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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)?
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