Biology of life and 3D spatial positioning

[KBCid]

I was under the impression that a cell/organism did have inherent positional control.

what gave you that impression?

Matter in the form of cell behaves in a certain way, matter in the form of a solar system behaves in a certain way, not entirely predictable but predictable to a rough degree. How does one show if movement is caused by inherent properties or not?

Matter in the form of a cell is not the basic matter that is used to form the cell. Cells are highly complex arrangements of matter in their own right. How do you suppose they become formed? Do you suppose that we could simply throw chemicals in a pot and poof you get a cell? The space shuttles complexity is many orders of magnitude simpler than a single cell in comparison. The matter that is used to construct a cell has no inherent positional control. You can certainly look up whatever research you feel backs your assertion but, I have researched this subject quite extensively. If you had read through this thread you would have found this;

Remaining Mysteries of the Cytoplasm
Nothing epitomizes the mystery of life more than the spatial organization and dynamics of the cytoplasm. How can a bunch of molecules, no matter how sophisticated, generate spatially complex behavior on a scale that is much larger than the molecules themselves? In my view, we will be done as cell biologists when we can predict the structure and dynamics of cells from DNA sequence. That goal is still some way off; indeed it is not yet clear if it is conceptually feasible. Below I identify three challenges, one general and two specific, that must be overcome if we are to make progress.
COLLECTIVE PROTEIN BEHAVIOR
Understanding how molecules work together to orchestrate cellular processes is the new frontier in basic cell biology. Reductionist approaches generated parts lists for many cellular processes and detailed biochemical information on some parts. Occasionally, studying a single part gave profound insight into large-scale behavior. Myosin-II in muscle contraction is an example, though we are still far from understanding how sarcomeres assemble. However, most cellular processes depend on multiple proteins and lack the quasi-crystalline organization of muscle. Invariably, we lack quantitative, predictive understanding of the collective behavior that generates such cellular processes...
...we may also need new conceptual approaches to understand how integrated behavior emerges from complex microscopic dynamics. ..
BUILDING THE CELL: LOCAL CONTROL VERSUS LOCAL SYNTHESIS
Physical organization and motility of cells requires spatially controlled biochemistry.
http://www.molbiolcell.org/content/21/22/3811.full

If there was an inherent control in the matter that forms a cell then they could easily define it. If there was inherent positional control at a cellular level then they could define it. Neither of these has inherent positional control.

I think the central dogma is a pretty good run down of how replication occurs. A mechanism was inferred and one was found, granted we don't understand everything about it but the same could be said of the constituents of matter or gravity or........
You have inferred a control system which, as far as I can see, is yet to be found.

The central dogma doesn't define how replication occurs. You are certainly welcome to reference any experimental evidence that does show how it works.
The control system is not yet to be found. The extent of It's boundaries are what is yet to be defined. Matter doesn't move itself.

[Proinsias]

I was under the impression that a cell/organism did have inherent positional control.

what gave you that impression?

Inherent probably wasn't a good word choice. Perhaps 'not obviously the work of intelligence' would be better.

Matter in the form of a cell is not the basic matter that is used to form the cell.

Then what is it?

If there was an inherent control in the matter that forms a cell then they could easily define it.

Why would it be easy?
The behaviour of basic matter, and what basic matter may be, isn't easy. If biology is built on basic matter which we can't yet define or understand I would expect theories of biology to have unknowns.

The central dogma doesn't define how replication occurs.

Again I think it gives a pretty good idea of the process. DNA>RNA>Protein gives a far better picture than other theories like that of spontaneous reproduction, rats from piles of hay and whatnot.

Do you expect this control system you are postulating to to be physical in nature? Is it something you expect to unravel and gain an understanding of like evolution>genetics or something that will need to be taken on inference?

[KBCid]

I was under the impression that a cell/organism did have inherent positional control.

what gave you that impression?

Inherent probably wasn't a good word choice. Perhaps 'not obviously the work of intelligence' would be better.

How might the requirement of intelligence be determined? If there is an assertion by a scientist that there could be a 1 in 10 to the power of 100 chance that such positional control could arise by chance would you assume that it must be a chance occurance?

Matter in the form of a cell is not the basic matter that is used to form the cell.

Then what is it?

structure in a cell is made from proteins, which are constructed from amino acids (folded into specific 3 dimensional forms) and the amino acids are formed from carbon, hydrogen, oxygen, and nitrogen into very specific arrangements. Each of the stages from building blocks to final protein form must be handled in space and time. Just as an intelligently designed factory operates on the processing of substrates to make final formations of matter so must the cells structure be built from substrates. None of the processing of matter used to form a cell is a chance occurance. It is precision movement at each stage exactly like any intelligently designed factory would operate.

If there was an inherent control in the matter that forms a cell then they could easily define it.

Why would it be easy?

because each of the material structures at each stage of being processed are open to empirical study. The same way crystalline structures are open to study.

The behaviour of basic matter, and what basic matter may be, isn't easy. If biology is built on basic matter which we can't yet define or understand I would expect theories of biology to have unknowns.

Biological structures are built on basic matter that is defined. You can study up on these here;
General Biology/Getting Started/Chemical Building Blocks of Life
http://en.wikibooks.org/wiki/General_Bi ... ks_of_Life

The central dogma doesn't define how replication occurs.

Again I think it gives a pretty good idea of the process. DNA>RNA>Protein gives a far better picture than other theories like that of spontaneous reproduction, rats from piles of hay and whatnot.

