Biology of life and 3D spatial positioning

[KBCid]

KBCid: Fair enough, I'll drop the crystal analogy and stick to biology in future. I look forward to the proposed experiments for testing.

As of my last interaction with colleagues who are delving into the physical truths of the 'system' I am pointing out, they will be focusing on substrate movements during the building of a cell since this is the area where it would be most visible and testable. They will most likely try various knockout experiments as this is the most logical method of reverse engineering a mechanism since it is indeed the base mechanism that allows for all others to be formed.

I appreciate evolutionary theory does not account for the prerequisites required by evolution, and that biology in general is struggling with how we got from chemistry to biology.

Keep in mind that the evolutionary model is a concept that doesn't provide a testable method which would show how its mechanism can affect living forms as they change from parent to offspring. At its very best the model describes what is observed. Genetic information changes ''somehow'' and the offspring are different in some ways from the parents. This is simply an observation of an effect. Evolution even if it could be described in a more scientific way would still be an effect. It is entirely dependant on there being a precision system of replication before it can even conceptually begin to function. Without a proper understanding of how such a system functions then the evolutionary concept can't provide a scientific explanation for how the observable effects occur.

May I ask if you have an objection to the idea of the evolutionary model? In that regardless of how we got to the point of biological organisms reproducing via selection and mutation, is it a reasonable explanation as to not the origin but the variety of life we see around us?

My objection to the model is that it is considered a cause to explain all the variety of life. Here is where you need to grasp the importance of the system that I am pointing out. All life... every organism that has ever come to exist beyond the first life forms owe their existence to the systematic replication of 3 dimensional form. So in truth the origin of life is a secondary consideration to this topic. The origin of every life form since the original is what is important if we want to have a scientific discussion about the evolutionary model. If you wish to delve into how life could evolve or change over time then we must be able to define how a code becomes translated into 3 dimensional structure. You would not exist unless there was a systematic function to take the varied genetic information from your parents and turn it into 3 dimensional form.
Think about it this way, A car begins as a concept on paper, its 3 dimensional form is encoded on the paper. What is required to take it from concept to reality? how does matter become formed into that 3 dimensional arrangement?
specific building blocks are controlled in space and time by mechanisms outside of themselves that constrain them into precise spatial positions. This is not a simple thing to accomplish. Factories to a great extent are examples of how matter can be controlled to produce functional formations. Since every existing factory has a foundation in physics then it is safe to say that any systematic control of matter must also have the same foundation. If matter is going to be constrained into a specifiable macro form then it requires that force from outside the matter to be manipulated must be applied to it according to the planes of movement it is required to move in. In the case of 3 dimensional structure it requires the application of force in 3 planes just to initiate movement in a specific direction. The other understanding necessary here is that after matter is set in motion it then requires a force to stop its movement in a precise location. What would be the simplest way you can conceive of to make such a function occur?

Personally I'm not convinced that the current evolutionary model of base pair changes & the environment are the main factors in variety of life.

How exactly do base pairs in the coding become changed? The revelation of genetic hotspots points to a control functioning since randomness cannot be described by having persistent hotspots. Since we have the experimental evidence against randomness then we are required to show how something can persistently vary in a limited number of locations within a coding structure that has the same definable composition from end to end. The current evolutionary model does not really explain how changes occur, it simply asserts that they do occur by a mechanism that is not yet defined empirically.

I think we may have missed something big, I think Davidson's papers about chromosomal rearrangement from back in the 70's chime in with doubts that I had talking to my professor after evolutionary lectures years ago and still linger. Unfortunately Davidson's papers are speculation, base pair changes and environment are something that can be controlled and is something I can prove to myself in a petri dish.

Indeed you would be correct because the living system is ultimately mechanical in its operation. It has specific causes and effects which can be replayed over and over. Everything in the system is testable if you know how to test for it. This is a key area that needs to be defined. We have to know how the changes are occuring and the random mutation concept just doesn't fly in the face of the evidence.

It will be interesting when this becomes more mainstream to see how evo's will try to overcome the laws of physics to keep their hypothesis relevant.

It will be very interesting if this becomes more mainstream, I don't think evo's will have a problem though as it doesn't really concern them. Your research seems focused on pre-evolution, or how matter got to the stage it can evolve.

