The Physics of Life versus Evolution 2.0

 

 

KI: State of science

1. P:011: I also found an immense chasm (chasm - a deep fissure in the earth, rock or another surface) between the version of evolution you find in the bookstore and what practising biologists understand evolution to be.
   YES: I agree with Perry. A lot of concepts used in life sciences are defined illogically and inconsistently. The first and very spectacular example is the definiendum of "evolution" - the fundamental concept to biology and life sciences. You can find around 20 very different definienda of this concept. Here are some examples from well-known dictionaries:

   1. any process of formation or growth; development.
   2. descent with modification from preexisting species.
   3. the change in the heritable characteristics of biological populations over successive generations.
   4. a process of gradual, peaceful, progressive change or development, as in social or economic structure or institutions.
   5. the change in the gene pool of a population from generation to generation by such processes as mutation, natural selection, and genetic drift.
   6. a motion incomplete in itself, but combining with coordinated motions to produce a single action, as in a machine.
   7. a pattern formed by or as if by a series of movements.
   8. a process of change in a certain direction.
   9. a process of gradual change that takes place over many generations, during which species of animals, plants, or insects slowly change some of their physical characteristics.
   10. the historical development of a biological group.
   11. one of a set of prescribed movements.
   12. the extraction of a mathematical root.

   This shows that science cannot provide a consistent model of life processes. I love this expression: "what practising biologists understand evolution to be" - I think the precise definition of evolution should be a starting point of any book devoted to life processes. To anyone I strongly reccomend to try to create a definition of evolution. All sources are available. But the definition should be understandable, logical and consistent, and the author should be proud of it and ready to defend it's any word. You will enjoy doing this!

2. P:011: Industries become incestuous {inˈsesCHo͞oəs} as they age (incestuous - excessively close and resistant to outside influence). They resist change because change threatens the status quo. Since all professions are run by good old boy clubs, innovations almost never come from the inside.
   
   For example, Bill Gates was a complete outsider to the computer business. Larry and Sergey, founders of Google, were newcomers to the search engine game. (Early on, they tried to sell their search technology to Yahoo! For $1 million, but Yahoo! turned them down).
   
   Fred Smith, founder of Federal Express, was a virgin in the shipping industry. Ray Kroc of McDonald's wasn't a restaurant veteran; he was a milkshake machine salesman. Lou Gerstner, who engineered a turnaround at IBM, had come from Nabisco and American Express. Before Jack Welch transformed GE, he was a chemical engineer.
   
   Mathematician and quantum physicist Barbara Shipman, a University of Rochester researcher, noticed that the shape of the honeybee’s dance closely mimics something in physics called the flag manifold. Benjamin Franklin, a printer and statesman, discovered that lightning comes from electricity. George Simon Ohm, who discovered "Ohm's law" of electricity, was a schoolteacher. Charles Darwin was a medical school dropout studying for the ministry when he took his famous trip to the Galapagos Islands on the HMS Beagle.
   
   Novel approaches usually come from outsiders. All these people had an outsider's point of view that enabled them to see something to which insiders were blind.

   YES: the scientific community is very incestuous and naturally opposes new ideas. In Poland, we have an expression: a circle of mutual adoration.
   There are two very interesting books "The Unnatural Nature of Science" by Lewis Wolpert and "The art of scientific investigation" by W.I.B Beveridge. Both authors describe how new ideas enter into the scientific community. As Beveridge said in his book, "the reception of an original contribution to knowledge may be divided into three phases:
   - during the first it is ridiculed as not true, impossible or useless;
   - during the second, people say there may be something in it but it would never be of any practical use;
   - and in the third and final phase, when the discovery has received general recognition, there are usually people who say that it is not original and has been anticipated by others".

   It seems that obstruction for novelty is a natural characteristic of the scientific community. When Galileo made his famous experiment with falling bodies, contemporary scientists rejected this fact because they were programmed by already acquired knowledge. The same happened with the rediscovery of cooperation in the living world (which was described by Russian scientists just after Darwin published his opus magnum) by Lynn Margulis. Her new thesis underwent three of Beveridge's stages. But what is really sad, and brings shame to the scientific community, nobody even tried to incorporate endosymbiosis into Darwinism. Nobody. It still remains an issue today, as pointed out in Evolution 2.0. Even now we can find in the bestsellers list of life such expressions as: "It is not struggle it is cooperation". Confusingly, we are unable to read that biological evolution may be both competitive and cooperative.

   This list of influential people who had no formal education only confirms the weakness of the scientific community. "What are the causative factors which generate this incestuousness?" - one may ask. I think that one reason for this is that no one really needs a true theory of life. All branches of science which help to win a war or earn money are developing very fast. The answer to the questions "How life emerged?" and "What is life?", regardless of how intriguing it may be, will not help to win a war. Other factors are: the way of financing researchers and the bad system of evaluation of products made by scientists - but these are to discuss in another book.