Does it? how does the RNA move in space and time to the proper point on the DNA to be transcribed? then how is this messenger RNA moved in space and time to the ribosome for translation? How are the specific amino acids which are used in the translation process moved in space and time to the ribosome to be formed into a protein? once constructed how is a protein moved in space and time to its final destination?
Once you can answer these questions then you can consider how such a system can be formed by chance since the entirety of this system is necessary for replication and without replication there is no evolution.

Do you expect this control system you are postulating to to be physical in nature? Is it something you expect to unravel and gain an understanding of like evolution>genetics or something that will need to be taken on inference?

All systematic control systems are formed from physical constituents. All systems are amenable to scientific study just as any reverse engineering study is. The only part of inference will be for how such a system can be formed since no one was there to see it happen. The simplicity here is that there is a limit to the minimal complexity of a replication system and part of that minimal requirement is the ability to control matter in 4 dimensions, 3 dimension in space and 1 dimension in time.
Evolution is entirely dependant on replication before it can have conceptual functionality and replication is entirely dependant on being able to re-build the same 3 dimensional structures over and over. So you come to this point where you must rationalise how a replication system can occur by chance to allow for the conceptual action of evolution to begin.
How simple is it to replicate 3 dimensional structures that are formed from matter that has no inherent positional control?

[Proinsias]

I really don't feel we're going anywhere here, I think I understand your position as well as I did back when I suggested I hold off on further posting until you have the experimental data that will elucidate the point. Oh well.

How might the requirement of intelligence be determined?

I have no idea. IQ tests are popular but getting your designer to sit one might be problematic. The only credible scientific outfit I can think of hunting for intelligence are SETI but they seem to be looking for pretty much the exact opposite of what the ID proponents are championing, http://www.teamseti.org/page.aspx?pid=1011 from the link:

Well, it’s because the credibility of the evidence is not predicated on its complexity.

If there is an assertion by a scientist that there could be a 1 in 10 to the power of 100 chance that such positional control could arise by chance would you assume that it must be a chance occurance?

I'd ask how the scientist came up with that number.

Each of the stages from building blocks to final protein form must be handled in space and time.

You seem to be asserting that biology, along with the rest of the physical world operates in space and time. I agree.

[quote=""KBCid""]Biological structures are built on basic matter that is defined. You can study up on these here;
General Biology/Getting Started/Chemical Building Blocks of Life[/quote]
I've got a working, if a little rusty, understanding of molecular biology and the building blocks of life, my stand alone chemistry is very poor. My point was not to expose my ignorance of the building blocks of biology, which fills many textbooks, but to elucidate that a bottom up understanding of so called 'basic matter' doesn't exist and isn't very basic. My understanding of particle physics doesn't go far beyond the occasional copy of New Scientist but is enough to see that's it's not well understood and is keeping some of the greatest living minds occupied and arguing. Your 'basic matter' is a profound mystery.
Water, as I've mentioned, is big part of the picture that we're still learning about it, from the Journal of Physical Chemistry last year:

The study of the structure and dynamics of water is one of the most exciting interdisciplinary research topics in science. Although it is one of the simplest molecules, water has myster- ious properties that have intrigued scientists of many different disciplines and that, despite its fundamental importance in science, technology, and the environment in our daily life, are far from being completely understood and are currently under active investigation.

linky
Once you can answer all the ground up questions from physics and chemistry you may be in a better position to infer the unknowns in biology to an intelligent designer.

Again I think it gives a pretty good idea of the process. DNA>RNA>Protein gives a far better picture than other theories like that of spontaneous reproduction, rats from piles of hay and whatnot.

Does it?

I despair. If the central dogma of molecular biology is no better than stating rats spontaneously generate from piles of hay I really don't know what to say.

how does the RNA move in space and time to the proper point on the DNA to be transcribed? then how is this messenger RNA moved in space and time to the ribosome for translation? How are the specific amino acids which are used in the translation process moved in space and time to the ribosome to be formed into a protein? once constructed how is a protein moved in space and time to its final destination?
Once you can answer these questions then you can consider how such a system can be formed by chance since the entirety of this system is necessary for replication and without replication there is no evolution.

I'm not trying to answer these questions, I've not been in a lab in years.
I was under the impression you were trying to answer these questions and forward all our understandings of biology. That you had some wonderful insight that was about to pull the carpet from below the feet of the woefully inadequate understanding of biology we are currently armed with.

Once you can answer these questions perhaps your inferred designer will be more obvious, perhaps not. Regardless I'd love to see the answers.

There seems to be two arguments running alongside each other, one, that biology cannot currently explain the origin of life which most people I think would agree with and, two, that biology is a bit like a factory and thus must have been designed like a factory. Most factories I'm familiar with have their origins in human beings, human beings originated from other biological organisms, the origin of biological organisms we're all a little hazy on. The only examples of intelligence I'm aware of are biological in nature or have a traceable source to biological organisms, the origins of biology are a mystery as far as I'm concerned and a mystery you're shedding little light on by highlighting answers we don't have with back up from scientific journals saying 'we don't know'.

[KBCid]

How might the requirement of intelligence be determined?

I have no idea. IQ tests are popular but getting your designer to sit one might be problematic.

Here is where you are not considering a basic understanding of ID or of intelligence in general. For some reason you feel that there is a need to be able to test the intelligence of the actual designer before an assertion of intelligent action can be asserted. This is the old show the designer position held by evolutionists which they use to make it appear that it is impossible for design to be judged without intimate knowlege of the desiner themselves.Intelligent agents recognise designed things because it exhibits properties that is typically left behind by an intelligent causal agency thus, it is not a necessity to know the designer prior to asserting intelligent action.