The origin of life is a separate issue from how it persists. The fact is that they will have to explain the existence of this system in order to have any chance of defining how each individual form of life is currently coming into existence. Without an explanation of how 3 dimensional formations are occuring then the evolutionary model as it now stands is only a possible partial explanation. If you wish to explain the origin of species' you will need to explain how code is translated into 3 dimensional structure. Thus the system is relevent at every replication event.
Its like being able to see the blueprint for a house and seeing the house but not having a proper understanding of how the house came form the print. How something is implemented is just as important for understanding as its beginning and end.

The idea of inherent control is also confusing me. From what I gather explainable phenomena = inherent, and unexplained phenomena = external, intelligent influence.

Ok let's explore this then. The simplest way is to envision you have 2 magnets 1/4" square by 1" long. When you bring one next to another they will both array themselves into a specific spatial formation. This is an inherent control, the same thing occurs in crystalline structuring. Now take 2 pieces of steel with the same dimensions as the magnets and bring them near each other. You should note right away that no matter how close they come there is no inherent forces causing spatial movement. you can arrange them in nearly any way you want and they will stay that way until an outside force is applied to them again. So if we wanted to mimic the spatial positions that occur inherently to the magnets with the steel parts to the same precision then we would have to apply outside forces to the steel in a systematic way. Try and consider what it would take for you to make something that provides such a funtion and it should become apparent just how complex such a function would be to make happen.

The engineering side puzzles me. I made a bicarb & vinegar volcano in the garden with my daughter today which took some thinking and planning, it didn't make me think all volcanoes take thinking and planning. It seems to me that you look at biological phenomena and think that as an intelligent engineer you could do something similar and thus there must be an intelligent engineer behind it all.

The part your missing in the volcano experiment was the temporal side of the equation. You made something that had a specific function in a specifiable time frame. The real thing isn't functioning in a specifiable temporal manner. It could blow today or a million years from now because a volcano is an effect whose cause is far below it. The forces that cause a volcano to occur are not inherent in its structure.
When you formed your structure each of the components you used were spatial and temporally positioned by your hands right? Do you realise what was actually involved mechanically in your simple construction? You as a causal mechanism chose substrates and then formed them into useable components which you then spatially arranged in a temporal manner to give it the final 3 dimensional form. Your eye hand coordination applied force to the substrates to move in space and time. You are one of the most expensive and complex construction tools ever formed. How much of you could be eliminated and still get the same results? Have a look at a 3D printer. These are quite neat contraptions that can actually form 3 dimensional structures without hands on human control. Such a system has all the minimal requirements that I have been talking about to control matter both spatially and temporally and this form of engineered product is as simple as we can mechanically arrange to perform such a function. If we eliminate any of the components it ceases to function. Irreducible complexity.
Everything in the printers formation has its basis in physics. There is no mysterious or magical causes within its functionality. Biological machinery has to have the same physics foundations if it has similar functionality in moving matter in space and time. If you want to control matter spatially then by the laws of physics you will be required to be able to apply force in a positive and negative direction on all 3 planes of existence. This is a minimal functional requirement. How you can make this function occur is going to have the same conceptual requirements that the living system will have. We don't need to know how the force is being applied in the biological application in order to know what would be minimally required for the function to occur. 'ANY' systematic control of matter in 3 dimensional space requires that force be applicable both positively and negatively in all 3 planes. There is no physical way around this requirement.
When scientists eventually begin to see the forest beyond the trees they will have to realise that such functionality cannot be formed in incremental steps since it is logically irreducible and since the evolutionary mechanism cannot even conceptually function until this system is functioning then it could not have come to exist by that mechanism. They will ultimately be left with the only explanation they are allowed... it formed by chance. This will be the equivalent to asserting that a bicycle could form by chance. Essentially not logically or rationally realistic. Irreducible complexity of this magnitude has only been observed to occur by intelligent design.

If you are still having conceptual problems understanding any of my points then feel free to define where and I will do my best to make it clear.

[Proinsias]

doh, said I'd to stick to biology then hit out with a volcano analogy....sorry.

I need a day or two to digest that.

[Neige]

If yes, does it mean that abiogenesis (being a stepwise process) requires the spatiotemporal control of matter?

Yes
Abiogenesis is a conceptual perspective of what might be possible and this should be understood to begin with. The point where the 3 dimensional control of matter would be required is where matter that has no inherent positional control has to be replicated into precise 3 dimensional arrangements which includes the ability to replicate structure changes.

