Biology of life and 3D spatial positioning

[KBCid]

KBC, wow this could really gain some momentum here. Do you think there could be a grant later on?
I have been waiting a few years for mechanical engineers to get into this area. I wouldn't be surprised if there is a paradigm shift within my lifetime:)

Bippy I am sure that if the scientist that I have submitted my idea too are interested enough they will find a method to bring it to the table. In my own work I cannot do that type of research since my employer chooses the projects according to their own criteria.
There will be a paradigm shift simply because the evolutionary hypothesis is wrong. As scientists get closer to understanding how structures are formed the reality of what must be happening will inevitably lead them to the correct understanding and as more mechanical engineers join the biological arena the understanding may come sooner than we think. I am hoping that the 6 submissions I have put out to various places friendly to ID will start them on this path and excellerate the process.
Secondarily I am hoping that there will be some who read these online posts and initially try to disprove it which will also help in the end as they will uncover more of the system that is there.

[bippy123]

Thanks again for all your hard work and info KBC, and I agree on what you said about evolution. By the way have you ever tried sharing this stuff with Perry Marshall ? I believe he's an engineer also . His theory is information theory.

Keep up the awesome work
God bless

[KBCid]

Thanks again for all your hard work and info KBC, and I agree on what you said about evolution. By the way have you ever tried sharing this stuff with Perry Marshall ? I believe he's an engineer also . His theory is information theory. Keep up the awesome work God bless

Bippy your understanding is appreciated. I have not yet submitted my concept to Perry but I will certainly send the paper I wrote, to him as well. It would be nice to see another engineer critically analysing this point since it is driven by information.
Did you realise that part of the 3D spatiotemporal positioning system requires that positional information to direct the positioning must be encoded? Think about it, how would a system define positional information to mechanisms that perform the actual positioning?
Here is something to consider if you haven't already. None of the cells in our body have any preferencial position relative to any other cell. A cell can be attached to any other cell at any point of its circumference. Since a cell is essentialy a spherical structure it is important to consider what the possible attachment points can be between two spheres. I invite you to give me a number that you feel would describe the possible number of locations. God, I really love mechanics and the one who allowed me to have it.

[KBCid]

Spatiotemporal mechanisms of life Abstract
Understanding how organisms measure and respond to space and time at a physical and chemical level is at the heart of a mechanistic understanding of life.
As physical beings, individual cells and whole organisms are bound by the four dimensions occupied by space and time.
... in biological systems a precise mechanistic understanding of how organisms react in four dimensions is only now emerging.
Research on telomeres, the specialized ends of chromosomes, reveals another connection between space and time. The length of telomeres is directly related to the age of an organism.
An intriguing feature of zebrafish fin growth lends further credence to the model in which space and time are interrelated. When amputated, fins grow back in the same amount of time whether they are fully amputated or only cut back by a small amount (Perspective, p. 614). Once a final position (in space) is reached, the process stops (in time).
In this issue, each of the Commentaries, Reviews and Perspectives demonstrates some aspect of the measurement or control of space and time in biological systems. They also demonstrate that an understanding of the basic measurements made by cells, whether it is the length of a DNA stretch, the length of a zebrafish fin or the number of daylight hours, helps us to restate the fundamental question of how biology works in space and time in specific mechanistic terms.
http://www.nature.com/nchembio/journal/ ... 7-593.html

Measuring Spatiotemporal Coordination in a Modular Robotic System Abstract
In this paper we propose and verify spatiotemporal measures of coordination in a modular robotic system. These information-theoretic measures estimate the generalized “correlation entropy” K2 and the generalized excess entropy E2 computed over a multivariate time series of actuators’
states, while standard deviation of E2 is minimized over both space and time. Actuators are shown to be well-coordinated in individuals with fastest locomotion. These results support our conjecture that direct ?tness functions can be approximated with generic selection pressures, leading towards information-driven evolutionary design. http://www.ict.csiro.au/staff/mikhail.p ... rected.pdf

Measuring collective behaviour of multicellular ensembles: role of space-time scales. Abstract
Living systems are spectacular examples of spatiotemporally organized structures. During the development of complex organization there is dynamic equilibrium between the local and global processes acting at the intra-and intercellular levels in multiple space and time scales. Although in modelling studies such spatiotemporal systems can be described by different space-time scales and at many organizational levels, the experimental quantities measured and predictions useful for practical applications are at a macroscopic (coarser or averaged) level/scale; these are limited by the resolution of the measuring method and experimental protocol. In this work, we address whether the spatiotemporal collective dynamics exhibited by a multiscale system can discriminate between,or be borne out by,the coarse-grained and averaged measurements done at different spatial and temporal scales. Using a simple model of a ring of cells, we show that measurements of both spatial and spatiotemporal average behaviour in this
multicellular ensemble can mask the variety of collective dynamics observed at other space-time scales, and exhibit completely different behaviours.
Such outcomes of measurements can lead to incomplete and incorrect understanding of physiological functions and pathogenesis in multicell ensembles. http://www.ncbi.nlm.nih.gov/pubmed/18535363

