"Miles Davis" is a molecular/cell biologist by training and career. He did contact me by email, asking to have an exchange in regards to abiogenesis - evolution. He is an atheist. He agreed that I publish our exchange here at my virtual library.
Miles: some evidence can be consistent with more than one conclusion?
Reply: Eventually. That depends on case to case to be analyzed individually.
Just to be clear what I mean here is an example:
Miles: Evidence:- A person A’s fingerprints are found on a murder weapon (let’s say it is a knife and the murder was a stabbing).
Some conclusions consistent with this evidence :
a. Person A is the murderer.
b. Person A handled the weapon at some point but is not the murderer.
c. Person A’s fingerprints were transferred to the murder weapon by some technical method by the murderer or their accomplice in order to frame person A.
d. Some sort of magic or supernatural effect caused person A’s fingerprints to appear on the weapon.
All the conclusions above are consistent with the evidence but only one leads to the conclusion that A is the murderer so we need a method by which we can determine which conclusion is correct?
Reply: Agreed.
Miles: We might disregard conclusion d. , at least initially, on the grounds that is seems so improbable that it would be a waste of time to investigate this possibility but the scientific method does not disregard any possible conclusions as we will see.
The best/scientific method is to seek more evidence but there might be a great deal of irrelevant evidence that we could waste time gathering so the scientific way to proceed is to form one or more hypothesis and then try to disprove that hypothesis.
Hypothesis: Person A is the murderer.
Then we ask what novel predictions does this hypothesis generate and look for evidence that tells us whether those predictions are true. I don’t want to belabour the point but just for clarity I’ll give one more example: Prediction:- Person A was at the scene at the time of the murder. If we find evidence that person A was somewhere else at the time of the murder then we have essentially disproved the hypothesis that person A is the murderer. It is still possible to come up with conclusions like:
Person A can perform long distance telekinesis and used this unique attribute to stab the victim.
Person A built a machine that mechanically stabbed the victim with the knife & then dismantled it at a later time.
But these seem extremely unlikely and would only be worthy of consideration if we had very good other reasons to think they might be true.
So, we can now treat the conclusion that person A is the murderer as highly unlikely. Please note that we have not proved 100% that person A is NOT the murderer. We must still be open to the possibility that new evidence will come to light to indicate that they did in fact stab the victim but our investigation will now look for other possible murderers and try to disprove the hypothesis that each one of them is the murderer.
I’m sorry if that was a bit long winded but it outlines the way that I think evidence should be considered & conclusions reached. Do you agree?
Reply: Agreed. I think all options should be put on the table, and considered as a possibility. As a side note, that is one of my criticisms on the current philosophical framework around historical sciences.
Design is excluded a prior as a possible explanation of unique events that supposedly happened in the past. You can read more about it here:
Historical sciences, and methodological naturalism
https://reasonandscience.catsboard.com/t1692-historical-sciences-and-methodological-naturalism
Miles: My second point about evidence is that each piece of evidence must be examined separately to determine its validity. It is crucial that only valid evidence is considered when we form hypotheses and draw conclusions. Do you agree?
Reply: yes. Each phenomenon has to be analyzed individually.
Miles: To demonstrate this, consider the stabbing example above. The initial evidence was that person A’s fingerprints were found on the murder weapon. If we check this evidence and find that the fingerprint match is incorrect or has been overstated or misinterpreted in some way, we must reject the statement “Person A’s fingerprints were found on the murder weapon”. It does not matter that someone once said it was true. It does not matter that we once thought it was true. We have checked, it is not true & we must reject it. Again, I ask whether you agree?
Reply: yes. Agreed.
OK, so I hope you will be able to agree with both these points about evidence since they should not be controversial. There may be other issues over what we can consider to be evidence or how best to analyse evidence but they can be dealt with if and when they occur in our discussion.
Now that it seems we both agree in a basic sense about how to handle and test evidence, hypotheses & conclusions I think we should pick a subject and make a start. My choice would be:
The origin of life on Earth.
I’ll briefly set out my position on this matter and you can let me know whether you are happy to start here and perhaps reply by setting out your position briefly. Then we can start to pick out pieces of evidence to examine, hypotheses to test and see if we can agree on a conclusion.
So, my short answer to the question “How did life on Earth originate?” is to say I don’t know; in fact, I’d say no human past or present knows the answer to this question.
That may not seem very helpful so a longer answer would be that there seem to be several possible answers to this question as listed below:
1. Chemical reactions and physical processes on the Earth from ~4.5 billion years ago till ~3.8billion years ago gave rise to the formation of something that we can consider to be a basic single celled living organism.
2. A basic single celled living organism arrived on the Earth ~3.8 billion years ago either on a comet, meteor or spacecraft.
3. A highly advanced but natural being assembled a basic single celled living organism using purely natural methods.
4. A supernatural being created a basic single celled living organism using purely supernatural powers.
There may be other possibilities not listed here but these are the ones that I can think of that fit the scientifically verified facts we know to be most likely true about life on Earth today, the history of life on Earth & how the Earth was formed. Please feel free to add to this list if you think there is one or more, I have omitted.
I consider the biblical account of the origin of life on Earth to be demonstrably false. We can explore the reasons for my rejection of this account if you think it should be included in the list of possible answers.
I also reject all the other creation accounts that I have heard e.g., the Hindu lotus flower story on the same grounds as I reject the biblical creation story.
Miles: I will happily give you my opinions about these three subjects but first I must insist that you consider the list of options that I gave for the origin of life on Earth. Do you agree with my list of four options?
Reply: yes, I do.
Miles: Would you like to include any other options?
Reply: I think I regards to origins of life, there are basically just following options:
1. unguided random events
2. physical necessity
3. design
The possible mechanisms to explain the origin of life
https://reasonandscience.catsboard.com/t2515-abiogenesis-the-possible-mechanisms-to-explain-the-origin-of-life
Miles: The biblical account is accurate and true but God engineered the Earth to appear to be 4.5 billion years old and placed rock strata, fossils, radioisotopes, geomagnetic data, ERV DNA sequences and a host of other physical and biological markers in such a way that human beings in 2021AD might be fooled into thinking the Earth was 4.5 billion years old & life evolved from a single common ancestor.
Reply: The timeline, when all happened, is a different topic. So I don't want to entertain that quest right now.
Miles: As I said in my previous email, I do not know how life originated on Earth.
Reply: First of all, it is not about knowing in absolute terms. Nobody has a time machine to go back. I use inference to the best explanation.
BAYESIAN PROBABILITY AND SCIENCE
https://reasonandscience.catsboard.com/t2721-bayesian-probability-and-science
and I also think saying " I don't know is unwarranted".
Here is why:
When you see a blueprint of a factory, with the precise instructions to make all machines, subparts, how to assemble each machine, interconnect them into production lines, organized production compartments, gates to permit the right materials to get in, and the end products go through error check and repair, and export, and then see the functional factory-build precisely upon the blueprint which you saw previously, and the operation of the factory close to perfection, controlled and directed by computers, directing thousands of processes simultaneously and adapting the production output by its demands, but have no clue of how both, the blueprint, and the factory, came to be: What is the obvious answer:
a) That an intelligent team of engineers, machine designers, etc. made the project, and skilled, intelligent labor workers, carpenters, masons, electricians, machine builders, etc. constructed the factory, or
b) that natural forces somehow made the blueprint, and random unguided forces brought the building materials together, and by luck, the factory was assembled precisely based on the blueprint instructions and started its production ? or
c) you have no way to conclude anything meaningful and feel justified to say: " I don't know"?
Here is the argument:
The factory maker argument
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument
Life comes only from life. That has never been disproven. Therefore, that should in my view be the default position.
