony: Information does not create life any more than the mechanical processes do. Even if you had all of the information, and all of the necessary mechanics in place, you would still have nothing but a corpse. Without that penultimate 'spark' of life, our bio-mechanical machinery is not alive. That is ultimately where all of the reductionalist/naturalist theories fail. It is not that they can't explain the machinery, it's that they can't explain the spark.-I agree with you in that technically a corpse still contains all the information that created life, but a corpse cannot read that information and therefore is dead. The 'spark' comes from the union of sperm and egg, which is two living items coming from two living sources. Thus life begets life and it is a continuum. The 'spark', as you put it, began 3.6-3.8 billion years ago and is not extinguished as yet. That is the true concept. Life appeared and hasn't left, and chance can't create that 'spark'. And the current so-called research into the OOL is doomed to failure, because human scientists can put together the chemicals, as Tony points out, but life will not appear. Still the same old rule. Only life makes life.

David: The other issue in live and dead animals is the availability of the information in the genome. This is really what creates life. The animal is dead because it can no longer access the life-running information. All the processes are stopped. In resuscitation failed organs (heart and brain) are supported until they can reacquire access to the information that runs life. Look at this quote:->David: I couldn't say it better. The emergence of life from the materials in living beings is due to the information in the codes of the genome and in all the modifiers of the genome complex. The Darwin folks seem very reluctant to get into the information issue, because recognition of the importance of that information is a direct threat to a mechanistic chance process of evolution being the correct interpretation. -
I know I am hit or miss on this conversation with my schedule lately, but I think you kind of missed the mark here. Information does not create life any more than the mechanical processes do. Even if you had all of the information, and all of the necessary mechanics in place, you would still have nothing but a corpse. Without that penultimate 'spark' of life, our bio-mechanical machinery is not alive. That is ultimately where all of the reductionalist/naturalist theories fail. It is not that they can't explain the machinery, it's that they can't explain the spark.