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 Idea for science journal Theory of Intelligent Design paper 
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Joined: Fri Sep 22, 2006 12:04 am
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Post Idea for science journal Theory of Intelligent Design paper
As you may know a science journal paper for the Theory of Intelligent Design has long been a gnawing goal complicated by a number of things, in addition to their unique politics. With this being theory that by any title is for including with source code for a computer model both have to be there at a place for downloading such a thing, not the theory all alone in a print journal with format for explaining lab research.

Where I stay within my niche that I have been in for decades and long before the ID controversy it’s no big deal to just for the heck of it see what it’s good for that might help improve an old computer model, make it even more fun to develop. And crossing a line into taboo theory, without going out of bounds of science, is something scientists dream of one day having been a part of. But have to first show how to get there, with something that goes with source code that is available at Planet Source Code that has long been the place for Visual Basic and still is.

In a science journal audience many would be all set to argue “evolution” and the other usual arguments not be interested in source code for an as simple as possible cognitive model of a typical brain of anything. Need to see what the theory looks like outside of the science journal format and expectations to appreciate its usefulness to science and science education.

Now that the source code with theory is available at Planet Source Code there is no longer the problem of only having download from a Google site, now have it looking like this:

Image

Even with a couple of its globes punched out, it still looks great. Their peer-review system (through awards) disqualified that outside junk, real well. System proved itself to be more resilient than thought. And science journals allow url’s that the researcher(s) put on the web (where there is no review for anything at all) which should make it easy for one that includes some peer review to be discussed in a normal paper for source code based work like this being online.

It is now possible to write a typical paper on source code that the journal audience would be interested in. Here’s one for Avida software I can use as a rough model for what to say where:

http://myxo.css.msu.edu/papers/nature20 ... omplex.pdf

They give url to their download site at:

http://myxo.css.msu.edu/papers/nature2003/

This type of paper greatly simplifies the problem of making the theory fit a science journal format. And impressing the Planet Source Code community is not as easy as it sounds. In some ways even harder because it has to impress more than just scientists with more than results of research on a gene or something it has to have awesomeness where they most know what else is on the internet for scientific code including GA’s. University professors get to see what some will in the future enter college knowing, be prepared for them.

A science journal paper is a good place for level of detail that audience would be most interested to know for ideas to use in their work. Paper would not dwell on Planet Source Code that is where the source code that includes the theory is downloaded, for any to join the fun. Takes care of the problem of having to try presenting the whole theory in few pages for them to judge from just that, in this case all supplemental material along with award from peer-review is right there.

Like above I can show an image of the screen, to get it into print. Not even mention missing globes, three then look just as excellent next to the big award. The theory is then accurately shown being useful where it most belongs not a pie in the sky idea that they need to judge for it to maybe someday be useful somewhere. Can this way get straight into what is most important they would be interested in knowing, in addition to all presented at Planet Source Code.

Being able to see the theory in a community that exchanges source code instead of research papers helps show what it is and why it started there not science journal format. And with the way it works out that the theory started in a community for source code exchange not science journal for lab research results they’re just left out of the science fun. It’s not because of any public policy against the theory it’s because of the theory having started there in the days I did not think the Theory of Intelligent Design was scientifically possible, that came later. Such a theory is inherently source code intensive, not surprising that's where it instead began the way it did.

It is easy for this community to be brushed off as a scientific nothing, yet it fills a respectable niche that made it easy to advance a computer model like this for basics of cognition. I doubt they like being snubbed either, so recognition that helps even up the score by getting them some respect will be empowering fun there too.

A science paper like this would be worth writing, and easy to publish. The science paper publisher might like knowing about a little about the source code related community, not be a rubbing it in kind of thing. And I would rather not have to take the theory out of context of what it is at Planet Source Code where it’s no big deal to have that included with an update to earlier model. To know what it is useful for all need to start with that example, go from there.