1. Living Cells store very complex genetic and epigenetic information through the genetic code, and over forty epigenetic languages, translation systems, and signaling networks. These information systems prescribe and instruct the making and operation of cells and multicellular organisms. The operation of cells is close to thermodynamic perfection, and its operation occurs analogously to computers. Cells ARE computers in a literal sense, using boolean logic. Each cell hosts millions of interconnected molecular machines, production lines and factories analogous to factories made by man. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks. Cells operate robot-like, autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advance and sophistication.
2. The origin of blueprints containing the instructional complex information, and the fabrication of complex machines and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup.
3. Therefore, the origin of biological information and self-replicating cell factories is best explained by the action of an intelligent designer, who created life for his own purposes.
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Miles: Unguided events do not have to be random. A chemical reaction is unguided but it is not random either. Unless you consider the physical laws to be the guiding agent which I would challenge because those laws are purely descriptive of our reality. I have no idea what you mean by physical necessity. I applaud the brevity of the phrase but that brevity is only useful if it conveys a clear meaning which, for me at least, it does not.
Reply: when I post a link, I do it for brevity's sake, in order for a reply not to be too long. But I recommend that you actually access the link , and read the information, because it is relevant to the topic, and elucidates what I mean.
Physical necessity & Physical laws
https://reasonandscience.catsboard.com/t2515-abiogenesis-the-possible-mechanisms-to-explain-the-origin-of-life
Stephen C. Meyer observed:
“There are neither bonds nor bonding affinities—differing in strength or otherwise—that can explain the origin of the base sequencing that constitutes the information in the DNA molecule”
(Signature in the Cell, 243).
As Paul Davies lamented,
“We are still left with the mystery of where biological information comes from.… If the normal laws of physics can’t inject information, and if we are ruling out miracles, then how can life be predetermined and inevitable rather than a freak accident? How is it possible to generate random complexity and specificity together in a lawlike manner? We always come back to that basic paradox”
(Fifth Miracle, 258).
A law of nature could not alone explain how life began, because no conceivable law would compel a legion of atoms to follow precisely a prescribed sequence of assemblage.
Paul Davies, The origin of Life, page 17
Werner Gitt summarized it this way:
“A necessary requirement for generating meaningful information is the ability to select from alternatives and this requires an intelligent, volitional entity.… Unguided, random processes cannot do this—not in any amount of time because this selection process demands continuous guidance by intelligent beings that have a purpose”
(Without Excuse, 50–51).
Miles: Design. OK, but design by who/what? I gave two design options one by a God and one by some advanced alien being/civilisation. Also, we need to be precise about the thing that was designed. In my opinion the only possibility considering other facts we know about the Earth and life we see today is a basic single celled organism. Do you agree?
Reply: We can reduce our investigation to either: An intelligent designer was involved to create life, or not. Physical necessity can be excluded, because
Luisi, The Emergence of Life; From Chemical Origins to Synthetic Biology, page 21
A deterministic answer assumes that the laws of physics and chemistry have causally and sequentially determined the obligatory series of events leading from inanimate matter to life – that each step is causally linked to the previous one and to the next one by the laws of nature. In principle, in a strictly deterministic situation, the state of a system at any point in time determines the future behavior of the system – with no random influences. To invoke a guided determinism toward the formation of life would only make sense if the construction of life was demonstrably a preferential, highly probable natural pathway.
We can also exclude aliens because that would demand an explanation of the origin of these folks as well. The identity of the designer can be left for an inquiry after it has been established, that design is the better causal agent rather than not.
Miles: The rest of your email, while interesting but mostly incorrect, is putting the cart before the horse.
Reply: Ok.
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Miles: I have proposed 5 possibilities, although I only proposed the 5th one for the sake of illustrating that all other possibilities seem somewhat absurd to me.
Reply: in regards to your example, I agree with all the options/possible explanations of the cause of the event. We want to elucidate if a designer is the most likely explanation of the origin of life, or not. As clarified in a previous email, physical necessity is not an option, since there is no necessity for nucleotides to line up in a specified complex order.
Miles: You have eventually made the statement "An intelligent designer was involved to create life, or not." which while true does not advance the discussion at all because it attempts to ignore the basic facts that we know about the Earth and life on Earth and leave open all manner of absurd ideas that will just waste a great deal of time.
Reply: I think it advances the discussion since we restrict the possible options to those which are really relevant.
Miles: Let me ask you a few simple questions. Please respond with short, ideally one word answers, so I can see whether we are starting from the same point or not. I have given my own one word answers to show how easy it is to answer these questions with a yes or no.
Please understand that I am not trying to avoid getting into the details,I just want to know whether you accept certain basic scientifically demonstrated facts or not.
1. Do you accept that the Earth is ~4.5 billion years old? My answer: YES.
2. Do you accept that all life on Earth evolved from a single common ancestor? My answer: YES.
3. Do you accept that all life on Earth is based on chemical reactions most of which are contained within structures we call cells? My answer: YES
4. Do you know how life originated on Earth? My answer: NO.
If your answers to these questions differ from mine then we have some work to do because we cannot proceed until we both agree on the answers to these questions.
Reply: All these questions are irrelevant to elucidate if intelligence was most likely involved to create life, or not. They are secondary questions which I am ok to discuss, but I think the quest of an intelligent designer was involved or not, is the most important one, and suggest we stick to attempt to clarify it, and then eventually can move on to those raised by you.
The age of the earth says nothing in regards of the question if God was involved in creating life, or not. Neither if there was a common ancestor. While we do not have absolute certainty how the first life form emerged, the evidence leads us to a very clear answer: Most likely, intelligence was involved. I have already given the reasons, which you were not willing to consider. Please do so.
1. Living Cells store very complex genetic and epigenetic information through the genetic code, and over forty epigenetic languages, translation systems, and signaling networks. These information systems prescribe and instruct the making and operation of cells and multicellular organisms. The operation of cells is close to thermodynamic perfection, and its operation occurs analogously to computers. Cells ARE computers in a literal sense, using boolean logic. Each cell hosts millions of interconnected molecular machines, production lines and factories analogous to factories made by man. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks. Cells operate robot-like, autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advance and sophistication.
2. The origin of blueprints containing the instructional complex information, and the fabrication of complex machines and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup.
3. Therefore, the origin of biological information and self-replicating cell factories is best explained by the action of an intelligent designer, who created life for his own purposes.
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Miles: Once again I'm disappointed with your reply. Those questions are not irrelevant, they are the very foundation we MUST establish before proceeding.
Reply: I disagree. When life started, and if it started from a common ancestor, says nothing about HOW it started, to name, if intelligence was necessary to instantiate it, or not. THAT is the relevant question, and if you insist in elucidating secondary questions first, we are done.
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Miles: I appreciate the attempt to simplify the syllogism but in my opinion it is still something of a mess. As it is written I still don't think it works as a valid syllogism but I'll leave that for now because almost no part of it can be justified as true & that is a much bigger problem than the structure. I have copied it in blue below with my comments in black
1. Blueprints, instructional information and master plans, and the making of complex machines and factories upon these are both always tracked back to an intelligent source which made them for purposeful, specific goals.
This cannot be justified as true because you use the word "always". You can only use this word if you have knowledge of all things past & present in all universes.
Reply: The algorithmic origins of life
https://reasonandscience.catsboard.com/t3061-the-algorithmic-origins-of-life
1. Creating a recipe to make a cake is always a mental process. Creating a blueprint to make a machine is always a mental process.
2. To suggest that a physical process can create instructional assembly information, a recipe or a blueprint, is like suggesting that a throwing ink on paper will create a blueprint. It is never going to happen!
3. Physics and chemistry alone do not possess the tools to create a concept, or functional complex machines made of interlocked parts for specific purposes
4. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind.