High-Resolution Quantification of Focal Adhesion Spatiotemporal Dynamics in Living Cells
Focal adhesions (FAs) are dynamic, multi-component protein complexes that serve as points of integration for both mechanical and chemical signaling,
while playing a central role in a variety of processes including cancer metastasis, atherosclerosis and wound healing [1], [2], [3]. Characterizing how these structures dynamically change is essential for understanding cell migration, which requires that adhesions are continuously remodeled as the cell moves forward. During motility, new adhesions are born at the leading edge of a protruding lamellipodia. They then enlarge and are either disassembled at the base of the protrusion in a process known as adhesion turnover, or become longer-lived structures that are eventually dismantled in the retracting tail at the rear of the cell [4], [5], [6]. In this cycle as well as other FA-mediated processes, FA dynamics are highly regulated by structural and signaling molecules...
http://www.plosone.org/article/info%3Ad ... ne.0022025

Computational Analysis of the Spatiotemporal Coordination of Polarized PI3K and Rac1 Activities in Micro-Patterned Live Cells
The results suggest that the initiation of the edge extension occurred before the activation of PI3K, which led to a stable extension of the free end followed by the Rac1 activation. Therefore, the results support a concerted coordination of sequential signaling events and edge dynamics, underscoring the important roles played by PI3K activity at the free end in regulating the stable lamellipodia extension and cell migration.
Directional migration plays an essential role in physiological and pathological conditions such as development, wound healing, and atherosclerosis [1]. Aberrant regulation of migration has been reported to indicate cancer metastasis [2]. Fibroblasts can also sense the spatial gradient of platelet derived growth factor (PDGF) and migrate to the wounded area [3], [4]. A typical migration procedure includes four steps: (1) extension of the lamellipodia; (2) formation of focal adhesions and stabilization of extension at the leading edge; (3) detachment of the focal adhesions at the tail; (4) contraction of the tail [1]. To coordinate these complex maneuvers for persistent migration, the cells need to sense the external cues, determine the migration direction and differentiate the molecular processes between the leading edge and the tail to achieve a polarity.
http://www.plosone.org/article/info%3Ad ... ne.0021293

Spatiotemporal patterns and transcription kinetics of induced RNA in single bacterial cells
Despite their relatively small dimensions, bacterial cells show a remarkable, rich internal subcellular organization that has captured the interest of researchers over the past decade. Many cytoplasmic and membrane proteins, particularly those involved in cell division, DNA replication, and chromosome segregation, have specific subcellular localizations that can change quickly over time in response to cell cycle progression, motility, and environmental cues. This dynamic and organized behavior is also true for bacterial chromosomal DNA. The use of GFP fusions and in situ fluorescence hybridization (FISH) have shown that every chromosomal locus has a defined subcellular address and is replicated and segregated into the new cell as part of an active and directed process. http://www.pnas.org/content/106/38/16399.full

Spatio-Temporal Organization of Replication in Bacteria and Eukaryotes (Nucleoids and Nuclei)
Early cytological experiments suggested that replication in bacteria occurs at a specific mid-cell position akin to the replication factories observed in eukaryotes (see below) (Lemon and Grossman 1998, 2000). However, accumulating evidence over the last decade suggests that after replication initiation, the replisomes are not stationary nor do they cluster (Jensen et al. 2001; Bates and Kleckner 2005; Berkmen and Grossman 2006; Reyes-Lamothe et al. 2008). Instead, it appears that the nucleoid serves as both the template and track for the replication machinery.
Accordingly, our current view is that the nucleoid itself is the major organizer of DNA replication in bacteria. Our premise is that understanding the spatial organization of bacterial replication requires an understanding of the structure and organization of the bacterial chromosome.
The ability to visualize individual chromosomal loci in live cells using fluorescent fusions to DNA binding proteins and their target sequences revealed a degree of spatial organization of the chromosome that had not been previously appreciated
http://cshperspectives.cshlp.org/conten ... 10389.full

Visualization of DNA Replication Sites in Mammalian Nuclei
DNA replication takes place at discrete sites in the cell nucleus, named replication foci. The spatial arrangements of these foci change in the course of S phase in a temporally regulated and reproducible fashion forming five distinct and highly conserved replication patterns. The organization of nuclear replication sites can be studied by electron and light microscopy techniques. This chapter describes several procedures for detection of replication foci in mammalian nuclei via indirect immunofluorescence microscopy.
http://www.springerprotocols.com/Abstra ... 7-815-7_23