That’s my idea for a science journal article. Do not have to compromise anything or anyone instead spreads the excitement to the lab research type community, without having to write outside what they’re used to publishing. The paper will not present the theory to be judged a theory or not, it is the usual description of something for download somewhere. Just have things they would have to see to believe that makes it of interest to read. That community can add their thoughts to others, but cannot judge for them. There would here be no conflict of interest, all stays fair, without the theory begging for a trashing with the old philosophy and evolution arguments that’s what it looks like being useful, with no shame in being where it is right now, doing well.

Explaining where the theory is now at seems to be the ultimate paper to write right now. If it works for you too then on something like this I can realistically set a goal for a rough draft ready here by New Years (Kansas time). What do you think?

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The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.
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Tue Dec 27, 2011 11:02 pm
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Post Re: Idea for science journal Theory of Intelligent Design pa
Well Brian it looks like in this thread I already need to cue your crickets:

http://www.abdn.ac.uk/~nhi708/classify/ ... ricket.wav

In an attempt to try to liven things up a bit, I already have over a page worth and it came out real nice I think. Only problem is their format worked so well it’s an obvious rewording of the paper for the Avida program. There is though a place to mention them to make up for it, I still consider Avida one of the best GA’s around for whoever found a way to get excited by one of those. William Dembski and others did write a paper about a hill climbing algorithm working better so it only figures that Avida is in it like somewhat like this. Their framework working for me too, is a compliment to them. Or at least whoever they got it from. Also have another way to figure out what I’m saying, by looking at what they did, maybe more helpful like that. Is at least a good place to start, get to see what it would look like where the Intelligence Design Lab is being written up the same way.

Avida article wrote:
A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.

I wrote:
A long-standing challenge to science has been to credibly explain to all whether or not there is any scientific merit to the Theory of Intelligent Design. We examined this issue by starting with its premise as basis for advancing an existing simple cognitive computer model, from which are derived operational definitions that more precisely describe the essence of intelligence, to in turn make it easy to conceptualize the overall process. There is a computer model with an included cognitive theory where purpose has all along been to provide a how-to type theory of operation for the circuit that the source code simulates. After taking literally the premise of the Theory of Intelligent Design it became a novel new theory useful to update earlier “Intelligence Generator” with a new model called the “Intelligence Design Lab” for one or two lobe brain configurations. Also explained is what science qualifies an “intelligent cause” event, for all to try to be the first to program. There was measurable success in this community with prior knowledge of such a computer model and included theory. There was first a made for source code pre-publishing peer review process to make sure there is no malware and works as advertised, which was accepted, then soon followed by compliments then month later honored with the Planet Source Code "Superior Coding Contest Winner" Award for Visual Basic. There here emerged clear example of a coherent Theory of Intelligent Design being useful in science and science education. These findings show that when explained this way there is tremendous scientific merit to the Theory of Intelligent Design already working in the community in which it came, to now explain here to a community more accustom to publishing research results and articles in a science journal.


This one was easy to get started:

Avida article wrote:
Charles Darwin’s theory of evolution 1, including its intertwined
hypotheses of descent with modification and adaptation by natural
selection, is widely regarded as one of the greatest scientific
achievements of all time. From the outset, Darwin realized that
“organs of extreme perfection and complication”, such as the eye,
posed a difficulty for his theory. Such features are much too
complex to appear de novo, and he reasoned that they must evolve
by incremental transitions through many intermediate states,
sometimes undergoing changes in function. There now exists substantial
evidence concerning the evolution of complex features that supports
Darwin’s general model 2–16. Nonetheless, it is difficult to
provide a complete account of the origin of any complex feature
owing to the extinction of intermediate forms, imperfection of
the fossil record, and incomplete knowledge of the genetic and
developmental mechanisms that produce such feature

I wrote:
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection1. That premise is widely regarded as one of the greatest scientific challenges of all time, to either find a use for or get rid of. Yet such features too complex to appear de novo from random means can be attributed to multiple levels of intelligence in the system that makes a living thing a born to be survivor, not an accident. There now exists substantial evidence concerning the origin of complex features that supports the Theory of Intelligent Design general model. Nonetheless, it is difficult to provide a complete account in such a brief article to explain how from the perspective of intelligence it is able to produce such features.