5. DNA stores codified information to make proteins, and cells, which are chemical factories in a literal sense.
Miles: The statement would be true if it specified on Earth and up to the present day. Or you could say "in human experience". This may seem like nit picking but I'm really trying to help you here.
Reply: Unless you can disprove the statement, it stands. Resorting to an unknown mechanism is unjustified.
Miles: 2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signalling networks.
This statement is more of a problem. It is in my opinion completely untrue. Just the first six words "Biological cells are a factory park" are a complete untrut. Biological cells are not a factory park.
Reply: Are Cells factories in a literal sense?
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#4490
Each cell hosts a large number of Ribosome factories, therefore, the statement IS true.
Ribosome: Lessons of a molecular factory construction
https://link.springer.com/article/10.1134/S0026893314040116
Nucleolus: the ribosome factory
https://www.ncbi.nlm.nih.gov/pubmed/18712681
Ribosome: The cell city's factories
http://www.open.edu/openlearn/nature-environment/natural-history/ribosome-the-cell-citys-factories
In the cell, there are production lines, in this case, manufacturing new proteins of many different sorts. New goods and products are continually being manufactured from raw materials. In cities this takes place in workshops and factories. Raw materials are transformed, usually in a sequence of steps on a production line, into finished products. The process is governed by a clear set of instructions or specifications. In some cases the final products are for immediate or local use, in others they are packaged for export.
The Cell's Protein Factory in Action
What looks like a jumble of rubber bands and twisty ties is the ribosome, the cellular protein factory.
https://www.livescience.com/41863-ribosomes-protein-factory-nigms.html
Miles: They may share some superficial similarities with factory parks but they are utterly different entities with utterly different purposes.
Reply: Biological Cell factories point overwhelmingly to set up by intelligent design
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7761
- factory portals with fully automated security checkpoints and control ( membrane proteins )
- factory compartments ( organelles )
- a library index and fully automated information classification, storage, and retrieval program ( chromosomes, and the gene regulatory network )
- molecular computers, hardware ( DNA )
- software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes )
- information retrieval ( RNA polymerase )
- transmission ( messenger RNA )
- translation ( Ribosome )
- signaling ( hormones )
- complex machines ( proteins )
- taxis ( dynein, kinesin, transport vesicles )
- molecular highways ( tubulins, used by dynein and kinesin proteins for molecular transport to various destinations )
- tagging programs ( each protein has a tag, which is an amino acid sequence ) informing other molecular transport machines where to transport them.
- factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
- error check and repair systems ( exonucleolytic proofreading, strand-directed mismatch repair )
- recycling methods ( endocytic recycling )
- waste grinders and management ( Proteasome Garbage Grinders )
- power generating plants ( mitochondria )
- power turbines ( ATP synthase )
- electric circuits ( the metabolic network )
Miles: Furthermore you include properties of biological cells "self-replicating, directed by genes and epigenetic languages and signalling networks" that are not shared with factory parks so within the statement itself you demonstrate that biological cells are not the same as factory parks.
Reply: I am a machine designer. The flow of information goes from the engineering department to the factory, where factory workers read the blueprints, and upon the information assemble the machines and eventually, even build factories. That is analogous to what cells do, only that in the cell it happens fully autonomously. The entire process is fully preprogrammed. No direct intervention of intelligence is required.
The interdependent and irreducible structures required to make proteins
https://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins
Miles: This statement is also untrue. DNA is not a blueprint.
Reply: DNA - the instructional blueprint of life
https://reasonandscience.catsboard.com/t2544-dna-the-instructional-blueprint-of-life
Cells in our body make use of our DNA library to extract blueprints that contain the instructions to build structures and molecular machines called proteins.
https://www.mpg.de/16227844/0107-mozg-keeping-sperm-cells-on-track-151300-x?c=2249
Miles: While it is true that people make that analogy it is just an analogy. Furthermore DNA contains zero instructional information. It does contain information but that information is not instructional. I know many people find this difficult to grasp but nowhere in DNA is there an instruction for anything.
Reply: you said that you published science papers, and are a professional in the field, and make such an uninformed claim? I start to doubt that you have the credentials that you claim to have.
What does DNA do?
DNA provides instructions for making proteins
https://www.yourgenome.org/facts/what-does-dna-do
DNA Is Called The Blueprint Of Life: Here’s Why
OCTOBER 26, 2017
DNA is called the blueprint of life because it is the instruction manual to create, grow, function and reproduce life on Earth similar to a blueprint of a house. 10
https://sciencetrends.com/dna-called-blueprint-life-heres/
Miles: Some DNA sequences have the ability under certain circumstances to interact with certain proteins. That interaction may lead to transcription or blockage of transcription or increase in the rate of transcription or replication of the DNA etc but there is no instruction. DNA does not tell any other molecule what to do.
Reply: DNA carries the instructions necessary for your cells to produce proteins that affect many different processes and functions in your body.
https://www.healthline.com/health/what-is-dna
Miles: Molecules, DNA, RNA, proteins and others interact according to the laws of physics and chemistry.
Reply: Physical necessity & Physical laws
Stephen C.Meyer, The return of the God hypothesis, page 216:
Rather than having a genetic molecule capable of unlimited novelty, with all the unpredictable and aperiodic sequences that characterize informative texts, we would have a highly repetitive text awash in redundant sequences—much as happens in crystals. Indeed, in a crystal the forces of mutual chemical attraction do completely explain the sequential ordering of the constituent parts. Consequently, crystals cannot convey novel information. Bonding affinities, to the extent they exist, cannot be used to explain the origin of information. Self-organizing chemical affinities generate highly repetitive “order,” but not information; they create mantras, not messages
The nucleotide sequence of DNA and RNA have an instructional function to make proteins and is NOT random but complex and specified, and not due to physical necessity or physical laws. And this is what events in a prebiotic land would need to produce: a minimal set of proteins .... and this kind of specification does not arise through chemical reactions ...... the result of a chemical reaction is not random. But the events dealing with an eventual chemical reaction would have been if there was not a mind guiding the events.
Life's Irreducible Structure, Michael Polanyi
Science mag, 1968
In Galileo's experiments on balls rolling down a slope, the angle of the slope was not derived from the laws of mechanics, but was chosen by Galileo. And as this choice of slopes was extraneous to the laws of mechanics, so is the shape and manufacture of test tubes extraneous to the laws of chemistry. The same thing holds for machinelike boundaries; their structure cannot be defined in terms of the laws which they harness. Nor can a vocabulary determine the content of a text, and so on. Therefore, if the structure of living things is a set of boundary conditions, this structure is extraneous to the laws of physics and chemistry which the organism is harnessing. Thus the morphology of living things transcends the laws of physics and chemistry.the codelike structure of DNA must be assumed to have come about by a sequence of chance variations established by natural selection. But this evolutionary aspect is irrelevant here; whatever may be the origin of a DNA configuration, it can function as a code only if its order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words is on a printed page. As the arrangement of a printed page is extraneous to the chemistry of the printed page, so is the base sequence in a DNA molecule extraneous to the chemical forces at work in the DNA molecule. It is this physical indeterminacy of the sequence that produces the improbability of occurrence of any particular sequence and thereby enables it to have a meaning-a meaning that has a mathematically determinate information content equal to the numerical improbability of the arrangement.
A deterministic answer assumes that the laws of physics and chemistry have causally and sequentially determined the obligatory series of events leading from inanimate matter to life – that each step is causally linked to the previous one and to the next one by the laws of nature. In principle, in a strictly deterministic situation, the state of a system at any point in time determines the future behavior of the system – with no random influences. To invoke a guided determinism toward the formation of life would only make sense if the construction of life was demonstrably a preferential, highly probable natural pathway.
