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The complexity of a living cell cannot be generated with a simple program
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Posted by: Gershom Zajicek M.D.
Objective: This thread will illustrate various aspects of complexity and their implication for the modeling of biomedical phenomena with CA.
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Three hypotheses account for the origin of life on Earth:
1. Life was generated from non living matter, or Abiogenesis.
2. Life is prevalent in the universe, known as Panspermia. On Earth it began by seeds of life arriving from outer space.
3. Life was created, as described in the first chapter of Genesis.
1a. The first hypothesis was tested experimentally. A “primitive soup” containing atoms molecules and water was treated with high voltage, or irradiated with U.V. or x-rays. In the following days, some basic organic molecules that form the building blocks of modern life aggregated spontaneously, yet did not replicate.
2a. The British astronomer Fred Hoyle was the proponent of Panspermia http://www.panspermia.org He believed that life on earth came from outer space.
3a. According to Genesis, life requires a different creation act than the rest of the universe.
Already Aristotle favored abiogenesis basing his hypothesis on the observed fact that some animals arise from putrid matter, or that plant lice arise from dew. In the 19th century this brand of abiogenesis was finally refuted by Louis Pasteur, which led to the conclusion that Life comes from Life (omne vivum e vivo). Yet the concept Life is too broad, and Rudolph Virchow replaced it with: Cells always emerge from cells (omnis cellula ex cellula).
The cell is the atom of life. If disrupted it dies. It is extremely complex. This complexity is conserved as such and passed from generation to generation. The first cells which appeared on earth were the archaea. They lack a nucleus and are called also prokaryotes. Then some invaded other cells, continued living in their cytoplasm, and became cell organelles, like mitochondria. (v. Lynn Margulis http://www.bio.umass.edu/faculty/biog/margulis.html ). In the same way cell nuclei were formed in eukaryotes.
The rest of the evolution can be summarized as a gradual assembly of cells into different organisms. When a sperm meets an ovum, both contribute to each other their enormous complexity. The complexity of the ovum cytoplasm surpasses its genetic complexity. Without this indispensable complexity which the two provide, life cannot exist.
There is a smooth transition between the inorganic and organic world. Atoms assemble into molecules, and molecules into complex macro molecules. None of these intermediary states actually lives. Life’s smallest atom is the cell.
Now imagine that life on earth is a computer, and its processes are computations. This bio-computer does not generate its complexity from scratch, or from some simple programs. It starts its computations from a baseline, the complexity of a cell. We ought therefore to distinguish between two kinds of complexity: NKS complexity, which can be generated with simple programs, and that of a cell, which cannot.
In order to exist, life needs a certain amount of complexity which initially arrived from outer space, and may have been arriving ever since.
More on cell complexity in: http://www.what-is-cancer.com/papers/ca/ca0.htm
Posted by: Tony Smith
The basic principles revealed by Margulis's substantive account of how prokaryotes begat eukaryotes are not difficult to also apply to the earlier step.
Lipid membranes growing and dividing without genetic instruction have been demonstrated and there are a few theories around as to how genetic information made the transition from punched cards to DVD-ROM. So the likely minimum is that we had an earlier symbiosis between membranes that enclosed a simpler autocatalytic proto metabolism and reproducible information from somewhere else entirely.
More likely there was more than one such pre symbiosis en route to something we might recognise today as life, with successful forms being adopted as new standard platforms for subsequent functional diversification. NKS has some important things to say about sources of variation.
A couple of asides may be helpful here:- beyond the kind of (Prigogine) emergence of order from coherent action of large numbers of individuals, vast populations over vast ages provide enough opportunities that some statistically very unlikely (proto) symbioses to be trialed
- while Pasteur may have found microorganisms there is no guarantee that we have yet seen more than a fraction of the complex chemical systems that inhabit the soil and the waters, a problem amplified by our practical need to build instruments that efficiently look for the things we expect to find
If we really do want to understand the origins of biological life, Mars or Europa might have more to say than a planet that has been reformed over and over by ever more evolved organisms.
Posted by: Gershom Zajicek M.D.
It appears as if the cell, and particularly its cytoplasm, is disordered. In reality it is a structured object with an origin and periphery. Its origin is the genome. Each gene is the starting point of a protein assembly line. First, its code is translated into a simple protein (peptide) which advances along the assembly line, and matures (differentiates) as it goes. When its time has come the protein molecule disintegrates. An illustration of such an assembly lines is in: http://www.what-is-cancer.com/paper...g/proteins.html
These assembly lines are processes, which originate in the genome and end in the cell’s periphery. Those unfamiliar with this ordered intricacy regard the cell as chaotic. Some claim that life can exist only on the borderline of chaos. In reality life is not at all chaotic. Neither is it sensitive to its initial conditions. Simply because the living cell does not start from an initial state. It inherits its ordered complexity from its ancestors.
Posted by: KGifford
Some possible flaws with hypothesis 2 and 3?
Even if the Earth was seeded by extraterrestrial life...it had an origin somewhere. Whatever processes involved in that environment--simple structure to complex structure is the only direction that makes sense. Returning us back to the idea that abiogenesis was the ultimate route.
If God (whatever that means...as I have discovered many definitions) was the demon involved in the push for cellular life...It still pulled together the inorganic of matter and force to organize viability. Suggesting that the natural intelligence of matter is not capable of such organization.
It seems such a simple task to watch crystals organize themselves into the most amazing of structures, to recognize that chemical nutrition supports vast quantities of life around the hot pots of the ocean. Is it such a stretch to imagine that the material universe fell upon the recipe for life all by its lonesome?
While the cell is the most basic of higher order life can the universe of bacteria and virus be neglected in the steps to cellular evolution? Is the cell truly the basic building block--or would it be DNA? How mathematically beautiful is that?
To reverse our look on evolutionary development and notice how determined the quantities in life are to provide statistical probability for complexity...doesn’t it stand to reason that the geology of the earth was vastly different from what it is now and may have been everything it necessarily needed to be to advance the probability for the inorganically complex to emerge into the organically simple? Maybe individual mitochondria playing house.
All you need is a serendipitous mixture of order and randomness. Doesn’t it seem the Universe is in very abundant supply of these?
Posted by: Gershom Zajicek M.D.
Let’s focus on observations:
No matter how life on earth started, today the atom of life is a cell, and microbes are also cells. Viruses or DNA cannot be regarded as atoms of life since they lack a metabolic machinery and do not replicate. In order to do so they have to penetrate a cell, mobilize its metabolism and replicate.
My point is that the cell does not generate its ordered complexity from scratch. It inherits it. Nor is it possible to generate such an ordered complexity with a simple program. After all the issue here is the universality of NKS. How universal are NKS computers if they fail to generate the complexity of a living cell?
Posted by: KGifford
Perhaps, I only know enough to be dangerous (or not enough to be fully articulate) with a medical physician. But, to see a simple program as a “direct path” to the complexity of the cell seems as erroneous and seeing bonobo chimps as the direct ancestors of Homo Sapiens.
I understand that the cell must inherit its formula and DNA is the code it passes on. So the analogy of the cell as the atom and DNA as its sub particles holds. But, to assume that the creative method was a chemical soup mixed with some electricity--viola, Frankenstein strikes--we have a fully realized cell, seems to be missing a gross amount of micro and macro evolutionary steps in process.
There is an issue between programs and intelligence. We know programs can be built to analyze, check themselves and evolve. We can even build a robot that learns how to walk, can eat by plugging itself in and might have the capacity to “replicate itself”...but alas that is not a sign of life affirming intelligence--is it?
I am suggesting, however, there are some “missing links” before the true cell emerged--from which to inherit any thing from. Viruses, simple bacteria and diatoms might hold "some" of the keys to those missing links.
Even the Creation Story in Genesis, as crude as it might be, eludes to the possibility of evolutionary process. Maybe "God" having its hand in the mix really only means the "logics (programs) and physics (chemicals) of universe" meeting at the right times and places.
The greater issue it seems to me is being able to grasp how the intelligence of inorganic complexity would organize itself into the flexibility of organic simplicity--turning the elements of random proximity and spontaneous probability into intentional organizations capable of distinguishing preferences for quality of existance.
I admit I am not familiar enough with NKS theory to suggest how it can apply to solving this question.
Posted by: Gershom Zajicek M.D.
In order not to get lost in speculations let’s concentrate on what is observed today. The issue is not how life started on earth, but how it propagates itself. No living entity known today generates its complexity from scratch. It inherits it.
I started this thread to call the attention of my colleagues in the exact sciences, to a phenomenon which does not have a counterpart in their realm. While the complexity of matter can be generated from its elements, there is no sign or an observation indicating that nature generates the complexity of a living cell from scratch.
More on cell complexity in: http://www.what-is-cancer.com/papers/ca/ca0.htm
Posted by: KGifford
If you do not expand your question to the creation of the cell and you do not use deduction and inference to look at as many parts of the whole picture as you can--I don't see that your “observations” will get you very far. Einstein, after all, explained how vital imagination is even above knowledge. Speculation without the meat of content is, indeed, pointless...but, I am not sure that my arguments are without that merit.
As the introduction in your link suggests, the biological chain is non-linear. Exactly my point about the course of micro and macro evolutionary steps being necessary to move from organic soup to the complexity of a cell.
The NKS model would need to discern when nonsense is a spatial opportunity to advance a macro transformation in its program. Quite frankly, if there is a failing in the model, it is here--as Biology has the fortune of exterior environment to push these opportunities along. I don’t see how a programming model can generate the kind of random crisis and motivations from “within” itself that a living organism must face in order to advance itself.
What is critical to realize in this process is that you have substance with its individual program and environment with its global program interacting to mix an outcome. Expecting a program to generate its complexity from wholly within is definitely a grand and, I believe, impossible notion.
Your position almost suggests that you do not embrace the concepts of evolution. But as we have never seen a cell spontaneously generate its complexity--nor have we seen the conditions that might support such an opportunity--given the incredible amount of time that is likely involved to accomplish such a task, I am surprised that your observations are so confined.
Exactly how did the single cell of primitive earth pass on the inheritable information for eyes, ears, noses, mouths and brains that we might even be having this conversation? I do not see how you can ask your question without asking who the first ancestral cell was and how it came to be?
The Exact Sciences must look at as many parts of the whole as it is able before drawing generalized conclusions. Suggesting that life “must” originate from outer space--which is certainly possible--still denies that somewhere, sometime, there was a specific course of time, forces and matter that pulled such life affirming complexity into its potential.
Posted by: MikeHelland
I would like to point out that there's a debate on the origins of life, and no one has cared to define life.
I think a human is alive.
I think a plant is alive.
I think a plank of wood is alive.
I think a solar system is alive.
There is no defining line anywhere between human life and the life of a star.
Using that as a starting point, the origins of life are identical to the origins of nature, presumably (until a better idea comes along) this would be the big bang.
So I offer hypothesis 4 to the original post:
4. All matter is life. There is no such thing as "non living"
That of course does not begin to discuss how something as magnifcant as a cell could evolve, but it does remove some of the "magical dust" required to get "life" from "non-life".
Just thought I'd throw that out.
Posted by: KGifford
Mike, I wholeheartedly agree and I’m pleased to see that I am not alone in that definition of life. But, I wonder if our friend Gershom might object, as it is clear his focus is on the biology of a cell.
My observation stands (as stated above), however that the greater issue seems, being able to grasp how inorganic intelligence would organize itself into the flexibility of organic intelligence--thus, transforming the elements of random proximity and spontaneous probability into “intentions” that are capable of distinguishing preferences for quality of existence and being able to do something about it.
Might we then also, “speculate” that a chemically rich rock is only some degree less intentional than a cell and that a galaxy or atom might be some other degree differently intentional than that rock? Taking us back to a conclusion that maybe the Total Universe, itself, possesses some proportion of intention...i.e. to evolve its original simplicity into all the complexity that it can be while establishing “a thriving balance of fitness and health” as its platform for quality?
Does NKS theory have the capacity for such a concept of such intentional intelligence? --Which I believe Gershom is suggesting--it can not...and, I also wonder if NKS is that robust.... ?!
Posted by: Philip Ronald Dutton
"Taking us back to a conclusion that maybe the Total Universe, itself, possesses some proportion of intention..."
Taking us back indeed... to pure Naturalism.
And hence, the end of free will.
Meaning that Nature herself decided that I should write this post.
Just a thought....
Posted by: KGifford
I don't get how the logic for the nixing of free will comes about.
No one said anything about absolute determinism or that the Universe even knows for certain where it is going. I suggest only that Universe may have a similar context of mandates it gets to work with as its resources towards an unknown potential list of optional complexities--the same way that any one of us humans has in our daily lives.
For example, I won't be changing the fixture of my DNA any time soon, nor the highly complex environment I get to interact in. But that is my palette of variables for an untold quantity of potentials waiting to be materialized into yet other finite certainties--that will only be added to the list of my variables (ether expanding or contracting the potentials of other options).
In my mind, Intention is fundamentally defined as free will. I might also suggest that the thing that distinguishes a human from another primate is the “proportion” of intention that we humans get to exercise towards the quality of our survival, instead of being as beholden to spontaneous instinct--as I might carry that idea further by suggesting that another primate has a higher “proportion” of intention than does a fish...a fish than a single cell...than a rock...than an atom.
Maybe, the proportion of intelligence in original universe was only to “choose” to stop being the same.
Posted by: Gershom Zajicek M.D.
In order not to get lost in fantasy and unnecessary speculations, I restrict my arguments to simple and clear statements.
My previous sections have shown that the living cell inherits an ordered complexity. It has an interior where protein assembly lines start, and a periphery where they end. Each gene is the starting point of a protein assembly line. The proteins advance (stream) along the assembly lines and when their time has come they disintegrate.
Despite this oriented turnover the appearance of the living cell remains invariant. It maintains a steady state (homeostasis), which indicates that for each dying protein molecule (A), a new one is formed:
Dead[A] = Born[A]
In order to satisfy this equality, the gene has to know the death rate of A , and adjust its production accordingly. This knowledge is called in my site, Wisdom of the Body (WOB). Its nature is one of the great medical mysteries.
More on WOB: http://www.what-is-cancer.com/paper...stconcepts.html
WOB in CA: http://www.what-is-cancer.com/papers/ca/ca93.htm
Posted by: John Gelles
When the body and its self-healing systems fail we look to the medical arts and sciences to add to self-healing the power of surgery, drugs, and care to overcome the failure.
The tools of NKS may have more to do with numerical and logical computation than with medicine and healing.
One starts with sensitivity, observation, explanation, understanding, accumulated knowledge, and wisdom, in the attempt to create an effective hospital staffed by specialists and generals.
A new kind of medicine is probably independent of NKS. Not that the principle of computational equivalence has no use in medical science -- it may very well simplify or help to improve statistical methods that take medicine out of the realm of prayer into the light of honest reporting and careful treatment.
Engineering may be the field that will most appreciate NKS. History may be where it is least needed. Medicine and economics have profound need of computation -- possibly NKS will contribute to progress in both disciplines.
Posted by: KGifford
Again Gershom, I wonder if your focus may be too restricted. But, I understand your drive to stick with substance that is concrete to you--the abstractions of hypothesis and theory can be too difficult to pin down to certainty. So far, I haven’t seen any evidence to pin God or life from outer space down to certainty, either--so we better stay away from those speculations as well.
You explain well the process of DNA replicating itself and keeping track of its life span--but, you still fail to explain how human cells “inherited” all of the data it possesses from those single cells floating around in the pond. From your website, I guess that is info that just isn’t “known” yet and can’t be discussed. What it seems to me, is that the cell, itself--learns--hence my discussion on “intention.”
I wonder if NKS might not have some contribution to understanding the process of DNA coding: How it determines a life span. How it adds (or subtracts?) genetic information to its evolving string, how it designates what is nonsense info in the code and what is substance intelligence--even if the cell or the body is an open black box--somehow it determines what it keeps and what it rejects towards quality survival...And it uses only four letters with very specific combinations to do it.
Where we are talking about organic properties, we are also talking about flexibilities and options in process ( “fuzzy probabilities” ) that inorganic materials “seem” to lack (as suggested earlier, and by virtue of my understanding of quantum mechanics, I am not convinced this is entirely so). Thus, NKS in engineering makes a lot of sense--where rigidity and purely mechanical endeavors are pursued.
Posted by: Philip Ronald Dutton
There was earlier talk about cells and how they inherit complexity of life and etc.
I was just thinking: How does a cell know when to die?
I assume that it carries around a discrete supply of oxygen. Does it replace that "quantum" of oxygen before it actually "runs out?" (uh oh, my cell oxygen is at 15% so I should now refill). If not, then would that imply that the cell can actually survive for a certain amount of time without oxygen? -- Maybe the cell uses all its oxygen and then remembers that, "oh boy! I better start looking for more oxygen because I have only 5 minutes until I will die!" So then it goes in search of oxygen during which time it is surviving without oxygen? If time goes long enough and it does not receive new oxygen, then it will die. But how does it know that too much time has passed??? How does the cell know when to run the "begin death process subroutine" ?
Just a thought which might be of interest to this conversation.....
Posted by: KGifford
Although I don't know all the technolingo, my understanding is that there are special strands of code at the ends of each DNA strand that carry this lifespan data. When the DNA replicates itself a little bit of this code is lost over a regular interim of time--until it finally runs out and instigates death.
Perhaps, when we ingest toxins and subject ourselves to undue stresses this course of time is shortened because the DNA is forced to spend a lot of unnecessary energy in repair.
I have investigated Gershom’s site, all be it, a skim here and there--as, a working girl can’t read it all--but it appears that his adherence to the cold hard facts is not as strict as he claims. Gershom does not discuss origins and is willing to say only that WOB is still a “mystery”--I believe that my concept of “intention” is not so different than his concept of WOB. But, I do have hypothesis, however, about origins--that I believe has sound basis in experimental science and math logics. In fact, while I do not embrace physics theory as the law, I do hold it dear that philosophy and theory are only useful if they have proven practical application.
I found the Book: “Love, Medicine and Miracles” by Bernie S. Siegel, very interesting. And I bring it up because he speaks at length about the power of the human to consciously (intention) intervene in self-healing. Gershom speaks at length about these concepts on his website. I, too, question the traditional methods of medical science and its approach to health and healing. And I also find greater wisdom, in a holistic approach. One of the greatest minds in medicine, Galen of old was very aware of this concept--which contributed greatly to his evolution as a physician.
Like Gershom’s physicist friend, Shin-Ichiro Terayama, having an approach to healing that is not “totally concrete” may lead to dismissals by the mainstream community as odd. That doesn’t mean there is not something to it--just that because there aren’t cold hard facts, people find it difficult to look and consider.
Posted by: Gershom Zajicek M.D.
Let’s remember that the main topic of our forum is neither medicine nor cancer, but NKS. For several years I have been involved in disease modeling with disappointing results. The tools were inappropriate. NKS provides a new dimension in the modeling of disease which I try to exploit. I am looking for a simple model of the Wisdom of the Body (WOB).
http://www.what-is-cancer.com/papers/ca/ca93.htm
Hitherto my approach was as follows: Grow a set of interacting CA which exhibit a directed complexity in the sense described above. The set maintains steady state and fulfils the equality Dead[A] = Born[A]. Now challenge it and look for non trivial response. Is it able to generalize?, or even be creative?