   Because of this innate feature of the scientific community, life processes are so poorly defined that educated people, like Perry, cannot fully understand them and scientists cannot fully explain them.

   So what should a person, who desperately wants to know what life really means, do?

   They can study for 20 years, finding obscure titles and previously unheard of scientists… or study the consistent model of life described in "The 59 keys for understanding the beginning of life".

3. P:081:
   Semmelweis was declined reappointment at the Vienna hospital in 1849. He moved to Hungary, where he took a position in a maternity ward. There, mortality rates also fell dramatically.
   Word of Semmelweis’ success spread across Europe… and so did opposition to his ideas.
   […]
   The term Semmelweis reflex refers to new knowledge being rejected because it overturns entrenched norms, popular beliefs and accepted paradigms.

4. P:086: People schooled in the Darwinian paradigm are blind to the import of McClintock's work

   YES. A good example of this is the book by Pier Luigi Luisi "The Emergence of Life - From Chemical Origins to Synthetic Biology" (2nd Edition) Cambridge University Press which was published in 2016. A reader may expect that from such an honourable publisher the information contained within would be as complete as possible and would delife what was promised in the title.

   It is undeniable that the book is a gathering of a vast number of items, but it is a typical product of the scientific community. A lot of quotes, all the reviews are positive, but no conclusions. Astonishingly, there was mentioned of mathematical game theory even though it has been into the life sciences decades ago. By refusing the importance of McClintock's work, the scientifioc community has shown that it is unwilling to change to new ideas and, is in fact, novelty-proof.

5. P:131: Darwin's version of evolution was admirable for its time. But as you can see now, his work i largely outdated. Worse yet, Darwin's theory experienced an immense setback in the 1930s with the Neo-Darwinian assumption of random copying errors. Darwinism has progressed from benign to destructive as Darwin's successors have consistently suppressed and torpedoed superior models.
   

6. P:217: scientists struggle to even agree on life's definition
   

7. P:000:
   

 

 

 

KI: Characteristics of mutations

1. P:033: A functional theory of evolution would require some other system to get the kind of mutations they were looking for, since "random" wasn't cutting it. Could there be specific types of mutations that performed certain evolutionary operations? Perhaps fruit flies don't progress by random copying errors, but by some other formula? What would that formula look like? I need to find out.

2. P:075: Yes, there is surely some vanishing small number of beneficial mutations that were generated by random accidental copying errors. But there's no way to be certain they were random. Experimentally, they're as rare as blasting fruit flies with radiation and getting a new species. […] Random mutations are philosophical and metaphysical assertions, not provable scientific theory. […] Only by proposing that the mutations afren't random, but rather follow some sort of formula or pattern. Then and only then can we have a properly scientific theory of evolution.

3. P:087: Does Transposition contradict Neo-Darwinism? If we're going to use consistent terminology, yes, it does. Neo-Darwinism by definition says: evolutionary changes are caused by random mutations and genetic drift.

4. P:088: Shapiro described life's adaptive formula as a "hierarchical operation of cellular control regimes" (665), and the cell itself as "systems all the way down" (666). He continued: "There are piecemeal coding sequences, expression signals, splicing signals, regulatory signals, epigenetic formatting signals, and many other 'DNA elements' ... that participate in the multiple functions involved in genome expression, replication, transmission, repair and evolution."
   After his talk, a smaller group huddled around him in the Fermilab cafeteria, peppering him with questions. Suddenly one guy "got" what dr Shapiro had been saying all night long.
   "You mean the mutations aren't random?" he asked.
   "No sir," replied dr Shapiro, "they are not random at all. When bacteria are comfortable, some mutations cannot be found in over ten billion cells. But when they're starving, the mutation frequency can go by a factor of > 100,000-fold and they develop new adaptations so they can survive" (658)
   Cell are capable of doing their own genetic engineering - a natural version of what scientists do in experiments in labs.

5. P:139: These findings build our confidence that progress is driven by adaptive mutations - modular reengineering of genes and chromosomes - not by random copyig errors.
   I don't know who insists more on random copyig errors, Marshall or Neo-Darwinists? Biological evolution could gradually change the mechanism changing the genetic design. On the beginning it was pure randomnes, later this mechanism could acquire some characteristics. But I am strongly convinced that randomness belongs to this characteristics. Randomnes may not only operate on single base pairs but also on blocks of base pairs.