Luisi, The Emergence of Life; From Chemical Origins to Synthetic Biology, page 21
Just like computer codes, the genetic code is arbitrary. There is no law of physics that says “1” has to mean “on” and “0” has to mean “off.” There’s no law of physics that says 10000001 has to code for the letter “A.” Similarly, there is no law of physics that says three Guanine molecules in a row have to code for Glycine. In both cases, the communication system operates from a freely chosen, fixed set of rules.
In all communication systems it is possible to label the encoder, the message and the decoder and determine the rules of the code.
The rules of communication systems are defined in advance by conscious minds. There are no known exceptions to this. Therefore we have 100% inference that the Genetic Code was designed by a conscious mind.
Physical laws which result in physical constraints, where chemical reactions are forced into taking a certain course of action is an often cited possible mechanism for the origin of life.
We are moving from chemistry to biology. Henceforward, life, it goes without saying, is independent of its chemical substrate, and its evolution does not follow paths that are predictable solely based on the laws of physics.
M. Gargaud · H. Martin · P. López-García T. Montmerle · R. Pascal Young Sun, Early Earth and the Origins of Life, page 95
Laurent Boiteau Prebiotic Chemistry: From Simple Amphiphiles to Protocell Models, page 3:
Spontaneous self-assembly occurs when certain compounds associate through noncovalent hydrogen bonds, electrostatic forces, and nonpolar interactions that stabilize orderly arrangements of small and large molecules. The argument that chemical reactions in a primordial soup would not act upon pure chance, and that chemistry is not a matter of "random chance and coincidence, finds its refutation by the fact that the information stored in DNA is not constrained by chemistry. Yockey shows that the rules of any communication system are not derivable from the laws of physics. He continues: “there is nothing in the physicochemical world that remotely resembles reactions being determined by a sequence and codes between sequences.” In other words, nothing in nonliving physics or chemistry obeys symbolic instructions.
Ulrich E. Stegmann: The arbitrariness of the genetic code March 2004 5
Some of the processes expected to involve semantic information are certainly not chemically arbitrary and, therefore, chemical arbitrariness is not a necessary condition for a semantic relation.
Miles: Furthermore biological cells are not "made". A biological cell will under certain circumstances divide giving rise to two daughter cells which are usually very similar to the parent cell. In multicellular organisms cells interact and combine to form tissues and organs. Every single cell in every single organism on Earth today can trace its parental lineage back to one single cell that was formed on Earth ~4 billion years ago.
Reply: Common descent, the tree of life, a failed hypothesis
https://reasonandscience.catsboard.com/t2239-evolution-common-descent-the-tree-of-life-a-failed-hypothesis
1. The DNA replication machinery is not homologous in the 3 domains of life. The bacterial core replisome enzymes do not share a common ancestor with the analogous components in eukaryotes and archaea.
2. Bacteria and Archaea differ strikingly in the chemistry of their membrane lipids. Cell membrane phospholipids are synthesized by different, unrelated enzymes in bacteria and archaea, and yield chemically distinct membranes.
3. Sequences of glycolytic enzymes differ between Archaea and Bacteria/Eukaryotes. There is no evidence of a common ancestor for any of the four glycolytic kinases or of the seven enzymes that bind nucleotides.
4. There are at least six distinct autotrophic carbon fixation pathways. If common ancestry were true, an ancestral Wood–Ljungdahl pathway should have become life's one and only principle for biomass production.
5. There is a sharp divide in the organizational complexity of the cell between eukaryotes, which have complex intracellular compartmentalization, and even the most sophisticated prokaryotes (archaea and bacteria), which do not.
6. A typical eukaryotic cell is about 1,000-fold bigger by volume than a typical bacterium or archaeon, and functions under different physical principles: free diffusion has little role in eukaryotic cells but is crucial in prokaryotes
7. Subsequent massive sequencing of numerous, complete microbial genomes have revealed novel evolutionary phenomena, the most fundamental of these being: pervasive horizontal gene transfer (HGT), in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment) of the Tree of Life concept
8. RNA Polymerase differences: Prokaryotes only contain three different promoter elements: -10, -35 promoters, and upstream elements. Eukaryotes contain many different promoter elements
9. Ribosome and ribosome biogenesis differences: Although we could identify E. coli counterparts with comparable biochemical activity for 12 yeast ribosome biogenesis factors (RBFs), only 2 are known to participate in bacterial ribosome assembly. This indicates that the recruitment of individual proteins to this pathway has been largely independent in the bacterial and eukaryotic lineages. 22
10. Like the origins of DNA replication, the promoters of bacterial and yeast genes have different structures, are recognized by different proteins, and are not exchangeable. The absolute incompatibility between prokaryote (e.g., E. coli) and eukaryote (e.g., yeast) origins of replication and promoters, as well as DNA replication, transcription, and translation machinery, stands as a largely unrecognized challenge to the evolutionary view that the two share a common ancestor.
Miles: PS FYI epigenetics is still DNA
Reply: Where is the Talin code, the histone code, and the Glycan code stored ?
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Miles: "Each cell hosts a large number of Ribosome factories, therefore, the statement IS true. " The claim you made is that cells are factories not that ribosomes are factories but neither claim is true.
Reply: You need to pay more attention. I wrote: 2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics.
A cell can be compared to an entire park of interlinked factories.
Miles:
Factory: A factory, manufacturing plant or a production plant is an industrial site, often a complex consisting of several buildings filled with machinery, where workers manufacture items or operate machines which process each item into another Neither a biological cell nor a ribosome meets that definition or even gets close to it.
Reply: Go and look up the link. Many science papers describe cells as factories. So this is taken directly from the scientific literature
Are Cells factories in a literal sense?
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#4490
The Molecular Fabric of Cells BIOTOL, B.C. Currell and R C.E Dam-Mieras (Auth.)
The central theme of both of these texts is to consider cells as biological factories. Cells are, indeed, outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products. The range of products is quite remarkable and encompasses chemically simple compounds such as ethanol and carbon dioxide as well as extremely complex proteins, carbohydrates, lipids, nucleic acids, and secondary products.
There in your own reply is that word "analogous" again . So by your own admission the syllogism is now not valid because the conclusion does not follow as a logical consequence from the premise.
Miles: You also make it clear in this reply that cells are different to factories because they are fully autonomous and factories are not. When you consider organisms as a whole the degree of autonomy is even greater. That is because life is a completely different category of matter to anything else.
Reply: Herschel 1830 1987, p. 148:
“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”
Miles: they are still making an argument from incredulity. At least I hope it is incredulity.
Reply: "Incredulous" basically means "I don't believe it". Well, why should someone believe a "just so" story about HOW reality came to exist? That is the THING that we are incredulous about - a *certain scenario* ( naturalism, cosmological, chemical, and biological evolution, abiogenesis, and Neo-Darwinism, and that irreducibly complex biological system, coded, instructed or specified complex information, and entire factory complexes composed of myriads of interconnected factories, full of computers and robotic production lines could emerge naturally ) that's only *imagined* about how various amazing abilities of animals and plants happened all by themselves, defying known and reasonable principles of the limited range of chance, physical necessity, mutations, and Natural selection. There are busy little molecular machines that let it untangle, replicate, and build according to plan. A large cadre of researchers continues to make new discoveries on a regular basis. Our mythology is that it explains life, but the system is far, far too complex to occur by accident, and requires that features to support many processes are required, making a path for its evolution very hard to surmise. DNA isn't the secret to life. It's a whole bunch of puzzles we don't have answers for. The proponent of naturalism is "incredulous" that an intelligent creator/designer could exist, beyond and behind our entire space-time continuum, who is our Creator. But there is nothing ridiculous about that - especially if you can't personally examine reality to that depth - how do you know nature is all that exists? What IS ridiculous (IMO) is trying to imagine a *naturalistic origin* of these things. What we need, is giving a *plausible* account of how it came about to be in the first place, and the " No-God hypothesis" simply doesn't cut the cake.