A better way to consider things is this "what is the possible complexity of an interactive machine that is attainable by chance in a single step?

How many machines of the level of the space shuttle have you observed to be formed by chance? remember science cannot prove a negative and it must bring evidence in a positive way. If an intellectual wishes to infer that chance can form something highly complex mechanically then they must have some evidence to show that the possibility is real and not imagined.
Ultimately the onus is not on intelligent design to show that it is capable of irreducibly complex mechanical formations since there is very little if anything that is functionally possible that we can't form. The onus of evidence is on those who are asserting chance as a causal possibility that must show evidence that it can indeed form the complexity necessary for the function to occur.

If there is an assertion by a scientist that there could be a 1 in 10 to the power of 100 chance that such positional control could arise by chance would you assume that it must be a chance occurance?

I'd ask how the scientist came up with that number.

That would be logical. However, the position your standing in is that ID must prove its position to eliminate chance. The problem of course is that no question has been asked or answered as to what chance can actually accomplish to allow you the luxury of requiring something else to knock it down. My question to you would be why do you seek evidence for ID? why not seek evidence for chance? It is a much more realistic position to assert that life was designed than that it occured by chance since you have never seen complexity of this nature by anything less than intelligent agency.

Each of the stages from building blocks to final protein form must be handled in space and time.

You seem to be asserting that biology, along with the rest of the physical world operates in space and time. I agree.

Making an asssertion that all physical forms operate in space and time is not what I am saying. Plywood in a factory does not operate itself through the factory. The steel in your car did not arrange itself and wait for a driver to come along. Existing in space and time is one thing being controlled is quite another.
When you order something online there is usually a 'handling' charge, why do you suppose that is? The answer is of course that your package doesn't deliver itself, it 'requires' an outside force to be exerted on it in order to go from where it is to where you want it. This is what must be defined in any explanation of structural organisation whether it be a space shuttle or a living body. Structure doesn't just repeat on accident or by chance. Repetition requires control.

[quote=""KBCid""]Biological structures are built on basic matter that is defined. You can study up on these here;
General Biology/Getting Started/Chemical Building Blocks of Life.[/quote]

I've got a working, if a little rusty, understanding of molecular biology and the building blocks of life, my stand alone chemistry is very poor. My point was not to expose my ignorance of the building blocks of biology, which fills many textbooks,...

Hmmm. if you are ignorant of the building blocks of life then how do you assert that they fill many textbooks?

The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T).
http://en.wikipedia.org/wiki/DNA

Now that didn't take any textbooks at all, it took approximately a line of text.Each of these four building blocks can be arranged in the DNA code in any order and there is absolutely no inherent control for any of them. The fact is if there were an inherent control life would not exist. From these basic building blocks every structure in life is directed. Each of them can be and has been tested to understand their properties and the conclusion is that there is no inherent reason for them to be arranged in any specifiable order. It is completely arbitrary.

...but to elucidate that a bottom up understanding of so called 'basic matter' doesn't exist and isn't very basic.

If that were true then I would not have a job. The nature of scientific inquiry is the ability to methodically test things and to be able to repeat the testing. All the physical things you percieve in space and time have properties that allow them to persist. The properties are testable which is how we made laws to define how things work. Without laws of understanding we would have no foundation to work with.

My understanding of particle physics doesn't go far beyond the occasional copy of New Scientist but is enough to see that's it's not well understood and is keeping some of the greatest living minds occupied and arguing. Your 'basic matter' is a profound

mystery.

Particle physics which is;
a branch of physics that studies the existence and interactions of particles that are the constituents of what is usually referred to as matter http://en.wikipedia.org/wiki/Particle_physics

is not what is being discussed in this thread. How matter itself come to exist or persists is not a necessary understanding required to work with the subject at hand. We are working with already existing matter amenable to testing by scientific method.

Water, as I've mentioned, is big part of the picture that we're still learning about it, from the Journal of Physical

Chemistry last year:

The study of the structure and dynamics of water is one of the most exciting interdisciplinary research topics in science

Once you can answer all the ground up questions from physics and chemistry you may be in a better position to infer the unknowns in biology to an intelligent designer.

Water is not the material arrangement that needs explaining. No matter how mysterious water may be it is not the matter that codes for life, it is not the matter that must form into very precise arrangements in order for replication to occur. The matter I am referring to may exist with a watery environment but its arrangement is not defined by water. In fact water works against monomer buildup. In most cases it requires the removal of water to make proper monomer linking.

Again I think it gives a pretty good idea of the process. DNA>RNA>Protein gives a far better picture than other theories like that of spontaneous reproduction, rats from piles of hay and whatnot.

Does it?

I despair. If the central dogma of molecular biology is no better than stating rats spontaneously generate from piles of hay I really don't know what to say.

If you believe that molecular biology does define how life arises from the genetic code I would surely like to read that book. As can be noted from all the peer reviewed references given in this thread they have not got a clue as to how things are being spatially controlled in 3 dimensions, they simply know that it is.

how does the RNA move in space and time to the proper point on the DNA to be transcribed? then how is this messenger RNA moved in space and time to the ribosome for translation? How are the specific amino acids which are used in the translation process moved in space and time to the ribosome to be formed into a protein? once constructed how is a protein moved in space and time to its final destination? Once you can answer these questions then you can consider how such a system can be formed by chance since the entirety of this system is necessary for replication and without replication there is no evolution.

I'm not trying to answer these questions, I've not been in a lab in years.