A summary of processes of abiogenesis according to wikipedia:

1. The early Earth had a chemically reducing atmosphere.
2. This atmosphere, exposed to energy in various forms, produced simple organic compounds ("monomers").
3. These compounds accumulated in a "soup", which may have been concentrated at various locations (shorelines, oceanic vents etc.).
4. By further transformation, more complex organic polymers – and ultimately life – developed in the soup.

From what I gather, point 2 is regarded to be feasible due to Miller–Urey experiment that demonstrated "how organic molecules could have spontaneously formed from inorganic precursors". Could you, please, comment on this? Does the discovery of the system of spatiotemporal control of matter somehow nullify this experiment?

[jlay]

From what I gather, point 2 is regarded to be feasible due to Miller–Urey experiment that demonstrated "how organic molecules could have spontaneously formed from inorganic precursors". Could you, please, comment on this? Does the discovery of the system of spatiotemporal control of matter somehow nullify this experiment?

Are you aware of the huge problems with this experiment and its results?

[Neige]

I'm not, to be honest. Did you notice me citing Wikipedia? Yeah, I'm quite ignorant as far as abiogenesis and experiments associated with it are concerned.

[bippy123]

I'm not, to be honest. Did you notice me citing Wikipedia? Yeah, I'm quite ignorant as far as abiogenesis and experiments associated with it are concerned.

Neige, here is why that experiment has been debunked many times that even evolutionists dont use it anymore.

http://creation.com/why-the-miller-urey ... biogenesis

[Neige]

Interesting. What this experiment seems to have produced are just some amino acids. They even have this on the same wiki page:
"No one has yet synthesized a "protocell" using basic components which would have the necessary properties of life."

Wow. I guess this answers my initial question to KBCid.

[Ivellious]

Neige, here is why that experiment has been debunked many times that even evolutionists dont use it anymore.

Indeed, you are correct...Those who accept evolution don't use this experiment (or any proposed experiments like it) to support evolution. Of course, the point is moot because it being wrong has zero bearing on whether evolution is true or not, and it has never been used as evidence for Darwinian evolution. But whatever, you technically are correct that no one uses abiogenesis experiments to support evolution.

[KBCid]

From what I gather, point 2 is regarded to be feasible due to Miller–Urey experiment that demonstrated "how organic molecules could have spontaneously formed from inorganic precursors". Could you, please, comment on this? Does the discovery of the system of spatiotemporal control of matter somehow nullify this experiment?

As you already know from other posts this is not an experiment that has bearing on the issue at hand. The other point that also has to be recognised is that there is no evidence whatsoever for there having been any accumulated building blocks of life in the fossil record. Without evidence to back a natural accumulation of ingredients then any supposition that they did is a belief and beyond scientific inquiry.

The question becomes "how could life originate without any evidence for a natural possibility" ?

There is one other point that needs to be made here. This system cannot be responsible for the origin of life. This is a replication system, its existence can only be asserted to be required in the first living system in order for it to persist. This system is required to exist at each point of replication from the first to the most recent. You could not logically exist without it. This system is the missing mechanism that would allow any concept of evolution to even become feasible. This is why it is relevant to any discussion about evolution at any time or place. no replication, no evolution.
So if anyone wants to posit evolution as a cause of lifes variety then we can properly demand the details of how cause and effect occurs. Simply asserting that random change happens is not a scientific explanation. Describing the effect of an undefined process is not an explanation of cause.
Since evolution cannot conceptually proceed without a 3 dimensional replication system functioning then any explanation that would involve any conceptual evolutionary mechanism must include an explanation for how replication functions.
Imagine trying to scientifically explain that houses come from plans without any description of how the plan can become the house. Suppose we were to say they evolve... is this a sufficient explanation? The physics / mechanics that take a code and translate it into 3 dimensional structures is not a simple thing by any stretch of imagination.

[Beanybag]

I'm not, to be honest. Did you notice me citing Wikipedia? Yeah, I'm quite ignorant as far as abiogenesis and experiments associated with it are concerned.

Neige, here is why that experiment has been debunked many times that even evolutionists dont use it anymore.

http://creation.com/why-the-miller-urey ... biogenesis

The specific experiment has been 'debunked', not the entire hypothesis.