Miles: some evidence can be consistent with more than one conclusion?
Reply: Eventually. That depends on case to case to be analyzed individually.
Just to be clear what I mean here is an example:
Miles: Evidence:- A person A’s fingerprints are found on a murder weapon (let’s say it is a knife and the murder was a stabbing).
Some conclusions consistent with this evidence :
a. Person A is the murderer.
b. Person A handled the weapon at some point but is not the murderer.
c. Person A’s fingerprints were transferred to the murder weapon by some technical method by the murderer or their accomplice in order to frame person A.
d. Some sort of magic or supernatural effect caused person A’s fingerprints to appear on the weapon.
All the conclusions above are consistent with the evidence but only one leads to the conclusion that A is the murderer so we need a method by which we can determine which conclusion is correct?
Reply: Agreed.
Miles: We might disregard conclusion d. , at least initially, on the grounds that is seems so improbable that it would be a waste of time to investigate this possibility but the scientific method does not disregard any possible conclusions as we will see.
The best/scientific method is to seek more evidence but there might be a great deal of irrelevant evidence that we could waste time gathering so the scientific way to proceed is to form one or more hypothesis and then try to disprove that hypothesis.
Hypothesis: Person A is the murderer.
Then we ask what novel predictions does this hypothesis generate and look for evidence that tells us whether those predictions are true. I don’t want to belabour the point but just for clarity I’ll give one more example: Prediction:- Person A was at the scene at the time of the murder. If we find evidence that person A was somewhere else at the time of the murder then we have essentially disproved the hypothesis that person A is the murderer. It is still possible to come up with conclusions like:
Person A can perform long distance telekinesis and used this unique attribute to stab the victim.
Person A built a machine that mechanically stabbed the victim with the knife & then dismantled it at a later time.
But these seem extremely unlikely and would only be worthy of consideration if we had very good other reasons to think they might be true.
So, we can now treat the conclusion that person A is the murderer as highly unlikely. Please note that we have not proved 100% that person A is NOT the murderer. We must still be open to the possibility that new evidence will come to light to indicate that they did in fact stab the victim but our investigation will now look for other possible murderers and try to disprove the hypothesis that each one of them is the murderer.
I’m sorry if that was a bit long winded but it outlines the way that I think evidence should be considered & conclusions reached. Do you agree?
Reply: Agreed. I think all options should be put on the table, and considered as a possibility. As a side note, that is one of my criticisms on the current philosophical framework around historical sciences.
Design is excluded a prior as a possible explanation of unique events that supposedly happened in the past. You can read more about it here:
Historical sciences, and methodological naturalism
https://reasonandscience.catsboard.com/t1692-historical-sciences-and-methodological-naturalism
Miles: My second point about evidence is that each piece of evidence must be examined separately to determine its validity. It is crucial that only valid evidence is considered when we form hypotheses and draw conclusions. Do you agree?
Reply: yes. Each phenomenon has to be analyzed individually.
Miles: To demonstrate this, consider the stabbing example above. The initial evidence was that person A’s fingerprints were found on the murder weapon. If we check this evidence and find that the fingerprint match is incorrect or has been overstated or misinterpreted in some way, we must reject the statement “Person A’s fingerprints were found on the murder weapon”. It does not matter that someone once said it was true. It does not matter that we once thought it was true. We have checked, it is not true & we must reject it. Again, I ask whether you agree?
Reply: yes. Agreed.
OK, so I hope you will be able to agree with both these points about evidence since they should not be controversial. There may be other issues over what we can consider to be evidence or how best to analyse evidence but they can be dealt with if and when they occur in our discussion.
Now that it seems we both agree in a basic sense about how to handle and test evidence, hypotheses & conclusions I think we should pick a subject and make a start. My choice would be:
The origin of life on Earth.
I’ll briefly set out my position on this matter and you can let me know whether you are happy to start here and perhaps reply by setting out your position briefly. Then we can start to pick out pieces of evidence to examine, hypotheses to test and see if we can agree on a conclusion.
So, my short answer to the question “How did life on Earth originate?” is to say I don’t know; in fact, I’d say no human past or present knows the answer to this question.
That may not seem very helpful so a longer answer would be that there seem to be several possible answers to this question as listed below:
1. Chemical reactions and physical processes on the Earth from ~4.5 billion years ago till ~3.8billion years ago gave rise to the formation of something that we can consider to be a basic single celled living organism.
2. A basic single celled living organism arrived on the Earth ~3.8 billion years ago either on a comet, meteor or spacecraft.
3. A highly advanced but natural being assembled a basic single celled living organism using purely natural methods.
4. A supernatural being created a basic single celled living organism using purely supernatural powers.
There may be other possibilities not listed here but these are the ones that I can think of that fit the scientifically verified facts we know to be most likely true about life on Earth today, the history of life on Earth & how the Earth was formed. Please feel free to add to this list if you think there is one or more, I have omitted.
I consider the biblical account of the origin of life on Earth to be demonstrably false. We can explore the reasons for my rejection of this account if you think it should be included in the list of possible answers.
I also reject all the other creation accounts that I have heard e.g., the Hindu lotus flower story on the same grounds as I reject the biblical creation story.
Miles: I will happily give you my opinions about these three subjects but first I must insist that you consider the list of options that I gave for the origin of life on Earth. Do you agree with my list of four options?
Reply: yes, I do.
Miles: Would you like to include any other options?
Reply: I think I regards to origins of life, there are basically just following options:
1. unguided random events
2. physical necessity
3. design
The possible mechanisms to explain the origin of life
https://reasonandscience.catsboard.com/t2515-abiogenesis-the-possible-mechanisms-to-explain-the-origin-of-life
Miles: The biblical account is accurate and true but God engineered the Earth to appear to be 4.5 billion years old and placed rock strata, fossils, radioisotopes, geomagnetic data, ERV DNA sequences and a host of other physical and biological markers in such a way that human beings in 2021AD might be fooled into thinking the Earth was 4.5 billion years old & life evolved from a single common ancestor.
Reply: The timeline, when all happened, is a different topic. So I don't want to entertain that quest right now.
Miles: As I said in my previous email, I do not know how life originated on Earth.
Reply: First of all, it is not about knowing in absolute terms. Nobody has a time machine to go back. I use inference to the best explanation.
BAYESIAN PROBABILITY AND SCIENCE
https://reasonandscience.catsboard.com/t2721-bayesian-probability-and-science
and I also think saying " I don't know is unwarranted".
Here is why:
When you see a blueprint of a factory, with the precise instructions to make all machines, subparts, how to assemble each machine, interconnect them into production lines, organized production compartments, gates to permit the right materials to get in, and the end products go through error check and repair, and export, and then see the functional factory-build precisely upon the blueprint which you saw previously, and the operation of the factory close to perfection, controlled and directed by computers, directing thousands of processes simultaneously and adapting the production output by its demands, but have no clue of how both, the blueprint, and the factory, came to be: What is the obvious answer:
a) That an intelligent team of engineers, machine designers, etc. made the project, and skilled, intelligent labor workers, carpenters, masons, electricians, machine builders, etc. constructed the factory, or
b) that natural forces somehow made the blueprint, and random unguided forces brought the building materials together, and by luck, the factory was assembled precisely based on the blueprint instructions and started its production ? or
c) you have no way to conclude anything meaningful and feel justified to say: " I don't know"?
Here is the argument:
The factory maker argument
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument
Life comes only from life. That has never been disproven. Therefore, that should in my view be the default position.