[KBCid]

Spatio-temporal Rho GTPase signaling – where are we now?
Summary
Rho-family GTPases are molecular switches that transmit extracellular cues to intracellular signaling pathways. Their regulation is
likely to be highly regulated in space and in time, but most of what is known about Rho-family GTPase signaling has been derived
from techniques that do not resolve these dimensions. New imaging technologies now allow the visualization of Rho GTPase signaling
with high spatio-temporal resolution. This has led to insights that significantly extend classic models and call for a novel conceptual
framework. These approaches clearly show three things. First, Rho GTPase signaling dynamics occur on micrometer length scales and
subminute timescales. Second, multiple subcellular pools of one given Rho GTPase can operate simultaneously in time and space to
regulate a wide variety of morphogenetic events (e.g. leading-edge membrane protrusion, tail retraction, membrane ruffling). These
different Rho GTPase subcellular pools might be described as ‘spatio-temporal signaling modules’ and might involve the specific
interaction of one GTPase with different guanine nucleotide exchange factors (GEFs), GTPase-activating proteins (GAPs) and
effectors. Third, complex spatio-temporal signaling programs that involve precise crosstalk between multiple Rho GTPase signaling
modules regulate specific morphogenetic events. The next challenge is to decipher the molecular circuitry underlying this complex
spatio-temporal modularity to produce integrated models of Rho GTPase signaling.
...Their ability to regulate so many different functions, in highly dynamic cellular contexts, implies that they are tightly regulated at the spatio-temporal level.
...I will then concentrate on a series of examples that illustrate the newly revealed complexity of spatio-temporal Rho GTPase signaling compared with the classic conceptual framework.
Spatio-temporal Rho GTPase signaling programs
Another insight provided by spatio-temporal Rho GTPase measurements is that complex spatio-temporal signaling programs that involve precise crosstalk between multiple GTPases are put in place by the cell to fine-tune specific morphogenetic events. For example, in the context of cell migration, FRET probes and biochemical experiments clearly indicate that all three canonical Rho GTPases are activated at the leading edge of migrating fibroblasts or other cells (Cho and Klemke, 2002; Itoh et al., 2002; Kraynov et al., 2000; Kurokawa et al., 2005; Nalbant et al., 2004; Pertz et al., 2006). This then begs the question of how crosstalk occurs between all three GTPases in time and space to regulate the leading-edge extension process.
Spatio-temporal signaling modularity and the need for systematic approaches
if Rho GTPase signaling involves the precise, coordinated action of multiple signaling modules in space and time, then the correct
description of a given cell behavior will require insight into all the players operating in each of the signaling modules. This will
require systematic approaches to identify and characterize all the components of the multiple signaling modules that cooperate to
regulate a given cellular process (cell migration, neurite outgrowth,phagocytosis, etc.).
http://jcs.biologists.org/content/123/11/1841.full.pdf


RESEARCH AREAS
Mechanobiology; Bioimaging & Biophysics of Gene Regulation
Summary
Physical signals from the extracellular matrix impinge on cellular geometry resulting in altered functional nuclear landscape and gene function. These alterations regulate diverse biological processes including stem-cell differentiation, developmental genetic programs and cellular homeostatic control systems. How such signals are integrated to the 3D spatio-temporal organization of the cell nucleus to elicit differential gene expression patterns are poorly understood. Using a multi-disciplinary approach, combining high-resolution live-cell imaging and mechanics experiments, our laboratory investigates the biophysical principles underlying the coupling between cellular geometric cues to the nucleus and its impact on gene regulation. Understanding the mechanical control of gene function in living cells has become a central theme in modern cell biology and biophysics. In this context, our laboratory’s approach is one that of modular, than molecular, in probing design principles underlying these cellular mechanical systems impinging on gene expression. In these projects, we engage in a number of collaborations, both theoretical and experimental, to quantitatively understand the coupling between cellular geometry and genetic information control.http://mbi.nus.edu.sg/g-v-shivashankar/

Mechanosensitive mechanisms in transcriptional regulation
Summary
Transcriptional regulation contributes to the maintenance of pluripotency, self-renewal and differentiation in embryonic cells and in stem cells. Therefore, control of gene expression at the level of transcription is crucial for embryonic development, as well as for organogenesis, functional adaptation, and regeneration in adult tissues and organs. In the past, most work has focused on how transcriptional regulation results from the complex interplay between chemical cues, adhesion signals, transcription factors and their co-regulators during development. However, chemical signaling alone is not sufficient to explain how three-dimensional (3D) tissues and organs are constructed and maintained through the spatiotemporal control of transcriptional activities. Accumulated evidence indicates that mechanical cues, which include physical forces (e.g. tension, compression or shear stress), alterations in extracellular matrix (ECM) mechanics and changes in cell shape, are transmitted to the nucleus directly or indirectly to orchestrate transcriptional activities that are crucial for embryogenesis and organogenesis. In this Commentary, we review how the mechanical control of gene transcription contributes to the maintenance of pluripotency, determination of cell fate, pattern formation and organogenesis, as well as how it is involved in the control of cell and tissue function throughout embryogenesis and adult life. A deeper understanding of these mechanosensitive transcriptional control mechanisms should lead to new approaches to tissue engineering and regenerative medicine.