"Surveys of textbooks find that the Miller–Urey study is the major (or only) research cited to prove abiogenesis." There has been many different experiments done that have improved upon miller-urey. Only miller-urey is mentioned in text books since there is no theory of abiogenesis, but the miller-urey provided some insight as to how it might have happened, i.e. a hypothesis. As it was the first experiment of its time, it is the one mentioned in text books. This is surely a dishonest way for any professional science critic to critique science - why not look at the actual science? See here for more examples of such experiments: http://en.wikipedia.org/wiki/Miller%E2% ... xperiments

Here's a paper that comments on some other experiments (DNA may have come before RNA): http://www.newscientist.com/article/mg2 ... tself.html

As well as possible asteroid and space hypotheses: http://www.popsci.com/technology/articl ... nate-space

[Proinsias]

KBCid:

We may have to agree to disagree until you have something testable. I think I have a decent grasp of what you are saying, it's just not in any way obvious to me that biology demands an intelligent designer. I get that humans move things in a complicated fashion and that when we look at biology things are also moving in a complicated fashion.

The theory of evolution had been proposed by Darwin & Wallace, at that time it was little more than an idea. It needed a mechanism of inheritance which via the discovered work of Mendel then Francis & Crick was shown to be dna. After the proposal of evolution the hunt was on for the mechanism, we found it and we're still working on understanding how it works. I'll grant a lot of the nuts and bolts of it are a mystery but the genotype/phenotype relationships in inheritance can be shown with a few pea plants and little time to the satisfaction of most.

At this stage I feel like the evolution skeptics pre-Mendel & Crick, disbelief in a theory that has no physical/experimental basis as yet. Time will tell I imagine.

[KBCid]

KBCid:
We may have to agree to disagree until you have something testable. I think I have a decent grasp of what you are saying, it's just not in any way obvious to me that biology demands an intelligent designer. I get that humans move things in a complicated fashion and that when we look at biology things are also moving in a complicated fashion.

You surely have the right to disagree.
However, I think you may not yet grasp this completely. What should be obvious is that matter that has no inherent positional cause 'must' have a scientifically definable cause for its precision movement in space and time. As I have asserted physics describes how matter can be moved. It requires an outside force to be applied in each of the planes of existence you wish to move it in. Since all living forms are 3 dimensional then you have no choice but to have the requirement of a 3 plane force application system. There is no conceiveable simpler mechanism possible within our understanding of physics.
Science is about making logical assertions based on what is known and since we can apply this understanding of physics in a logical manner then is falls within the scientific method. My position is that such a system 'must' exist in order to form 3 dimensional structures and that such a system has a minimal level of complexity that can be inferred based entirely on this understanding of physics. All designed matter moving systems have this fundamental understanding applied within their ordering. So to assert that you disagree with the concept would actually require you to assume that something other than the known laws of physics for the motion of matter would be applicable. Laws of physics are laws for a reason... they are not theories or hypothesis;

Several general properties of physical laws have been identified (see Davies (1992) and Feynman (1965) as noted, although each of the characterizations are not necessarily original to them). Physical laws are:

1) True, at least within their regime of validity. By definition, there have never been repeatable contradicting observations.
2) Universal. They appear to apply everywhere in the universe. (Davies, 1992:82)
3) Simple. They are typically expressed in terms of a single mathematical equation. (Davies)
4) Absolute. Nothing in the universe appears to affect them. (Davies, 1992:82)
5) Stable. Unchanged since first discovered (although they may have been shown to be approximations of more accurate laws—see "Laws as approximations" below),
6) Omnipotent. Everything in the universe apparently must comply with them (according to observations). (Davies, 1992:83)
Generally conservative of quantity. (Feynman, 1965:59)
7) Often expressions of existing homogeneities (symmetries) of space and time. (Feynman)
Typically theoretically reversible in time (if non-quantum), although time itself is irreversible. (Feynman)

Physical laws are distinguished from scientific theories by their simplicity. Scientific theories are generally more complex than laws; they have many component parts, and are more likely to be changed as the body of available experimental data and analysis develops. This is because a physical law is a summary observation of strictly empirical matters, whereas a theory is a model that accounts for the observation, explains it, relates it to other observations, and makes testable predictions based upon it. Simply stated, while a law notes that something happens, a theory explains why and how something happens.
http://en.wikipedia.org/wiki/Physical_law

The theory of evolution had been proposed by Darwin & Wallace, at that time it was little more than an idea. It needed a mechanism of inheritance which via the discovered work of Mendel then Francis & Crick was shown to be dna. After the proposal of evolution the hunt was on for the mechanism, we found it and we're still working on understanding how it works.

actually you nor they have 'found it' yet. The complete mechanism is not defined. You have no idea how 3 dimensional form can go from a code to actual structure. This is exactly what I am adressing here. I am showing the physical necessities required by the laws of physics to perform the the action that has to occur in order for code to become 3 dimensional form and you are arbitrarily disagreeing with that without having and other rationale to apply instead. This is not how the scientific method works since you would need to haave some foundation to work from. In my case I cite laws of physics. In your case you don't cite anything else other than it will remain a mystery to you even in the face of the logic of physics.