1. Living Cells store very complex genetic and epigenetic information through the genetic code, and over forty epigenetic languages, translation systems, and signaling networks. These information systems prescribe and instruct the making and operation of cells and multicellular organisms. The operation of cells is close to thermodynamic perfection, and its operation occurs analogously to computers. Cells ARE computers in a literal sense, using boolean logic. Each cell hosts millions of interconnected molecular machines, production lines and factories analogous to factories made by man. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks. Cells operate robot-like, autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advance and sophistication.
2. The origin of blueprints containing the instructional complex information, and the fabrication of complex machines and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup.
3. Therefore, the origin of biological information and self-replicating cell factories is best explained by the action of an intelligent designer, who created life for his own purposes.
==========================================================================================================================================
Miles: Unguided events do not have to be random. A chemical reaction is unguided but it is not random either. Unless you consider the physical laws to be the guiding agent which I would challenge because those laws are purely descriptive of our reality. I have no idea what you mean by physical necessity. I applaud the brevity of the phrase but that brevity is only useful if it conveys a clear meaning which, for me at least, it does not.
Reply: when I post a link, I do it for brevity's sake, in order for a reply not to be too long. But I recommend that you actually access the link , and read the information, because it is relevant to the topic, and elucidates what I mean.
Physical necessity & Physical laws
https://reasonandscience.catsboard.com/t2515-abiogenesis-the-possible-mechanisms-to-explain-the-origin-of-life
Stephen C. Meyer observed:
“There are neither bonds nor bonding affinities—differing in strength or otherwise—that can explain the origin of the base sequencing that constitutes the information in the DNA molecule”
(Signature in the Cell, 243).
As Paul Davies lamented,
“We are still left with the mystery of where biological information comes from.… If the normal laws of physics can’t inject information, and if we are ruling out miracles, then how can life be predetermined and inevitable rather than a freak accident? How is it possible to generate random complexity and specificity together in a lawlike manner? We always come back to that basic paradox”
(Fifth Miracle, 258).
A law of nature could not alone explain how life began, because no conceivable law would compel a legion of atoms to follow precisely a prescribed sequence of assemblage.
Paul Davies, The origin of Life, page 17
Werner Gitt summarized it this way:
“A necessary requirement for generating meaningful information is the ability to select from alternatives and this requires an intelligent, volitional entity.… Unguided, random processes cannot do this—not in any amount of time because this selection process demands continuous guidance by intelligent beings that have a purpose”
(Without Excuse, 50–51).
Miles: Design. OK, but design by who/what? I gave two design options one by a God and one by some advanced alien being/civilisation. Also, we need to be precise about the thing that was designed. In my opinion the only possibility considering other facts we know about the Earth and life we see today is a basic single celled organism. Do you agree?
Reply: We can reduce our investigation to either: An intelligent designer was involved to create life, or not. Physical necessity can be excluded, because
Luisi, The Emergence of Life; From Chemical Origins to Synthetic Biology, page 21
A deterministic answer assumes that the laws of physics and chemistry have causally and sequentially determined the obligatory series of events leading from inanimate matter to life – that each step is causally linked to the previous one and to the next one by the laws of nature. In principle, in a strictly deterministic situation, the state of a system at any point in time determines the future behavior of the system – with no random influences. To invoke a guided determinism toward the formation of life would only make sense if the construction of life was demonstrably a preferential, highly probable natural pathway.
We can also exclude aliens because that would demand an explanation of the origin of these folks as well. The identity of the designer can be left for an inquiry after it has been established, that design is the better causal agent rather than not.
Miles: The rest of your email, while interesting but mostly incorrect, is putting the cart before the horse.
Reply: Ok.
=========================================================================================================================================
Miles: I have proposed 5 possibilities, although I only proposed the 5th one for the sake of illustrating that all other possibilities seem somewhat absurd to me.
Reply: in regards to your example, I agree with all the options/possible explanations of the cause of the event. We want to elucidate if a designer is the most likely explanation of the origin of life, or not. As clarified in a previous email, physical necessity is not an option, since there is no necessity for nucleotides to line up in a specified complex order.
Miles: You have eventually made the statement "An intelligent designer was involved to create life, or not." which while true does not advance the discussion at all because it attempts to ignore the basic facts that we know about the Earth and life on Earth and leave open all manner of absurd ideas that will just waste a great deal of time.
Reply: I think it advances the discussion since we restrict the possible options to those which are really relevant.
Miles: Let me ask you a few simple questions. Please respond with short, ideally one word answers, so I can see whether we are starting from the same point or not. I have given my own one word answers to show how easy it is to answer these questions with a yes or no.
Please understand that I am not trying to avoid getting into the details,I just want to know whether you accept certain basic scientifically demonstrated facts or not.
1. Do you accept that the Earth is ~4.5 billion years old? My answer: YES.
2. Do you accept that all life on Earth evolved from a single common ancestor? My answer: YES.
3. Do you accept that all life on Earth is based on chemical reactions most of which are contained within structures we call cells? My answer: YES
4. Do you know how life originated on Earth? My answer: NO.
If your answers to these questions differ from mine then we have some work to do because we cannot proceed until we both agree on the answers to these questions.
Reply: All these questions are irrelevant to elucidate if intelligence was most likely involved to create life, or not. They are secondary questions which I am ok to discuss, but I think the quest of an intelligent designer was involved or not, is the most important one, and suggest we stick to attempt to clarify it, and then eventually can move on to those raised by you.
The age of the earth says nothing in regards of the question if God was involved in creating life, or not. Neither if there was a common ancestor. While we do not have absolute certainty how the first life form emerged, the evidence leads us to a very clear answer: Most likely, intelligence was involved. I have already given the reasons, which you were not willing to consider. Please do so.
1. Living Cells store very complex genetic and epigenetic information through the genetic code, and over forty epigenetic languages, translation systems, and signaling networks. These information systems prescribe and instruct the making and operation of cells and multicellular organisms. The operation of cells is close to thermodynamic perfection, and its operation occurs analogously to computers. Cells ARE computers in a literal sense, using boolean logic. Each cell hosts millions of interconnected molecular machines, production lines and factories analogous to factories made by man. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks. Cells operate robot-like, autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advance and sophistication.
2. The origin of blueprints containing the instructional complex information, and the fabrication of complex machines and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup.
3. Therefore, the origin of biological information and self-replicating cell factories is best explained by the action of an intelligent designer, who created life for his own purposes.
===========================================================================================================================================
Miles: Once again I'm disappointed with your reply. Those questions are not irrelevant, they are the very foundation we MUST establish before proceeding.
Reply: I disagree. When life started, and if it started from a common ancestor, says nothing about HOW it started, to name, if intelligence was necessary to instantiate it, or not. THAT is the relevant question, and if you insist in elucidating secondary questions first, we are done.
===========================================================================================================================================
Miles: I appreciate the attempt to simplify the syllogism but in my opinion it is still something of a mess. As it is written I still don't think it works as a valid syllogism but I'll leave that for now because almost no part of it can be justified as true & that is a much bigger problem than the structure. I have copied it in blue below with my comments in black
1. Blueprints, instructional information and master plans, and the making of complex machines and factories upon these are both always tracked back to an intelligent source which made them for purposeful, specific goals.
This cannot be justified as true because you use the word "always". You can only use this word if you have knowledge of all things past & present in all universes.
Reply: The algorithmic origins of life
https://reasonandscience.catsboard.com/t3061-the-algorithmic-origins-of-life
1. Creating a recipe to make a cake is always a mental process. Creating a blueprint to make a machine is always a mental process.
2. To suggest that a physical process can create instructional assembly information, a recipe or a blueprint, is like suggesting that a throwing ink on paper will create a blueprint. It is never going to happen!
3. Physics and chemistry alone do not possess the tools to create a concept, or functional complex machines made of interlocked parts for specific purposes
4. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind.
5. DNA stores codified information to make proteins, and cells, which are chemical factories in a literal sense.
Miles: The statement would be true if it specified on Earth and up to the present day. Or you could say "in human experience". This may seem like nit picking but I'm really trying to help you here.