6. P:259: Mutations aren't random, they're goal directed.
   Evolution 2.0 events reverse information entropy. The actions cells take to comunicate wich each other, edit their genomes, engage in symbiotic relationships, exchange DNA with other cells, and formhybrids increase information and order in the universe. Novelty comes from the cells themselves.
   

7. P:
   

 

 

 

KI: Information theory

1. P:057: It is common in information systems jargon to say that data only becomes information after meaning is assigned to it. In DNA, the ribosomes assign meaning to the code in messenger RNA. The message in DNA is meaningful because the cell has a system for understanding it.
   YES & NO: By saying "data only becomes information after meaning is assignet to it" the author suggests an "outside action". He programmes the readers mind that there sould be something or someone that performs the action of assignment. Yet information can emerge spontaneously and can be spontaneously interpreted too.

2. P:076: ... mice and humans sharing 99% of the same genes

3. P:167: Only about 3 percent of the genome codes for proteins.

4. P:182: "Spontaneously",... "go on to produce", ... "mutation via faults in replication", ... "We have evolution!" is the RNA hypothesis in a nutshell, but it contains no mention of code at all.
   The preceeding explanation moght soun okay until you remember that a digital code must be established before any kind of self-replication can be possible. A code will only function in the context of an encoder and decoder. Plus, amino acids aren't code. A string of nucleotides all by itself is not a code.
   Chemicals all by themselves don't communicate. No one has ever demonstrated that chemical reactions alone can generate codes.

5. P:205: Information is a set of rules that operate in addition to the laws of physics.

6. P:217: Design is when an idea precedes its embodiment.

7. P:238: The same program provides unique instructions to the several hundred different types of cells in the human body; it dictates their relationship to each other in three-dimensional space to make organs, as well as in a fourth dimension, the timeline of growth and development.

8. P:00:

 

 

 

KI: Life emergence

1. P:058: Messenger RNA is strings of code, generated by an encoder (RNA polymerase). This leaves us with the obvious mystery. Where did the original code in the DNA strand come from?
   

2. P:179: Dawkins at the time was a professor at Oxford University. One of his admirers had created a special endowment for him, The Charles Simyoni Chair for the Public Understanding of Science.
   One of the callers asked Dawkins about the Origin of Life. He replied that it was “a happy chemical accident”.
   A happy chemical accident?
   What kind of answer was that? And this is Oxford's "Professor of the Public Understanding of Science”?!
   What if Isaac Newton had watched the apple fall out of the tree, and instead of formulating a theory of gravity, he had proclaimed it happy accident? I was shocked Dawkins didn’t get laughed right out of the studio.

3. P:180: Most theorists put replication before protein synthesis, but you can't have one without the other.

4. P:181: As a communication engineer, my objection to the RNA hypothesis is that to evolve any kind of cell, RNA would have to self-replicate. But the RNA strand formation you read about in the literature is not code-based self-replication. It is similar to crystal growth, which does not use codes at all!
   RNA strand formation in a chemical lab is not in any way, shape, or form the same as DNA transcription and translation. In DNA transcription and translation, in order to convert code to proteins, you need a ribosome to transcribe the message. But in order to have a ribosome you have to have a plan for building a ribosome first. A ribosome is partly made from RNA. So before that, you have to have a code in the RNA.
   Many books and papers on the Origin of Life only discuss the assembly of the chemicals themselves. Nothing we know about chemicals tells us where codes come from.

5. P:192: All codes are created by a concious mind; there is no natural process known to science that creates coded information.
   […]
   If you want to dismiss the ideao of design in biology, you have to demonstrate where information comes from first.

6. P:203: So far as anyone knows, information is not an emergent property of matter.

7. P:205: But I could find no formula or transformation that turns matter or energy into inforamtion. This is pecisely what the Evolution 2.0 Prize seeks to discover.

8. P:00:

 

 

 

KI: Creation of novelty

1. P:072: For many decades the Neo-Darwinian Modern Synthesis has claimed that adding noise to a signal can occasionally impróve its content. Beneficial random mutations, together with natural selection, were allegedly the key for everything. If this were actually the case, I would have to agree that Mother Nature would possess a truly amazing built-in tool of continuous improvement.
   

2. P:259: The actions cells take to comunicate wich each other, edit their genomes, engage in symbiotic relationships, exchange DNA with other cells, and formhybrids increase information and order in the universe. Novelty comes from the cells themselves.
   