Physical geometry. The very thing that gives life its abilities and allows it success in existence is only eclipsed by how physical geometry can persist through replication. Matter is some how controlled so that when it is arranged into a living system it can pass on its 3 dimensional form.
What does it take to replicate 3 dimensional forms of matter that have no inherent formational cause such as crystals or snowflakes.

[KBCid]

Mechanosensitive mechanisms in transcriptional regulation
Summary
Transcriptional regulation contributes to the maintenance of pluripotency, self-renewal and differentiation in embryonic cells and in stem cells. Therefore, control of gene expression at the level of transcription is crucial for embryonic development, as well as for organogenesis, functional adaptation, and regeneration in adult tissues and organs. In the past, most work has focused on how transcriptional regulation results from the complex interplay between chemical cues, adhesion signals, transcription factors and their co-regulators during development. However, chemical signaling alone is not sufficient to explain how three-dimensional (3D) tissues and organs are constructed and maintained through the spatiotemporal control of transcriptional activities. Accumulated evidence indicates that mechanical cues, which include physical forces (e.g. tension, compression or shear stress), alterations in extracellular matrix (ECM) mechanics and changes in cell shape, are transmitted to the nucleus directly or indirectly to orchestrate transcriptional activities that are crucial for embryogenesis and organogenesis.
http://jcs.biologists.org/content/early ... 5.abstract

...Nuclei of embryonic stem cells appear to have their very specific 3D chromosomal organization that differs from the position the same chromosomes have in differentiated cells (Wiblin et al., 2005).
It was also shown that the 3D nuclear order of chromosomes within the same cell type is inherited during mitosis: daughter cells will show an organizational pattern that resembles their parental cell (Cremer et al., 2001; Gerlich et al., 2003; Essers et al., 2005). Moreover, the chromosomal order within the 3D nuclear space is evolutionarily conserved (Tanabe et al., 2002) strongly suggesting that the structural organization of the nucleus that is relevant to its stability and overall function has been established

Telomeric organization in normal cells.
As shown by live cell imaging, telomere positions in the 3D nucleus are not static. Telomeres can move in the interphase nucleus (Molenaar et al., 2003). The distances they move vary (ibid). Telomeres are organized in a very typical way within the 3D space of the nucleus. Normal lymphocytes of mouse or human origin show a cell cycle-dependent organization of telomeres in their interphase nuclei. In an unperturbed nucleus and under optimal growth conditions, telomeres are widely distributed throughout the nucleus in normal G0/G1 cells (Weierich et al., 2003; Chuang et al., 2004). S-phase cells display a similar pattern of telomere organization and, in addition, show replicative structures of telomeres (Chuang et al., 2004). In G2, telomeres assemble into a telomeric disk, first observed by us (Chuang et al., 2004). Human keratinocyte cell lines with flatter nuclei perform less reorganization of telomeres but also exhibit a dynamic cell-cycle-specific organization (Ermler et al., 2004). Thus, telomeres reorganize in the 3D space of the nucleus during a normal cell cycle (Fig. 3). At no time during a normal cell cycle do telomeres of normal cells come into such close association that they form clusters or aggregates (Chuang et al., 2004). In fact, telomeres of normal cells do not overlap (Chuang et al., 2004).
http://atlasgeneticsoncology.org/Deep/3 ... 20053.html

[KBCid]

Spatiotemporal chemical dynamics in living cells: From information traficking to cell physiology
Abstract
...stop-action movies of signal traficking in living cells are created; these have revealed a new level of spatiotemporal chemical organization within cells.
1. Introduction
Molecular sciences, including molecular biology, genomics, proteomics, and crystallography, have now described life in unprecedented depth and breadth. Yet these descriptions have not improved significantly the rate of drug discovery. Themolecular defect in sickle cell anemia was discovered nearly a half-century ago, yet in 50 years what treatments has this knowledge yielded?
The defects in oncogenes were found in the 1970s, and those in cystic fibrosis and Duchenne muscular dystrophy were discovered in the 1980s, but we have yet to see signi?cant improvements in clinical care. Whatever scienti?c insightsmight have been gained,molecular science has not yielded sufficient insight to provide bettercare for patients.
So what have we missed? By so thoroughly embracing structural reductionism, we have learned a great deal about the system’s parts without really understanding how the system works. For example, a list of the capacitors, resistors, and the other functional parts found in a television set are not sufficient to deduce how a television works. As the parts list of the human genome is much longer than that of a television set, and the behavior of its components more subtle, it is not surprising that molecular biology has not yielded the anticipated cornucopia of new drugs. Living cells require networks of enzymes and receptors with large numbers of feedback loops under conditions held far from thermodynamic equilibrium. Therefore, the properties of individual isolated components can never adequately model the dynamic chemical processes that underlie cell functions. The part cannot explain the whole; to understand how all of the parts of a cell work in concert, the parts must be studied in their cell biological context at a time-scale relevant to the physico-chemical processes under study.