Reply: Unless you can disprove the statement, it stands. Resorting to an unknown mechanism is unjustified.
Miles: 2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signalling networks.
This statement is more of a problem. It is in my opinion completely untrue. Just the first six words "Biological cells are a factory park" are a complete untrut. Biological cells are not a factory park.
Reply: Are Cells factories in a literal sense?
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#4490
Each cell hosts a large number of Ribosome factories, therefore, the statement IS true.
Ribosome: Lessons of a molecular factory construction
https://link.springer.com/article/10.1134/S0026893314040116
Nucleolus: the ribosome factory
https://www.ncbi.nlm.nih.gov/pubmed/18712681
Ribosome: The cell city's factories
http://www.open.edu/openlearn/nature-environment/natural-history/ribosome-the-cell-citys-factories
In the cell, there are production lines, in this case, manufacturing new proteins of many different sorts. New goods and products are continually being manufactured from raw materials. In cities this takes place in workshops and factories. Raw materials are transformed, usually in a sequence of steps on a production line, into finished products. The process is governed by a clear set of instructions or specifications. In some cases the final products are for immediate or local use, in others they are packaged for export.
The Cell's Protein Factory in Action
What looks like a jumble of rubber bands and twisty ties is the ribosome, the cellular protein factory.
https://www.livescience.com/41863-ribosomes-protein-factory-nigms.html
Miles: They may share some superficial similarities with factory parks but they are utterly different entities with utterly different purposes.
Reply: Biological Cell factories point overwhelmingly to set up by intelligent design
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7761
- factory portals with fully automated security checkpoints and control ( membrane proteins )
- factory compartments ( organelles )
- a library index and fully automated information classification, storage, and retrieval program ( chromosomes, and the gene regulatory network )
- molecular computers, hardware ( DNA )
- software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes )
- information retrieval ( RNA polymerase )
- transmission ( messenger RNA )
- translation ( Ribosome )
- signaling ( hormones )
- complex machines ( proteins )
- taxis ( dynein, kinesin, transport vesicles )
- molecular highways ( tubulins, used by dynein and kinesin proteins for molecular transport to various destinations )
- tagging programs ( each protein has a tag, which is an amino acid sequence ) informing other molecular transport machines where to transport them.
- factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
- error check and repair systems ( exonucleolytic proofreading, strand-directed mismatch repair )
- recycling methods ( endocytic recycling )
- waste grinders and management ( Proteasome Garbage Grinders )
- power generating plants ( mitochondria )
- power turbines ( ATP synthase )
- electric circuits ( the metabolic network )
Miles: Furthermore you include properties of biological cells "self-replicating, directed by genes and epigenetic languages and signalling networks" that are not shared with factory parks so within the statement itself you demonstrate that biological cells are not the same as factory parks.
Reply: I am a machine designer. The flow of information goes from the engineering department to the factory, where factory workers read the blueprints, and upon the information assemble the machines and eventually, even build factories. That is analogous to what cells do, only that in the cell it happens fully autonomously. The entire process is fully preprogrammed. No direct intervention of intelligence is required.
The interdependent and irreducible structures required to make proteins
https://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins
Miles: This statement is also untrue. DNA is not a blueprint.
Reply: DNA - the instructional blueprint of life
https://reasonandscience.catsboard.com/t2544-dna-the-instructional-blueprint-of-life
Cells in our body make use of our DNA library to extract blueprints that contain the instructions to build structures and molecular machines called proteins.
https://www.mpg.de/16227844/0107-mozg-keeping-sperm-cells-on-track-151300-x?c=2249
Miles: While it is true that people make that analogy it is just an analogy. Furthermore DNA contains zero instructional information. It does contain information but that information is not instructional. I know many people find this difficult to grasp but nowhere in DNA is there an instruction for anything.
Reply: you said that you published science papers, and are a professional in the field, and make such an uninformed claim? I start to doubt that you have the credentials that you claim to have.
What does DNA do?
DNA provides instructions for making proteins
https://www.yourgenome.org/facts/what-does-dna-do
DNA Is Called The Blueprint Of Life: Here’s Why
OCTOBER 26, 2017
DNA is called the blueprint of life because it is the instruction manual to create, grow, function and reproduce life on Earth similar to a blueprint of a house. 10
https://sciencetrends.com/dna-called-blueprint-life-heres/
Miles: Some DNA sequences have the ability under certain circumstances to interact with certain proteins. That interaction may lead to transcription or blockage of transcription or increase in the rate of transcription or replication of the DNA etc but there is no instruction. DNA does not tell any other molecule what to do.
Reply: DNA carries the instructions necessary for your cells to produce proteins that affect many different processes and functions in your body.
https://www.healthline.com/health/what-is-dna
Miles: Molecules, DNA, RNA, proteins and others interact according to the laws of physics and chemistry.
Reply: Physical necessity & Physical laws
Stephen C.Meyer, The return of the God hypothesis, page 216:
Rather than having a genetic molecule capable of unlimited novelty, with all the unpredictable and aperiodic sequences that characterize informative texts, we would have a highly repetitive text awash in redundant sequences—much as happens in crystals. Indeed, in a crystal the forces of mutual chemical attraction do completely explain the sequential ordering of the constituent parts. Consequently, crystals cannot convey novel information. Bonding affinities, to the extent they exist, cannot be used to explain the origin of information. Self-organizing chemical affinities generate highly repetitive “order,” but not information; they create mantras, not messages
The nucleotide sequence of DNA and RNA have an instructional function to make proteins and is NOT random but complex and specified, and not due to physical necessity or physical laws. And this is what events in a prebiotic land would need to produce: a minimal set of proteins .... and this kind of specification does not arise through chemical reactions ...... the result of a chemical reaction is not random. But the events dealing with an eventual chemical reaction would have been if there was not a mind guiding the events.
Life's Irreducible Structure, Michael Polanyi
Science mag, 1968
In Galileo's experiments on balls rolling down a slope, the angle of the slope was not derived from the laws of mechanics, but was chosen by Galileo. And as this choice of slopes was extraneous to the laws of mechanics, so is the shape and manufacture of test tubes extraneous to the laws of chemistry. The same thing holds for machinelike boundaries; their structure cannot be defined in terms of the laws which they harness. Nor can a vocabulary determine the content of a text, and so on. Therefore, if the structure of living things is a set of boundary conditions, this structure is extraneous to the laws of physics and chemistry which the organism is harnessing. Thus the morphology of living things transcends the laws of physics and chemistry.the codelike structure of DNA must be assumed to have come about by a sequence of chance variations established by natural selection. But this evolutionary aspect is irrelevant here; whatever may be the origin of a DNA configuration, it can function as a code only if its order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words is on a printed page. As the arrangement of a printed page is extraneous to the chemistry of the printed page, so is the base sequence in a DNA molecule extraneous to the chemical forces at work in the DNA molecule. It is this physical indeterminacy of the sequence that produces the improbability of occurrence of any particular sequence and thereby enables it to have a meaning-a meaning that has a mathematically determinate information content equal to the numerical improbability of the arrangement.
A deterministic answer assumes that the laws of physics and chemistry have causally and sequentially determined the obligatory series of events leading from inanimate matter to life – that each step is causally linked to the previous one and to the next one by the laws of nature. In principle, in a strictly deterministic situation, the state of a system at any point in time determines the future behavior of the system – with no random influences. To invoke a guided determinism toward the formation of life would only make sense if the construction of life was demonstrably a preferential, highly probable natural pathway.