If the answer is not of importance then why post to the thread since it is entirely about the question of how matter is controlled in space and time. This is tantamount to trying to understand how a car motor functions without looking under the hood or how a factory works by only looking at the material going in at one end and finished structures coming out the other. Who in their right mind would not want to look inside the factory to understand how the matter that goes in is arranged into the final form that comes out?

I was under the impression you were trying to answer these questions and forward all our understandings of biology. That you had some wonderful insight that was about to pull the carpet from below the feet of the woefully inadequate understanding of biology we are currently armed with.

I have answered the question. Precise spatiotemporal control of matter requires an irreducible highly complex control system. Life cannot

replicate without it. This is an extremely wonderful insight from physics and mechanical engineering for those who are not mechanically inclined. The woefully inadequate understanding that biology currently has is because they are not looking at the system in play. They are doing a great job of identifying the individual players and nearly nothing in the way of how they are being applied in space and time.

Once you can answer these questions perhaps your inferred designer will be more obvious, perhaps not. Regardless I'd love to see the answers.

The important questions have already been answered. all that is left to define is the exstent of the irreducibly complex system that is operating to allow life to form and replicate.

There seems to be two arguments running alongside each other, one, that biology cannot currently explain the origin of life which most people I think would agree with

and they have not.

and, two, that biology is a bit like a factory and thus must have been designed like a factory. Most factories I'm familiar with have their origins in human beings, human beings originated from other biological organisms, the origin of biological organisms we're all a little hazy on. The only examples of intelligence I'm aware of are biological in nature or have a traceable source to biological organisms, the origins of biology are a mystery as far as I'm concerned and a mystery you're shedding little light on by highlighting answers we don't have with back up from scientific journals saying 'we don't know'.

Biology is entirely like a factory... an autonomous factory. There is code, there are mechanisms, there is shipping, there is handling, there is electronic messaging, there is waste disposal, there is error correction, there is everything that is currently observed as a basic necessity of any intelligently designed factory and the additional functionality of autonomous operation. Life exhibits all the properties of an intelligently designed system and I can say that based on my intimate experience of designing systems. No one has any experience with chance organization being able to form such factories because it doesn't happen naturally. Organization of this complexity, irreducibility and magnitude have only been observed as a result of intelligent agency. Occams razor determined that we should never infer anything more than is necessary or anything less than is necessary to explain something and with this in mind can you think of anything other than intelligence that anyone has observed that can cause the organization of matter into a functional system like life has?

[bippy123]

Making an asssertion that all physical forms operate in space and time is not what I am saying. Plywood in a factory does not operate itself through the factory. The steel in your car did not arrange itself and wait for a driver to come along. Existing in space and time is one thing being controlled is quite another.
When you order something online there is usually a 'handling' charge, why do you suppose that is? The answer is of course that your package doesn't deliver itself, it 'requires' an outside force to be exerted on it in order to go from where it is to where you want it. This is what must be defined in any explanation of structural organisation whether it be a space shuttle or a living body. Structure doesn't just repeat on accident or by chance. Repetition requires control.

To me this is the key that has me so fascinated by this theory. If repetition requires control then its logical to say that a controller being there from the beginning is the most reasonable explanation here.

Ill be right back, im going outside to thow a pile of leaves in the air, when they comes back down they will have formed a cat

[KBCid]

To me this is the key that has me so fascinated by this theory. If repetition requires control then its logical to say that a controller being there from the beginning is the most reasonable explanation here.
Ill be right back, im going outside to thow a pile of leaves in the air, when they comes back down they will have formed a cat

This is probably one of the most overlooked points in the entire evolutionary debate. Evo's love to sqeeze everything into the 'it evolved' concept but, in order to 'evolve' it is entirely dependant on replication. Once you touch this point you have encountered the Evo's corner since there is no evolution without replication they can't sqeeze it into their happy place.
You know Bipp it amazes me how many people work for a living... producing physical objects who never really analyse how the process works. Man has done his best to automate construction processes and yet we still need people to perform many of the functions actually 'required' in order to complete the process. What would be nice is if people would realise just what part they play in the scheme of these processes. Our bodies and minds perform the basic movements of materials in almost every case. We move things with precision in 3 dimensional space without hardly a thought and yet this is one of the most critical things in the process. precision control of matter in time and space.
Strangely this is also our creators claim to fame... He precisely controlled matter to do his bidding from the beginning, he caused it to be formed into all the systems we observe. even the commonly observed sun with planets circling in precision orbits is incredibly hard to imagine occuring by chance. To get a grip on how hard this would be to arrange just imagine how hard it would be to get a bunch of small magnets to circle one very large one without flying away or falling in.

What causes an orbit to happen?
Orbits are the result of a perfect balance between the forward motion of a body in space, such as a planet or moon, and the pull of gravity on it from another body in space, such as a large planet or star. An object with a lot of mass goes forward and wants to keep going forward; however, the gravity of another body in space pulls it in. There is a continuous tug-of-war between the one object wanting to go forward and away and the other wanting to pull it in.
These forces of inertia and gravity have to be perfectly balanced for an orbit to happen. If the forward movement (inertia) of one object is too strong, the object will speed past the other one and not enter orbit. If inertia or momentum is much weaker than the pull of gravity, the object will be pulled into the other one completely and crash.
http://www.qrg.northwestern.edu/project ... orbit.html

If you would like to try a little test of this there is a place to go try it;
Can you put the moon in orbit?
http://edinburghcreationgroup.org/moon-orbit.php

[Beanybag]

If you would like to try a little test of this there is a place to go try it;
Can you put the moon in orbit?
http://edinburghcreationgroup.org/moon-orbit.php

For what it's worth, I typed in 20 for angle and 5 for force and created a stable orbit on my first try.