3. P:00:

 

 

 

KI: Way of thinking

1. P:047: Many standard terms in biology are simplistic and misleading. […] Turks had dozens of words for tactile sensations that we have no equivalent for in English. Our vocabulary for the genome is similarly limited. Narrow language limits our thinking.
   YES: our vocabulary for life is similarly limited. A huge ammount of concepts still remain undefined. Inuits have around 40 to 50 words for snow (eg.: Qanik: snow falling; Aputi: snow on the ground; Aniu: Snow used to make water). Swedes have about 25 (eg.: Blötsnö – wet, slushy snow; Drivsnö – snow that is blown into troublesome snow drifts; Aprilsnö – snow in April, according to suspicion signifies plenty of food for the coming season; Hårdsnö – compacted hard snow; Konstsnö – artificial snow; Kramsnö – squeezy snow, perfect for making snowballs; Julesnö – snow at Christmas; Klabbsnö – wet, warm snow for building snowmen). Samis have about 180 (eg.: Guoldu- “A cloud of snow which blows up from the ground when there is a hard frost without very much wind.”; Skava- Very thin layer of frozen snow; Skavvi- “Crust of ice on snow, formed in the evening after the sun has thawed the top of the snow during the day.”; Soavli- Slushy snow). Scots - 421 [Source]
   Imagine now how a Scotsman can discuss with a Tanzanian about snow or different stages of frozen water. It is very difficult to understand something new if we don't have the appropriate models in our minds. Nor do we have models of the compounds of this "something" or the processes which influence it.
   Because of this we need to create or discover new concepts and explain them in a logical and consistent way. As an example, here are a few new terms from The Physics of Life: evolutionary ratchet, resergy and pursuance.
   Moreover, some terms which seem to be understood very well need to be redefined and clarified. One such term is information, which will be looked at in more detail later.
   
   One more very important issue, Perry touches here, is "limitation of our thinking". The way we think definitely allows us to understand, or not to understand, investigated topics. When I started to promote The Physics of Life, I unconsciously started to feel that a lot of people think in a very different way than I do. Things and concepts that are obvious to me were unknown or incomprehensible to others. We return here to the problem of discussion on the frozen water between Tanzanian and Scotsman. Later, as I became more experienced in promotion, I discovered that people generally think in the reductionst way, some are able to think in a systemic way, but only a few are able to think in the, very important to life sciences, game theory way.
   
   As you can see I have introduced three brand new concepts without giving their precise definitions. Is it a mistake? Not at all. I consciously postponed it because we will soon talk about, not three ways of thinking, but about ten or more. The book "The Macroscope" by Joël de Rosnay confirmed my conviction that there is a huge gap between reductionist and systemic thinking. But the book "Roadmap to reality", by Thomas Elpel, had a great impact on the further development of humankind's limitation of thinking.
   
   The author states that our understanding of the world is restricted by our individual perception and our own way of thinking. He also explains the ten, hierarchical, worldviews:

   • preconsious
   • magical
   • mythical
   • sequential
   • systems
   • holistic
   • mystical
   • observer
   • non-linear
   • universal

   Although I don't fully agree with this hierarchical classification, I was strongly attracted to this book. The book is superbly written, it explains complicated concepts in a very simple way that almost anyone can understand. The first six worldviews are written in an informative and consistent way which adheres to the principles of The Physics of Life. The last four I am unable to give my opinion on as they deal with such subjects as speed of light, wave-particle duality etc, which are not included in The Physics of Life. Moreover, certain concepts have a completely different definition which clash.

   The quotes which captured my attention were:
   Mythical thinkers are disproportionately favored in elections
   The worldview of the majority of Americans is between Mythical and Sequential.
   We construct a reality based on models of how we would like that reality to be, not on reality itself.
   and
   People don’t want complicated answers. They want a person or doctrine to give them simple solutions to avoid the effort needed to study and understand sophisticated issues.
   [More quotes from the "Roadmap to reality"]

   After reading this book I came to the conclusion that one should think in an Absolute Way of Thinking. Roughly speaking it means that one should fluently use the knowledge from some given scientific disciplines and should not have cultural prejudices nor subjective biases. You can find the introduction, which will help you to study this issue, under the link: Absolute Thinking

2. P:111: In other words, division of labour wasn't invented by Henry Ford or Adam Smith or ancient tribesmen - it was invented by bacteria.

3. P:190: I saw another kind of value in opening this up to the general public. Albert Einstein said: "It should be possible to explain the laws of physics to a barmaid".
   […]
   I got a generous sampling of the beliefs of thousands of people all over the world, and obtained a deeper appreciation for the principle that werever possible, you should prefer a simple explanation over a complex one - especially after witnessing the elegance of a crisp, one-paragraph idea versus four pages of ramblings!

4. P:252: Modern science was birthed from the belief that to discover and quantify the order of the natural world was an act of worship.
   Listen to this from the mouths of the great science pioneers themselves...