Modify the set and check again.
More in http://www.what-is-cancer.com/papers/ca/ca01.htm
Posted by: Gershom Zajicek M.D.
In his book Wolfram talks of “The complexity”, while there may be many kinds of complexity. Since Life does not generate complexity from scratch we ought to distinguish between two kinds of complexity: NKS complexity, which can be generated with simple programs, and that of a living cell, which cannot.
True, rules 30 and 110 generate immense complex patters, still it does not indicate that their complexity matches that of a living cell. One wonders how universal is Wolfram’s computer if it fails to emulate the complexity of a living cell? Or might his universal computer be only a conjecture?
More in http://www.what-is-cancer.com/papers/ca/ca01.htm
Posted by: Gershom Zajicek M.D.
Wolfram divides CA into four classes. The first three are somewhat regular, and the last is really complex. Such a classification reminds of the counting system of the primitive man: One, two, three, many (infinity). Can’t we generate additional classes with different complexities?
We might apply here Cantor’s method for determining set cardinality. The first transfinite number is called aleph-sub-zero. It is the cardinal number of the set of positive integers, also called countably infinite. Each CA is defined by a triplet {Rule, r, k}, where r is the number of neighbors and, k the color.
The set of positive integers may be regarded as a CA{Rule, 0, 1}. Rule means add one to the current state, no neighbors, and one color. Next is CA{Rule, 1, 2}. Since we can establish a one-to-one correspondence with the positive integers, its cardinality is aleph-sub-zero. Rule is finite (<=256). Some of the CA in this set e.g., CA{rule = 30}, CA{rule = 110}, generate a complexity which belongs to Wolfram’s class-4. Raising {r, k} step by step, we shall soon conclude that the cardinality of all discrete CA in Wolfram’s book is aleph-sub-zero.
None has cardinality C which is the cardinality of the set of real numbers.
One wonders, given CA{Rule[Real], r [Real], k[Real]}, might it be possible to generate complexity more complex than that generated by aleph-sub-zero CA? If so, how universal is CA{Rule 110}, which obviously cannot emulate the complexity of CA{Rule[Real], r [Real], k[Real]}?
http://www.what-is-cancer.com/papers/ca/ca0.htm
Posted by: Gershom Zajicek M.D.
Edward N. Lorenz, was a research meteorologist at MIT who created a model for weather forecast, and discovered the Butterfly effect?
One day, as the legend says, Lorenz was busy computing his weather forecast (Lorenz model). After an elaborate work he got hungry. He stopped the program, saved the state parameters of his weather model, and went for a snack. When he returned, he restored the model's state and continued computing, whereupon he discovered that the numbers he observed on the screen differed from those which he observed before having the snack. He soon realized than whenever he stopped and resumed the computation of his differential equations, the results changed. His model was sensitive on initial conditions, and was therefore chaotic.
Then he discovered the butterfly effect, whereby the flapping of a butterfly's wings may change the model’s initial conditions so that somewhere on the globe the weather turned into a tornado.
What is generally misunderstood, that the real weather is an ongoing process which lacks any initial conditions. In reality the initial conditions of Lorenz’s model never occur. Also life is an ongoing process which may have started once (Genesis), but now it cannot be sensitive on initial conditions, simply since it lacks any initial conditions. Since an extreme sensitivity on initial conditions is a prerequisite of Chaos, life is not chaotic! In other words, the chaos model is inadequate to capture the intricacy of life.
Cells can be grown in a tissue culture, which consists of fluid and essential ingredients for growing cells. After some time they start dying and have to be transferred into a new dish with a fresh medium. Each such a transfer may be regarded as a new initial condition. Nevertheless, the cells don’t get chaotic, since they carry their own initial conditions and complexity, which they inherited from their parents. Life is a never ending ongoing process.
http://www.what-is-cancer.com/papers/ca/ca0.htm
Posted by: Karl Smith
Originally posted by Philip Ronald Dutton
There was earlier talk about cells and how they inherit complexity of life and etc.
I was just thinking: How does a cell know when to die?
I assume that it carries around a discrete supply of oxygen. Does it replace that "quantum" of oxygen before it actually "runs out?" (uh oh, my cell oxygen is at 15% so I should now refill). If not, then would that imply that the cell can actually survive for a certain amount of time without oxygen? -- Maybe the cell uses all its oxygen and then remembers that, "oh boy! I better start looking for more oxygen because I have only 5 minutes until I will die!" So then it goes in search of oxygen during which time it is surviving without oxygen? If time goes long enough and it does not receive new oxygen, then it will die. But how does it know that too much time has passed??? How does the cell know when to run the "begin death process subroutine" ?
Just a thought which might be of interest to this conversation.....
Oxygen diffuses across the cell membrane. If the cell is in an environment in which there is more oxygen on the outside than on the inside oxygen will diffuse into it. Therefore, it is only important that the body keep the cells in an oxygenated environment.
And yes, a cell could live for a short time without oxygen. Cells actually use ATP for energy. ATP can be produced aerobically or anaerobically. Anaerobic resperation, however, produces deadly byproducts and far less ATP.
Posted by: Gershom Zajicek M.D.
Cells “don’t know when to die!” They are eliminated by other processes which I call collectively Wisdom of the Body (WOB). There are two mechanisms of cell death: Controlled (apoptosis) and arbitrary (necrosis).
The body is composed of tissue units, each made of cells. In the healthy organism cell death is controlled and for each dead cell, a new one is formed.
Dead[cell] = Born[cell]
In order to satisfy this equality, the organism has to know when a cell dies, and when to replace it with a new one. This knowledge is called in my site Wisdom of the Body (WOB). Its nature is one of the great medical mysteries.
http://www.what-is-cancer.com/papers/ca/ca93.htm
Microbes and other agents kill cells arbitrarily. Nevertheless WOB senses the loss and stimulates cell production. The issue is explained in depth in my site: Streaming tissues: http://www.what-is-cancer.com/paper...reamtissues.htm
Here is another mystery: I can at will prolong the life of many of my cells. However I doubt whether it merits to be described in this forum, which is dedicated to discuss NKS, and not cell death. However, if the forum coordinator finds it important and creates a specialized section for this topic, e.g. The secrets of the Wisdom of the Body, I shall be pleased to explain how I improve the survival of my cells.
Otherwise you are invited to visit my site :
Cancer and Wisdom of the Body (WOB)
http://www.what-is-cancer.com/
Posted by: Gershom Zajicek M.D.
Although Wolfram’s book shows how to generate complexity, it says very little how to reduce or simplify it. Which is a pity since I encounter it in my practice. Among other my task is to reduce the extreme complexity of the human organism to a manageable number of components, otherwise cure is unthinkable.
In the search for ideas and methods to simplify the human organism, I discovered Aristotle’s ‘Four Causes’. Aristotle was a biologist with a thorough understanding of medicine. I believe that his ‘Four Causes’ were intended to simplify the complexity of Nature, although he himself does not mention complexity. In order to apply them today they have to be recast in a modern form.
Nature presents itself to us as change, and Aristotle distinguishes between four causes of change. Suppose that you are watching on your monitor an evolving CA. You pause, observe the CA state and ask what are the causes that will shape the next one? According to Aristotle this change has four causes:
1. Material cause, is the CA structure.
2. Formal cause, is its rule.
3. Efficient cause, is the processor which drives the program to the next state.
These three, account for the change in Wolfram’s CA. However they do not suffice to describe change observed in medicine (life), when the last cause has to be considered as well.
4. Final cause, or what is the purpose of this change?
A good philosophical treatment of the Four Causes is in:
http://faculty.washington.edu/smcohen/320/4causes.htm
Their significance in the description of disease is in: http://www.what-is-cancer.com/papers/fourcauses.html
Since lacking the fourth cause CA are inadequate to model disease. I therefore modified them in two ways: 1. Cells collect resources. 2. Their life is finite: http://www.what-is-cancer.com/papers/ca/ca14.htm
In this setting the Final Cause is Optimality. Each living form thrives to optimize itself. Optimization is the hallmark of life. http://www.what-is-cancer.com/papers/ca/ca48.htm
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p.s. What might be the final cause of the CA which I am watching on my monitor? To get me a salary. . . When you broaden your scope, the final cause is everywhere, even in Physics…
Posted by: Jim Edinger
I am new to this forum and I think there are many good ideas presented here. Like some in this forum, I too am searching for ways to develop valid models of cellular processes. In this vein, developing an idealogy for optimality in cells or in metabolism is difficult. It ultimately requires a purpose that defines the conditions of optimality. For example, enzymes catalyze reactions inside cells and this collective set of reactions is metabolism. One measure of an optimal enzyme is that the enzyme catalyzes its reaction at a rate close to the diffusion controlled limit (~10^12 per sec.). If one measures these types of kinetic constants in vitro, one finds that most enzymes, that are not at control points of metabolism, are within a factor of 2 of this limit. The purpose here is that these enzymes be fast enough to not create a bottle neck in metabolism.
This is a biological context that one misses when one simplifies a complex system into something that can be represented as a CA. The challenge for NKS and CA experiments is to bridge that knowledge gap between simple CA rules that result in complex patterns and the biological mechanisms that result in the complexity of life.
Posted by: Jason Cawley
The NKS idea is that simple programs can model natural systems, both those giving simple behavior and those giving complex behavior. It is not limited to elementary CAs, which are simply one example of a class of simple programs. Any simple program set up to reproduce the behavior of a natural system can be an NKS model.
In the case of enzymes, some of the relevant behavior is already well understood and fairly simple. Chemical reaction equations and the way they change in the presence of a single catalyst can be modeled by conventional equations - or made discrete if one wants, a first difference version of the same relationships.
Complexity enters on other levels of analysis (e.g. why does this protein molecule catalyze reaction A? - a microstructure issue) or from the interaction of a number of these processes going on in parallel and linked to one another. If they are completely independent - no overlap of reactants etc - then a reductive analysis gets you everything available on the reaction level alone.
But in general they are not. Maybe they compete for reactants. Maybe they change the concentration of reactants for another enzyme. Some subset of them may influence rates of formations of catalytic enzymes themselves. The networked connection of these things is where one can see complexity specifically on this level of analysis.
And all of this occurs in a system or phase space of parameters or boundary conditions perhaps set by higher level processes. One does not need to model those as well (all at once) but instead one needs parameters in the enzyme level model. It is not true that one can't know anything unless one knows everything, and science as Popper put it is the art of systematic simplification, or noticing what we can profitably ignore when looking at a particular problem.
How complicated is the resulting behavior, though? It is not at all obvious that it is particularly complicated. An organism would not find it particularly helpful to have e.g. a concentration of growth hormone that varies as wildly as possible in space and time. Not what it is after. Complexity may emerge in some subsystem anyway - or a form of randomness might be usefully exploited (e.g. in sampling a space of possible antigens to recognize all sorts of foreign pathogens).
But predictable results are often required, and that will limit the complexity of individual subsystems. In addition, natural systems need some mechanism to achieve things, that is simple enough as a mechanism that it can be implimented with available biological components, and be reasonably robust against all sorts of modes of failure.
One therefore should start with the assumption that simply subsystems behaving in predictable ways are interacting robustly to achieve overall results well confined in some parameter space. They may need to respond to various signals or have some built in range. But they won't just connect everything to everything else in random ways, resulting in uncontrolled information spread and hypersensitivity to all inputs.
What NKS does suggest about some biological systems that do produce complex looking results, is that there may often be a simple algorithm beneath those results, able to produce them without the bio equivalent of a million lines of C code. Sometimes 1-3 lines of Mathematica is a more likely place to look for a model. Of a specific feature or subsystem, of course, not of the whole organism at all levels of analysis put together. We know those are reasonably long programs, because we can see the lines of code themselves (DNA sequences). We just can't decode them (yet).
If you think about it, this is already part of everyday biological intuition in the idea of a gene. Which is, after all, the idea that a recognizable small subset of a much more complicated program is directly linked, through causal pathways much simpler than the whole organism, to various clearly dependent outcomes. Or in other words, that there are routines involved that aren't many lines long that produce important effects. So, NKS thinking says, look for simple programs as subroutines. And be prepared to find that a single simple program may be responsible for plenty of behavior.
This program and behavior relation is not restricted to that level of analysis either. It may arise between e.g. a hormone producing region and a diffusing influence field, or a signalling array between neighboring cells or regions, or a node and arc network relation between linked messenger proteins, etc. The "programs" may be at the systems biology level in other words.
I hope this helps.
Posted by: Gershom Zajicek M.D.
Even if you know the optimal state of individual enzymes, their function as a group, may be far from optimal. Which is a good example that a whole is more than the sum of its parts. Nevertheless our metabolism is always optimal. Optimality is the hallmark of life.
In order to model optimality with CA you need several prerequisites:
1. Enzymes are processes, that operate in interacting chains.
2. The context of an enzymatic reaction is the set of enzymes involved in it.
3. Optimization involves the entire context.
Take the citric acid cycle, which actually is a vortex whose optimality depends on all enzymes involved. http://www.what-is-cancer.com/papers/ca/ca86.htm
How to model it? You start with a small CA set, let them interact and evolve, and try to adjust their state parameters so as to optimize an attribute. By trial and error. Such an experimentation helps you to grasp intuitively what’s involved and how to proceed. Hopefully you will find out how to grow a CA ensemble which will optimize itself. Which is precisely what I am looking for.
http://www.what-is-cancer.com/papers/ca/ca48.htm
Posted by: Jim Edinger
The equations that describe enzyme kinetics in isolation and in metabolic context are well described. Many people have written very good metabolic modeling programs that are very adequate to quantitate these ideas (B. Paulsson, P. Mendez, S. Leibler among others). I have used Gepasi by P. Mendez to model a very simple metabolic pathway that has been extensively studied as a kinetic system. As described in NKS, this very simple system, consisting of 2 enzymes, an input rate and an output rate, evolves into a chaotic or complex system when the measure is the concentration of the intermediates in the pathway. Using kinetic constants that are close to the invivo values for the glyoxalase pathway in erythrocytes, I do not see a steady state system; it behaves as a more complex system that oscillates around the steady state.
In terms of systems biology, the philosophy of NKS and a deducible reductionist approach to complex systems is the only viable analytical approach. It seems to me that CA is very suitable to analyzing gene array data and proteomic data sets over a time course (or between diseased and normal tissue). Does anyone know of individuals that have chosen this type of analytical method? One could assign a particular CA cell to a gene or protein and test different rules for its evolution in time and attempt to predict the future state of the gene. This can be compared directly to gene expression data.
Posted by: Gershom Zajicek M.D.
Although Wolfram’s book shows how to generate complexity, it says very little how to reduce or simplify it. Which is a pity since I encounter it in my practice. Among other my task is to reduce the extreme complexity of the human organism to a manageable number of components, otherwise cure is unthinkable.
In the search for ideas and methods to simplify the human organism, I discovered Arthur Koestler’s notion of the Holon.
http://www.campusprogram.com/refere...r_koestler.html
A Holon is something that is simultaneously a whole and a part. Viewed from the perspective of larger things, the Holon is a part. Viewed as an entity in its own right, it is a whole that has parts. Like an atom which when viewed from above (chemistry) is a unit, while when viewed from below (quantum mechanics) it is an universe of quanta.
The cell which may be regarded as an atom of life, has similar properties. From the viewpoint of the organism it is a unit, while encompassing a universe of sub cellular structures.
Life is a Holon
The organism may be structured into the following Holons: organism -> organ -> tissue -> cell. Facing the higher hierarchies each Holon is viewed as an atom. "The members of a hierarchy, like the Roman god Janus, all have two faces looking in opposite directions: the face turned toward the subordinate levels is that of a self-contained whole; the face turned upward toward the apex, that of a dependent part" Each Holon is a node in a hierarchical tree, or Holarchy. - Arthur Koestler.
The definition of a Holon and Holarchy is arbitrary. It is a way to simplify complexity.
CA-holon: http://www.what-is-cancer.com/papers/ca/ca74.htm
Organism as a Holon: http://www.what-is-cancer.com/paper...andDisease.html
Posted by: Gershom Zajicek M.D.
Laplace (1749-1827) believed that if we knew the current state of all things in the universe and the forces acting on them, we could predict events with certainty. The concept is known as Laplace's Demon. By the end of the 19th century the demon was banished from physics by quantum mechanics, which regards the universe as random. Then came chaos theory according to which the universe is unpredictable. Today complexity makes the demon even less appealing, since the computability of the universe is limited.
Imagine a computer made of atoms. Since information flow from atom to atom cannot exceed the speed of light, there is a limit to its computing power. According to Bremermann no material system whether artificial or living can compute more than 2 x 10e47 bits per second and per gram of its mass. http://pespmc1.vub.ac.be/ASC/BREMER_LIMIT.html
Many similar demons dwell in our conceptual world which might be called complexity demons. Like the notion that the universe is a computer, and we are its computations. Or the universal computer mentioned in Wolfram’s book, whose universality is compromised by Bremerann’s limit. We may therefore distinguish between two kinds of complexity. One which can be generated with NKS, and a complexity demon which cannot.
Now imagine that life on earth is a computer, and its processes are computations. Apparently life is also constrained by Bremermann’s limit since it does not generate its complexity from scratch. It starts its computations from a baseline, the complexity of a cell. This issue was discussed in a previous section: http://forum.wolframscience.com/sho...s=&threadid=245
More on cell complexity in: http://www.what-is-cancer.com/papers/ca/ca0.htm
Posted by: jonny
To answer some earlier points, it is being suggested that:
1). Cells are the atomic unit of life
2). Cells inherit all their complexity.
3). Cells are static where Dead[A] = Born[A]
In my opinion these statements are not very useful. Instead I would suggest the following:
1). The subjective 'randomly varying replicator' is the atomic unit of life.
2). Inheritance is not perfect. Cells inherit their parent's complexity plus any additional complexity conferred by mutation. In this way complexity alters over time.
3). Cellular homeostasis results from a highly dynamic set of interlocking feedback loops where the point of balance fluctuates according to data harvested from the environment.
These alterations allow us to 'restrict our arguments to the simple and clear statements'.
1). Life is the result of the non-random replication of randomly varying replicators.
2). Imperfect inheritance can generate from scratch all the complexities of life. The gradual differentiation of starting conditions is responsible for the variation and complexity we observe.
3). A cell is not a closed system. Homeostatis is not the same as stasis. Cells do not remain in a 'steady state' but respond to their immediate and extended environment.
Over time both the internal state of a cell and the starting conditions it confers on its progeny can and do change.
Jonny
Posted by: Gershom Zajicek M.D.
Homeostasis was coined by the French physiologist Claude Bernard (1813 – 1878). Despite continuous turnover, for short periods of time, our (adult) body does not change its appearance. You may experience homeostasis by watching a lake. Despite continuous water inflow and outflow, for short periods of time its surface remains constant.
In a lake homeorhesis (rhesis = flow) might be more appropriate. I apply it also to describe the flow of material and cells in the body. For every cell born one has to die Dead[cell] = Born[cell]
http://www.what-is-cancer.com/paper...eamorganism.htm
Since cells beget cells {omnis cellula e cellula) they inherit their features as well as their complexity. As cells mature their complexity is affected by outside factors. This additional complexity is not inherited. We may therefore distinguish between the inherited cell complexity, or genotype, and acquired complexity, phenotype.