[Danieltwotwenty]

If you would like to try a little test of this there is a place to go try it;
Can you put the moon in orbit?
http://edinburghcreationgroup.org/moon-orbit.php

For what it's worth, I typed in 20 for angle and 5 for force and created a stable orbit on my first try.

I tried what you did Beany and it was not orbiting in the dotted line.

[KBCid]

For what it's worth, I typed in 20 for angle and 5 for force and created a stable orbit on my first try.

So you were able to make this happen;

The Moon has a nearly circular orbit (e=0.05) http://www.windows2universe.org/the_uni ... moon1.html

Of course part of the scientific method means that it is repeatable. strangely I can't get the effect you think you did.

[bippy123]

KBC correct, and it's a corner that evos get squeezed into that is impossible to get out of.
I think that most people these days forget how much human itelligence and involvement is needed for replication because most people see only the end product and forget how much people are actually involved in the process .

But that is definitely something that is noticed by engineers, which is why I envision a future where engineers will be more involved in the area of the biology of life. I see the darwinists fighting it tooth and nail, but eventually that paradigm shift will happen, and when it does it will be a doozy.
It will be such a huge shift that atheism and naturalism will have their legs cut out from under them.
Some exciting times are ahead of us

[Proinsias]

I'm not asserting chance. I'm not even sure what it means for someone to 'assert chance'.

It is a much more realistic position to assert that life was designed than that it occured by chance since you have never seen complexity of this nature by anything less than intelligent agency.

I think it is more realistic to say we don't currently know how biological life on earth originally arose.

Hmmm. if you are ignorant of the building blocks of life then how do you assert that they fill many textbooks?

I'm assuming the many molecular biology textbooks I've not read contain information I'm ignorant of, as I've not read them.

If the answer is not of importance then why post to the thread since it is entirely about the question of how matter is controlled in space and time. This is tantamount to trying to understand how a car motor functions without looking under the hood or how a factory works by only looking at the material going in at one end and finished structures coming out the other. Who in their right mind would not want to look inside the factory to understand how the matter that goes in is arranged into the final form that comes out?

I wanted to look under the hood of biology so I went to college and university to study biology. To me your current position is tantamount to understanding a car by looking under the bonnet and inferring it has its ultimate origin in an intelligent agent capable of controlling all matter from the beginning.

I have answered the question. Precise spatiotemporal control of matter requires an irreducible highly complex control system.

How do you differentiate between "movement" & "precise spatiotemporal control"?

Life cannot replicate without it. This is an extremely wonderful insight from physics and mechanical engineering for those who are not mechanically inclined. The woefully inadequate understanding that biology currently has is because they are not looking at the system in play. They are doing a great job of identifying the individual players and nearly nothing in the way of how they are being applied in space and time.

I really don't see the wonderful insight.
I see a lot of examples from biology asserting ignorance and the need for further study across a diverse range of problems. All of which involve movement, as that's what matter does. I see you unifying all these mysteries by claiming there is some sort underlying control system but I see no control system.

The important questions have already been answered. all that is left to define is the exstent of the irreducibly complex system that is operating to allow life to form and replicate.

A quick glance through the papers you cited in this thread shows quite a few unanswered questions, I can't find an example where you answered one of the problems you brought to light. Explaining than an arm develops in space & over time, that genetic material has a profound effect on the phenotype of an organism, that both the genotype and the phenotype operate in space in time, or that chromosomal position as they line up in the nucleus varies between tissue types doesn't really explain much at all - if the chromosomes of the different tissues of a given organism all lined up in a similar fashion would this undermine your theory at all?

We move things with precision in 3 dimensional space without hardly a thought and yet this is one of the most critical things in the process. precision control of matter in time and space. Strangely this is also our creators claim to fame... He precisely controlled matter to do his bidding from the beginning, he caused it to be formed into all the systems we observe. even the commonly observed sun with planets circling in precision orbits is incredibly hard to imagine occuring by chance.

That may be why I'm having difficulty in singling out biology as the work of an intelligent agent, your hypothesis stretches that bit further to incorporate control of all matter from the beginning.
Perhaps the thread should be renamed "Precise 3D Spatio-Temporal Control of all Matter Since The Beginning" or maybe "Change".
How do we determine what control is inherent and what is not if God precisely controlled matter to do his bidding from the beginning? not to mention the free will/determinism issues that crop up.

[KBCid]

I'm not asserting chance. I'm not even sure what it means for someone to 'assert chance'.

There is only 2 choices to form a basis from. If you don't feel that ID is plausible then it would be chance.

It is a much more realistic position to assert that life was designed than that it occured by chance since you have never seen complexity of this nature by anything less than intelligent agency.

I think it is more realistic to say we don't currently know how biological life on earth originally arose.

One could certainly assert that position if you don't understand mechanics or the physics required.

If the answer is not of importance then why post to the thread since it is entirely about the question of how matter is controlled in space and time. This is tantamount to trying to understand how a car motor functions without looking under the hood or how a factory works by only looking at the material going in at one end and finished structures coming out the other. Who in their right mind would not want to look inside the factory to understand how the matter that goes in is arranged into the final form that comes out?

I wanted to look under the hood of biology so I went to college and university to study biology. To me your current position is tantamount to understanding a car by looking under the bonnet and inferring it has its ultimate origin in an intelligent agent capable of controlling all matter from the beginning.