I'll grant a lot of the nuts and bolts of it are a mystery but the genotype/phenotype relationships in inheritance can be shown with a few pea plants and little time to the satisfaction of most.
At this stage I feel like the evolution skeptics pre-Mendel & Crick, disbelief in a theory that has no physical/experimental basis as yet. Time will tell I imagine.

Actually the laws of physics do have physical and experimental backing which is why they are laws. It doesn't matter if the matter being moved is being moved by a human or the matter being moved is within a biological organism. Matter requires an outside force to be moved and a very complex system to be moved precisely. Such a system would be required to be functional within the first organised living system that has a systematically reproducing 3 dimensional form.
So even though you may not agree with the implications that would be demanded by this understanding the facts are that there are laws that have never been disputed which define how matter can be affected.

[Proinsias]

Yeah, I'm aware of the laws of physics & physical law, I don't see how citing them supports your theory of intelligent design.

I get that understanding how matter moves and interacts is a complicated business, especially in biology & when things get very small.

You have no idea how 3 dimensional form can go from a code to actual structure.

The central dogma of molecular biology is a decent idea in my book. We've come a long way since the first proposals of evolution. If you can take it to the next level, go for it.

[KBCid]

Yeah, I'm aware of the laws of physics & physical law, I don't see how citing them supports your theory of intelligent design.

Every observable instance of precision construction of matter that as no inherent positional control has been intelligently designed and it fundamentally comes down to this one constraint; The only way to consistently arrange matter into specific 3 dimensional formations is by systematic control of matter. Intelligent design has been the only observable cause for the occurance of such systems because of the systems necessary minimal / irreducible complexity.

I get that understanding how matter moves and interacts is a complicated business, especially in biology & when things get very small.

You have no idea how 3 dimensional form can go from a code to actual structure.

The central dogma of molecular biology is a decent idea in my book. We've come a long way since the first proposals of evolution. If you can take it to the next level, go for it.

Yes it is very complicated and the central dogma doesn't address how it occurs so you can't even point to that for any scientific rationale. The entire hypothesis of evolution simply asserts that random changes in the blueprint happen and the outcome of an event they can't scientifically define spits out 3 dimensional formations called life. What exactly is being scientifically explained? I can come in fresh today with no foreknowlege and make the very same observation and yet no one knows exactly how changes are occuring scientifically or how a change in code = 3 dimensional form. But, if such an observation is all you need to understand how life occurs then your level of evidentiary requirements is much lower than most of the people I know including myself.

[Proinsias]

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

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.

I'm not suggesting the central dogma explains how life originates but it gives a pretty good window into how it persists and perhaps some clues as how it came to be.

It wouldn't surprise me if we find a mechanism that gets us away from using words like 'random', 'error' or 'accident', I'm not a big fan of that sort of terminology but it's really just another way or saying 'we don't know yet'. I suspect the rabbit hole goes a deep as we can be bothered to look.

As I've said before I'm more than eager to see the carpet pulled from beneath the feet of modern biology. The central dogma & genetics united the different branches of biology with a common language & system. I think you're going to have to do better than attributing the unknowns in the current system to aliens or God. If there is a control system in there, let's see it. The same was asked of the original proponents of evolution and a mechanism was found which has kept the scientific community happy and busy for coming on a hundred years. You are claiming there's more to it but I'm seeing little but inference.

edit:

Following a thread on steel abrasion elsewhere brought up the point that our lack of understanding of water has a direct impact on our understanding of protein folding. That much of our knowledge of water is phenomenological, ie top down. The reliance of biology on water is huge and it seems the complexity of water is well beyond out current means. Just a thought, not sure how relevant it is but one of those pleasant coincidences where my love of rubbing bits of metal on abrasive surfaces coincides with my love of biology. His point was if water is deeply complex to the point we can't account for all of its properties then understanding steel is a long way away, I imagine the same goes for biology multiplied many times.