These concepts were tested experimentally and are therefore valuable.
It seems to me that the concepts which you raised cannot be tested experimentally. Like:
1). The 'randomly varying replicator' is the atomic unit of life.
3). Cellular homeostasis results from a highly dynamic set of interlocking feedback loops where the point of balance fluctuates according to data harvested from the environment.
I agree with you that:
2). Inheritance is not perfect
Posted by: jonny
You said "[cells] .. inherit their features as well as their complexity".
I think it would be more accurate to say that cells inherit their starting conditions. From the genes arise the cell and it is the random alteration of the starting conditions coupled to a selective environment that leads to the gradual accumaltion of complexity.
You also questioned whether my statement 'The 'randomly varying replicator' is the atomic unit of life' is verifiable. Let me assure you that it has been. Here is a break down:
1). That life consists of replicators (sexual and asexual) is not in question (see cell biology)
2). That replicators vary randomly via mutation has been demonstrated succesfully (see geneticts)
3). That non-random selection pressure kills some replicators while promoting others is supported by experimental evidence (see Darwin).
Therefore it follows that "Life results from the non-random replication of randomly varying replicators".
Unless you are religious then you can have no problem with this statement because it is far from controversial. Rather is a restatement of the founding principle of biology.
Finally. You suggest that homeostatic regulation via feedback has not been tested experimentially. I beg to differ and cite the science of cybernetics and biochemistry in my defence.
Posted by: MikeHelland
Jonny,
>Therefore it follows that "Life results from the non-random replication of randomly varying replicators".
>Unless you are religious then you can have no problem with this statement because it is far from controversial. Rather is a restatement of the founding principle of biology.
I'm not religious, but I have a problem with the statement. I think of life as everything that is observed. Like a cloud. A cloud isn't the result of replicators, I don't think.
Of course, in the context of biology you'd get less disagreement, but in science at large how can you say your statement is verifiable when what we've really done is simply take for granted an arbitrary defintion of life that agrees with the conclusion we want?
Posted by: Gershom Zajicek M.D.
I agree with you that “cells inherit their starting conditions”
You said :”it is the random alteration of the starting conditions coupled to a selective environment that leads to the gradual accumulation of complexity”.
Who showed experimentally that the alterations are random?
I agree with you that: 1). That life consists of replicators (sexual and asexual) is not in question (see cell biology)
You wrote 2). That replicators vary randomly via mutation has been demonstrated succesfully (see geneticts)
You might be interested in my criticism of genetics:
http://www.what-is-cancer.com/papers/bewareofgene.html
That replicators vary randomly via mutation has NEVER BEEN DEMONSTRATED! It is an ASSUMPTION. Please look at the other thread which deals with randomness.
http://forum.wolframscience.com/sho...s=&threadid=167
The next statement is obvious: "3). That non-random selection pressure kills some replicators while promoting others is supported by experimental evidence (see Darwin)."
Your conclusion reminds me of arguments by scholastic philosophers. You decided that randomness exists and “Therefore it follows that "Life results from the non-random replication of randomly varying replicators". Yet randomness does not exist as such it is in the eye of the beholder.
You said: “Finally. You suggest that homeostatic regulation via feedback has not been tested experimentially. I beg to differ and cite the science of cybernetics and biochemistry in my defence.”
The existence of homeostasis is obvious to any physician. Yet it is not based on negative feedback!!
My dear friend you are brainwashed with randomness. Look at your organism there is nothing random in it! Take my advice if a doctor treats you with randomness, ask a non random one for a second opinion.
Posted by: Gershom Zajicek M.D.
Although creativity is linked with complexity. Not every complexity may be regarded as creative. Take for instance the evolution of the logistic equation and its progression to chaos. Some chaotic regions reveal structure, while other resemble noise.
http://www.pha.jhu.edu/~ldb/seminar/logdiffeqn.html
Wolfram’s book depicts evolving chaotic CA which might be regarded as creative, yet their structures appear and vanish. Creativity involves more than a turnover of unexpected structures. In order to be relevant these creations ought to persist for a while. When this happens creativity becomes an innovation.
The growing embryo displays both kinds of creativity. Areas of intense cell turnover and fleeting structures are embedded in regions of innovation where the limbs are formed.
I developed a CA system in which rapid turnover and innovation occur side by side. As the CA evolves its cells (bits) continually change. Despite being chaotic it ultimately settles down and maintains its appearance.
http://www.what-is-cancer.com/papers/ca/ca126.htm
A river illustrates the notion of bounded chaos. Its water changes chaotically, while its banks are relatively stable.
Posted by: Gershom Zajicek M.D.
The Sepher Yetzirah, or Book of Creation, is one of the oldest Jewish religious texts to be found outside the Bible. It was written between the 3rd -6th century. It elucidates how God permuted and transformed the 22 letters of the Hebrew Alphabet to form the foundation of his creation and how he combined these letters to generate the words by which "He depicted all that was formed and all that would be formed."
The Book of Creation is an interesting attempt to handle complexity.
According to a Jewish legend God actually consulted the Book of Creation during his creation, and the book illustrates that creation proceeded algorithmically. The 22 letters of the Hebrew alphabet were placed in a circle and permutated. As the circle oscillated back and forth, the words emerged and were transformed into real objects. The algorithm is illustrated in Chapter 4:16. Stones means letters, and houses are groups of letters.
“Two stones build 2 houses
Three stones build 6 houses
Four stones build 24 houses
Five stones build 120 houses
Six stones build 620 houses
Seven stones build 5040 houses
From here on go out and calculate
that which the mouth cannot speak
and the ear cannot hear”.
http://members.fortunecity.com/patrickm/231kaplan.htm
Several centuries later Alan Turing defined a universal machine that is able to simulate any other Turing machine. Some computer experts regard our universe as a huge Turing machine. According to Church-Turing thesis it is generally assumed that an algorithm must satisfy the following requirements:
1.The algorithm consists of a finite set of simple and precise instructions that are described with a finite number of symbols.
2.The algorithm will always produce the result in a finite number of steps.
3.The algorithm can in principle be carried out by a human being with only paper and pencil.
4.The execution of the algorithm requires no intelligence of the human being except that which is needed to understand and execute the instructions.
http://en.wikipedia.org/wiki/Church-Turing_thesis
Although Turing’s algorithm seems better than that of the Book of Creation, God did use neither algorithm. He knew that nothing proceeds faster than the speed of light and with these algorithms it may take eons until his creation will be completed. Not that eons should disturb the timeless almighty. He was simply more creative than a Turing machine. He first thought of his creation, he then said “Let there be. . “ and created us in a parallel fashion.
http://www.what-is-cancer.com/papers/ca/ca01.htm
Posted by: Gershom Zajicek M.D.
Complexity as such is uninteresting. Yet it poses a threat to our existence. Imagine being placed in a complex maze when you desperately search for the way out otherwise you might starve to death. In order to save yourself you have to simplify and look for a pattern which points the way out.
Our interest in complexity is driven by the urge (need) to simplify it. One way to grasp it is by creating complex systems in order to simplify them. The more difficult the simplification, the more interesting is the system. The ease of simplification may thus serve as a measure of the system complexity.
Let's start with the complexity of the class-4 in Wolfram’s book (p. 231) which is easily simplified. You generate a CA set which displays calss-4 complexity and apply the following transformation. For every state, sum up its elements and you will get a number. In this way you may simplify any evolving CA in Wolfram’s book into a series of numbers.
The Mandelbrot set is somewhat more complex. It has two simplifying features. It is self similar, and has a fractal geometry.
What about noise which generates unpredicatable patterns? In a previous section it was mentioned that whenever noise is multiplied by itself it does not become more complex. Thus noise cannot generate complexity. In addition noise does not exist as such in nature and therefore does not pose a threat to our existence.
Life cannot be simplified at all. Any attempt to simplify it generates inconsistencies.
http://www.what-is-cancer.com/papers/ca/ca0.htm
Posted by: Mark McAndrew
The instant anything exists (as opposed to not existing) you have the concept of binary, therefore numbers and mathematics. That means infinite complexity explodes from the most simple condition possible: Is or Is Not. ('There is no try' - Master Yoda)
The Universe is fundamentally binary and what we see as particles, waves and even our consciousness is merely the result of huge persistent structures of 'on-space' and 'off-space' interacting. (Are these words or just pixels?)
We know all life is biology, all biology is chemistry, all chemistry is physics, all physics is maths, all maths is binary patterns. Everything is binary patterns.
Ultimately, it's blatantly obvious complexity needs no designer because then God could not exist (being complex as he is) and neither could anything else. Logic (and NKS) confirms that all you need is a 1 and a zero, something and nothing, and bang! Infinity.
Maybe God tried to tell us all along? "I am the One..."
Posted by: Vasily Shirin
<Quote>
We know all life is biology, all biology is chemistry, all chemistry is physics, all physics is maths,
all maths is binary patterns. Everything is binary patterns.
</Quote>
Who "we"?
Chemists don't beleive chemistry is physics.
Physicists don't beleive physics is math.
Methematicians don't beleive math is binary patterns.
I can't even agree that life is biology - it
depends what definition of "life" and "biology"
we are using.
Posted by: Jesse Nochella
Gershom, I think I have a useful tool in development that you can use for looking at cellular automata as a kind of body. Go to "Cellular Automata with Live Input".
Posted by: Mark McAndrew
Vasily Shirin, you are of course correct. I should have said, "I reckon" rather than, "We know." Especially on a math-related forum. My apologies.
Anyway, I still reckon!
Posted by: Gershom Zajicek M.D.
Hi Mark,
I suggest that you brush up your theology. Do you really mean that the One is a one of a binary number?
The One is the “infinite” and “timeless” of Western and Eastern Religions. In order to be grasped by finite beings like you he created the world in which we live and endowed us with the language of mathematics with which you may regard the One’s creation as a finite binary computer.
http://www.what-is-cancer.com/paper...ndtheology.html
http://www.what-is-cancer.com/paper...minddisease.htm
Posted by: Vasily Shirin
The logic "A is B, B is C, ..., Y is Z, and Z is just a bunch of bits" is an essence of Wolfram's philosophy, it's not Mark's invention.
I would rather beleive that A is not B,
even if it appears to be made of Bs. To explain the stability of atom, people had to introduce special force that keeps the thing together. Do we know how many additional laws and forces should be introduced to explain properties of proteins? (Even properties of crystals cannot at this moment be fully explained by known forces - as far as I know). So, here's my conjecture:
Every entity (that deserves the title of entity) has properties that cannot be deduced from properties of its parts.
I suspect this conjecture in fact has very ancient origin, but don't know who was the first to mention it - Platon?
Posted by: IvanKrasnyj
- Have a look at the B.Fuller Synergetics. He defines synergy also as the “behavior of integral, aggregate, whole systems unpredicted by behaviors of any of their components or subassemblies of their components taken separately from the whole.” (101.01-102.00, Synergetics)
http://www.bfi.org/synergetics/index.html
Fuller's Synergetics differs greatly from synergetics notion as self-organization of complex systems, used for ex. in Russia. Fuller assumes geometric neighborhood relations as basic reason for complex behavior.
I haven't found references to Plato at the BFI site.
Posted by: Mark McAndrew
Hey, I never claimed to invent anything! Many people have thought for years that reality is fundamentally digital (and by fundamentally, I mean just two states). After all, there is no such thing as 'analogue' anywhere in Nature, it just looks like it on large scales. Reduce that argument to its natural end, and voila! A binary Universe.
Stephen Wolfram's breakthrough - for that is most certainly is - is showing that incredibly complex structures can be created and sustained in the simplest binary system. NKS is indeed something wonderful - otherwise we wouldn't be on this forum, no?
And as for brushing up on my theology? For shame, sir! Here I am, trying to learn about maths for the first time since school - is that not enough for you?
If God exists, I bet he's as baffled by maths as anyone because it's the one thing he didn't create. He discovered it, same as the rest of us.
Posted by: Vasily Shirin
there's apparently some gap in Wolfram's reasonings. Suppose reality is digital. And we know that rule 110 is universal. Does it follow from here that if we run CA with this rule long enough, human beings will emerge in this simulation?
As usual, opinions will differ.
Some will beleive that yes, we will get human beings. I don't belong to this camp.
So, for me, it's somehow clear (I don't know why, by the way) that human beings will not materialize inside your computer running rule 110.
But what follows from here? Either that not ALL reality is digital, or ... I cannot say
that rule 110 is NOT Universal, because
it's proved to be such - so, it follows that
universality of rule 110 doesn't matter - it's not relevant if we want to explain the reality. This certainly contradicts Wolfram's theory (universality of rule 110 is a central point of the whole Wolfram's philosophy - he certainly beleives the impact of it goes far beyond abstract theory of computations)
Posted by: Vasily Shirin
To illustrate further what I mean by previous post, I constructed 2 possible dialogues between beveiver in Wolfram's theory (B) and non-beleiver (NB).
Dialogue 1
-------------
NB: Do you beleive that if we run rule 110 on a computer with 10^80 bits of memory,
human beings will eventually materialize inside a computer?
B: Yes, I beleive so.
This is the end of dialogue 1, because NB has nothing to say: position of B is perfectly consistent.
Dialogue 2
-------------
NB: Do you beleive that if we run rule 110 on a computer with 10^80 bits of memory,
human beings will eventually materialize inside a computer?
B: No, I don't think so. However, I think that some different rule being run on a different computer really brings humans to life at some point.
NB: Why different rule will be any better than rule 110? Rule 110 is known to be universal, and the whole idea of universality is that no other rule is fundamentally better than this one!
Same question arises with respect to different computer: why is it any better? Do you beleive that result of program run on IBM PC would be fundamentally different from result of the same program run on Sun workstation?
B: ...
[ Please substitute your response here ]
Posted by: Jesse Nochella
In regard to recent postings on this thread:
First, any thought about digital universe ideas etc. I think would benefit from reading Jason Cawley's post "The class 3 problem, PCE, and a cup of coffee".
As for your argument about Vasily, universality means the whole enchilada, and human beings, on the IBM and the Sun workstations; and on a sheet of graph paper, too. So long as you've got an infinite space to work on, you can make Macy's day parades, nuclear fireballs, nice long beaches, sweet bike tricks—all that stuff. Call it a big claim, but thats what this universality thing is all about.
10^80 bits aint good enough. We don't even know how much there really is to any literal object to place a limit like that. Besides, it's misleading to think of a system of a limited size as requiring less effort to make.
By running rule 110, I assume you mean from random initial conditions. Again thinking about things in finite terms complicates the matter and so it may seem perplexing just what random initial conditions we would use for our simulated beings, knowing they would come out. Basically the solution to this is to simulate a the rule guided by infinite random initial conditions, by making what is in essence a kind of background that corresponds to a computation that generates its own randomness in some way, and never repeats.
I'm sure that we would all look quite different at a cellular automaton printout. But hey, it's all in the representation. Maybe a speck of dust would recognize it immediately.
Gershom, I quote:
"Yet what are these ‘bodies’ which control our reasoning? For neuroscientists embodiment means the central nervous system (CNS) and its sensory organs. Some include also the autonomous nervous system which among other conveys our emotions. Which leaves out myriad processes in the body. Yet true embodiment includes all of them. It involves the entire complexity of the organism"
Why stop with the whole organism? What does it all really involve? Where is the threshold?
I think it can be defined in terms of NKS; and that is something we could actually do. So I pose the question of why do we not go down further? What's the stopping point. I don't know what R. Brooks said or what he had in mind, but my own ideas and take on embodiment is: likewise to the fact that all that we are is nothing but our bodies, I have this suspicion that the universe to us has more to do with our processes of perception and analysis than anything else, and that the body is actually a really fluid concept that can be described in terms of things like computational reducibility and irreducibility, and that we can actually go up all the way to the smallest distances, and to the edge of physical limits in general, to define what we can readily manipulate, and thus what is in a sense a part of our true body.
How does that idea sound?
Posted by: Vasily Shirin
OK, human beings come to life in a computer if we run rule 110 long enough.
Question: does a crystal feel pain when we take a hammer and break it to pieces?
Pain is a part of our reality. Some can argue that our feelings are unimportant,
all that is important is our reflexes - they
can be described in terms of 0s and 1s. Still, pain is REAL. If we leave pain out of the picture, then we don't cover entire reality.
At this point, we open a Pandora box:
if there's something that our model doesn't predict, there can be something else, and something else - so the model is flawed.
So, how about crystal?
Posted by: Gershom Zajicek M.D.
Dear Vasily,
Look at me. My name happens to be Crystal. Do I feel pain? You can’t ask me since I am in a coma. Before this fateful event I was treated in our psychiatric ward for a delusion that I was generated by rule 110.
Although pain is a part of your reality. How do you know that I am in pain? And yet you assert that if we leave pain out of the picture, then we don't cover the entire reality.
At this point, we open a Pandora box. . .etc.
So, how about me Mr. Crystal?
http://www.what-is-cancer.com/paper...wmedicine0.html
Posted by: Lawrence J. Thaden
Never mind the human being emerging from Rule 110, let's work on turning base metals into gold.
Posted by: IvanKrasnyj
S.W. gives profound classification of the CA, but I failed to find any one, providing conservation of initial elements. All the discussed CA models may happen useful for different applications, regarding phenomena of reproduction, competition and propagation of anything. These phenomena pertain to complex systems. CA used for the tasks, utilize large-block elements, which may appear and disappear.
However, when we discuss simple basic elements of matter, generating particles, atoms and molecules, which constitute living cell, one should consider these elements as entities and provide conservation rules for them at each step of CA evolution. Simple entity as far as it is already being supposed existing, couldn't disappear to nowhere, or appear from nothing.
To get plausible model of reality, based on simple entities, one needs to provide entity conservation rules, let entities move, group and rearrange. To provide global rules applicability, you'll have to get rid of the model borders, - for ex. make a wraparound Universe, so as each model would present a little closed digital World. Hopefully your supercomputer would process big enough Universe to show up emergent elementary particles' ensembles grouping. As for the living cell incipience, this regards several more levels of grouping properties emergence, - particles to atoms, moleculas, substance mixtures at different conditions... we do not live so long :)
Albeit, we could arrange several stages of modelling, - first understand particles ensebles grouping. Then, choosing right initial state conditions. We could force particles grouping to arrange atoms, substance mixtures and finally, get to virtual chemical process experiments (to speed up natural experiments).
As regarding the "Crystal's pain", - the hammer is not appropriate instrument for the task, because it would break up rules in the micro-Universe. To see the pain, you'll need to inject a "violent being" to your Universe and have a look at synapses' activity of your victim. All these fantasy requires inconceivable, and probably, unattainable resources. I guess, supergrouping properties require super-quantity resources to emerge.
Furthermore, I consider rectangular lattice models the worst choice for modeling of Nature's basic elements' behavior. There are no simple rectangular lattice structures in the Nature...
If we'll manage to guess the true basic mechanics of the Nature and see it's conformance to Reality (say, regarding particles interactions), all further stages of modelling, including the living cell, would be just a matter of time.