 

 

 

KI: On evolution

1. P:130: Cooperation, Not Survival of the Fittest

2. P:145: Most important, what we've learned about Evolution 2.0 is:

   1. It is not slow or gradual; it is fast.
   2. It is not accidental; it is organised.
   3. It is not purposeless; it is adaptive.
   4. Natural selection isn't star of the show; Natural Genetic Engineering is.
   […] these bring us to a brand new understanding of evolution - Evolution 2.0. Evolution 2.0 is defined as the cell's capacity to adapt and to generate new features and new species by engineering it's own genetics in real time.

3. P:222: Some years ago, Dawkins wrote a famous GA software program to demonstrate how Darwinian evolution might successfully work. He entered the following random string of letters into the program.

   WDLTMNLT DTJBKWIRZREZLMQCO P

   One letter at a time, his program evolved this string of letters. After only 43 iterations, by randomly changing letters and deleting results it didn’t want, the program reached its preprogrammed goal of the following sentence:

   METHINKS IT IS LIKE A WEASEL

   This was heralded as a success. However, Dawkins’ software program was programmed to compare each new sentence to the goal sentence and either select it for continued “mutation” or reject it based on whether it more closely resembled the goal than the previous mutation. But his very own “1.0” Darwinian evolution explicitly forbids preprogrammed goals! So Dawkins’ “Weasel” experiment had nothing to do with the true Neo-Darwinism.

4. P:250: Evolution doesn't have to be competitive; it can be cooperative. If evolution is purposeful... if all codes need designers... then the universe is a purposefull place, not a blind, pitiless, indifferent place. Evolution 2.0 saves you from the bitter, nihilistic corset of Darwinsm.

5. P:000:

 

 

 

KI: Does life reverse the 2 law of thermodynamics

1. P:228: Aging is accelerated by loss of genetic information, the same information entropy we talked about in chapter 9.

2. P:000:

 

 

 

KI: Intelligence

1. P:229: We can't know for certain now whether cells are self-aware or not, other than to say that some very competent researchers report that cells have impressive decision-making capabilities. Here's what we do know:

   • Cells learn from past events.
   • Cells grasp relationships between themselves, other cells and objects in their environment.
   • Cells exchange code with each other when triggered by certain conditions.
   […]
   Your brain exercises one kind of intelligence (decision-making ability and capacity to anticipate the future), while your immune system employs a different kind of intelligence. The intelligence that makes your body operate like a silent, well-oiled machine is not lesser than the intelligence of your brain; it's jus different.

2. P:236: a single cell possesses more intelligence than a multibillion-dollar search engine.

3. P:000:

 

 

 

KI: The author's attitude

1. P:188: But I still need a sparring partner. Deep down, what I really wanted was to be able to punch someone and get them to punch right back. Someone really smart. Someone relentless, who wouldn't indulge any of my nonsense, someone who would challenge every fact and assumption I've shared so far. Iron sharpens iron. I knew that I might come up with all kinds of wievs that could satisfy my own belief system. But we're all prone to self-deception.

2. P:216: I am suggesting that biology must draw upon an additional level of scientific principles beyond traditional physics, including linguistics, information theory and signal processing. Perhaps even art, music and architecture.

3. P:190:

4. P:257: Darwin's original full book title was, after all, "On the Origin of Species be Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life". In it, Darwin wrote: "The civilised races of man will almost certainly exterminate and replace, the savage races throughout the world". Remarking on social institutions that care for the poor in his later book "The Descent of Man, and Selection in Relation to Sex", Darwin wrote: "Excepting in the case of man himself, hardly any one is so ignorant as to allow his worst animals to breed".
   
   Racism, eugenics and genocide are totally logical if Darwin's understanding of humans is correct and we are not spiritual beings. Darwinism is racist and inhumane.

 

 

 

KI: The basic question

1. P:270: Matter and energy don't tell you where they come from.
   YES: As far as life science is concerned, we are very close to an accurate explanation of how life arose. However, we have no idea how matter, energy and their properties emerged, and how came to being something like the emptiness of the universe - the place where matter and energy are dispersed and behave guided by their properties.

 

Struggle for Survival or Cooperation? Information is not an emergent property of matter

 

 

 

Quote:

Life cannot be understood unless one first learns to comprehend the language and to understand the alphabet in which it is composed. It is written in the language of: mathematics, system theory, theory of stability, game theory, set theory, information theory, chemistry, biology, cybernetics and economics; and its characters are: dilemmas, gerpedelution, How Life Is Competing model and other cognitive models of The Physics of Life, without which it is humanly impossible to comprehend all about life. Without knowing them one wanders about in a dark labyrinth.