... In another example of information distribution, waves have clearly defined directional properties. Longitudinal NAD(P)H waves allow neutrophils to aim superoxide production in the direction of target cells (Kindzelskii and Petty,2002).

...Due to their physical nature, waves are also characterized by ignition sites. In neutrophils, one calcium ignition site has been found to
be the lamellipodium. As calcium waves are repetitively triggered from this site, it displays a rudimentary form of cell memory. Depending upon the latest direction cue, this ignition site can reorganize at different locations on the plasma membrane.

...Thus, the processes underlying cell behaviormore closely resemble the decision making processes of a computer than the dynamics of a stirred
chemical reactor.
http://www.sownar.com/silvercluster/Spa ... iology.pdf

NETWORK DYNAMICS AND CELL PHYSIOLOGY
In the past year,many prominent molecular biologists have pointed out the pressing need for theoretical and computational tools to show the spatial and temporal organization implicit in the way that macromolecules are ‘wired together’ to create a living cell. The molecular signals that control the proliferation of mammalian cells are extremely complex, and Kohn’s map of this network has become an icon of the challenges that confront any attempt to fathom a realistic cellular control system.
What tools do we have to help us understand how the precise spatio-temporal organization of a cell arises from the molecular interactions of the protein machinery inside?
Spontaneous spatial and temporal organization of dynamical systems is, therefore, the unifying principle of the ‘last step’ of computational molecular biology.
http://www.sbs.utexas.edu/genetics/Lite ... iology.pdf

[Beanybag]

While I actually do appreciate your ability to gather all these different papers on this topic, they're all pretty interesting (I only read every other one or so), I wonder if you notice that none of them support the hypothesis of ID nor deny the theory of biological evolution.. They simply raise questions and show research. Do you think, perhaps, that you have overstepped the boundary of legitimate reason here by trying to assert a conclusion without sufficient justification? I just find it strange that none of this deters you. I suppose it's admirable in some manner, but it's also a little foolish.

[KBCid]

While I actually do appreciate your ability to gather all these different papers on this topic, they're all pretty interesting (I only read every other one or so), I wonder if you notice that none of them support the hypothesis of ID nor deny the theory of biological evolution.. They simply raise questions and show research. Do you think, perhaps, that you have overstepped the boundary of legitimate reason here by trying to assert a conclusion without sufficient justification? I just find it strange that none of this deters you. I suppose it's admirable in some manner, but it's also a little foolish.

There is no need to appreciate anything. In fact no one is forcing you to read any of it but, if you are reading them then you should see a common thread in every area of research. Why do you suppose that is? If everywhere a researcher looks in a living system they see spatiotemporal control being exhibited what would be the logical conclusion?

How much of a stretch of logic and reason is required to assert that a 3 dimensional replication system requires a spatiotemporal control system for the matterial structure it reproduces?

A foolish assertion here would be that there is no systematic spatiotemporal control system but you can imagine whatever makes sense to you. I'm going with the observable evidence. The living system requires a system to spatiotemporally control matter in order to replicate 3 dimensional form.

[bippy123]

KBC, how dare you make logical sense about a subject that would force beanie to go against his cherished and faith-based worldview?
your not playing fair man;)

[Pierson5]

While I actually do appreciate your ability to gather all these different papers on this topic, they're all pretty interesting (I only read every other one or so), I wonder if you notice that none of them support the hypothesis of ID nor deny the theory of biological evolution.. They simply raise questions and show research. Do you think, perhaps, that you have overstepped the boundary of legitimate reason here by trying to assert a conclusion without sufficient justification? I just find it strange that none of this deters you. I suppose it's admirable in some manner, but it's also a little foolish.

There is no need to appreciate anything. In fact no one is forcing you to read any of it but, if you are reading them then you should see a common thread in every area of research. Why do you suppose that is? If everywhere a researcher looks in a living system they see spatiotemporal control being exhibited what would be the logical conclusion?