Posted by: Tony Smith
The biggest problem in thinking about all this is that we are immersed in a world which at our scale looks as though conservation is primitive. But when you actually do experiments you find persistent features emerging very readily.
Clearly the computing scale (and techniques) needed to simulate anything that is likely to provide a convincing demonstration is not within sight, so what I've been trying to do since my burst of experiments in the couple of years after NKS came out, is to do mental experiments cleared as well as I can of preconceptions.
The first thing that becomes obvious is that all simple rules applied to a sufficiently small space relatively soon settle into a persistent cycle (including period 1 cycles as a trivial case). As biological critters the very idea that conservation is achieved through sustained cycles should be second nature, but we have been indoctrinated with the idea that physical conservation is intrinsically different. It isn't. And if you can get past those barriers, the strangeness of quantum mechanics starts to seem a lot less strange.
But don't expect to see more than the most primitive hints emerge on a (readily computable) orthogonal grid, not even in rhombic dodecahedra, even if they are more elegant.
Posted by: IvanKrasnyj
To simulate Nature's fundamental structure of matter, we need to choose one correct model among the variety of possible CAs, conforming the NKS concept. I suppose, there should be not more than one TRUE mechanism for fundamental structure of matter, providing all observable phenomena.
To get closer to the desired CA model features, gedanken experiments certainly may be helpful. I've tried to work out a series of logical steps in this direction and stated the concept in Simulational Metaphysics essay.
It would be nice to hear any critical opinions on the issue. Are there any sound alternatives possible at each stage of the model development besides the proposed? Next, we could also discuss special software requirements for this kind of CA model.
Speaking of entities conservation, I mean the very basic principles for keeping just a cell contents and permitting its shifts to neighbouring cell in each CA phase. No long jumps are possible. The very basic conservation rules would provide further grouping properties conservation and elements aggregation.
It's nice to meet hands-on programmers of the NKS applications. I could hardly find a lot of time for the task. It's also weird to imagine spatial interaction even for several rhombic dodecahedra. I use 3ds Max for the task and need to rotate the scene each time to understand voxels' relations. Software rules implementation in this case is a must to see basic grouping and shifting algorithm in details. It's funny, but for ex., 5x5x5 tiling space pack of rhombic dodecahedra contains exactly 365 polyhedra. The f.c.c lattice packing differs greatly from the ortogonal one, as well as Cartesian coordinate system differs from Synergetics coordinates.
It would be also interesting to find out how do emergent grouping properties depend upon the digital Universe size in the suggested model.
Posted by: Vasily Shirin
Gershom,
I don't understand what you mean by your last post. My point was that CA cannot be a model of reality. Example of its deficiences is the fact
that real phenomena like pain cannot emerge in a computer simulation. Why they cannot emerge? You have to be a crystal yourself to know whether crystals feel pain or not. Ivan suggested
(if I understand him correctly), that if CA can simulate
particles, this could be enough. But what if particles feel pain, too? And what if their feelings affect their behaviour? (it would be
very strange if not). Then you, unfortunately,
come to conclusion that you cannot model just anything, except maybe statistical properties -
which, as far as I know, can be modelled by much
simpler means, even with respect to human beings
(e.g., advertisement agencies study statistical
effects of their ads). To do studies like this, you don't need to know the rules governing behaviour of elementary particles.
Posted by: IvanKrasnyj
There is a conventional opinion in biology,- "No brain, no pain." Plants and invertebrates do not feel pain. Professor Wenche Farstad from Norway recently investigated the issue:
http://www.animalactivism.org/resou...tory.php?pr=118
Pain is an important signal for creatures. Moreover, some people like the feeling... :) But these are biological problems though, and we are rather far from them at this point.
I consider particles behavior depends only of their mutual spatial location, but not of their mood or feelings. :)
And forget about fortuity at basic elements scale. This world is absolutely deterministic. Statistical reports just reflect degree of information loss due to generalization processes. As I wrote in my concept, in Reality we just do not know in advance what shall we meet on the road.
Posted by: Vasily Shirin
Sorry, Ivan, but your reference to conventional opinion in biology doesn't dound very convincing.
Biologists still insist, for example, that the whole
evolution can be explained by random mutations.
When you ask them how probability of, say,
10^(-1000000) can ever materialize, their responce
goes along the lines of "well, why not - if you
try long enough". 10 or 20 billion years is
long enough for them.
Can I propose an experiment for you,
which is relatively easy to implement (easier
than simulating universe populated by dodecahedrons). Capture any biologist (for greater accuracy of experiment, he should be a specialist in evolution theory),
and ask him to compare two values:
10^100000 and 10^1000000.
I bet the second value will turn to be by 10 times greater.
The last thing you can rely on is opinion of biology professors (I had a pleasure to know some)
Posted by: IvanKrasnyj
I wouldn't evaluate biologist's contribution and abilities here. The biologists are payed by government to decide if the creatures feel pain. The government qualifies them to be authorities in this sphere in order to relax animal activists.
Pain pertains to conscious creatures. In our case, generally speaking, we assume a huge simulation model of Reality where a projection of conscious creature may exist. This wouldn't be just a cinema screen. The model should provide absolute likeness of the natural objects behavior, dependent of the environment, but in limited model space and under another time scale. Also the media would differ. For ex. we'll assume software only implementation.
The question is: Does the software implementation of conscious creature feel pain and persieve the reality? The answer would require analysis of the software objects behavior, likewise performed by Professor Wenche Farstad from Norway. The answer will be positive. The behavior of the objects corresponds to notion of pain.
Posted by: Vasily Shirin
In other words, you (along with government-paid biology authorities) confirm that if we take a piece of paper and start painting squares black and white accoring to rule 100, or some other rule, some combinations of these squares will represent human beings, which not only behave like human beings, but feel pain like human beings. Right?
Posted by: IvanKrasnyj
Vasily,
Your question just contains information storage metaphor. It doesn't matter how information is being kept. The key feature is system behavior as reaction to intervention.
No any creature could "connect" to other creature's brain in order to intercept his/her perception flow. At least, a task of feelings mapping should always persist. Thus, we could draw conclusions about feelings experienced by other creatures only basing on their behavior, including internal physicochemical processes, observed nervous system state and structure. Hence, any object (no matter of inhabitance media), demonstrating dynamic behavior, dependent of our intervention and corresponding to our notion of pain, should be qualified as suffering. Don't forget to take in account, that " feeling of pain" should be also concerned with the inhabitance media. Pixel shifts make sense for pixel-creatures, living in pixel-world. They do not know, that they are made of pixels. It is your's comprehension of the model. Pixel-creatures will demonstrate their behavior and we would consider their reaction to our intervention as suffering.
Rule 110 doesn't care of entity conservation principle, thus it couldn't be nominated to the tasks of basic structure of matter modelling.
... we take a piece of paper and start painting squares black and white...
First, I insist on conservation principle implementation, so you'll need to shift cells filling, but not only mark them. Next, people, paper, computers and the Universe wouldn't live so long to perform the task of a conscious creature behavior modelling. In Realty simple events happen at a speed of light and presumably seize a Plank's unit of time, - 10^-44 sec. BlueGene/L makes 71 TFlops. How long would it take it to simulate motion of several basic elements to one santimeter shift by shift at the Plank's scale lattice? Each shift needs to be performed by the processor.
I even hope just to get closer to particles interaction simulation, assuming deliberate choises of initial states and very small Univerce size. Living cell modelling is not within sight, as Tony said.
The next trouble concerms the major difference between reality and its model, - the strictly deterministic behavior of basic elements at fundamental scale of Reality and fortuous behaviour of anywise complex fundamental blocks for the model of any kind. Here I mean the existence of stationary ether dislocations in space, happening on the road and triggering random events for complex construction blocks of the model. The hardware is a mandatory part of the model. That is also the reason why computers, providing interface between Reality and Simulation are not eternal. We'll be principally unable to provide required reliability for the Planck' scale voxel model of a huge complex system, like conscious creature behaviour.
Answering to your question in other words, if you'll succeed to build such a model, no matter of information storage design, you can easily consider the creatures suffering. At least, currently this is the implication, people assume for notion of pain, regarding any kind of creatures.
Posted by: Vasily Shirin
How about cartoons in computer game? Do they feel pain? Based on their behaviour, they do.
How about reality in computer game? When you'are shooting marsians in one room, does another room exist? Or it's created on the fly as soon as you enter it?
How do we know that remote stars really exist if we have never seen them? Maybe, they will be created on the fly when we develop necessary instruments?
What strikes me in all proposed constructions
of modelling Universe is the lack of originality. These mechanistic ideas are hundreds of years old. In a recent history, they were the basis of marxist ideology. It was used to enslave a billion people. You mentioned government-sponsored research in biology: in USSR, all research was government-sponsored. There were 100,000 Ph. Ds
in economics - their dessertations proved beyond reasonable doubt that USSR has the most advanced economy in the history of human kind. At the same time, stores were empty, and buying a bottle of milk was a challenge (we used to go to Moscow -
250 km one way - to buy 400 grams of butter), and
only two things could be purchased relatively easily: vodka and bread (except some periods
when they were not available)
They used to say: look, guys, more and more countries in the world select communism - it's
just a matter of time to see the whole world following our suit. Doesn't this logic sound familiar?
Wolfram says: more and more phenomena get explained based on deterministic, materialistic platform. Consequently, one day we will be able to
explain the rest. And he proves that if this possible at all, it can be possible with CA simulation. He is right! He really proved the equivalence of all mechanistic models to just rule 110 alone!!!
He just forgot this little "if".
Posted by: IvanKrasnyj
Originally posted by Vasily Shirin
How about cartoons in computer game? Do they feel pain? Based on their behaviour, they do.
Computer simulations are rather different. What we've already discussed was CA applications for fundamental structure of matter simulation. The key feature for this class of simulators is natural grouping and rearrangement of basic elements. The ensembles of these elements would discover emergent properties. Super-grouping ensembles, if being ever achieved in simulation, would also show up emergent super-phenomena like conscious creautres behaviour.
Frankly speaking, the model, proposed in Simulation Metaphysics essay do not belong to CA (it may require CA definition extension), as it utilizes far-away neighboring rules and assumes following to simple entities conservation rules.
There may be used different initial states for the CA. And there's nothing common with computer games. Computer games are just entertainments with preprogrammed scenery.
How about reality in computer game? When you'are shooting marsians in one room, does another room exist? Or it's created on the fly as soon as you enter it?
There's no common with Reality in computer games. We should differ between imitation and simulation. I assume simulation, based exceptionally on fundamenatal rules for basic Plank's scale elements could replace natural physical experiments if could prove its plausibility in simple cases.
How do we know that remote stars really exist if we have never seen them? Maybe, they will be created on the fly when we develop necessary instruments?
Good question, but not a new one. Anyone can make up a lot of theories, but there are common principles used to check out their plausibility, - for ex., "least action" principle, Occam's Razor... this discussion better suits philosophy newsgroups.
What strikes me in all proposed constructions
of modelling Universe is the lack of originality.
I've suggested exact solution for the discrete space-time model, demanding computer testing. The concept corresponds to properties of isotachy, kekinema and renovation, mandatory for any discrete space-time model and never available before. The task require supercomputer facilities, absent in Russia. The best supercomputer cluster in Moscow provides 300 GFlops, but top 500 supercomputer list just starts at 1000 and ends with 71000 GFlops.
Wolfram says: more and more phenomena get explained based on deterministic, materialistic platform. Consequently, one day we will be able to explain the rest. And he proves that if this possible at all, it can be possible with CA simulation. He is right! He really proved the equivalence of all mechanistic models to just rule 110 alone!!! He just forgot this little "if".
- I've already explained that CA definition needs to be extended. First, to include far-away neighboring rules to provide non-locality properties of the model of Universe. And second, to provide simple entity conservation rules, which present basic mechanism, providing emergent properties accumulation, and encapsulation.
Posted by: Gershom Zajicek M.D.
Is the water in a cup complex? You might regard it as a pile of isolated water molecules randomly tossed around. Their velocity is distributed according to the Maxwell-Boltzmann distribution.
You are wrong! Actually each water molecule is an oriented vector whose front is occupied by an oxygen atom and the rear by the two hydrogen atoms. Each vector head attempts to get as close as possible to the rear of other vectors, generating complex structures. The Maxwell-Boltzmann distribution presumes that water is isotropic. Molecules behave like isolated billiard balls. Yet these tiny vectors molecules interact and do not resemble billiard balls. Water is anisotropic.
However since the interaction among water molecules is extremely weak, it may be neglected or ignored, which is how statistical mechanics regards water. Which illustrates the central themes of this thread:
1. There does not exist a reliable complexity measure, and the definition of complexity is arbitrary.
2. Randomness does not appear as such in nature. It is a convenient way to describe it.
3. The Maxwell-Boltzmann distribution does not reveal all that nature has to offer. It is an approximation to nature’s complexity.
Water memory
Some believe that water has a memory. Small impurities change its structure and affect its response, in the same way as impurities do to a semiconductor. Water thus remembers its impurities. Which explains why no two snowflakes are the same. Each remembers different impurities.
Homeopathic medicine relies on water memory during treatment. A drug dissolved in water is diluted many times, until only traces of the drug remain. This method, known as potentiation, is believed to enhance the effect of a drug.
Oriented complexity
Once you let water flow its complexity becomes oriented. Like in the river that reveals recurring patterns, whorls, and other structures, which depend on its bed and will disappear during stagnation. Or the water flowing from a faucet whose structure depends on the faucet outlet and water velocity.
Oriented complexity is the hallmark of life. Processes in organism are streams of matter, like in the protein assembly line. It starts at the gene which encodes a particular protein. After this information is translated it directs RNA molecules to assemble amino acids into small chains called peptides which gradually grow and become more and more complex whereupon they are called proteins. The growing protein molecule streams away from the gene site toward the cell periphery where it becomes an enzyme.
Since the organism maintains a steady state, for each molecule which starts its voyage at the gene site one dies at the periphery. The molecules obey the fi-fo rule, (the molecule that is formed first also dies first).
Additional reading: The Streaming Organism:
http://www.what-is-cancer.com/paper...eamorganism.htm
http://en.wikipedia.org/wiki/Streaming_organism
Posted by: Vasily Shirin
> I've already explained that CA definition needs to be extended.
No matter how you extend it, it will still be equivalent to Turing machine. So, the basic claim remains that Universe can be modelled as Turing machine.
Turing thesis states that our intuitive notion of "purely mechanical" procedure can be formalized as Turing machine. Turing machine, in turn, is an abstraction of our own, human way of implementing "rules". It's quite possible to imagine that different kind of intelligence might produce different definition of "purely mechanical" procedure, which is not equivalent to ours (so we will never fully understand it). Which will not prevent us from using this "supernatural machines", like we are using electricity while having no clue of how it works. For example, I believe we will soon discover a way of utilizing "intelligence" of bacteria to solve our own practical problems.
Posted by: Vasily Shirin
I found a good article that elaborates on common misconceptions about Turing machines:
http://plato.stanford.edu/entries/church-turing/
Posted by: IvanKrasnyj
Originally posted by Vasily Shirin
So, the basic claim remains that Universe can be modelled as Turing machine.
1. - Of course. Turing machine, bluntly speaking, is a synonym of computability. Human logic operates entities with discrete states TRUE, FALSE (sometimes, NON DEFINED state) and rules to change between the states. I'd like to note, that at this point, those who claim that Universe can be modeled as Turing machine (or "Universe is a computer" (c) E.Fredkin), should bury continuity principles together with infinities and uncertainities it brings, and rely on discrete space-time concept. Comprehension of this fact will lead us to very long and important consequences. My proposal to extend CA definition is just a step in this direction.
2. Let's assume alien logic differs from human logic. We'd never know this and never need to know. Any kind of alien behaviour we'll always MAP to human logic (formal logic) and our model of the reality. The very sense of "understanding" of any phenomenon means that somebody's personal model of reality matched the logics of the phenomenon in such a way, that a satisfactory forecast of the phenomenon may be performed. Finaly, any person operates his own personal logic. In most cases people's behavior just looks similar. Any person is alien...
3. The third issue concerns generalization principles in simulation. My comprehension of complexity is strictly hierarchical. I mean that first we need to start modeling from the very basic elements and discover emergent properties of ensembles of these elements. Moreover, we need to use the discovered ensembles of basic elements on the next level of modeling and set up corresponding initial states for the next level of simulation. We are not justified to substitute the discovered model of proton with a ball. Balls wouldn't group as primary proton models and wouldn't discover emergent grouping properties.
Any generalized model (and this also concerns Gershom's models) will provide limited correspondence to reality and would never show up emergent grouping properties of its elements. Though, taking in account a long chain of complexity levels, it may occure useful for a certain modelling tasks. Anyway forecasting power of generalized model would depend mostly upon preprogrammed sceneries of the elements behavior.
Posted by: Vasily Shirin
>Any kind of alien behaviour we'll always MAP to humane logic (formal logic) and our model of the reality
You are mistaken. We know just infinitesimal part of reality. We will certainly know more in the future, and, I'm sure, during your lifetime you will see more discoveries leading far beyond our current, mechanistic worldview. Still, I advise that you should read the article about Turing thesis I referred to in my prev. post.
There's no need to involve aliens. Such "aliens" are all over the place; our own body is an example of such "alien".
You have to realize that position you're advocating is something that was historically called "vulgar materializm".
Posted by: IvanKrasnyj
Originally posted by Vasily Shirin
>Any kind of alien behaviour we'll always MAP to humane logic (formal logic) and our model of the reality.
- You are mistaken.
Are you denying here subjective comprehension in general? There's no matter how much do we currently know about the Universe. At any level of knowledge our comprehension would remain subjective.
I'm sure, during your lifetime you will see more discoveries leading far beyond our current, mechanistic worldview.
- So, you confirm, that our current worldview is mechanistic...
and believe that future would give us a new logic?
There exists a plenty of questions laying behind the borders of knowledge at any time. They call this faith. I even consider current notion of fields and forces as related to sphere of faith. We always apply to belief if we have no explanation for a phenomenon... If the explanation wouldn't be mechanistic, one should necessarily consider it a question of faith.
However, one can find a lot of studies beyond our current, mechanistic worldview even nowadays. For ex.,- "Sri Aurobindo or the Adventure of Consciousness", "Life After Life", Chiromancy, Astrology and etc. :)
You have to realize that position you're advocating is something that was historically called "vulgar materializm".
I do not advocate any particular philosophic doctrine, I even hardly could find any, really matching to the concept.
How can one qualify the description of metaphysical (directly unobservable) fundamental structures, which may provide simulation process and posess forecasting power? This site just gives me a good chance to discuss the proposed concept and particular technique for its testing with interested researchers.
Vulgar Materialism denies personal specifics of consciousness and considers consciousness as physiological function of organism. As for my concept, I even do not pretend to make a model of living cell yet. It's too early to discuss such a huge levels of complexity.
Here I consder complexity as hierarchy of grouping for elements' ensembles, showing up new emergent properties, as we extend our Universe model size.
Posted by: Vasily Shirin
>So, you confirm, that our current worldview is mechanistic... and believe that future would give us a new logic?
Yes, I confirm that; however depressing it could be, this is true. Now it looks like a historical impasse, but I strongly believe things will change in the future.