Then this became another fill in the blanks too:

Avida article wrote:
To examine the evolutionary origin of a complex feature in much
greater detail than has previously been possible, we have performed
experiments with digital organisms—computer programs that selfreplicate,
mutate and compete 17–26. As Daniel Dennett 27 has emphasized,
“…evolution will occur whenever and wherever three conditions
are met: replication, variation (mutation), and differential
fitness (competition)”. By using this tractable system, we aim to
shed light on principles relevant to any evolving system. Digital
organisms are also of interest as computer scientists and engineers
explore ways to apply evolutionary principles to program design,
engineering and robotics 28–31. The next section describes our
experimental system, including the logic functions that digital organisms
can use to obtain energy. There follows a case study of the genomic
and phenotypic changes in a population that evolved an especially
complex function, and then a functional-genomic analysis of the
first genotype able to perform that function. Next we compare the
trajectories and solutions of many populations that independently
evolved this same function, and we conclude by examining the
influence of different selective environments on the propensity of
digital organisms to evolve the function.

I wrote:
To examine the intelligence related origin of a complex feature in much greater detail than has previously been possible the theory had to over time become a serious scientific challenge to ones with programming skills that make them most able to understand how it works and what it’s useful for. What applies to these computer models can be expected to also apply to an emerging systems biology that attempts to reduce living things to their schematic circuit. It is not that in another paradigm the concept makes sense here Natural selection based answers are not useful to develop this theory their core models are here entirely different and require specific terminology, are not interchangeable and are to be kept separate from each other.


That flowed into the start of next section but then required going freestyle:

Avida article wrote:
Experimental system

Avida is a software platform for research on digital organisms. To
convey what digital organisms are, it is helpful to compare them
with computer viruses. Digital organisms are self-replicating....

I wrote:
Experimental system

The Intelligence Design Lab is a software platform for cognitive research that is available for download at Planet Source Code has theory that is useful for what can be coded, emergent levels of intelligence are expected to still speciate without natural selection in a model that includes molecular intelligence.

Image
Image
http://www.planet-source-code.com/vb/sc ... 5&lngWId=1

In the included theory of operation all living things are linked over time by a self-learning molecular intelligence that “cycles” one replication at a time over billions of years lifetime to arrive at us in its genetic memory in the present. We can this way explain as far back as the origin of life where there were already self-assembling cellular organelle that did not evolve they are chemical reactions common to this planet’s chemistry. Not leaving intelligence out of the equation makes possible theory for another way to explain how living things work.


Then I gave Avida a reference so it's not like I'm trying to hide my wrongdoing or down their model just using it to help write a science article, that at least we know Nature will accept:

I wrote:
Because of the core model producing intelligence not a Genetic Algorithm such as Avida[2] a Natural Selection variable is not required to produce digital organisms. This modeling method produces digital organisms by considering all levels of intelligence that may or may not include neural brain that like here be modeled separately, or use same computer algorithm to represent its living genome. What happens is for the most part decided by the intelligence(s) in the virtual world. How long each can sustain cellular level systems determines lifetime which are normally near infinite in cyberspace because of their virtual parts/components never wearing out or getting broken. Not having a limited life span here indicates the molecular level system not included, is not because of natural selection variables needed somewhere in this multi-level model.

This source code is for simple to program next generation personal computer scale origin of intelligence simulations that are as alive as science can make them, because of intelligence being first and foremost included. There is a cognitive model with a four requirement system that is useful to rule things intelligent or not.