The difference here of course is that I / we are not simply looking under the bonnet. We are looking at all the parts that form, and are used to form the whole. If I were to take you on a 3D tour of a functioning engine how would you know design from chance possibility?
Why does it require intelligent agency to form a motor or a space shuttle or a watch? how come we don't see things of this type of complexity just naturaly occuring?
My inference to ID is based on observable evidence for what has already proven the causal ability to form matter into arrangements of this 'type' of complexity.
I am certainly not asserting in my theory that the intelligence that formed life could control 'all matter' from the beginning as this would be a religious belief. I do have beliefs aside from this particular mechanical / physics position but I am not relying on a belief to state the position.

I have answered the question. Precise spatiotemporal control of matter requires an irreducible highly complex control system.

How do you differentiate between "movement" & "precise spatiotemporal control"?

Replication / repetition of 3 dimensional form. This is the difference between looking at a tree and seeing the forest that a tree is a small part of. Matter can certainly be moved by random forces in the environment and not be spatially controlled. However, if an arrangement of millions or billions of substrate components keeps forming the exact same 3 dimensional structure repeatedly then there is a cause which is not random and when we consider that the components must move through space and time in order to become part of that final structure then it requires a 'precision' control of both spatial and temporal aspects. Physics and mechanics.
Here is an example;
You are walking down the beach and you encounter a precise 1 foot cube of sand with 5 perfectly flat sides that you can view... you keep walking down the beach and you encounter another cube that is precisely the same as the last.... you keep going and you see many more as you go and at some point you realise that they are placed at a specific distance from each other.
Now what would you logically infer 'could' be causal to that observable evidence and why? It is after all simply sand on a beach.

Life cannot replicate without it. This is an extremely wonderful insight from physics and mechanical engineering for those who are not mechanically inclined. The woefully inadequate understanding that biology currently has is because they are not looking at the system in play. They are doing a great job of identifying the individual players and nearly nothing in the way of how they are being applied in space and time.

I really don't see the wonderful insight.
I see a lot of examples from biology asserting ignorance and the need for further study across a diverse range of problems. All of which involve movement, as that's what matter does. I see you unifying all these mysteries by claiming there is some sort underlying control system but I see no control system.

If you don't see the insight then you need to develop an understanding of both physics and mechanics.
When the Wright brothers asserted that man could fly in a heavier than air machine everyone laughed at them because it was common understanding by the scholars and college educated at that time that such was impossible.

Airplanes
Flight by machines heavier than air is unpractical (sic) and insignificant, if not utterly impossible. Simon Newcomb

Heavier-than-air flying machines are impossible.
Lord Kelvin, British mathematician and physicist, president of the British Royal Society, 1895.

It is apparent to me that the possibilities of the aeroplane, which two or three years ago were thought to hold the solution to the [flying machine] problem, have been exhausted, and that we must turn elsewhere.
Thomas Edison, American inventor, 1895.
http://en.wikiquote.org/wiki/Incorrect_predictions

The truth of the matter then and now is simply a lack of understanding of both physics and mechanics. If you wish to understand what I am asserting then you should get a grip on both of these well understood disciplines. Otherwise you are relegated to taking someone elses word for it.

The important questions have already been answered. all that is left to define is the exstent of the irreducibly complex system that is operating to allow life to form and replicate.

A quick glance through the papers you cited in this thread shows quite a few unanswered questions, I can't find an example where you answered one of the problems you brought to light.

I have not brought any problems 'to light'. The problems have been brought to light by the investigators making the observations. But, I am defining an answer to their problem. Systematic control of matter in space and time. How does that not answer their problem?
You have 2 choices here, you can observe what is happening in the body or a cell and assert that those particular formations repetitiously happen by chance... or they occur because of a control system. It is ultimately your choice to make.
If you feel my answer doesn't answer the problem then what would you propose it could be? since there is only 2 possible answers then your position has to be chance, there is no middle ground or third option. If however, you feel that an explanation for the observable phenomena could not be chance then you have no choice but to agree with my assertion that a control system is required to cause the observable phenomena.

Explaining than an arm develops in space & over time, that genetic material has a profound effect on the phenotype of an organism, that both the genotype and the phenotype operate in space in time, or that chromosomal position as they line up in the nucleus varies between tissue types doesn't really explain much at all

Well since I am not making any of those assertions as an explanation for anything then you would be quite right that such a perception of what i'm saying doen't explain anything. The truth is that this entire paragraph is an essential restatement of the scientifc observations made by the observers in the papers cited.
Your first point that "an arm develops in space & over time" would be doing nothing more than stating the truth. Doesn't everything in our existence develop in space and over time?
The part you appear to be missing at every turn is HOW these things are able to be formed in both space and time. It seems strange that you have read this thread and not seen one instance where I explain how things are able to be formed in space and time.

if the chromosomes of the different tissues of a given organism all lined up in a similar fashion would this undermine your theory at all?

Not at all. My position and theory is to define what is minimally required for the pattern to repeat. If you see a 3 dimensional pattern of matter occuring then you can assert one of 2 things it occurs by chance or its controlled. In my entire observational experience I have never observed precision repetition occuring by chance, have you?

We move things with precision in 3 dimensional space without hardly a thought and yet this is one of the most critical things in the process. precision control of matter in time and space. Strangely this is also our creators claim to fame... He precisely controlled matter to do his bidding from the beginning, he caused it to be formed into all the systems we observe. even the commonly observed sun with planets circling in precision orbits is incredibly hard to imagine occuring by chance.