You know, children often despise the views of their parents; when current generation of marxist university professors retires, their students will merrily throw away old theories.
It's not about astrology. Our own existence is a miracle. We have miracles all over the place, we just got used to them and don't pay attention. Why do we ignore them? Because we're in denial, as
dictated by dogmas of our materialistic religion.
Posted by: Gershom Zajicek M.D.
1. Self organization, or organization without a central organizing authority.
2. Emergence of an unforeseen behavior.
3 Their behavior cannot be explained by decomposing the system into sub-parts.
4 The system is an ongoing process.
5. The system adapts creatively to unforeseen challenges of the environment
6. In order to survive it optimizes its organization.
7. The ability of the system to perform a task is triggered by the environment.
8. Some complex systems may propagate their design.
Creativity is defined as an unexplained behavior or adaptation.
Optimization is defined as; Given a set of constraints by the environment, the system organizes itself so as to minimize their undesired effects to it.
Some examples of complex systems:
1, The Internet.
2. Eco-system.
3. Networks like electricity and highways.
4. The metabolic network of the organism collectively called here as Wisdom of the Body (WOB)
http://www.what-is-cancer.com/papers/ca/ca93.htm
A complex system may be simple and uncomplicated like the one which I designed. It consists of two cellular automata, and displays properties 1-7 of the list.
http://www.what-is-cancer.com/papers/ca1/ca167.htm
Posted by: Gershom Zajicek M.D.
The term autopoiesis, which means "self-production" was originally introduced by Chilean biologists Francisco Varela and Humberto Maturana in the early 1970s. They attempted to create simple models which capture the essence of the living organism, like:
Its identity remains constant while its components continually change.
It is a whole (holon) despite the dynamics of its component parts.
It is self organizing, can repair itself, and its properties emerge.
The original model was written in FORTRAN and placed in a lattice. The unit had a interior wrapped in a membrane through which it interacted with the exterior. You are invited to experience a more sophisticated autopoiesis model, the proliferon, which applies two powerful tools, JAVA and CA.
http://www.what-is-cancer.com/papers/ca1/ca174.htm
The experiment illustrates a profound philosophical question. Are living organisms teleological? Do they have an end purpose? The proliferon has two end purposes: To mature and produce offspring.
Posted by: SteveA
Posted by: mick whieldon
An interesting NKS relavent subject - EPIGENETIC INHERITANCE.
http://www.wsu.edu/theinnovators/march/news-2.html
Posted by: Gershom Zajicek M.D.
The genome is regarded today as blueprint of the organism. Despite the great hopes in the “Book of Life” it turned out to be not more intelligent than a telephone directory or better the yellow pages, which tell you who is doing what but fail to reveal how it is done.
Unfortunately the Book of Life does not indicate how the complexity of the organism is generated. Biologists distinguish therefore between two realms: genetics or the blueprint, and epigenesis, where complexity emerges. While the first may be investigated by reduction, epigenesis can be understood only phenomenologically (which is explained in the other thread).
All this is bad for business, which had embraced Book-of-Life-start-ups with love. Soon disenchantment with the Book of Life drove bio-stocks downward. In order to save their business companies created new buzzwords, e.g., epigenetics and proteomics. Methylation which is the hallmark of epigenetics is a new way to control genes which is not determined by heredity. True, it is a first step to a new level of complexity but a very modest one. Despite the similarity of the names epigenetic and epigenesis they are utterly different from each other.
Their difference may be illustrated with simple CA systems. A CA rule and its initial conditions might be regarded as CA-gene. Yet once you iterate, you are actually practicing epigenesis. Even better, you might regard the set of CA rules as system genes, while their initial conditions are no more than their epigenetics.
Check it in the following site:
http://www.what-is-cancer.com/papers/ca1/ca167.htm
Posted by: Gershom Zajicek M.D.
Complexity of life
The complexity of a living cell cannot be generated with a simple program
http://www.what-is-cancer.com/paper...ityofliving.htm
No living entity known today generates its complexity from scratch.
http://www.what-is-cancer.com/paper...entityknown.htm
The cell is the atom of life
http://www.what-is-cancer.com/paper...ecellisatom.htm
The complexity of the genome
http://www.what-is-cancer.com/paper...ofthegenome.htm
The complexity of a living cell is ordered
http://www.what-is-cancer.com/paper...xityordered.htm
The complexity of life is oriented
http://www.what-is-cancer.com/paper...dcomplexity.htm
Wisdom of the Body (WOB)
http://www.what-is-cancer.com/paper...omofthebody.htm
Model of the Wisdom of the Body (WOB)
http://www.what-is-cancer.com/paper.../modelofwob.htm
WOB and cell death
http://www.what-is-cancer.com/paper...ndcelldeath.htm
Autopoiesis
http://www.what-is-cancer.com/paper...autopoiesis.htm
Holon - A complexity unit
http://www.what-is-cancer.com/paper...plexityunit.htm
The hierarchical arrangement of our organism into attractors is entirely arbitrary
http://www.what-is-cancer.com/paper.../attractors.htm
Epigenesis in Cellular Automata
http://www.what-is-cancer.com/paper...genesisinca.htm
A simplified model of protein assembly
http://www.what-is-cancer.com/paper...elofprotein.htm
Action memory of a blastocyst
http://what-is-cancer.com/papers/ca...yblastocyst.htm
Chaos
Chaos does not exist as such in Nature
http://www.what-is-cancer.com/paper...oesnotexist.htm
Life is not chaotic
http://www.what-is-cancer.com/paper...snotchaotic.htm
Chaos and creativity
http://www.what-is-cancer.com/paper...dcreativity.htm
EEG and Chaos
http://www.what-is-cancer.com/paper...eegandchaos.htm
Heraclitus and boundary chaos
http://what-is-cancer.com/papers/ca...oundedchaos.htm
Complexity attributes
Complexity spectrum
http://www.what-is-cancer.com/paper...ityspectrum.htm
Properties of a complex system
http://www.what-is-cancer.com/paper...mplexsystem.htm
The Complexity Demon
http://www.what-is-cancer.com/paper...lexitydemon.htm
Transfinite complexity
http://www.what-is-cancer.com/paper...ecomplexity.htm
Optimality is a property of a process ensemble
http://www.what-is-cancer.com/paper...isaproperty.htm
Simplification
http://www.what-is-cancer.com/paper...plification.htm
Information theory and complexity
http://what-is-cancer.com/papers/ca...ationtheory.htm
Robot psychology
Robot intelligence
http://www.what-is-cancer.com/paper...ntelligence.htm
Soul and complexity
http://www.what-is-cancer.com/paper...dcomplexity.htm
Memory of a complex system
http://www.what-is-cancer.com/paper...ryofcomplex.htm
Action memory
http://www.what-is-cancer.com/paper...ctionmemory.htm
Orientation memory
http://www.what-is-cancer.com/paper...ationmemory.htm
Emotions
http://www.what-is-cancer.com/paper...ty/emotions.htm
Metaphysics
Bergson and Complexity
http://www.what-is-cancer.com/paper...dcomplexity.htm
Complexity and free will
http://www.what-is-cancer.com/paper...andfreewill.htm
Metaphysics and complexity
http://www.what-is-cancer.com/paper...dcomplexity.htm
Popper and complexity
http://www.what-is-cancer.com/paper...dcomplexity.htm
The first universal computer
http://www.what-is-cancer.com/paper...salcomputer.htm
The illusion of time
http://www.what-is-cancer.com/paper...usionoftime.htm
Relative time
http://www.what-is-cancer.com/paper...elativetime.htm
The issue here is the universality of NKS
http://www.what-is-cancer.com/paper...issuehereis.htm
Nature is neither complex nor simple
http://www.what-is-cancer.com/paper...thercomplex.htm
Popper and complexity
http://www.what-is-cancer.com/paper...dcomplexity.htm
CA and Aristotle’s Four Causes
http://www.what-is-cancer.com/paper...ndaristotle.htm
Intelligent design and complexity
http://www.what-is-cancer.com/paper...igentdesign.htm
Phenomenology of complexity
http://www.what-is-cancer.com/paper...fcomplexity.htm
Embodiment
http://www.what-is-cancer.com/paper.../embodyment.htm
Phenomenology of Artificial Intelligence
http://www.what-is-cancer.com/paper...fartificial.htm
Evolution of Intelligent Design
http://what-is-cancer.com/papers/ca...intelligent.htm
Randomness
http://www.what-is-cancer.com/papers/ca/randomness.htm
Posted by: Enexseenge
How on earth would one isolate out a particular process, label it's functionality within the parameters of "it's system" and then discard all other processes which have been isolated out as irrelevant separate systems, and at the same time attempt to find the emergent pattern within the "chaos".
Does each system that is isolated out have it's own behavior and rules? or are there universal rules that are emergent in information transfer functions, whether or not they manifest within constructs of physicality?
Could these emergent rules exists in a non physical relation that extends beyond the physicality of the universe? And that the manifestations of physicality are simply chance assemblies of a finite systems which function within a particular set of rules which are sourced from the "Sea" emergent rules which exists independent of physical representations??
It seems that there is a problem in the way that things are formulated in thought, not that this can be transcended in an instance, but their is a limiting framework from which we can approach things with. For one, my experience with NKS has been that only under the possibility that there exists a framework, or universe, which is independent of physicality and composed of information transfer functions that are not necessarily in action, but available to systems which will allow those functions to arise, only with that type of permeability can we find emergent behavior which can relate complex processes together in a "new kind of way" a way that shows us something we do not yet know... But then again, I am all about hypothetical thinking, and non of what I say is based on fact.
The issue with the cell, it does not have initial conditions it self from scratch, but it inherits these conditions from it's ancestors. Are you then to say that at no point within the cells functioning would you be able to draw out emergent rules which explain it's interactions in a way that parallels the actual process which could be used to observe different degrees of the system under the same rule, and that only from observation of the ancestral gift would one be able to find emergent rules?
If so, then this is similar to what i was saying.
The DNA has many forms from which it could express it self through, not all of these forms are currently in existence, yet their must be some aspect of DNA which we could find that would allow us to see the emergent behavior in, say, two different systems. For example, we could see how various arrangements of DNA would lead to different systems, and from observing the differences in these systems we could classify a degree of variance, a degree of "flexibility" within cellular formation which would be in relation to the initial conditions of the DNA...
Perhaps it is simply our inability to interact with matter at that level that prevents us from learning more about it. We are relying too much on theories and not correlating enough with physical data, not that this data exists yet, which is why i say there is a limitation to how we approach things, and that limitation is within our tools which we use to observe with.
When we touch down at that level of cells we are course, and we are invasive, we are not silent observers, we need to find a way then to make an experiment which would observe cell interactions in much finer detail... There is some work being done on this at the University of Washington http://faculty.washington.edu/afolch/
which you might find interesting.
Links to UW's Center for Nanotechnology research topics: Biological Nanosystems
http://www.nano.washington.edu/rese...table=materials
Posted by: Arion
Originally posted by Gershom Zajicek M.D.
My previous sections have shown that the living cell inherits an ordered complexity. It has an interior where protein assembly lines start, and a periphery where they end. Each gene is the starting point of a protein assembly line. The proteins advance (stream) along the assembly lines and when their time has come they disintegrate.
I am in no way qualified to debate this, I also highly doubt that I have so much as a tenth of the background of which most of you have, even so, I find this debate highly intriguing, anyway, on to my reply.
As per your quote does that alone not stand to compliment the NKS theory? In most of the examples within Stephen's does it not show small structures being created, changing, and then disappearing (in essence, dying)?
Posted by: Gershom Zajicek M.D.
Each assembly line is an oriented process obeying the fi-fo rule. The first molecules formed at the gene site, are also the first to die at the end of the line. It’s not enough to show that structures are created and destroyed, which is the essence of turnover. It has to be oriented. My question is. where does NKS mention turnover ? And where does it mention oriented turnover?
http://www.what-is-cancer.com/paper...g/proteins.html
Posted by: Gershom Zajicek M.D.
Complexity is the key attribute of life. Even the smallest living organisms like the microorganisms are extremely complex. Each is an individual cell distinct from the inanimate matter in which it exists. Actually the cell is an atom of life. Some believe that life can originate from inorganic matter, which has not yet been verified experimentally.
The cell is the atom of life: http://www.what-is-cancer.com/paper...ecellisatom.htm
Simplify or remove the complexity of a living cell and it will cease to exist as such and become inanimate. There are two laws which characterize matter and life: Conservation of energy and the conservation of mass. Yet life is characterized by a third law, the conservation of minimal complexity. Imagine the following experiment. Take a suspension of bacteria and heat it to 100 degrees centigrade. The first two conservation laws still hold. However the heat reduces (destroys) complexity and turns the bacteria to inanimate matter.
On the other hand you may cool the cells to near absolute zero. They will maintain their complexity, and show signs of life when warmed up to our room temperature. This experiment supports the assumption that cells may travel unharmed in outer space. They may have seeded our planet when the primordial soup cooled to a complexity preserving temperature. They probably continue seeding it even today, when comets enter our atmosphere.
Panspermia: http://www.what-is-cancer.com/paper...ityofliving.htm
Posted by: Enexseenge
" Each is an individual cell distinct from the inanimate matter in which it exists."
Please go into more detail about this if you would..
I feel that the cell is not distinct from the inanimate matter in which it exists..
I think that where the complexity of the living system comes from is in implicate rules that live within a specific configuration of molecules. The complexity of the living system has more so to do with the subtle effects within the interactions of matter, then with some spark of life..
Could not this atom of life actually be a process of implicate rules that are existing within specific arrangements of inorganic matter?
The functionality that is observed within the cell could be composed from the "deeper" levels that exist in domain of the molecules, and the complexity of the living cells is a colligation of these molecular interactions that perpetually maintains it self in application... Application which is derived from the observed functionality.
Posted by: Gershom Zajicek M.D.
Each cell is covered by a membrane which separates it from its neighborhood. The membrane serves as interface between the cell and environment and controls the transfer of energy and matter. The membrane determines the individuality of the cell and its nature. However the membrane is not an independent organelle, it is an integral part of the cell’s complexity.
Imagine an oil droplet immersed in water. Its outer fat layer is the interface between the droplet and water and yet it is not different from the other oil molecules. We call this outer layer a membrane while in reality it is not a separate structure. Now add to the water drops of different dyes and you will realize that some will penetrate the oil droplet. We call them lipophilic (oil-lovers). Their access into the droplet is controlled by the so called membrane and in order to penetrate it they better be called “membrane lovers”
The cell is an extremely complex droplet, with a so called membrane which is an integral part of this complexity. More, this membrane is continually renewed, it is part of an oriented process (stream) from the cell interior. It is continually turning over in an ordered way.
You ought to distinguish between qualities of the cell itself and qualities which we attribute to the cell. Like the membrane which is our view how the cell is structured. Or “oil loving” which is our way to interpret what this droplet does.
You may feel that the “cell is not distinct from the inanimate matter in which it exists” The oil droplet is distinct? And so is the cell.
You think “that where the complexity of the living system comes from is in implicate rules that live within a specific configuration of molecules.” While the complexity is obviously there the rules are not part of it. These are qualities which we attribute to the cell. We might as well propose that a guardian angel accounts for this complexity.
When a cell is born it inherits its complexity, membrane and individuality from its parent cell as stated by Rudolf Virchow (1858). "Omnis cellula e cellula" (where a cell arises, there a cell must previously have existed).
http://www.what-is-cancer.com/paper...ecellisatom.htm
Posted by: Enexseenge
Thank you for your response..
I think i understand what you describing in more detail now..
The part about all cells come from cells makes sense..
As in saying, that we cannot "Create a cell" from the bottom up, unless we are a cell our selves..
So if we were to see a functionality within the cell,
for example the protein "walker" that is currently an interest in nanotechnology research.
A protein structure within the cell that transports molecules by walking around the cell membrane.
If we were to isolate out that particular process we may study it extensively and find vast amounts of information about how it works, but all of that information we have found is specific to that isolated system it self, and it is not part of the complexity of a "unit cell"..
But it is part of the complexity of a specific process which may or may not actually be "within a cell" when it is existent..
So what can "generate" the complexity of a living cell?
Another living cell?
Posted by: Gershom Zajicek M.D.
Isolating single processes of a cell is the essence of medical research. If you want to study an enzyme which converts a substance A to B, you place the enzyme in a test tube, add substance A and observe how substance B is created. This what biochemistry is about. In the intact cell the three substances are processes.
The enzyme is a protein encoded in the DNA and born there. It then travels from the site of its birth to the site where it will meet substance A. As it travels through the cell it interacts with other molecules differentiates and when mature it is ready to convert substance A to B. Substance A just crossed the cell membrane and streams toward the site where it will encounter the enzyme. The newly formed B substance will then travel somewhere else.
What the biochemist observes in the test tube is a static representation of three ongoing processes. A three dimensional projection of a multidimensional complexity. It’s like trying to capture the essence of a river in a glass of water. Chemically river and glass hold water yet when placing the river in a glass it loses its organization inherent in its stream. Isolation of your “protein walker” is a simplification of complex dynamics. A faint shadow of what really happens in the cell.
More on this in
1. Streaming proteins http://www.what-is-cancer.com/paper...g/proteins.html
2. A model of protein assembly: http://www.what-is-cancer.com/paper...elofprotein.htm
Biological complexity is always inherited. Yet not the entire complexity has to be inherited. When sperm and egg unite, each contributes its “minimal complexity” from which the immense complexity of the organism emerges.
My main research objective is to find ways for simplifying this complexity without losing its essence.
Posted by: Garrett Neske
Cellular automata are appropriate models for phenomena like biological growth and neuron excitation, but they cannot readily model the basis for this growth and excitation; they merely show how these phenomena occur in discrete space and time.
Unfortunately, networks seem to be getting very little attention in comparison to other NKS programs like CA and Turing machines. I believe that if one is to take an NKS approach to modeling biological complexity, it is necessary to employ networks. Biology has never been very conducive to mathematical study. We know that continuous models such as PDEs and other systems based on constraints are inadequate in 21st century computational biology. NKS provides a fresh perspective on bio-modeling. Nevertheless, I do not believe that cellular automata, with their rigid structures, can work in modeling anything but the simplest biological processes. Networks have no such rigid structure and are, in effect, dimensionless, for they model interactions not necessarily orientations.
Posted by: Gershom Zajicek M.D.
Biological modeling has a long history, nevertheless most models are too simplistic and rigid. http://www.what-is-cancer.com/papers/ca/ca01.htm
In order to model life phenomena one has to realize that life is a process. The organism is a set of interacting processes. Traditional modeling tools like differential equations or PDEs are too rigid for modeling processes. The inadequacy of time series involving random numbers, e.g. random walks, was discussed previously. The same applies to genetic algorithms whose evolution and interaction is driven by random numbers.
http://www.what-is-cancer.com/papers/ca/randomness.htm
The game of life was the first modern tool for modeling processes yet it is too rigid for simulating life. Neural nets are still poor models for processes encountered in the organism. We are left with CA. Please visit my latest creation:
Swarm intelligence http://www.what-is-cancer.com/papers/ca1/ca184.htm
May this be simulated with networks? Can you model processes with networks? If so please indicate how.