How much of a stretch of logic and reason is required to assert that a 3 dimensional replication system requires a spatiotemporal control system for the matterial structure it reproduces?

A foolish assertion here would be that there is no systematic spatiotemporal control system but you can imagine whatever makes sense to you. I'm going with the observable evidence. The living system requires a system to spatiotemporally control matter in order to replicate 3 dimensional form.

You may want to read what he wrote again. He's not saying the system isn't required, or doesn't exist. None of us are arguing that...

I wonder if you notice that none of them support the hypothesis of ID nor deny the theory of biological evolution.. They simply raise questions and show research. Do you think, perhaps, that you have overstepped the boundary of legitimate reason here by trying to assert a conclusion without sufficient justification?

It's your conclusion (biological design/evolution is false) that he's talking about.

[KBCid]

You may want to read what he wrote again. He's not saying the system isn't required, or doesn't exist. None of us are arguing that...
It's your conclusion (biological design/evolution is false) that he's talking about.

The fact is in this case that to deny a designer as a requirement to explain the origin of the system then you must deny that the system is what I am saying it is. However, If you both recognise and don't deny that the system exists then you should realise logically that replication cannot occur without it.
Knowing this you should have no problem in asserting a logical alternative hypothesis for how natural causes could form the system prior to replication if you don't accept my hypothesis.
This is your paradox. You are restricted by your own belief system to only allowing natural causes to explain everything and you have all been happy in waving the magic wand of evolution at everything and feeling that the explanation is sufficient. Now you are faced with something that you can't wave your wand at and make go away.
I and many others are quite interested in seeing how you attempt to explain the occurance of an extremely intricate and irreducibly complex spatiotemporal control system by chance alone and you have no hypothetical mechanisms to rely on to provide a hypothetical explanation.
No replication, no evolution.

[KBCid]

KBC, how dare you make logical sense about a subject that would force beanie to go against his cherished and faith-based worldview? your not playing fair man;)

I am a bad bad man... I should be flogged, I should be purged.

In the beginning there was nothing but chemicals and then suddenly from out of nowhere a highly complex irreducible system to control the replication of matter begins to function by chance.

ye shall all bow down and worship the great god chance.

[bippy123]

KBC, how dare you make logical sense about a subject that would force beanie to go against his cherished and faith-based worldview? your not playing fair man;)

I am a bad bad man... I should be flogged, I should be purged.

In the beginning there was nothing but chemicals and then suddenly from out of nowhere a highly complex irreducible system to control the replication of matter begins to function by chance.

ye shall all bow down and worship the great god chance.

Kbcid you deceiver you lol

On a serious note I vote for this thread to be stickied . It is incredibly fascinating and will probably be the new paradigm shift in the biology of life. It's about time the engineers started getting in on it.
Do I hear anymore votes?

[KBCid]

On a serious note I vote for this thread to be stickied . It is incredibly fascinating and will probably be the new paradigm shift in the biology of life. It's about time the engineers started getting in on it.
Do I hear anymore votes?

I too would like to see it stickied until it has run its course. I'm fairly sure that there won't be much in the way of argument from the evo's / atheists simply because there is no ready made arguments that they can grab to argue it and they don't really possess the intellectual capacity to properly discuss it in a logical manner. However, there are a great many who will understand what is being said and will understand the implications that can't be avoided and maybe they like me will be convinced of the necessity for an intelligent designer and make a choice as to who it may be.

Bippy here is one of the simple explanitory letters I have sent to some of the ID sites out there. See if this helps your understanding a bit since I haven't posted it in this manner yet;

Replication of life and 3D Spatiotemporal control
by: KBCid

The question of the origin of life as well as the persistence of life has been a long standing mystery of scientific inquiry since man has sought to explain scientifically how these thing occur. In order to help guide how we explain these mysteries we have formulated several conceptual hypothesis and by scientific method have tested to see what makes the most logical sense of the observable evidence produced.
Our scientific inquiry has opened a plethora of understandings about a majority of the individual components that take part in the living system but almost nothing that would help to explain how such a system came into existence nor how it persists. With this paper I hope to change those problem based on an understanding of mechanical engineering, system mechanics and physics.