That may be why I'm having difficulty in singling out biology as the work of an intelligent agent, your hypothesis stretches that bit further to incorporate control of all matter from the beginning.

My theory / hypothesis does not include any beliefs I may hold for validity. We are each free to assign whatever intelligent agent we want to as the agent responsible for the systems origin. If you want to assert the deity of any religion conceived so far you are free to do so because my theory has no dependancy on who the designer may be. I could just as easily hold a belief it was fairies and this would have no bearing or effect on the theory being presented since it simply points to intelligence being required. If it makes you feel better you can assume a currently unknown intelligent agent and then focus on the actual point being made about intelligent agency being a requirement.

Perhaps the thread should be renamed "Precise 3D Spatio-Temporal Control of all Matter Since The Beginning"

'Since The Beginning' of what? can you define precisely what had a beginning?

or maybe "Change". How do we determine what control is inherent and what is not if God precisely controlled matter to do his bidding from the beginning? not to mention the free will/determinism issues that crop up.

I believe it wise to let this last point you made stand on its own as it appears you have an issue with a religious position aside from the physics / mechanics position of this thread.

[Proinsias]

KBCid, I appreciate the thoughtful responses. I'm cherry picking and mixing up, if I miss something you'd like me to answer let me know.

I have not brought any problems 'to light'. The problems have been brought to light by the investigators making the observations. But, I am defining an answer to their problem. Systematic control of matter in space and time. How does that not answer their problem?

These were not papers I was aware of, you brought them to my attention as support for your theory. They all raise questions. Systematic control of matter in space and time does not answer their questions, most if not all of the papers you mention are by writers who are aware of 3d spatial control in a systematic fashion.

The first link you posted in this thread:
Tissue-specific spatial organization of genomes
http://genomebiology.com/content/5/7/R44
It appears to me to be a paper on tissue specific chromosome behaviour. The title alone suggests the authors are comfortable with the idea of precise 3D spacial control. It's a paper attempting to investigate the interplay between tissue type and chromosomal positioning at division. They seem to have found some sort of a relationship , even two chromosomes that: "Remarkably, the preferential radial positioning of at least two chromosomes, 18 and 19, has been evolutionarily conserved over 30 million years". The authors seem fully aware that there is 3d spatial control of matter through time involved in what they are investigating, what they don't know are the mechanisms involved in chromosome positioning and how that impacts the phenotype of the cell" "The spatial positioning of chromosomes within the interphase nucleus is often nonrandom".

However, if an arrangement of millions or billions of substrate components keeps forming the exact same 3 dimensional structure repeatedly then there is a cause which is not random and when we consider that the components must move through space and time in order to become part of that final structure then it requires a 'precision' control of both spatial and temporal aspects. Physics and mechanics.

As you say physics & mechanics. They Might Be Giants say it better than I could: http://www.youtube.com/watch?v=Zbgul1NpEA8 , they recently updated the song and made it sound rubbish but more scientifically accurate

Matter can certainly be moved by random forces in the environment and not be spatially controlled.

Could you give an example?

When the Wright brothers asserted that man could fly in a heavier than air machine everyone laughed at them because it was common understanding by the scholars and college educated at that time that such was impossible.

Yes, lots of people laughed at them. And then they flew. And that's why we still talk about them. They solved a 3d spacial positioning problem.

The part you appear to be missing at every turn is HOW these things are able to be formed in both space and time. It seems strange that you have read this thread and not seen one instance where I explain how things are able to be formed in space and time.

It's the how I'm interested in. If you could elucidate on the physics & mechanics behind the distribution of chromosomes around the nucleus and then give a physical & mechanical explanation as to how the chromosome arrangement before division impacts the phenotype of the cell I'm all ears.

I could just as easily hold a belief it was fairies and this would have no bearing or effect on the theory being presented since it simply points to intelligence being required.

What precise 3D control mechanism is responsible for chromosomal variance over tissue type? intelligent fairies lovingly manoeuvre them.

He precisely controlled matter to do his bidding from the beginning, he caused it to be formed into all the systems we observe.

Perhaps the thread should be renamed "Precise 3D Spatio-Temporal Control of all Matter Since The Beginning"

Since The Beginning' of what?
can you define precisely what had a beginning?

You brought it up with "his bidding from the beginning". The biological flavour to the argument seems incidental.
No.

[KBCid]

I have not brought any problems 'to light'. The problems have been brought to light by the investigators making the observations. But, I am defining an answer to their problem. Systematic control of matter in space and time. How does that not answer their problem?

These were not papers I was aware of, you brought them to my attention as support for your theory. They all raise questions. Systematic control of matter in space and time does not answer their questions, most if not all of the papers you mention are by writers who are aware of 3d spatial control in a systematic fashion.

So you agree that most of the writers recognise that 3d spatial control is happening in a systematic fashion but you assert that me stating that "Systematic control of matter in space and time does not answer their questions". Well if you look at this carefully you will realise that they are asserting an explanation (systematic control) for the observation they have made, what they have questions about is the extent of the details for how the system is functioning. This is ultimately what they want to know. But....
The details of how the 'system' is 'implemented' is not what I am asserting to explain. I am agreeing with the investigators that there is a 'system' of 3D spatial control functioning and further I am asserting that it is necessary to be functioning in order for 3 dimensional structures to be formed and for replication to occur. There is no logical way to repicate without a systematic control.