Image

There is a simple system configuration to look for that because of being self-learning has a hidden way of adapting to and controlling its environment. Instead of random change, the exact mechanism that produced anything is important especially where like transposon making memory address changes and other system expected processes like this form of good guess. There is here a reason why things change over time like they do. Leaving it to random accidents is here not accepted need to at least know it was cosmic ray or other damage that molecular intelligence would see as random change, but would normally be expected to be intentional changes in response to learning. This goes beyond the usual theory rigor, in search of better answers to what makes a genome and what comes from it a tenaciously controlling entity.

From this system structure we can derive a method to illustrate metabolic circuits from systems biology, as a most simple cognitive model that also works for neural brains that accomplish the same using neurons. Simplifies the task of comparing one system to another and the placing of molecular interactions in an overall circuit that may have both molecular and cellular going at the same time, is then not a single circuit there are two systems working at the same time to separate out. Makes the purpose of things more clear cross disciplines, from even source code community, to molecular biology, to cellular biology, to multicellular biology that includes cognitive science where the human brain has many parts that still all together reduce to the same simple system.

All not in cognitive science can be glad they don’t need to make sense of all in neuroscience or even be proficient in Visual Basic to make good use of this theory. Just need what is most important to know about intelligence, be able to recognize it. Can then also fill in what is not yet known in science models with what this model predicts missing or is happening in the part of the circuit it is in. All in biology then makes more sense, because of all being easier to model, at any level of detail.

Discussion

There is now a simple yet challenging cognitive model already being useful in the source code community to apply by the lab research type community that at the same time helps find reason in a debate where it never was as simple as a theory being impossible. In science, almost anything is possible, obviously even this theory. And for what it’s worth science wants such things developed, just because they can, even where just to see what it can in time develop into. Trying to stop all from trying, is simply unscientific, best for all who remember it’s old days can just lighten up about ID because the way science works all even their institutes must start with accepted theory, then work from there. Having accepted theory is here better than having nothing.

Academia needs to be aware of in the future entering their classrooms or discussed there. This will in turn become their working knowledge of the Theory of Intelligent Design. As with a Theistic Evolutionary it is possible to add religious significance to a scientific theory, but that does not rule it out. There is nothing to get shook about, like science will stop because of it, just have to find a way to adapt to the acceptable theory that now exists. Need to be more specific as to which theory and what they understand from it.


Like with programming an intelligent design event to a programmer that loves a-life I next want to add more for them to apply to their work to include in this paper, take it to the edge of science without falling off for their community to have fun with, but I have not thought of what they need yet. Something to at the same time win them a Nobel Prize in their field would work, can maybe go on that idea. Let me know if you have any, for leaving them glad for the read, find this theory totally awesome too.

_________________
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The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.
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Thu Dec 29, 2011 3:15 am
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Post Re: Idea for science journal Theory of Intelligent Design pa
Seeing how the forum is so asleep slow it made sense that I at least talk to myself through this writing project, after again going over the Avida based material I wrote it made it hard to add in what else needed to be covered. So I focused on its lead (can be its Abstract) paragraph that has to in few words as possible sum up the issue and article/paper, then came up with this much more information containing short read. It now starts off with only 5 words from the Avida paper, the rest is original phrasing to keep the information flowing to end with learning there is already online software for experimenting with intelligent cause:

Quote:
A long-standing challenge to science has been to credibly to all put into scientific context this premise: “The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.” It can seem that the 2004 Dover, PA trial settled that issue but not having had a coherent theory back then does not rule out one in the future being discovered. The court order was against a school board ID policy not a theory. Further, religious implications that were said to make the theory unscientific are contradicted by Theistic Evolution and other religious denominations who self-styled whole religions around scientific theory. Where even for just the benefit of those who at least expected a genuine attempt with the rules kept the same for all theories it remained a scientific challenge to explain what the premise operationally defines as “intelligent cause” whereby there is an emergence of intelligence from intelligence. With science not allowing from anyone including those who argue against the premise holding true any supernatural deity in place of observable repeatable expermentable mechanisms the issue was found to boil down to a phenomenon that can be experimented with that easily scientifically qualifies as an “intelligent cause”. This article describes the online one or two lobed “Intelligence Design Lab” that includes a Theory of Intelligent Design to among other things operationally define “intelligence” and explain how to work program towards a never seen before “intelligent cause event”.