Życia nie da się zrozumieć, jeśli wpierw nie nauczy się jego języka i odróżniania liter, z jakich zostało zbudowane. A jest to język: matematyki, teorii systemów, teorii stabilności, teorii gier, teorii mnogości, teorii informacji, chemii, biologii, cybernetyki i ekonomii; literami zaś są: dylematy, dylematy iterowane, gerpedelucja, model Jak Gra Życie i inne modele poznawcze Fizyki Życia, bez pomocy których niepodobna ludzkim umysłem pojąć zjawiska życia. Bez ich znajomości jest to bowiem próżne błądzenie po mrocznym labiryncie.

 

 

 

General:^

Reading "Evolution 2.0" had a major impact on me. It is a great book and Perry did a very good job. I feel some kind of allegiance with him, as an engineer and entrepreneur who also has a very strong scientific background. On the other hand, I feel some kind of opposition. While starting my investigation into the essence of life and its origins, I came to the same conclusions as Perry did. Seeing that the models offered by evolutionists are noncoherent and that modern science hasn't even provided a logical and consistent definition of evolution. In 2009, I came to the same conclusion, that any science devoted to life is, as Perry has shown in 2015, "in the bushes". However, I took another way of thinking and this led me to The Physics of Life, which encapsulates all my theories and discoveries into one volume.

My scientific background originates from creating and investigating physical and mathematical models, mainly their reactions to disturbances. It is the field of the theory of stability. I started to ask some simple questions and tried to answer them myself, bearing in mind that the present models may be inaccurate and should be rebuilt.

Evolution 2.0 is very important because it shows that scientists, at their own request, found themselves at a dead end. If some facts did not fit their theory, they were sweeping them under the carpet, instead of trying to think about whether the theory should changed or supplemented or not. I think "Evolution 2.0" will create a new impact (at least it impacted on me a great deal). I admit that after writing my "The Physics of Life" I was pinned down by the attitude of some of my readers. A lot of them tried to classify my theses to their own worldviews & biases. And instantly, when a single element didn't fit in it, they rejected the whole.

Nevertheless, some of my explanations contradict what Perry has written and I still hope to cooperate with him because: The community as a whole doesn't listen patiently to critics who adopt alternative viewpoints. Although the great lesson of history is that knowledge develops through the conflict of viewpoints. If you simply have a consensus, it generally stultifies. It fails to see the problems of that consensus and it depends on the existence of critics to break up that iceberg and permit knowledge to develop. This is in fact one of the underpinnings of democratic theory. It is one of the reasons why we believe in notions of free speech and it's one of the great forces in terms of intellectual development. - Walter Gilbert who in 1986 coined the term "RNA World".

I prepared myself for the beginning of this cooperation. Initially, I will list all of Perry's theses and I will gradually write my responses to them.

 

 

 

Random copying errors or a formula? (page 34, 87):

★ Page 34: Could there be specific types of mutations that perform certain evolutionary operations? Perhaps fruit flies don't progress by random copying errors, but by some other formula? What would that formula look like? I need to find out.

Page 87: Does transposition contradict Neo-Darwinism? If we are going to use consistent terminology, yes, it does. Neo-Darwinism by definition says evolutionary changes are caused by random mutations and genetic drift.

 

The Evolution 2.0's main accusation against evolutionists is: the randomness of mutations based on the assumption that the randomness occurrs on the level of nitrogen base pairs. I also noticed that the mechanisms that change the genetic design are not well explained, so far. However, I saw that the "mutations", whatever they are and whatever their source of creation is, have a lot in common with "disturbances" used in the theory of stability. Therefore, not delving too much into the causes and mechanisms of mutation, I started to investigate how disturbances influence the behaviour of gerpedelution. I named this simulation a Small evolution

I will not pay so much attention to the character of mutations. From the very beginning (on the level of RNA base pairs copying) they were random, later the improvement machinery of biological evolution transformed the random changes into changes having their own characteristic. As it did with absorption: primarily it was simple chemical affinity, and now some living objects use claws, fangs and sophisticated hunting techniques.

 

 

 

 

(page 58):

★ Where did the original code in DNA strand come from?

 

 

 

 

 

(page 111):^

★ In other words, division of labour wasn't invented by Henry Ford or Adam Smith or ancient tribesmen - it was invented by bacteria.

 

It wasn't even invented by bacteria. Division of labour is pushed through the selection function because it is a victory factor for the living objects who have it. If, in a set of homogenous living objects, which can be either cells within a multicellular organism or individuals in a human society, a disturbance during the copying of its genetic design occurs, which causes that these homogenous objects specialise and exchange resources, it raises the ability of the set to achieve its purpose of life. So this disturbance, which is recorded in the DNA, goes through selection and is passed down to subsequent generations. Specialisation & exchange are favourable because they lower the operating costs of the set. Why they lower the operating costs is explained by the law of comparative advantage.