(Tissue-specific spatial organization of genomes) appears to me to be a paper on tissue specific chromosome behaviour. The title alone suggests the authors are comfortable with the idea of precise 3D spacial control. It's a paper attempting to investigate the interplay between tissue type and chromosomal positioning at division. They seem to have found some sort of a relationship , even two chromosomes that: "Remarkably, the preferential radial positioning of at least two chromosomes, 18 and 19, has been evolutionarily conserved over 30 million years". The authors seem fully aware that there is 3d spatial control of matter through time involved in what they are investigating, what they don't know are the mechanisms involved in chromosome positioning and how that impacts the phenotype of the cell" "The spatial positioning of chromosomes within the interphase nucleus is often nonrandom".

Recognizing that a system is functioning should have been the first thing 'anyone' should be able to rationalise based on the observable evidence, it is not a comfort position. Recognizing that chance cannot explain a spatially ordered construction should not be some great revelation by a scientist to the rest of the world. Any orderly replication process known requires a control that does not naturally occur.
Sytematic is the essence of nonrandom, in fact I could virtually interchange the two in any sentence that either could be in. So with that all said... What problem do you have with my assertion that there is a 3 dimensional spatiotemporal control system functioning within all living things? You are saying that my theory doesn't explain anything for you but let's really have a look at what my theory is intended to explain;

A 3 dimensional spatiotemporal control system is asserted by me to explain 'how' the matter used to form a cell is able to be arranged, repetitiously in a temporally definable manner.

Do you get the gist of what I am saying here? I am agreeing with the typical observer of lifes phenomena and making a concise statement of what rationale would logically explain the observable evidence. So, my theory that a control system is required to explain the phenomna is minimally what any other logic based intellect should also assert, right?
Or do you propose in opposition that a temporally definable formation can happen by chance, repetitiously?

However, if an arrangement of millions or billions of substrate components keeps forming the exact same 3 dimensional structure repeatedly then there is a cause which is not random and when we consider that the components must move through space and time in order to become part of that final structure then it requires a 'precision' control of both spatial and temporal aspects. Physics and mechanics.

As you say physics & mechanics. They Might Be Giants say it better than I could: http://www.youtube.com/watch?v=Zbgul1NpEA8 , they recently updated the song and made it sound rubbish but more scientifically accurate

I don't see an explanation or a corrolation between the sun and life. Maybe you can simply state what you mean the best you can.

Matter can certainly be moved by random forces in the environment and not be spatially controlled.

Could you give an example?

I am sure that anyone could including you.

When the Wright brothers asserted that man could fly in a heavier than air machine everyone laughed at them because it was common understanding by the scholars and college educated at that time that such was impossible.

Yes, lots of people laughed at them. And then they flew. And that's why we still talk about them. They solved a 3d spacial positioning problem.

Ummm no they did not solve "a 3d spacial positioning problem". They resolved a missunderstanding of mechanics with properly applied physics, and just as there where a great many in that time who didn't properly understand physics we too have many educated people in this time period who simply don't understand the physics required to allow for such a process of 3 dimensional formation to occur.

The part you appear to be missing at every turn is HOW these things are able to be formed in both space and time. It seems strange that you have read this thread and not seen one instance where I explain how things are able to be formed in space and time.

It's the how I'm interested in. If you could elucidate on the physics & mechanics behind the distribution of chromosomes around the nucleus and then give a physical & mechanical explanation as to how the chromosome arrangement before division impacts the phenotype of the cell I'm all ears.

So what you want from me is the blueprint of the machine in the finest detail before you will entertain my theory as explanitory right?
If we had a completely mapped blueprint of how the system is implemented then there would be no need to have a theory. A theory is a conceptual explanation for phenomenon that has some of the answers but not all. I too propose to explain what is necessary minimally but not to explain it in complete blueprint level schematics. So if you need a schematic to entertain a theory then you are looking in the wrong place since we will all be detailing the schematic for some time to come.
Interestingly this has been one of the things I pointed out about the ToE that doesn't seen to affect its status as a valid theory. Since it gives no level of understanding about the mechanics beyond just as assertion of systematically observed effects.... stuff changes and the stuff that continues to exist was better at survival than the stuff it came from.

However, unlike evolutionary theory I do propose to provide a greater level of understanding for what functionalities are necessary for such a system as I am theorising to operating in order to allow for 3 dimensional structures to be replicated in a temporally defined manner.

Now listen carefully here is part of the explanation.
Such a system that can exhibit the functionality observed in life 'requires' the ability / functionality of being able to control the movement of matter in a precision manner that can only be explained physically by being able to apply force to matter on all three planes of existence at once.

This is the application of a physics understanding to explain mechanics. Now with this very limited part of the explanation I am providing so far do you comprehend what I have said? what does this mean to you?

What precise 3D control mechanism is responsible for chromosomal variance over tissue type?

One that can control matter in 3 planes of physical existence and a fourth plane in time.

intelligent fairies lovingly manoeuvre them.

Only if there is no mechanical way to allow it to function autonomously. Ever see a lamp that comes on automatically when you come near it? This is what we mechanically inclined people call automation. It makes peoples lives easier because it allows for processes to function without constant or direct intelligent intervention. This is one of the effects that has been observed as a product of intelligent causation... 'only'. Your computer is also a highly automated mechanism by design. I could hit a button on it an walk away forever and it would sit there and perform without my intervention all the while I am gone. Lifes systems run in an even more complex automation process. What are the odds that such a system can naturally form?

So I have provided a direct physics based partial explanation of the system necessary for life to reproduce and you can begin with that explanation if you wish to attempt to refute and then we can move on to further physics based explanation when I am sure you grasp
this initial point.