The text from Planet Source Code that will next be on the screen does a good job of explaining what that is, so with their next downloading the software and theory not much seems to need to be said after that. To not distract from its purpose of introducing the lab & theory the article can be kept short. Maybe include a new flow-chart type diagram for the circuit followed by one from model, so they’ll have the cognitive model and its theory of operation part in print in front of them to study, seems that’s all they need. Not need to mention Avida that would distract too.

After the above paragraph, I think the rest is just piecing something together from what I already have to work with.

_________________
Premise:
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.
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Fri Dec 30, 2011 5:11 am
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Post Re: Idea for science journal Theory of Intelligent Design pa
Just to keep something of a paper going I kept working on the lead/Abstract paragraph so it says the right things to make the reader have to read this one.

Quote:
A long-standing challenge to science has been to responsibly put into scientific context this premise: “The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.” It can seem that the 2004 Dover, PA trial settled that issue but not having had a coherent theory back then does not rule out one in the future being discovered, the court order was against a school board ID policy not a theory. Furthermore, as with Theistic Evolutionists who religiously use scientific theory such religious implications are not grounds for dismissal, nor are arguments that attempt to falsify the theory with supernatural deities in place of observable repeatable expermentable mechanisms. With the rules kept the same for all sides/theory the issue was found to boil down to a phenomenon that scientifically qualifies as an intelligent cause whereby there is spontaneous emergence of an intelligence from another level of intelligence. This article describes the online Intelligence Design Lab source code that includes in theory of operation a Theory of Intelligent Design to among other things better operationally define intelligence and explain how to program towards a never seen before intelligent cause event. How this predictive theory uniquely applies to biology and human (chromosomal Adam and Eve) origin will also here be introduced.

There would next be what it looks like on Planet Source Code, followed by summing up the theory real fast, maybe along with some from the full version of the theory on qualifying biological intelligence that was too much detail for theory included with the Intelligence Design Lab. Can maybe also put the already better edited version of that theory in the open access online supplementary information, along with software with the Windows compatible .exe that is not in the Planet Source Code download. I’ll have to check on that, but think I found what I need for an awesome lead paragraph for any science journal. Starts off with a hint of Avida paper in it but the article does not need to compare that model or keep following their exact structure, just be the same idea for something similar yet has differences.

So there you have it, just in time to say I had a rough draft of something here for by New Years, Kansas time. Have to now wish all another happy New Year to you, and a changing science.

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The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.
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Sun Jan 01, 2012 1:53 am
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Post Re: Idea for science journal Theory of Intelligent Design pa
The above attempts at trying to rush the right thing to say are now so outdated I cringe to read them. I must update the thread with what I now have, which is short and sweet and to the point. The theory itself would be included in Supporting Information.

Systems Biology and the Theory of Intelligent Design.

In the same way the NIH/NLM Visible Human Project had to be followed by the Human Genome Project another challenge of even greater scale to follow that is emerging from systems biology, where the ultimate goal is to fully map and model the chemical processes of living things. The National Center for Biotechnology Information is already in the early stages of its development with the BioSystems Database they describe here:

“The NCBI BioSystems Database was developed as a complementary project
to (1) serve as a centralized repository of data; (2) connect the
biosystem records with associated literature, molecular, and chemical
data throughout the Entrez system; and (3) facilitate computation on
biosystems data.”

http://www.ncbi.nlm.nih.gov/Structure/b ... about.html

This database may not yet be much of an attraction, but such a project can in the future take on an unexpected life of its own. Systems biology is an area of science that takes all of us towards better understanding what it is that makes living things alive, intelligent. And success in showing what is most important to show happening in the system of something that is some level cognitive has a way of on its own leading to surprising models.