Posted by: Enexseenge
Greshom..
I was reading about your WOB and watching your CA experiment run.
I noticed that you have these moods which correspond to specific states that the CA entity would be in.
I was wondering if you feel that the "Wisdom of the body" has an intelligence in a way, an intelligence which feels the state of things in a certain way. A certain way which is very important to consider.
I am interested in how you feel about our awareness as individuals in relation to the more general "wisdom of the body" which "Lives" in the body’s complexity.
It seems you are connecting things very intimately, for example the swarm intelligence is the WOB.
This WOB sounds like something that lives within all biological interactions, some sort of intelligence, but not a neural intelligence of conceptual relations within the brain of a human..
But a intelligence which is the ability for a entity (cell or otherwise) to "know" what is happening..
Posted by: Gershom Zajicek M.D.
WOB is a medical metaphor accounting for the fact that we are unconscious of the 99.999% occurrences in our body. They proceed by themselves without our interference. What we regard as our free will affects only marginally this amazing universe. Despite our ignorance we are pretty well alive. Many (if not most) of our diseases are self healing. In order to discuss rationally this amazing gift of our organism to keep us alive, we need a nice metaphor, WOB.
Aristotle called it soul. It resides in animals and plants and is mortal. Yet soul, also a metaphor, serves other purposes as well. Hindus favor an immortal soul. Catholics need it to drive sinners into Hell. Descartes regarded the organism as a complex machine with an immortal soul to handle some non mechanistic properties of our body. Bergson called it élan vital and so on. I prefer WOB since it is devoid of metaphysical or religious connotations.
Actually WOB has two meanings: 1. The set of processes in the body, and 2 Their optimal control. It is an attribute of complexity and emerges with it. When sperm and egg unite, each is equipped with a relatively simple WOB whose complexity is still enormous. During the coming years the organism becomes more and more complex, its WOB emerges and gets smarter.
I was pleased to realize that with two interacting CA I can simulate WOB and illustrate what the Aristotelian soul might be.
Soul and complexity: http://www.what-is-cancer.com/paper...dcomplexity.htm
WOB http://www.what-is-cancer.com/papers/ca/ca93.htm
WOB http://www.what-is-cancer.com/paper...omofthebody.htm
Posted by: Enexseenge
Hello again..
I was reading through your web page and found this,
R[i+1] = R[D(i), W(i), M(i)]
W[i+1] = W[D(i), M(i)]
M[i+1] = M[R(i), R(environment, i)]
I think that this can be extended to any process in general which is a system of orientation..
S + A = R + E
a state of structure = S
plus
an affecter signal = A
equals
The state of the structure within the reception of A, = R
plus
the expression which is the signal that tells other structures the state which R is in, = E
Posted by: Gershom Zajicek M.D.
Two institutions continually search for truth, religion and philosophy including science. One wonders what is all this fuss about the quest for truth and we are told that this yearning to know the truth is part of human nature which distinguishes it from animals and plants.
We are endowed with many inborn faculties and instincts which assist us to survive in a hostile world. None of these includes a quest for truth drive. We are driven by an immense curiosity to find out how nature operates, while its truth value is less interesting to us. Curiosity is an attribute of life. Apparently this quest for truth is a myth or better a deception spread by the two powerful institutions. As rational beings we realize that our existence is in jeopardy. Nature poses a threat to our existence and in order to survive and protect ourselves we have to understand its ways.
In the past we turned to religion for guidance in this dangerous world. This is when truth was born. It was absolute and ultimate. Religion portrayed a secure world where truth lovers are safe. As humankind broadened its horizons this truth seemed to contradict their findings and the scientific truth was born. The two kinds of truth have different meanings. While the opposite of religious truth is a lie, error or fallacy are the opposites of scientific truth. Above all scientific truth was never absolute. It was always willing to reexamine itself.
With the mounting prestige of science it appeared as if soon it will replace religion. It all started when Darwin came up with the theory of evolution and natural selection which illustrated how nature manages without a creator. Evolution theory became the central dogma of a new religion which was called by Houston Smith, Scientism.
Creationists jumped on the scientist bandwagon and declared that the book of Genesis is a scientific document. They soon realized that their theory fails to account for the fossil record and rephrased it as the theory of intelligent design (ID). Neo-darwinists were furious. They were eager to highlight its inconsistencies while ignoring their own, which are indeed formidable. After all both theories explain the past and lack any predictive value. One may favor one over the other but none may be forbidden. This is what genuine science is about, it tolerates ideas. Unfortunately neo-darwinists abandoned this maxim. The issue is not about truth but about power.
Intelligent design and complexity http://www.what-is-cancer.com/paper...igentdesign.htm
Intelligent design and swarm intelligence: http://www.what-is-cancer.com/paper...ignandswarm.htm
Posted by: Enexseenge
I was reading at Lippincott Schwartz's web page and came across a question while reading this bit from her web page i thought you might help me with.. Or that may interest you.
"Unlike inanimate systems, the functional systems of the cell are selected for a purpose and have an unbroken history stretching back to the origin of life. New functions arise only by tinkering with already existing biological machinery rather than being built from scratch. It is useful when studying any new process or phenomena, therefore, to ask what other functions it might have evolved from or be related to. One example that comes to mind is membrane resealing, a phenomenon which only recently has been characterized (McNeil and Steinhardt, 1997). The plasma membrane of cells is constantly being torn or disrupted and must be resealed. There is no doubt that membrane resealing is an ancient cellular function since without it cell content and integrity could not be maintained. Recent studies have shown that resealing involves Ca+- mediated fusion of endosomal membranes with the plasma membrane rather than plasma membrane expansion to fill in a perforated region (Terasaki et al., 1997). This finding raises the question of whether other Ca+ mediated processes of fusion with the plasma membrane, including synpatic vesicle fusion (and synaptic vesicle biogenesis from endosomes), have evolved as specialized adaptations of the more basic wound healing process. By asking how different processes are related to each other and to the historical evolution of cells, fundamental properties of a system often can be identified and used to generate testable hypotheses."
So what is know about this more basic "wound healing process".
It's not really a theory is it?
Just a vague reference to the unknown of what we are working with?
Posted by: Gershom Zajicek M.D.
The first sentence “the functional systems . . . have an unbroken history stretching back to the origin of life”, is another way of stating that the cell inherits a minimal complexity from its ancestors. Apparently this minimal complexity cannot be generated from inorganic matter. I favor the theory of panspermia according to which the first chunk of living complexity arrived on earth from outer space. As we speak (write) life continues arriving from outer space.
http://www.what-is-cancer.com/paper...ityofliving.htm
Membrane resealing is a process that starts at the genome site. Molecules which are encoded there gradually flow outward, differentiating as they go and when reaching the cell boundary they replace the existing membrane which is broken down (catabolism). In other words the cell membrane is continually replaced by a new one. What may appear as resealing, is actually a replacement.
Wound healing is a different story. While membrane turnover operates in a cell, wound healing is the property of cell populations. It is the basic manifestation of the self healing capacity of the organism. Membrane turnover actually underlies wound healing and the sentence “synaptic vesicle fusions . . .[are] adaptations of the more basic wound healing process,” is flawed.
http://www.what-is-cancer.com/paper...ming/injury.htm
Membrane fusion can be modeled with two CA. You plant two zygotes. When they mature they touch each other and fuse into one continuous CA.
Posted by: Enexseenge
Thank you for your response again.
I think that there is a block that prevents us from understanding what is taking place beyond the specific phenomena that are being isolated out from extremely complex systems and defined in terms of their processes.
And then we organize a variety of described phenomena together in a way which defines their interconnectivity relationships, and supposedly describes the next level of the system.
For example, Schwartz says that,
"New functions arise only by tinkering with already existing biological machinery rather than being built from scratch.
It is useful when studying any new process or phenomena, therefore, to ask what other functions it might have evolved from or be related to."
How come we do not have an understanding of the original process, if forever we are looking at already oriented systems then how are we to go back to the original state which allowed the complexity that is being exhibited in newer processes to arise in the begging?
If we could look at that original functionality then I think we could understand our way from the bottom up instead of taking already extremely complex functions and intellectual relating them together trying to describe only that specific system which was the orientation.
For example, the first encasing which held "the atom of life".
And isn't what we are after a more general theory which accounts for the arrival of the complexity from a very simple system, a theory that could allows us to display how certain random structures would unfold which were sensitive to initial conditions which we gave? And if we were to input an already known system, then we could have a display which would mirror what we actually find in nature within those specific initial conditions (genetic material)
How does the D.N.A adapt?
Posted by: Gershom Zajicek M.D.
Heraclitus http://www.what-is-cancer.com/paper...oundedchaos.htm
In order not to get lost let’s start (philosophically) from scratch. What we perceive is change and no more. Everything else are explanations, models or just so stories. Our only concern is how to survive in this change. Fortunately we inherited faculties which keep us alive, called here Wisdom of the Body (WOB), which keeps also other living beings alive.
WOB http://www.what-is-cancer.com/paper...ontentswob.html
Somehow we humans inherited also the faculty of reasoning (consciousness), and realized that change may cause suffering. From then and onward we invested all our mental faculties to avoid suffering, e.g., religion, and science. We apply them to understand change. By understanding I mean having a theory, belief or a story which will protect us from suffering.
So if Mr. Schwartz says "New functions arise only by tinkering. . .” it is one explanation of change to which I respond: Life (WOB) is creative! Think of all these pessimists (Darwinists) who claim that life evolved through adaptation to random changes. Randomness does not exist as such in nature. It is a way to explain change. Take away randomness and their theory falls apart. Life is creative.
Randomness http://www.what-is-cancer.com/papers/ca/randomness.htm
This change which threatens our existence does not provide clues how life started, or how complexity evolved, and what is creativity. All these so called beautiful and esthetic theories are only explanations. So why do people cherish them? Because science or religion means power over the other! (Michel Foucault)
Posted by: Enexseenge
Alright..
Then what about this minimal complexity..
This atom of life..
If it has a Minimum complexity, then can we say that at this level the system is within it's "first" orientation.. The orientation which allows the Atom to hold it self together and further it's existence.
Could you for example, evolve this minimum complexity into a further complex state or process if you were to control environmental factors which are affecting the most basic "limit" of complexity which lives within the "Atom of life"?
Posted by: Gershom Zajicek M.D.
Let’s start with observations.
1. Microbes are the smallest cells living an independent life, observed in nature.
1a. Viruses are smaller but cannot live independently.
2. The complexity of the smallest microbe is immense.
2a. The smallest microbe on earth illustrates what such a minimal complexity might be. It might be regarded as an atom of life. When divided into its parts it ceases to exist. (Atom in Greek means indivisible)
2b Despite ongoing research nobody succeeded to generate such a complexity from organic or inorganic molecules.
3. Most (if not all) microbes do not live isolated, they live in populations called bio-films which by themselves are living organisms. An isolated microorganism is only a temporary (transient) state.
4. Properties of the atom of life
4a Is an open system exchanging matter and energy with the environment.
4b Its structure is oriented. In other words it is a set of oriented processes.
4c Despite an ongoing turnover it maintains its appearance. This feature is known as steady state, homeostasis or homeorhesis.
4d It is optimal.
4e It reproduces.
Properties 4b,4c and 4d are collectively called Wisdom of the Body (WOB).
In other words, the atom of life is an open system with a WOB.
The proliferon is the simplest artificial construct illustrating these properties.
http://www.what-is-cancer.com/papers/ca1/ca167.htm
5. Whenever atoms of life aggregate they create open systems with a WOB. For instance bio-films are also open systems with a WOB and so are we.
Posted by: Enexseenge
3. Their behavior cannot be explained by decomposing the system into sub-parts.
Now it is this issue that i feel must be looked into more deeply, and i do believe that an understanding can arise of the system in it's whole operation without the need to divided it into a description of interacting subparts (and this is where our error in understanding arises)..
And also without a vague reference which simply labels it's complexity and gives no more room for development or theory or more detailed understanding.
My idea is that such complex process can exist in a "non programmed" computer type simulation (artificial neural network) which does not execute a process of calculations to arrive at a specific solution related to a particular process (and then discombobulates these into a unity of operation, haha), but operates under this same "strange attractor" type rule..
For example a neural network which orients it self in a similar way to how the cell orients it self.
The input would be a process which exists within the whole nueral network as a transference of two structure's states which are separated by a "empty space", where one is the "affecter" which sends signals, and the other is the structure under observation which could be considered the "cell". And the inputs (or perhaps at the "press of a button" from the experimenter) come into the receptive structure which then alters under the affect of the reception of that input and develops a "new" structure which then again is "hit" by another input and again another affect which displaces the system and causes it to "re-orient" it self within the new conditions which have arisen due to the input, and this continually happens..
The out put would be the "new structure" which has oriented it self to the input and has been "frozen" in time in order to observe it.
Is this not what the out put is? unless you might considered a more complex system like a human which "Reaches out" its arm to represent it's out put.
But in terms of information it self as the entity which are observing,
Is it not the new structure which ahs oriented it self in terms of the affect of the reception of a input... which is the output?
Posted by: Gershom Zajicek M.D.
I fully agree with your statement:” i do believe that an understanding can arise of the system in it's whole operation without the need to divide[d] it into a description of interacting subparts”
This is precisely what the concept of a minimal complexity is about. It is the amount of complexity necessary to sustain the life of a living entity like a bacterium. Currently we cannot explain how this minimal complexity sustains life, and the dissection of the bacterium will not clarify it. So we define a variable called WOB (Wisdom of the Body) which “knows” how to sustain the life of a bacterium. WOB has two meanings: 1. The process set and 2. The faculty to optimally control the set. WOB is also an open system.
We may now define a hierarchy of complexities in all manifestations of life:
WOB(i+1) = Sum[WOB(i)].
For instance Bio-film[WOB] = Sum of all bacterial WOBs
http://www.what-is-cancer.com/paper...llistheatom.htm
In embryogenesis WOB(0) is the zygote and WOB(n) is the newborn. This iteration illustrates a basic property of life. As the complexity of a living process emerges each of its stages is equipped with a WOB. In other words each stage is an emerging WOB.
Posted by: Gershom Zajicek M.D.
Darwin’s theory of natural selection explains evolution in terms of three independent factors:
1. Each living entity has a genetic memory which contains a blueprint of the organism that is manifested by its phenotype. The genetic memory and blueprint may change randomly (mutation) in an unpredictable way, leading to a change of the phenotype.
2. Genetic memory is inherited.
3. Blueprint changes affect the chances of the individual to survive in the hostile environment. Actually the environment "selects" the best fitting individuals.
http://www.what-is-cancer.com/paper...erspective.html
The theory has little to say about the immense variability of life. It seems even to contradict itself since a selection of the fittest actually reduces variability contributed by the non-fitting who are eliminated. Selection seems to filter variability. Many properties are conserved (universal) and appear in diverse species like similar brains and limbs, and many metabolic processes. For example, roughly 15 percent of our genes are like those of bacteria, 25 percent are like those of single-celled fungi, 50 percent are like those of fruit flies, and 70 percent are like those of frogs. How might these conserved universal properties account for variability? Above all how does complex novelty, like the brain or eye arise?
In the recently published book “The Plausibility of Life: Resolving Darwin's Dilemma “, Marc W. Kirschner and John C. Gerhart introduced the theory of "facilitated variation". Structure is never inherited as such only genes (blueprint) are inherited. Suppose that when sperm and ovum unite the sperm carries a mutation in one of its genes, its effect will be constrained by the evolving embryo known as phenotype. Phenotypic variation is biased by the structure that evolves. The authors illustrate their idea by the following example. Suppose that you give a monkey a pen and paper, and let it randomly scribble, how long will it take until it writes “Monkey”? Next let the monkey hit typewriter keys, its chances to type “Monkey” will obviously improve. Finally if you let the monkey type on a computer keyboard with a spell checker that eliminates non English words, it may succeed.
Many species have conserved genetic blueprints and when their genes change (mutate) the outcome will be constrained. This is why phenotypic variation cannot be random. It is biased and creative. Kirschner and Gerhart provide interesting ideas how complexity evolves.
In a previous section the hierarchy of living complexity was defined as:
WOB(i+1) = Sum[WOB(i)]. WOB has two meanings: 1. The process set and 2. The faculty to optimally control the set. WOB is also an open system.
http://www.what-is-cancer.com/paper...gcomplexity.htm
Whenever two living entities merge or change they are subject to this recursion. Any change (mutation) will be constrained by the WOB which emerges from this change. This recursion is a concise expression of how “facilitated variation” operates during evolution.
Posted by: Gershom Zajicek M.D.
The monkey parable by Kirschner and Gerhart illustrates the major criticism of neo-Darwinism, randomness cannot generate novelty.
http://www.what-is-cancer.com/paper...edvariation.htm
Suppose that you give a monkey a pen and paper, and let it randomly scribble, how long will it take until it writes “Monkey”? Next let the monkey hit typewriter keys, its chances to type “Monkey” will obviously improve. Finally if you let the monkey type on a computer keyboard with a spell checker that eliminates non English words, it may succeed.
According to the theory of intelligent design, in order to create novelty the monkey needs assistance by a super-being. On the other hand, Kirschner and Gerhart’s theory, called “facilitated variation’ is more convincing. Structure is never inherited as such only genes (blueprint) are inherited, and structure constraints genetic expression. Phenotypic variation cannot be random. It is biased and creates novelty.
There is more to structure than just its appearance. Biological structure has a wisdom (WOB) which constraints gene expression. WOB is optimal and will facilitate only genes which improve optimality.
Darwinism http://www.what-is-cancer.com/paper...s.htm#darwinism
Randomness and creativity: http://www.what-is-cancer.com/paper...mness.htm#creat
Randomness cannot generate complexity: http://www.what-is-cancer.com/paper...ess.htm#examine
Posted by: Gershom Zajicek M.D.
J. E Lovelock regards the surface of Earth as a kind of super-organism called Gaia. Life has evolved and still evolves as a complex web, "A self-regulating entity with the capacity to keep our planet healthy by controlling the chemical and physical environment". Gaia is a biosphere that controls itself. An ecosystem in which life and its environment are coupled. It was born in the "primitive soup", has been evolving ever since, and we differentiate in it.
http://www.what-is-cancer.com/paper...ismDecline.html
In order to grasp how Gaia, the super-organism evolves, consider for a while how your organism evolves. Imagine yourself living in a growing embryo. It is three months old and you are its brain. Unlike other embryonic brains you posses a consciousness, remember your past, and observe other organs in the growing body. You are the thinker and theorist. You were born from a gastrula as an elongated hollow tube, as you became older you twisted, convoluted, and now you are proud of being a real brain. Other organs evolved as well. The heart started as a hollow tube, twisting once or twice until its four chambers became visible. The kidney proceeded through somewhat more complex states, and so did other organs.
You wonder, what drives these changes? Since each organ is composed of several cell populations, your body somehow determines which cells will continue dividing and which will cease to exist. Your body selects the best fitting cells and adds them to the different organs. This process of cell selection is called differentiation.
Did your body evolve (differentiate) by natural selection as Darwin put it? How does your body select the fittest organs? The best fitting heart, has to match the best fitting lung, kidney and other organs. A weak heart will not pump enough blood into an oversized lung. Thus in order to select the best fitting heart, the organism has to consider all other organs in the body.