Luisi, The Emergence of Life; From Chemical Origins to Synthetic Biology, page 21
Just like computer codes, the genetic code is arbitrary. There is no law of physics that says “1” has to mean “on” and “0” has to mean “off.” There’s no law of physics that says 10000001 has to code for the letter “A.” Similarly, there is no law of physics that says three Guanine molecules in a row have to code for Glycine. In both cases, the communication system operates from a freely chosen, fixed set of rules.
In all communication systems it is possible to label the encoder, the message and the decoder and determine the rules of the code.
The rules of communication systems are defined in advance by conscious minds. There are no known exceptions to this. Therefore we have 100% inference that the Genetic Code was designed by a conscious mind.
Physical laws which result in physical constraints, where chemical reactions are forced into taking a certain course of action is an often cited possible mechanism for the origin of life.
We are moving from chemistry to biology. Henceforward, life, it goes without saying, is independent of its chemical substrate, and its evolution does not follow paths that are predictable solely based on the laws of physics.
M. Gargaud · H. Martin · P. López-García T. Montmerle · R. Pascal Young Sun, Early Earth and the Origins of Life, page 95
Laurent Boiteau Prebiotic Chemistry: From Simple Amphiphiles to Protocell Models, page 3:
Spontaneous self-assembly occurs when certain compounds associate through noncovalent hydrogen bonds, electrostatic forces, and nonpolar interactions that stabilize orderly arrangements of small and large molecules. The argument that chemical reactions in a primordial soup would not act upon pure chance, and that chemistry is not a matter of "random chance and coincidence, finds its refutation by the fact that the information stored in DNA is not constrained by chemistry. Yockey shows that the rules of any communication system are not derivable from the laws of physics. He continues: “there is nothing in the physicochemical world that remotely resembles reactions being determined by a sequence and codes between sequences.” In other words, nothing in nonliving physics or chemistry obeys symbolic instructions.
Ulrich E. Stegmann: The arbitrariness of the genetic code March 2004 5
Some of the processes expected to involve semantic information are certainly not chemically arbitrary and, therefore, chemical arbitrariness is not a necessary condition for a semantic relation.
Miles: Furthermore biological cells are not "made". A biological cell will under certain circumstances divide giving rise to two daughter cells which are usually very similar to the parent cell. In multicellular organisms cells interact and combine to form tissues and organs. Every single cell in every single organism on Earth today can trace its parental lineage back to one single cell that was formed on Earth ~4 billion years ago.
Reply: Common descent, the tree of life, a failed hypothesis
https://reasonandscience.catsboard.com/t2239-evolution-common-descent-the-tree-of-life-a-failed-hypothesis
1. The DNA replication machinery is not homologous in the 3 domains of life. The bacterial core replisome enzymes do not share a common ancestor with the analogous components in eukaryotes and archaea.
2. Bacteria and Archaea differ strikingly in the chemistry of their membrane lipids. Cell membrane phospholipids are synthesized by different, unrelated enzymes in bacteria and archaea, and yield chemically distinct membranes.
3. Sequences of glycolytic enzymes differ between Archaea and Bacteria/Eukaryotes. There is no evidence of a common ancestor for any of the four glycolytic kinases or of the seven enzymes that bind nucleotides.
4. There are at least six distinct autotrophic carbon fixation pathways. If common ancestry were true, an ancestral Wood–Ljungdahl pathway should have become life's one and only principle for biomass production.
5. There is a sharp divide in the organizational complexity of the cell between eukaryotes, which have complex intracellular compartmentalization, and even the most sophisticated prokaryotes (archaea and bacteria), which do not.
6. A typical eukaryotic cell is about 1,000-fold bigger by volume than a typical bacterium or archaeon, and functions under different physical principles: free diffusion has little role in eukaryotic cells but is crucial in prokaryotes
7. Subsequent massive sequencing of numerous, complete microbial genomes have revealed novel evolutionary phenomena, the most fundamental of these being: pervasive horizontal gene transfer (HGT), in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment) of the Tree of Life concept
8. RNA Polymerase differences: Prokaryotes only contain three different promoter elements: -10, -35 promoters, and upstream elements. Eukaryotes contain many different promoter elements
9. Ribosome and ribosome biogenesis differences: Although we could identify E. coli counterparts with comparable biochemical activity for 12 yeast ribosome biogenesis factors (RBFs), only 2 are known to participate in bacterial ribosome assembly. This indicates that the recruitment of individual proteins to this pathway has been largely independent in the bacterial and eukaryotic lineages. 22
10. Like the origins of DNA replication, the promoters of bacterial and yeast genes have different structures, are recognized by different proteins, and are not exchangeable. The absolute incompatibility between prokaryote (e.g., E. coli) and eukaryote (e.g., yeast) origins of replication and promoters, as well as DNA replication, transcription, and translation machinery, stands as a largely unrecognized challenge to the evolutionary view that the two share a common ancestor.
Miles: PS FYI epigenetics is still DNA
Reply: Where is the Talin code, the histone code, and the Glycan code stored ?
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Miles: "Each cell hosts a large number of Ribosome factories, therefore, the statement IS true. " The claim you made is that cells are factories not that ribosomes are factories but neither claim is true.
Reply: You need to pay more attention. I wrote: 2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics.
A cell can be compared to an entire park of interlinked factories.
Miles:
Factory: A factory, manufacturing plant or a production plant is an industrial site, often a complex consisting of several buildings filled with machinery, where workers manufacture items or operate machines which process each item into another Neither a biological cell nor a ribosome meets that definition or even gets close to it.
Reply: Go and look up the link. Many science papers describe cells as factories. So this is taken directly from the scientific literature
Are Cells factories in a literal sense?
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#4490
The Molecular Fabric of Cells BIOTOL, B.C. Currell and R C.E Dam-Mieras (Auth.)
The central theme of both of these texts is to consider cells as biological factories. Cells are, indeed, outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products. The range of products is quite remarkable and encompasses chemically simple compounds such as ethanol and carbon dioxide as well as extremely complex proteins, carbohydrates, lipids, nucleic acids, and secondary products.
There in your own reply is that word "analogous" again . So by your own admission the syllogism is now not valid because the conclusion does not follow as a logical consequence from the premise.
Miles: You also make it clear in this reply that cells are different to factories because they are fully autonomous and factories are not. When you consider organisms as a whole the degree of autonomy is even greater. That is because life is a completely different category of matter to anything else.
Reply: Herschel 1830 1987, p. 148:
“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”
Miles: they are still making an argument from incredulity. At least I hope it is incredulity.
Reply: "Incredulous" basically means "I don't believe it". Well, why should someone believe a "just so" story about HOW reality came to exist? That is the THING that we are incredulous about - a *certain scenario* ( naturalism, cosmological, chemical, and biological evolution, abiogenesis, and Neo-Darwinism, and that irreducibly complex biological system, coded, instructed or specified complex information, and entire factory complexes composed of myriads of interconnected factories, full of computers and robotic production lines could emerge naturally ) that's only *imagined* about how various amazing abilities of animals and plants happened all by themselves, defying known and reasonable principles of the limited range of chance, physical necessity, mutations, and Natural selection. There are busy little molecular machines that let it untangle, replicate, and build according to plan. A large cadre of researchers continues to make new discoveries on a regular basis. Our mythology is that it explains life, but the system is far, far too complex to occur by accident, and requires that features to support many processes are required, making a path for its evolution very hard to surmise. DNA isn't the secret to life. It's a whole bunch of puzzles we don't have answers for. The proponent of naturalism is "incredulous" that an intelligent creator/designer could exist, beyond and behind our entire space-time continuum, who is our Creator. But there is nothing ridiculous about that - especially if you can't personally examine reality to that depth - how do you know nature is all that exists? What IS ridiculous (IMO) is trying to imagine a *naturalistic origin* of these things. What we need, is giving a *plausible* account of how it came about to be in the first place, and the " No-God hypothesis" simply doesn't cut the cake.