Where a cognitive model is kept on a scale within limits of science and technology it is possible to program this “Intelligence Design Lab” now available for download from Planet Source Code:

Image
Image
http://www.planet-source-code.com/vb/sc ... 5&lngWId=1
(See Supporting Information for text of theory with detail added for this article.)

Software with compiled code for Windows, and earlier version of the model:

http://intelligencegenerator.blogspot.com/

In this how-to part of the computer science community exact biological detail is not required, yet what applies to this simple computer model can be expected to also apply to the most complete that may one day be possible from systems biology. Both models must most clearly show the multicellular intelligence level of the system, with one based on a BioSystems Database model organism only having to go into much finer biological detail.

Electronics based schematics can simplify testing and visualization of the underlying principals of a self-learning system, in-silico where there is this RAM memory in the system to model with. This helps sort out the components of a cognitive biosystem.

Image

Molecular streams traveling through the nuclear membrane address various chromosome territories, so logically end up in the Addressing side of the RAM chip. The DNA part of memory (gene action responses) logically belong in the right Data side of the RAM chip. All sensory inputs have their place as well as mechanisms that can produce a change in Data or Address to take a guess leading to transposition to new RAM address or code change at the same address. The RAM can be made any height necessary for all genes in each chromosome that has a 3D position inside a nucleus that connects to the outside environment through a spherical nuclear membrane with pores that can be conceptualized as addressing pins that address a specific internal chromosome and location. Shown on top here would be the confidence changing circuitry monitors how all is going between sensory and
Addressing, which can output a signal for RAM changing events such as transposition or hypermutation type code change to gene data.

All visionary projects have to start somewhere. For systems biology the best place is with a how-to computer model that pulls out all the science-stoppers to provide novel new theory that further helps show what is possible. Here all living things are linked over time by a self-learning molecular intelligence that “cycles” one replication at a time over billions of years lifetime to arrive at us in its genetic memory, in the present. From its model are derived operational definitions that can more precisely describe the essence of intelligence. It is all together a very intelligent glimpse of the future of science for even future scientists who may still be in grade school, and on up, where a not as impossible sounding as once thought Theory of Intelligent Design is found to love systems biology too…

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The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.
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Mon Feb 27, 2012 6:41 am
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Post Re: Idea for science journal Theory of Intelligent Design pa
I have been going over how the article ended up having to say, and it now looks like it’s down to minor grammar and understanding changes that can be included in the final text of the article. Everything it absolutely needed still seems to all be there, so here is the first draft to be sent to NCBI to show what is planned for publishing:


Systems Biology and the Theory of Intelligent Design.

In the same way the US National Library of Medicine’s “Visible Human Project” had to be boldly followed by its “Human Genome Project” another great scientific challenge is emerging from the science of “systems biology” that has already led to an ambitious “BioSystems Database” project described here:

“The NCBI BioSystems Database was developed as a complementary project
to (1) serve as a centralized repository of data; (2) connect the
biosystem records with associated literature, molecular, and chemical
data throughout the Entrez system; and (3) facilitate computation on
biosystems data.”

http://www.ncbi.nlm.nih.gov/Structure/b ... about.html

The ultimate goal of systems biology is to provide models with full circuit diagrams of living things, in resolution to the finest cellular and molecular detail possible. Yet for hundreds of years new scientific knowledge has only lead to new questions to answer, with certainly no sign yet that everyone is almost out things that need more study. As a result, a complete BioSystems Database for even a most simple model organism becomes a tremendous multidiscipline lab and programming challenge that can easily take decades for halfway complete, but hopefully by then there will be enough information to model an entire cell/bacterium, that behaves like the real-thing.