According to the Gaia hypothesis, our evolution is determined by all entities (organs) on earth. Gaia evolution is actually an ongoing differentiation of a super-organism.
When Spinoza searched for God he found Him all over Gaia (pantheism). It seems to me that when he read Genesis chapter-1, “God said: Let us make man in our image, after our likeness” Spinoza might have preferred: "Let us make Gaia in our image, after our likeness.”
Posted by: Enexseenge
Gershom,
I am enjoying this discussion, and just wanted to let you know i plan on responding in time.. when i have time..
Specifically about the zygote before it becomes a whole, while there exists two different precursor states from the male and female...
I was wondering why you say that those two precursors do not have WOB?
haha, and this might seem a little out of context..
But do you know about when the first hint of a basic "nervous" cell appears within a developing human? what are the first "cell types" to be created in the creation of a human system.
And also, this WOB seems to be able to be applied to non living things, and might be a property of any structure (of information!!! Not physicality) which exhibit’s a “nested” pattern, or functionality that holds it self together.
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Unavoidable implications of an affect due to a specific arrangement of "relative" elements which relate to that specific structure which we observe.
These implications which become the manifestation which unfolds due to the interaction between the substance and an affecter are the parameters of the WOB of any system.
WOB I feel might be extended beyond “cells”…
I think it all must relate together under the same rule…
Minimum complexity is inherited by the next instance no matter the system under observation…
For example, a flame to paper..
The affect of the flame within the structure of the paper causes an unavoidable implication which is the alteration of the form of that paper, so as to suit the new “minimum complexity” which was forced into being by the "energy" of the affecter...
something drives this minimum complexity to be held, we have tried to label it terms of many equations of energy and matter, and statistical appropriations towards phenomena, but we are still missing the big picture.
Posted by: mick whieldon
Ive come up with an interesting idea I call Quantosynthesis.
Its an abiogenetic model similar in its nature to Nucleosynthesis. The deterministic model poses a very very strong anthropic principle.
It works in like the whole genetic coding assemblage utilises microscopic physical pathways - which itself is a coded network that 'exists' in all matter and space and is indeed the quantum 'foam' itself. It works in water.... and quarks... and galaxies. Its quite simple when you get it.
Essentially, the form of the body is there at the beginning of time- thats the conclusion.
All the rest is emergent gnomons forming the diversity of forms we see around us. So there is a simple system which exhibits immense complexity and I think that it underlies the whole physical biology. Its my Quantosynthesis model. Also it allows the scientist to concieve of a god that made man in his image without the need to become conventionally religeous as such. It has changed the way I see the world. But I might just be mad.
Mick, Aug 2006.
Posted by: Gershom Zajicek M.D.
Darwin's theory of natural selection has three ingredients:
1. Each living entity has a genetic memory that contains a blueprint of the organism that is manifested by its phenotype. The genetic memory and blueprint may change randomly in an unpredictable way, leading to a change of the phenotype.
2. Genetic memory is inherited.
3. Blueprint changes affect the chances of the individual to survive in the hostile environment. Actually the environment "selects" the best fitting individuals.
http://www.what-is-cancer.com/paper...erspective.html
More concisely: Evolution consists of two basic types of processes: Those that introduce random genetic variation into a population, and those that affect the frequencies of existing variation. We have seen previously that randomness does not exist in nature, it is a concept to describe nature.
http://www.what-is-cancer.com/papers/ca/randomness.htm
The following thought experiment ought to highlight the shortcoming of random variation. First we ought to examine the notion of pseudo-randomness. Pseudo-random numbers are derived from a known starting point (seed) by repeated iteration, while “truly” random numbers are generated by radioactive decay. All known statistical tests for randomness cannot distinguish between the two. Even a rule 30 cellular automaton may serve as an efficient pseudo random generator (NKS p.315)
Now assume that genetic variation is not random but pseudo-random. You would not know the difference, since no statistical test can distinguish between them. Natural selection would have been driven by a deterministic process like rule 30 CA. The initial condition might be set by the Creator, thus taming the somewhat heretic theory of evolution.
Why stop here? Apparently other kinds of pseudo-random processes might drive variation as well. It seems to me pathetic that genetic algorithms (GA) still rely on traditional pseudo-random generators which drive the program to an inconclusive local maximum. They were led astray by the simplistic and naive assumptions of the theory of natural selection.
Finally let's turn to Cardinal Ratzinger (now Pope Benedict XVI). After describing the scientific elements of neo-Darwinian theory, then-Cardinal Ratzinger asked: "What response shall we make to this view [evolution]? It is the affair of the natural sciences to explain how the tree of life in particular continues to grow and how new branches shoot out from it. This is not a matter for faith. But we must have the audacity to say that the great projects of the living creation are not the products of chance and error."
http://www.freerepublic.com/focus/f...n/1527751/posts
Shouldn't we embrace deterministic pseudo-randomness for unraveling the mystery of life?
http://www.what-is-cancer.com/paper...ntroduction.htm
Posted by: mick whieldon
Chance and error happen during the evolution of a process which divines mass from space - over all scales.
Faith is needed to trust that the initial condition of 'zero to healing man' was somehow intentional - a vision.
In the course of Quantosynthesis, the automatic IS the intentional.
Posted by: Gershom Zajicek M.D.
Could you imagine a world to which Darwin’s model of evolution does not apply?
Let’s turn first to the French biologist Lamarck who claimed that traits acquired during life may be inherited. For instance Giraffes which have to stretch their necks to reach leaves high in trees, have offspring with slightly more elongated necks. This version of Lamarckism is naďve and refuted by any living Jew. Ever since the time of Abraham all Jews in the history were circumcised yet none of their offspring was ever born without a foreskin (prepuce). Although the macro-world does not follow Lamarck’s model, in the micro-world Lamarckism is still relevant.
Neo-darwinism is based on three pillars:
1. Each living entity has a genetic memory which contains a blueprint of the organism that is manifested by its phenotype.
2. Genetic memory cannot be affected by any organ in the organism. It is “deaf” to the outside world, and may change only randomly (mutation).
3. Blueprint changes affect the chances of the individual to survive. Actually the environment "selects" the best fitting individuals.
http://www.what-is-cancer.com/paper...esisbetween.htm
Now imagine a world in which life lacks a genetic memory. Obviously offspring would have inherited traits acquired during the life of its ancestors. Such a condition existed on earth when it was covered by the “primeval soup”. According to the Russian biologist Aleksandr Oparin, life on earth developed through gradual chemical evolution of carbon-based molecules floating in the primeval soup. As these molecules polymerized they gradually started replicating and their offspring inherited their acquired traits. DNA may have appeared much later (after million years) whereupon Darwin’s model became relevant. (Liane Gabora, J. Theoret. Biol. 241: 443 - 450, 2006)
Does this imply that the establishment of genetic inheritance made Lamarck’s model irrelevant? Not at all. Neo-Darwinists claim that genetic memory is “deaf” to the outside world. Which seems to me even more ridiculous than the hope that in the future Jews will be born without a foreskin. Since all processes in the organism continuously interact why should they spare the blueprint? Genetic memory is influenced by other organs. Lamarckism is ready for its comeback.
I favor the view that life on earth appeared from outer space. (panspermia).
http://www.what-is-cancer.com/paper...tyofliving.htms
Posted by: Enexseenge
##Gershom,
I like this! Welcome back.
Now you say “Lamarckism” is ready for a come back.
You said that the micro world would be more of a domain for this type of “memory” to transfer,
“Genetic memory is influenced by other organs. Lamarckism is ready for its comeback. “
The influence upon the genetic memory, very interesting..
And you consider that this is actually taking place?
What entities interact with the blueprint beyond RNA?
an experiment I come up with is that we can continually encode a specific gene, we encode the RNA over and over and over never ceasing, and we see if this causes any change in the blueprint.
What other elements interact with the blueprint?
And if a macro scale phenomena is to be represented in the micro world, then what other ways besides the encoding of RNA would you relate to this macro scale phenomena in terms of the blueprint?
Posted by: Gershom Zajicek M.D.
Emergence is an attribute of complex processes (systems). As a complex process evolves new structures and patterns emerge. They are novel, unpredictable and cannot be deduced from the parts which make the process. The new pattern is generally associated with a new behavior of the process (system) that was not pre-programmed. We ought to realize that most complex systems are ongoing processes which evolved from some initial condition. The only complex system which was created as such is outlined in the first chapter of Genesis.
Nevertheless we read that “Biology (including biological evolution) can be viewed as an emergent property of the laws of chemistry. Chemistry (including the evolution of both elements and molecules over time) can be viewed as an emergent property of the laws of physics. Most of the laws of physics themselves as we experience them today appear to have emerged during the course of time making emergence the most fundamental principle in the universe and raising the question of what might be the most fundamental law of physics from which all others emerged”. (Wikipedia)
This kind of emergence is different from the above. Biology, chemistry and physics, do not exist as such in nature. They are theoretical constructs (hierarchies) to describe nature and as such they are static. Here emergence means a transformation which cannot be deduced from laws of the lower scientific hierarchy. Nevertheless many scientists do not distinguish between the two kinds of emergence. They claim that when nature becomes more complex it selects its novel (emerging) behavior from a huge domain of the possible, by pruning the less advantageous. This domain of the possible is purely theoretical. Nature does not select anything it simply emerges. Yet these theoreticians lack the necessary concepts to describe this kind of emergence. They even claim that the pruning rules are consequences of the laws of science, and so will work universally.
We may thus distinguish between two views of complexity:
1. Platonic, which regards complexity as invariant.
2. Process oriented, which regards complexity as evolving.
The first still applies traditional physical concepts to complex processes, e.g. entropy, or random walk. Yet real processes do not “walk randomly” and measures like entropy fail to predict their behavior. Nevertheless these “Platonists” enforce their view on the interpretation of bio-medical complexity which seems to me unfortunate.
http://www.what-is-cancer.com/paper...ess.htm#entropy
http://www.what-is-cancer.com/paper...ness.htm#cadont
Cellular automata offer an opportunity to investigate the evolution of process complexity and its emerging behavior.
http://www.what-is-cancer.com/papers/ca1/ca167.htm
http://www.what-is-cancer.com/papers/ca1/ca178.htm
Posted by: Gershom Zajicek M.D.
Death is a term that is used to describe the permanent ending of life. Since life is manifested by complexity we may ask whether “death” is applicable also to other complex processes. First we ought to realize that most if not all complex systems are actually complex processes. Complexity is not created as such, it evolves from less complex conditions.
Some complex processes never die, e.g. the weather, which exists as long as our earth does. The weather does not die it only mutates. Today’s weather is not sensitive to initial conditions. It is an ongoing process and obviously lacks initial conditions. For the same reason it is immune to butterfly effects. The same applies to life as such which appeared on earth eons ago and will never die. It is organized as a super-organism, called Gaia which encompasses all life processes. http://www.what-is-cancer.com/paper...utionofgaia.htm
Apparently other complex processes, e.g. economy, stock market or even the internet will exist as long as we will. They will not die, only mutate. We may thus generalize and assume that processes which depend on life will hardly ever die.
How come that the human, the hallmark of life actually dies? The definition of death depends on our viewpoint. Whether we regard man as an isolated process, which started during fertilization, or as a part in a more general process known as food chain. It is defined as: A succession of organisms in an ecological community that constitutes a continuation of food energy from one organism to another as each consumes a lower member and in turn is preyed upon by a higher member. (Answers.com). Gaia may be regarded as a web of food chains.
Plants serve as food chain origins. They apply sun energy to polymerize simple inorganic molecules, e.g. water and carbon dioxide. All other members in the food chain are incapable of polymerizing inorganic molecules. They require simple organic molecules like sugars or amino acids. Complexity evolves by polymerization of simple organic molecules. When a member of the food chain dies, its complexity is degraded to simple complex building blocks which serve as initial conditions (primers) for the complexity generation of the next member (process) in the chain. Death of a chain member is far from being an annihilation, it is a mutation.
The human destiny is expressed by Rabbi Akavya Ben Mahalel: "Reflect upon three things and you will never come to sin: Know from where you came, to where you are going, and before whom you are destined to give an accounting.
" 'From where you came' - From a putrid drop; 'To where you are going' - To a place of dirt, maggots, and worms; 'And before whom you are destined to give an accounting' - Before the King of Kings, The Holy One, Blessed Be He."
The putrid drop initiates a process known as a human being . When his time has come he mutates into a different process. From the Gaia perspective the place of dirt, maggots, and worms is a process in the food chain which takes care of the dead individual and prepares his remnants as primers for the next chain member. Death is actually a process mutation. Not “dust to dust, or ashes to ashes”, which are essentially inorganic and cannot serve as primers for life. Maggots, worms, microbes and fungi, keep the food chain ticking.
More on this in a Hebrew poem: http://www.what-is-cancer.com/poems/mavet.html
Posted by: Gershom Zajicek M.D.
“Physicists come from a tradition of looking for all-encompassing laws, but is this the best approach to use when probing complex biological systems?” This question was posed by Evelyn Fox Keller in an essay published in Nature (Nature 445, 603 (8 February 2007)). Does biology have laws of its own that are universally applicable?
“Today, biologists are faced with an avalanche of data, made available by genomics and by the development of instruments that track biological processes in unprecedented detail. To unpack how proteins, genes and metabolites operate as components of complex networks, modeling and other quantitative tools that are well established in the physical sciences — as well as the involvement of physical scientists — are fast becoming an essential part of biological practice.”
Apparently traditional mathematical tools are of little help to deal with biological complexity. Physicists yearn for some kind of a law which might serve as a starting point in their effort. Evelyn Fox Keller is concerned that biologists often pay little attention to debates in the philosophy of science, like whether there are laws of biology. As if these issues were solved in the exact sciences.
All these so called laws of physics are no more than models that were extremely successful in describing many aspects of our reality and fail to untangle the complexity of life. Yet life is an essential part of our reality which cannot be ignored anymore. In his book Phenomenon of Life (1) Hans Jonas states that most of what we encounter on the surface of earth is intimately intertwined with the dynamics of life. A fact which was hitherto ignored by the exact sciences, which attempt to understand (describe) life by reducing it non life (matter).
In order to proceed the exact sciences ought to get rid of their conceptual crutches, which they regard as universal laws. Like Newton’s “laws” which have been always irrelevant to biological processes.
Physics as a fable: http://www.what-is-cancer.com/papers/physicsfable.html
References
1. Hans Jonas The Phenomenon of Life- Toward a Philosophical Biology
Northwestern University Press Evanston Ill 2001
Posted by: Chris Humphrey
One of those question that I see asked over and over, is how can there be highly complex life without some prior highly complex agent to create it.
Here’s the truth of the matter, the complexity we observe developing is only a temporal view of a cognitive system that contains a duality, one of temporal time and one outside the field of time, Eternity.
Complexity in all its form does not exist as a temporal design, but as an eternal form. A singularity. Order is inherent, moving toward the eternal.
Remember the movement of time from past to future is our experience. According to basic laws of physics there is no clear distinction between to two, outside our cognitive experience.
What we observe as time and movement between a simple ordered state and higher ordered state is merely a cognitive movement between the two aspects of time, one of eternity, Were all things are complete whole forms and the temporal state of becoming.
To anthropomorphize an omnipresent intelligent force that builds from the ground up, existing in the field of temporal time, tinkering as it goes, negates the eternal principle.
"I am the Alpha and the Omega, the first and the last, the beginning and the end."
The noun alpha and omega has 2 meanings:: : the first and last; signifies God's eternity,
the basic meaning of something; the crucial part
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Temporal: Man
Let me approach this from architectural view point. When we build a structure using regular geometry, small mistakes in the initial measurements will be amplified as the construction progresses, until a point is reached were the initial small instability surpasses and overwhelms the stability factors causing a catastrophic collapse, destroying the intended design.
Eternal: God
Now edge of chaos with dynamics of a dissipative physical components is were this scenario happens in reverse.
The instant all the physical and dynamic elements arrive they cause a catastrophic constructive collapse toward a higher ordered state. ( “Eternal true forms” ) This state of creative instability is referred to as “edge of chaos” Coined by Doyne Farmer this state exist between the chaotic regime and the order regime. These attractors self-construct, by drawing energy and order from its environment.
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This scenario is central to evolution, it is how biological systems self organize, and evolve.
It is also counter intuitive because it is diametrically opposed to how we believe the universe operates.
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All creation or destruction of forms, or morphogenesis, can be described by the disappearance of the attractors representing the initial forms, and their replacement (by capture) by the attractors representing the final forms. Rene Thom
Posted by: Gershom Zajicek M.D.
Chris! The arguments which you raised may be investigated within three realms: Theology, metaphysics, and science.
1. Theology: God or Brahman is the eternal and timeless and cannot be grasped by us. He therefore decided to present himself in a manner that we can grasp. You may chose one of the following possibilities:
1a Hinduism: What we observe is Maya or illusion
1b Pantheism: What we observe are manifestation of God (Spinoza)
1c All what He wants us to understand is inherent in His creation (Genesis).
You state that: "I am the Alpha and the Omega, the first and the last, the beginning and the end."
Answer: Since you have a beginning and an end you are mortal.
Contrary to what you claim, complexity does not exist in the eternal realm since we cannot grasp the eternal and yet we grasp complexity.
2. Metaphysics: The “higher ordered state” is a Platonic idea, represented on earth by a “simple ordered state”
3. Science: The name of the game is to investigate your statements scientifically. This is what the present thread is about. You are invited to examine some ideas which were presented here before.
http://www.what-is-cancer.com/papers/ca/complexity.htm
Posted by: Chris Humphrey
My argument was intended to be scientific, by straddling what we know about time, complexity and chaos.
The alpha omega quote I’m referring to eternity as central organizing point. An attractor, creating a field of temporal movement.
This dynamic can be observed in the relationship between a black hole and all other celestial spheres in our galaxy. This central singularity creates a stable but cyclical field around it.
These cycles are the key to generating complexity.
Posted by: Gershom Zajicek M.D.
“What Computers Still Can't Do” written by the philosopher Hubert L Dreyfus (1) exposes the shortcoming of Artificial Intelligence (AI), like the claim that in order to act intelligently people must have a model of the world in their mind. Which is known as mental representation of the world. According to Herbert Simon this model is a system of symbols which serve as representations of reality, and since computers manipulate symbols they may act intelligently like people. Dreyfus maintains that disembodied machines cannot mimic human intelligence and hitherto he was right. The embodiment concept is discussed elsewhere.
http://www.what-is-cancer.com/paper...fartificial.htm
One may argue that today’s computers, are still too slow for such a task. What about computer systems, like the WEB? Might the WEB act intelligently? “Not at all!” says Dreyfus, since the WEB is disembodied. True, it has some embodiment, like SKYPE or VOIP yet this is not enough. The WEB is only a tool and not an intelligent machine.
What Dreyfus fails to realize is that the WEB is a living system embodied by its users. So why can’t it be intelligent? Elsewhere I mentioned other living systems, like the stock exchange which cannot be labeled as intelligent. What kind of embodiment is required to make an intelligent system?