I will begin by showing where scientific inquiry is focusing in order to help answer the questions that have so far eluded us. A good reference to the problem was elucidated by Howard Petty in this paper;

Spatiotemporal chemical dynamics in living cells: From information trafficking to cell physiology
Howard R. Petty
Molecular sciences, including molecular biology, genomics, proteomics, and crystallography, have now described life in unprecedented depth and breadth. Yet these descriptions have not improved significantly the rate of drug discovery...
So what have we missed? By so thoroughly embracing structural reductionism, we have learned a great deal about the system’s parts without really understanding how the system works. For example, a list of the capacitors, resistors, and the other functional parts found in a
television set are not sufficient to deduce how a television works. As the parts list of the human genome is much longer than that of a television set, and the behavior of its components more subtle, it is not surprising that molecular biology has not yielded the anticipated cornucopia of new drugs. Living cells require networks of enzymes and receptors with large numbers of feedback loops under conditions held far from thermodynamic equilibrium.
Therefore, the properties of individual isolated components can never adequately model the dynamic chemical processes that underlie cell functions. The part cannot explain the whole; to understand how all of the parts of a cell work in concert, the parts must be studied in their cell biological context at a time-scale relevant to the physico-chemical processes under study.
http://www.sownar.com/silvercluster/Spa ... iology.pdf

In his discourse on the subject Howard has correctly defined the problem with how we have been try to understand things. We have been studying individual components within the system without paying enough attention to how they are systematically controlled which is analogous to not seeing the forest for the trees.

As an engineer I have been studying the mechanics of life for nearly 10 years to see if I can make some mechanistic sense of how it works in a cause and effect manner. However, my study had been impaired by the limited inquiry of science into simply defining the properties of the components without much inquiry into how the components are functioning within a greater system. In the past five or so years our technology has improved to the point where we can now observe life at the level of its three dimensional activity and with this information now coming to the forefront I am able to discern the system in a more comprehensible mechanistic way.
There are numerous studies that have come out showing that every part of the living system is tightly controlled both spacially (in 3 dimensions) and temporally (in time) in order for replication and the continued function of life to occur. We can observe this control occurring within cells themselves and at a higher level where cells are organized with each other and so far none of the scientists have been able to provide even a hypothetical explanation for how such spatiotemporal organization is being produced much less how it could have originated.

I would say that the problem they are having in providing a hypothetical explanation isn't so much that nothing can be imagined that could be explanatory it is rather that every explanation that could be imagined has historically been the result of intelligent agency and such explanations are not allowed within the paradigm of naturalism which is currently used to guide scientific inquiry. In this paper I am going to explore past this stumbling block following the evidence where it leads based on what is known scientifically.

Life is composed of components of matter with very specific arrangements that are specifiably arranged in both spatial and temporal organization. This is the observable evidence. So let's first explore what is known about how matter can be arranged. In all of our experience and observations we have found that matter can only be arranged into specific arrangements in two ways;

1) Matter can self arrange its spatial positioning based on its inherent physical properties which we have observed in the case of crystalline structuring and in the formation of snowflakes. In every case where such ordering occurs we have been able to deduce what is causing the spatial organization to occur.
2) Any matter that is not controlled by an inherent physical property to self organize requires an outside force to act on it in order to move it spatially.

So, when we observe that matter is exhibiting the effect of being spatially controlled then we only have two options to look for, either it is an inherent property of that matter or it is a controlling force outside the matter itself. The living system exhibits an outside control for the matter that makes up its structure. Thus, we are left with defining how such a control can systematically function.

The systematic control of matter has typically been the work of mechanical engineers applying the known rules of physics to forming matter into specific shapes or organizations and engineering has been one of the oldest used properties of intelligence since before recorded history. So there is no shortage of concepts for how to systematically arrange matter into specific organizations. In most of the historic methodologies envisioned it required the direct action of an intelligent agency to create an arrangement such as using moulds or hand shaping (clay) to give a few examples. As technology advanced we found that we can create machines to do the hand work for us, but the fact remained that even the machines had to apply the same outside force to the materials we wanted to have shaped. One of the most recent technologies used to form matter is called CNC machining. This type of control for shaping matter required a three dimensional coordinate system to be created in order to provide a code for the shaping machinery to be able to perform its function in both space and time. Even at this level of technology it is a given that we can only organize matter by being able to apply force in three separate directions, namely the X, Y and Z axis. Each of these individual axis are used to provide a referenceable method of defining 3 dimensional space in a coded format that can be used to give instruction to mechanisms that need to move precisely within these dimensions.
In all this technological marvel we have found a very fundamental rule to always be in effect when we want to organize matter into specific 3 dimensional shapes. To be able to move matter into specific 3 dimensional forms we must be able to apply force to the material in all three planes. There are no shortcuts, there is no loopholes in physics. This is a fundamental understanding by any mechanical engineer and any physical science. It is undeniable.

With this understanding established we know that the control system within life MUST be able to apply force to matter in 3 dimensions in order to control its movement in space. This is an 'irreducible' constant for any systematic 3 dimensional control system. However, this is only one aspect of its irreducibility. There are many other aspects of such a system that are just as irreducible to the control of matter spacially. Even though we know that we must minimally be able to apply force in 3 separate planes the application of these forces must also be controlled in how they are applied. Random force applied in any direction would eliminate any precision and replicability in a formation process. This understanding forces the rationalization that a precision spatial positioning system must minimally be able to apply force in a variably controlled manner in three separate planes which makes this its minimal irreducible level in order to conceptually affect the spatial positioning of matter. Even with this said we are still not done with defining everything necessary to control matter spacially.