 

 

 

 

(page 119):

★ Modern research increasingly suggests that animals can pass on learned traits to their to their offspring and that there really is a "memory" of past events overlaid onto DNA. This memory is flexible and adaptive.

 

 

 

 

 

Struggle for Survival or Cooperation? (page 130, 250):^

★ Page 130: Cooperation, Not Survival of the Fittest.

Page 250: Evolution doesn't have to be competitive; it can be cooperative. If evolution is purposeful...

 

First: evolution is not purposeful (having a purpose), like planets revolving around the Sun are not purposeful either. The Solar System and biosystem have their natural tendencies. The natural long-range tendency of biological evolution is to perfect the objects subjected to it. It perfects them by optimising in two orthogonal directions. The first is the ability to absorb resources and the second the ability to multiply. This optimisation depends, of course, on interactions between other living objects.

Second: Biological evolution is neither cooperative nor competitive. It is cooperative and competitive at the same time. The orthogonality of improvement is the second feature of biological evolution.

 

 

 

 

(page 139):

★ These findings build our confidence that progress is driven by adaptive mutations - modular reengineering of genes and chromosomes - not by random copying errors.

 

 

 

 

 

(page 180):

★ Most theorists put replication before protein synthesis, but you can't have one without the other.

 

 

 

 

 

Natural emergence of code/novelty (page 182, 206, 217, 290, 291, 292):

★ Page 182: "Spontaneously"... "go on to produce"... "mutation via faultes in replication"... "we have evolution!" is the RNA hypothesis in a nutshell., but it contains no mention of code at all.
The preciding explenation might sound okay until you remember that a digital code must be established before any kind of self-replication can be possible. A code will only functionin the context of an coder and decoder. Plus amino acids aren't code. A string of nucleotides all by itself is not a code.
Chemicals all by themselves don't communicate. No one has ever demonstrated that chemical reactions alone can generate codes. It's not nearly enough to have "hardware". You have to have software too. Remember, the genetic code is crucial to all life and its ability to reproduce.

Page 206: But I could find no formula or transformation that turns matter or energy into information. This is precisely what the Evolution 2.0 Prize seeks to discover.

Page 217: Design is when an idea precedes its embodiment.

Page 290: If some natural way exists to convert energy into code, nobody's discovered it yet.

Page 291: Still, natural selection can only select what exists. Natural selection can never create anything out of thin air. It can't make cold toas hot, and, since information entropy is irreversible, natural selection can't reverse it. Natural selection is only as good as what comes before it.
Noise doesn't add, it substracts.
Likewise, natural selection doesn't add, it substracts.
So, how can the classic Darwinian model work if it's a one way ticket to decay, degradation, and extinction? How can anything evolve if Neo-Darwinism has no workable mechanism for adding novelty?

Page 292: If you've ever grown a business or competed in a basketball tournament, you know that a round of eliminations all by itself doesn't create anything.
The best natural selection can do with noisy data is select the least noisy piece of data. But the data will be still be noisy and inferior. Natural selection can slow entropy down, but it is powerless to reverse it.

 

The first question we should answer is "How chaos can transform into something targeted?"

The system above is a platform driven by chaotically moving particles colliding with it. Thanks to the pawl platform can move only in one direction. Ratchets are the simplest form of mechanisms. They can be mechanical, as in our example, electrical and others. Generally, ratchet is a mechanism that restricts behaviour of the system in a given dimension(s) and allows it in another(s). It directs chaos, it creates natural tendency of systems.

 

 

 

 

(page 190):

★ I saw another kind of value in opening this up to the general public. Albert Einstein said: "It should be possible to explain the laws of physics to a barmaid". This was also a place where I was learning to explain my own ideas to everyday folks.

 

 

 

 

 

(page 192):

★

1. DNA is not merely a molecule with a pattern; it is a code, a language, and an information storage mechanism
2. All codes are created by a consious mind; there is no natural process known to science that creates coded information
3. Therefore DNA was designed by a mind.

 

 

 

 

 

Information is not an emergent property of matter (page 203):^

★ Page 203: So far as anyone knows, information is not an emergent property of matter.

 

If one accepts the definition of information as follows: information is an (interpreted) sequence of states, the natural emergence of information became obvious.

Due to the natural tendency of nucleotides (both ribo- and deoxyribo-) to form chains, the sequences of states form naturally. Because each nucleotide can be in four possible states (its state depends on one of the 5 nitrogenous bases attached to it) the formed chain is a sequence of states, which is information. Because properties of given sequences of ribonucleotides differ it is the simplest form of interpretation of this information; RNA particles constitute the information because it is a sequence of states and plays the role of interpreter because a given sequence results in a given property (given functionality) which differs from properties of other sequences of ribonucleotides.