At the time when AI (artificial intelligence) was named by John McCarthy, Wittgenstein's philosophical investigations came out against mental representations. Heidegger had already done so in 1927 with “Being in Time”. Yet the AI researchers still ignore it. They are followed by neuroscientists who place mental representations into the brain. Other regard the brain as a computer. A neural net of representations. They ought to wake up from their Cartesian slumber and turn to phenomenology which is the motto of the present trail.
An intelligent machine can be created only if adopting the viewpoint of phenomenology, which criticizes the notion of mental representation. Yet phenomenology does not point the way to the creation of an intelligent machine. It only explains why Cartesian reductionism is wrong. Nevertheless it is a basis from which AI ought to continue. To me phenomenology is a way to tackle complexity. Embodiment is an attribute of a complex system. It can be realized even in a relatively simple two CA system.
http://www.what-is-cancer.com/papers/ca1/ca167.htm
http://www.what-is-cancer.com/papers/ca1/ca143.htm
References
1. Hubert L. Dreyfus What Computers Still Can't Do: A Critique of Artificial Reason
ISBN 0-262-54067-3
http://globetrotter.berkeley.edu/pe...eyfus-con0.html
Posted by: Gershom Zajicek M.D.
Complex systems may be divided into three qualitative groups:
1. The whole is the sum of its parts, e.g. molecules of an ideal gas, or the set of integers.
2. The whole is more than the sum of its parts:
2a Like water in a container (at room temperature). Its molecules are not dispersed randomly. Each water molecule is a dipole, and tends to partially align itself with other molecules.
2b Or the following sentence :” My information content is more than the sum of the letters in me”
2c Wolfram CA classes 3 and 4 (p. 231)
3 The whole controls its parts (and is obviously more than the sum of its parts). Such systems obey the allometric law , or power law, which describes the relationship between the whole (W) and its parts (p). Like in the following equation: p = a * W ^ b or Log[p] = Log[a] + b * Log[W].
Kleiber (1930) described the relationship between the mass (M) of an organism and its basal metabolic rate (BMR) which applies to the majority of animals, BMR= a * M ^ 0.75 . Thus a cat, having a mass 100 times that of a mouse, will have a BMR roughly 31 times greater than that of a mouse.
Since all living systems obey similar relationships, the allometric law may be regarded as their attribute. However it is observed also in some non-living complex systems. The law indicates that living systems are constrained by a relative shortage of vital substances like oxygen which drives the basal metabolic rate (BMR) and determines the size of an animal. Since oxygen is scarce, the organism controls its distribution among the organs. Brain is the most privileged, then come the kidneys, heart muscles and bones. The power law thus indicates that the whole actually controls its parts. It has a wisdom which is called here Wisdom of the Body (WOB).
WOB has two meanings: 1. It is the set of interacting processes, and 2. It is an optimizing principle. Processes in the body interact so as to keep it optimal.
WOB in CA: http://www.what-is-cancer.com/papers/ca/ca93.htm
Allometric law in cancer: http://www.what-is-cancer.com/paper...cmetastasis.htm
Posted by: Gershom Zajicek M.D.
A recent essay, “Rules of engagements “ by Doyle and Csete, published in Nature (1) starts with the following sentence:: “Complex engineered and biological systems share protocol-based architectures that make them robust and evolvable, but with hidden fragilities to rare perturbations.” I agree with the authors that “engineers can learn from biology” and wonder whether they grasped the essence of biological (life) complexity. The authors assure us that:” Biological systems are robust and evolvable in the face of even large changes in environment and system components, yet can be extremely fragile to small perturbations. Such universally robust yet fragile (RYF) complexity is found wherever we look.” True, life is universally robust but is it really fragile? Take for instance diabetes and cancer which the authors regard as: “conditions resulting from faulty biological control mechanisms, normally so robust as to go unnoticed.” Even the authors imply that these diseases are far from being fragile. So what led them astray.
It all started when Descartes proposed that man is a complex machine (with a soul). From then and onward physicists and engineers applied their concepts to handle complexity. Newton applied his “laws” to the real world. Then came Laplace's clockwork universe, which despite its immenseness could be generated from some simple laws. Yet the artificial world supporting us and our culture became more and more complex. Suddenly we realized that the weather is essentially unpredictable and found relief in the theory of chaos and its butterfly effect. Ignoring the fact that real butterflies do not initiate hurricanes. Nevertheless life’s complexity was explained by its terms.
Chaos: http://www.what-is-cancer.com/paper...oesnotexist.htm
The computer provided a mechanistic explanation of our brain. And then came the Internet, which is more complex than any computer and inspired the authors to tackle life’s complexity. Although “Chaos, fractals, random graphs and power laws inspire a popular view of complexity . . . . A different, more rewarding take on complexity focuses on organization, protocols and architecture” . . . . “So biologists can learn from engineering. The Internet is an obvious example of how a protocol-based architecture facilitates evolution and robustness.” The authors conclude:” All life and advanced technologies rely on protocol-based architectures.”
Indeed the Internet is protocol driven, yet what about the stock exchange with its internet dependency, is it also a protocol based complex system? If it were I might devote my time to search for a protocol to make me rich. Life is far more complex than the stock exchange. And yet the authors want us believe that: “All life and advanced technologies rely on protocol-based architectures.” Advanced technologies, yes, but not life! There is a limit to the complexity of protocol based systems and since life is not protocol based it is far more complex. In order to progress the authors and engineers ought to investigate how life’s complexity emerges without relying on protocols.
Why not turn our attention to a simple two CA system called proliferon, and ask the authors to define protocols that control its behavior.
http://www.what-is-cancer.com/papers/ca1/ca167.htm
===References===
1 John Doyle & Marie Csete
Rules of engagement
Nature 446, 860 (19 April 2007)
Posted by: Gershom Zajicek M.D.
Ask any expert what is aging and you get the following answer: Aging is a gradual deterioration of physiological function with increasing age, associated with decreasing performance, and increasing probability of mortality. You may not find anything wrong here because you were raised to regard aging as a deterioration. It is a Cartesian heritage according to which the organism as a sophisticated machine whose components deteriorate randomly. Its aging is studied within the realm of Reliability Theory.
In order to prolong the life of a machine you equip it with redundant components so that when one dies the other takes its place. Reliability-theory experts believe that aging is driven by an ongoing (random) deterioration of vital genes. In order to attain old age you ought to be equipped with redundant vital genes.
Hitherto demographic models seemed to support this view, since from the age of 20y and onward the mortality rate known as Gompertz equation rises exponentially, exactly as in malfunctioning machines. Then came an “unpleasant” surprise. People lived longer and when they passed the age of 85 years their mortality rate started declining (!). Beyond the age of 100y the mortality rate approaches asymptotically a constant value. In other words, if you cross the age of 80y and you are still healthy, your chances to cross the 100y mark continually improve. Instead of celebrating the initiation of longevity, scientists were disappointed since all their models fail.
Don’t despair, soon they will adapt their models and theories to the new reality and the human organism will continue deteriorating at their will. They are still mesmerized by the machine metaphor and fail to realize that aging is not driven by random deterioration of components. Actually aging is a creative process. Suppose that you follow the growth of a newborn without realizing that occasionally it may die. You may now regard it as a living system whose properties emerge. Like the weather, a living system that never dies. Would you regard weather as a system of randomly deteriorating components? The same applies to our organism. It is a set of interacting processes called here WOB (Wisdom of the Body), that are continually rejuvenated and hardly ever deteriorate.
http://www.what-is-cancer.com/paper...stconcepts.html
The organism is driven by an independent process, destruction, which it continually attempts to repair. As long as the destruction rate is less than the repair rate, the organism continues living and when destruction gains the upper hand it dies.
Aging is an ongoing process by which WOB attempts to creatively withstand external threat. What appears to us as age deterioration is a successful attempt to sustain life. The appearance of a healthy elderly is a token of his capability to handle external threat. So, despite an external threat our fate lies in our hands.
Late life mortality
http://www.what-is-cancer.com/paper...femortality.htm
How to slow down aging:
http://www.what-is-cancer.com/paper...wdownaging.html
Aging in CA
http://www.what-is-cancer.com/papers/ca/ca63.htm
http://www.what-is-cancer.com/papers/ca1/ca165.htm
Posted by: Gershom Zajicek M.D.
Reading the fat NKS book I wondered what bugs him? The central idea is obvious, you can generate complexity with simple programs. Then you read about emergence of order from randomness (Chapter 6) which I like less, as explained earlier in this thread.
http://www.what-is-cancer.com/paper...s/compFrame.htm
Recently in a short article which appeared in his blog
http://blog.wolfram.com/2007/09/my_...unive.html#more
Wolfram spelled out what really bugged him: “Physicists often like to think that they're dealing with the most fundamental kinds of questions in science. But actually, what I realized back in 1981 or so is that there's a whole layer underneath.” It is governed by very simple rules that can generate all sorts of rich and complex behavior.
Then came the first question: “. . what about our physical universe? Could it be operating according to one of these simple rules? “Of course, that's not at all how most of today's physicists like to think. They like to imagine that by pure thought they can somehow construct the laws for the universe--like universe engineers” In other words they continue being Platonists searching for the truth in the world of ideas. Might this imply that Wolfram is somewhat different?
“So in a sense we have to go below space and time--to more fundamental primitives. What might these be?” A network of interacting programs in which space and time do not apply. Such a network does not exist in a space. “There is not a ‘space’ there but a bunch of points.” Which are actually connections. The programs exchange pieces of the network. “And in general each possible sequence of rule applications might correspond to a "different branch of time".”
Then comes the hammer:” But now we're deriving something like that for the universe: we're saying that these networks with almost nothing "built in" somehow generate behavior that corresponds to gravitation in physics.” He then mentions two ideas alien to physics: 1. That physical theories could emerge from something more fundamental and 2. “. . our whole universe and its complete history could be generated just by starting with some particular small network, then applying definite rules.”
All these ideas so weird to physicists simply indicate that Wolfram started thinking biologically. His small network might be regarded as a mathematical zygote from which our theoretical universe emerges.
We are told that Wolfram developed Mathematica for studying these “weird” ideas. Why not create a tool which will model a simple causal network of programs which exchange pieces of the network. As a starter he might consider my proliferon.
http://www.what-is-cancer.com/paper.../comp2Frame.htm
Posted by: Gershom Zajicek M.D.
Now that we embraced Wolfram as a biologist, let’s see what kind of biologist he is.
http://www.what-is-cancer.com/paper...s/compFrame.htm
Biological phenomena may be explained within two frameworks : Reductionistic and Holistic. The first applies physical reasoning to explain life, and is known as Cartesian reductionism. The other explains life as a whole and is less concerned with reduction. Its philosophy is outlined in : Hans Jonas The Phenomenon of Life- Toward a Philosophical Biology
Northwestern University Press Evanston Ill 2001 Here are some examples; R and H stand respectively for reductionism and holism:
The Gene: R: Unit of heredity which determines physical-chemical processes in the body. DNA -> RNA -> protein.
H: Is a manifestation of complex network interacting with processes of the body. It might be likened to a typewriter which types the four letters, ATGC yet the typing mechanism is also part of the gene.
Brain: R: Brain electrical activity (action potentials) accounts for our reasoning. In the future, reasoning will be read off this activity. H: The electrical activity is an epi-phenomenon of a vast and complex biochemical machinery which includes neurons and glia (supporting cells). It is embodied, which means that the entire organism participates in neural activity.
Evolution: R: Results from the selection by the environment of individuals carrying beneficial genes. H: Is the evolution of the food chain network, otherwise known as Gaia.
An in depth explanation is provided here: http://www.what-is-cancer.com/paper...lexityFrame.htm
Reductionism paved the way to today’s technological innovations. However it fails to explain important phenomena of modern life, e.g., Economy, weather, and global warming. The Black-Sholes equation won’t make you rich. Apparently the holistic approach of Warren Buffet is more effective. The Lorenz attractor shows that a system of differential equations cannot predict weather and ends in chaos. The babble about global warming results from the lack of holistic mathematical tools, which hopefully Mathematica will provide.
Since Wolfram drove my attention to CA, I devoted my research to evaluate their potential for holistic explanation of biological phenomena. http://www.what-is-cancer.com/paper...s/compFrame.htm
Now Wolfram came with an even more intriguing concept: A simple causal network of programs which exchange pieces of the network. Will this gem be presented to us in the next Mahematica edition?
Posted by: Gershom Zajicek M.D.
We were pleased to read that a three color machine is the simplest possible universal Turing machine and congratulate the winner who proved it.
http://blog.wolfram.com/2007/10/the...e_simplest.html
At this occasion we turn again to NKS Chapter 12 and read: “In essence, therefore, the Principle of Computational Equivalence introduces a new law of nature to the effect that no system can ever carry out explicit computations that are more sophisticated than those carried out by systems like cellular automata and Turing machines.” Reading this we wonder whether this “law of nature” applies also to life?
What we perceive around us is change. An ongoing and continuous change to which even Kant’s “the thing in itself” does not apply. There is not a thing out there, only change. Fortunately we are equipped with two faculties for handling this change: A memory to store it and a mind to interpret it. For interpreting change, mind applies innate and acquire memories. While the change there is essentially continuous our mind freezes and makes it discrete.
Wolfram regards change as a process, which may be regarded as a computation, assuring us that “all processes, whether they are produced by human effort or occur spontaneously in nature, can be viewed as computations” and “Computational Equivalence applies to essentially any process of any kind, either natural or artificial.” Therefore the “Principle of Computational Equivalence can be viewed in part as a new law of nature.”
Wolfram thus presumes that this “law of nature” governs also change. A Platonic idea which we mortals cannot grasp since it is obscured by change. So far so good, yet what about continuity? Cellular automata and most of the other computational systems that are discussed in his book are discrete. Does it imply that the change that surround us is also discrete?
Wolfram: “It is my strong suspicion that at a fundamental level absolutely every aspect of our universe will in the end turn out to be discrete. And if this is so, then it immediately implies that there cannot ever ultimately be any form of continuity in our universe that violates the Principle of Computational Equivalence.”
Wolfram: “In a sense the most basic defining characteristic of continuous systems is that they operate on arbitrary continuous numbers. But just to represent every such number in general requires something like an infinite sequence of digits. And so this implies that continuous systems must always in effect be able to operate on infinite sequences.”
What Wolfram prefers to ignore is that mathematics, be it discrete or continuous is a way to describe change, and cannot fully reproduce the continuity of the change that surrounds us. Thus Computational Equivalence is far from being a new law of nature. It is a creation of Wolfram’s mind which is busy interpreting the ongoing continuous change. It may be regarded as an important law of mathematics, a valuable tool for modeling phenomena of nature, but not a law of nature.
Vive la petite difference!
http://www.what-is-cancer.com/paper...s/compFrame.htm
Posted by: bsdwork
Gershom Zajicek M.D. you are most so right, Darwin was a revelation indeed.
__________________
A thing well said will be wit in all languages.~John Dryden
online prescription drugs
Posted by: Gershom Zajicek M.D.
Recently in his blog, Wolfram mentioned a new interpretation of space and time. http://blog.wolfram.com/2007/09/my_...unive.html#more
Let’s first examine two current interpretations of space.
“Normally in physics one thinks of space as some kind of background, in which matter and particles and so on separately exist” writes Wolfram. Some regard space as a container in which events happen, that existed even before the Big Bang, and we evolve in it. Poetically speaking, the Big Bang might be regarded as a fertilization of a primordial uterus.
Mandelbrot draw our attention to the possibility that space might be a fractal with its own geometry. Now Wolfram proposes that space might be a network and cautions us not “to imagine that the points in the network have actual defined positions in some background space.” He then adds “What's interesting, though, is that when a network gets big enough, its combinatorics alone can in effect define a correspondence with ordinary space.”
What about time? :” Current physics tends to say that time is just like space--just another dimension.” In other words time is a container extension into a higher dimension. Such a simple extension seems not to work in a fractal space. How then define time in a fractal space? I leave it to you as an exercise in a thought experiment.
Wolfram has a another suggestion. Suppose that space is a network of programs. “In programs, moving in space might correspond to looking at another part of the data, but moving in time requires executing the program.” “For networks, pretty much the most general kind of program is one that takes a piece of network with one structure, and replaces it with another.”
“But now we're deriving something like that for the universe: we're saying that these networks with almost nothing "built in" somehow generate behavior that corresponds to gravitation in physics.” This is Wolfram’s space. Actually it is a space-time. The programs are the space while each executes its own time. Similar space-times are inherent in life.
http://www.what-is-cancer.com/papers/ca/ca67.htm
Wolfram: ”Special and general relativity are things that physicists normally assume are built into theories right from the beginning, almost as axioms (or at least, in the case of string theory, as consistency conditions). The idea that they could emerge from something more fundamental is pretty alien” Yet Wolfram believes that ”. . .our whole universe and its complete history could be generated just by starting with some particular small network, then applying definite rules.” I hope that he does not mean our physical universe but the way we interpret it.
More on Wolfram’s biological thinking
http://www.what-is-cancer.com/paper...lexityFrame.htm
Posted by: Gershom Zajicek M.D.
Change is the fundamental attribute of nature. Life is a process which interprets change. In order to do so life has to sense change and remember the previous change. Sensing change triggers movement, either toward change or away from it. The three attributes, sensing , memory and movement, distinguish life from non life (but do not define life). While in the physical world, movement has to have a cause, movement of a life form is triggered. It is triggered by change.
The decision whether to move toward a change, or away from it, is handled by an entity, which controls the change in the living being, called here Wisdom of the Body (WOB). Every life form is bounded (covered with a membrane) and distinguishes between its personal change (self) and the change which it faces. Unlike inorganic matter, life’s wisdom (WOB) is inherited.
http://www.what-is-cancer.com/paper...lexityFrame.htm
Evolution is an ongoing improvement of WOB to handle change. (Survival of the fittest WOB).
At a certain stage of evolution, life entities acquired a mind, which assists WOB to interpret change.
The human mind broadened its change interpretation capabilities by creating religion, science and philosophy. While the three disciplines claim to understand reality, they are no more than means to interpret change.
Posted by: Gershom Zajicek M.D.
RIEDENSCHNEIDER (Lawyer)
...They got this guy, in Germany.
Fritz something-or-other. Or is it.
Maybe it's Werner. Anyway, he's got
this theory, you wanna test something,
you know, scientifically--how the
planets go round the sun, what
sunspots are made of, why the water
comes out of the tap--well, you gotta
look at it. But sometimes, you look
at it, your looking *changes* it. Ya
can't know the reality of what
happened, or what *would've* happened
if you hadden a stuck in your goddamn
schnozz. So there *is* no 'what
happened.' Not in any sense that we
can grasp with our puny minds. Because
our minds... out minds get in the
way. Looking at something changes
it. They call it the 'Uncertainty
Principle.' Sure, it sounds screwy,
but even Einstein says the guy's on
to something.
RIEDENSCHNEIDER
...Reasonable doubt. I'm sayin',
sometimes, the more you look, the
less you really know. It's a fact. A
proved fact. In a way, it's the only
fact there is. This heinie even wrote
it out in numbers.
The Man Who Wasn't There
by Joel Coen and Ethan Coen
http://www.answers.com/topic/the-ma...t=entertainment
v. Change http://www.what-is-cancer.com/paper...xity/change.htm
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