The next level in such a system must be the part that drives the application of the three separate planes of force. It should be obvious that this system cannot simply apply forces in an independent fashion. Each of the planar force appliers must be directed in how they individually apply force to the matter being affected. Thus a driver / controller is also a necessary part of a 3 dimensional control system.

Our next consideration in this system is to define how the driver can accurately direct the planar force appliers. Since we can't infer that there is an intelligence actively providing orchestration then the driver must give instruction based on stored information and this stored information must be able to accurately define, by instruction, specific spatial positioning. So how can spatial position information be stored? We have found through various scientific methods that you need to minimally define three points relative to a home point. When you use your GPS device to find your way in the world it is functioning by this very method. It uses three points in space and a home point in order to define your location in 3 dimensional space. There is no simpler method of being able to define a 3 dimensional position. You must have four definable points being delineated by whatever type of informational coding you use.

Another part of this irreducibly complex system is the information storage and retrieval system. Such a system must be able to store information on a medium and then be able to retrieve it in a temporal manner so that a physical construction can be correctly formed.
This means that whatever you wish to construct in 3D must be driven in an orderly manner just the way a house or car or anything is built.
This is where the temporal consideration comes into full effect. If we try to build a house by starting with the roof then it will fail. All physical structures that are formed must have an orderly manner of construction and the construction material need to arrive at the time they are needed. As intelligent agents we know this based on every single thing we have ever made in 3 dimensional space. The correct direction and timing must be correlated to ensure that construction proceeds correctly.

The final part of this system is of course the production of the substrates that need the 3 dimensional guidance to begin with. We should all know that it does no good to have people ready to build a house on site if there are no materials for them to build with. The same is true for any type of structural formation system. The material substrates must occur as they are needed in order for the positioning system to place the substrates in the right place and at the right time they are needed during the construction process.

Essentially all of the above MUST be arranged before the spatiotemporal control system can function. There are no shortcuts or alternatives to be found since it all works within the known laws of physics and has been logically and empirically tested as a minimum on every front. It is irreducibly complex.

So what does this mean to us as it relates to the origin and persistence of life from a scientific perspective?

This means that replication cannot begin without the spatiotemporal control system being in place.
It means that life as we know it cannot persist without this system.
It means that the prevailing concept of evolution cannot begin without this system
It means that chance could not have formed such a system
It means that an intelligent designer is necessary to initially form such an irreducibly complex system to allow for replication and persistence.

This is what led me from an evolutionary perspective to the Intelligent design concept. You can't build this system in a stepwise manner nor can you logically assert that it could occur by chance. You are left with only one possibility. Life was designed.

After reading through everything I could find on the subject of intelligent design I was especially captivated by Professor Michael Behe's description of irreducible complexity. I finally found another way of saying 'minimal complexity required'. It was his argument that allowed me to see the depth of meaning in this terminology as it applies to the living system.
It is unfortunate that Professor Behe hadn't further plumbed the depths of how far irreducible complexity could be applied within the system of life but, in any case his references to things such as the flagellum still hold true even in the face of the hypothetical evolutionary way of overcoming it. This understanding that I am bringing forward was the missing piece in his argument though it may not initially be apparent why.

When Professor Behe spoke about the components of the flagellum all being necessary for its function this is absolutely a true statement just as my own statement about the spatiotemporal system is true. The difference between our individual assertions was that evolutionists imagined that the flagellum’s irreducible complexity could be overcome by an evolutionary method of over forming and then reduction to a lesser form though they never delved into how any formation could could have occurred to begin with. With my argument evolutionists cannot attempt to invoke the mechanism of evolution because frankly evolution cannot occur until my system is in place and it would be a test of logic to think that such a system could accidentally perform that action. No replication, no evolution.
The truth for Behe's flagellum point is still valid once he incorporates the reality of this paper into it, as it would require the explanation of how something can be precisely constructed in 3 dimensional space and how it's parts could be subsequently rearranged into a totally different irreducible arrangement.

So for those who take the time to understand the concept of this paper there will be some truths that cannot be avoided based on simple logic and physics;

1) You can't precisely replicate 3 dimensional structures of matter without a spatiotemporal control system
2) You can't have evolution without a spatiotemporal control system
3) You can't form a spatiotemporal control system by chance
4) The living system requires a spatiotemporal system of control in order to persist

I would like to thank all the intelligent design proponents for their input and especially Professor Behe for his logic and reason.
If anyone who receives this paper is interested in discussing this subject further just reply me at this e-mail; --------------------