At least for now, it’s too early for there to be BioSystems Database files with all the numbers needed to fully bring to life a model organism, but that’s the dream for those working on the computer science related challenges of this awesome systems biology problem. And here, success in showing what is most important to notice happening in the system of something at some level cognitive has a way of on its own leading to surprising paradigm changing models and theory. Where a cognitive model is kept on a scale within limits of current science and technology it is now at least possible to program an “Intelligence Design Lab” that includes theory of operation where no matter how it’s explained, only one name to call it immediately comes to mind:

Image
Image
http://www.planet-source-code.com/vb/sc ... 5&lngWId=1
(See Supporting Information for text of theory with detail added for this article.)

Software with compiled code for Windows and earlier version of the model:

http://intelligencegenerator.blogspot.com/

In this how-to computer science community exact biological detail is not required, making this model possible to experiment with from there. Technology willing, the BioSystems Database project makes possible Intelligence Design Labs for virtual living things that automatically become increasingly realistic as their biosystem database becomes more detailed.

What applies to this simple computer model applies to the most complete someday possible. Both models must as clearly as possible start with the upper level self-learning (intelligence) system that can be (as below) multicellular brain, or single-cell animal (protozoan, stem cells) cellular, or molecular level only that self-learns through time by replication of genetic memory. Each level of self-learning reduces to the same circuit, which further simplifies visualization of what’s most important to notice happening in a system that is also “intelligent”.

Image

Here we can very literally say that: All in (systems) biology makes sense, somewhere in the (above) circuit. Where this were showing molecular intelligence of a cell, streams traveling through the nuclear membrane address various chromosome territories are logically placed inside the (left) Addressing half of the RAM chip, as part of its chemical addressing/signaling system. The genes of DNA belong in the (right) Data side of the RAM chip. The RAM can be made any height necessary for all genes in each chromosome that has a 3D position inside a nucleus that connects to the outside environment through a spherical nuclear membrane with pores that can be conceptualized as addressing connections that address a specific internal chromosome and location. All sensors/sensory have their place connecting into addressing of RAM, and these connections may be monitored by a Confidence circuit that can produce a change in Data or Address to take a guess leading to transposition to new RAM address, or code change at the same address.

Living things can be conceptualized as each being one thought cycle of their now billions year old self-learning molecular intelligence (same circuit) that stays going through time by replication. If our brain worked this way then it would replicate and replace itself every few thoughts (and without losing contents of memory) thus stay going almost forever. Unfortunately, cells cannot replace themselves that quickly. Our thought cycles exist as a brain wave/cycle rhythm within the one single self-learning memory system, but (where physics willing) the system could just as well at the same time reproduce and replace itself (and stored memories) at regular wave/cycles.

A multicellular intelligence model (such as Intelligence Design Lab) that includes the molecular intelligence level would adapt and reproduce over generations, without needing a mutation/selection Genetic Algorithm. In this modeling method you do not have to reduce the effects of every thing happening in the environment to a “natural selection” variable, the non-intelligent influences from environment are simply modeled in. As in real life the food supply may vary or a volcano could be programmed into the model which destroys a part of the virtual world and cover other areas with ash, then what happens with the virtual living things, happens. None need to start with a conclusion about environmental influences. This does more to test hypotheses that came from other theory, with different variables in its core model/algorithm.

This model easily allows germ line (inherited) cell epigenetic systems where there can be upstream sensory molecules involved in downstream regulation of morphology changing genes that may have a confidence circuit to control translocation to new address or code change at same address. The circuit sorts out and make sense of some of the most baffling phenomena of them all.

The how-to computer science community now has a model to work with that removes the usual science-stoppers to produce a paradigm changing theory to help systems biology along. It is evident that all who now know-how are OK with such a bold and daring way of seeking new knowledge in a very real uncharted scientific territory, just waiting to be pioneered by anyone with the talent. And even at the NCBI level great visionary projects have to start somewhere, preferably with a prototype to show what is ultimately possible where all think really really big. Therefore, insight into the future of the science of systems biology, must include a model from where scientists of all ages can be found who know intelligent causation events as something that can be programmed, and its Theory of Intelligent Design loves systems biology too…

_________________
Premise:
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.
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Thu Mar 08, 2012 4:44 pm
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