 

 

 

 

(page 205, 216):

★ Page 205: Information is a set of rules that operate in adittion to the laws of physics.

Page 216: I am suggesting that biology must drawn upon an additional level of scientific principles beyond traditional physics, including linguistics, information theory, and signal processing. Perhaps even art, music, and architecture.

 

 

 

 

 

(page 217):

★ Scientists struggle to even agree on life's definition

 

 

 

 

 

(page 222):^

★ This was heralded as a success. However, Dawkins' software programme was programmed to comapare each new sentence to the goal sentence and either select it for continued "mutation" or reject it based on whether it more closely resembled the goal than the previous mutation. But his very own "1.0" Darwinian evolution explicitly forbid preprogrammed goals! So Dawkins' "Weasel" experiment had nothing to do with true Neo-Darwinism.

 

I could hardly believe that what you have written is true, because if it is, it means that Richard Dawkins does not really understand the mechanisms of evolution. Of course biological evolution has no final design stored in it, and it does not compare how far the present design is from completion. The selection process rejects those objects which are, put simply, worse for the completion of their life purpose.

 

 

 

 

(page 229):

★

1. Cells learn from past events
2. Cells grasp relationships beteween themselves, other cells, and objects in their environment
3. Cells exchange code with each other when triggered by certain conditions
4. Cells rewrite their own code
5. Some cells organise themselves into colonies

 

 

 

 

 

(page 246):

★ When you allow nature to simply tell its own story, when you subtract randomness from the equation and replace it with the goal-seeking systems, evolution, in the form of Evolution 2.0, finally begins to make sense. You find that real-world biology doesn't support atheism at all. Itspeaks to a world that's even more amazing than most people dared to believe.

 

 

 

 

 

(page 270):

★ You know, all those atheists you're arguing with are just devotes of a different form of fundamantalism.

 

 

 

 

 

(page 270):

★ Matter and energy don't tell you where they come from.

 

 

 

 

 

(page 274):

★ Any scientist who takes his work seriously has no choice but to say, "I don't know what its function is, but my job is to fully engage in the systematic study of the structure and behaviuor of this until I do. So until I have a complete working model that describes the entire system in exact detail, I have no right to assume these stretchesof DNA are junk".

 

 

 

 

 

Information Entropy (page 290):

★ A very common reply to this is, "Sure, entropy, the tendency toward disorder and decay, always increases in a closed system. But you can decrease entropy within the Earth by adding energy fromthe outside. In other words, you can always put the cold toast back into the toaster and heat it again". […]

 

 

 

 

 

(page ):

★

 

 

 

 

 

Evolutionary mechanism for adding novelty (page 291-292):

★ Still, natural selection can only select what exists. Natural selection can newer create anything out of thin air.
[…]
How can anything evolve if Neo-Darwinism has no workable mechanism for adding novelty?
[…]
If you've ever grown a business or competed in a basketball tournament, you know that a round of eliminations all by itself doesn't create anything.
The best natural selection can do with noisy data is select the least noisy piece of data. But the data will still be noisy and inferior. Natural selection can slow entropy down, but it is powerless to reverse it.

 

To answer this question let's analyse a specific tournament of two, for example, hockey teams: Reds (R) and Whites (W). They play a match, if there is a tie, then they continue until the next goal is scored. So we have the winner and the loser. A team should be understood as a group of players (lets name it GP) and a set of tactics used by them to play (ST). Let's define an ability to win (ATW) as a function of GP and ST.

ATW = ATW(GP,ST);

Basically, the ability to win depends on the quality of players and the tactics they use.

The ability to win of each team is evaluated after the match. Those who won had better ATW. Now, some very biological processes happen: the losers are rejected, the winners are cloned. The players are duplicated, and their tactics as well. Theoretically, as a result of the cloning, we have two teams with an equal ability to win. Because Whites won, we have two W teams. In order to distinguish them let's add a suffix. We have W1 and W2 teams.

They start to play, one wins. Let it be W2. Then W1 is rejected and W2 is cloned into two teams: W2a and W2b. And this is a continual process.

If the ATW of both playing teams is equal, then one wins by "luck" or "chance". But during the cloning something might have happened that weakened the ATW of one team. They play and this team loses emphatically. The winner is cloned. The conclusion is that if, during the duplication, the ATW is weakend this feature does not pass onto the next generations.

Now consider the duplication during which the ATW of one team is strengthened. This team wins the match. The conclusion is that if, during the duplication, the ATW is strengthened this feature will pass onto the next generations.

So the strengthening mutations are selected and passed down to the next generations. I named this mechanism - evolutionary ratchet. A ratchet, as a mechanism, is the simplest one. Similarly, a bit is the simplest unit of information.

 

 

 

 

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