Biology of life and 3D spatial positioning

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Biology of life and 3D spatial positioning

#1

Post by KBCid » Wed Jun 27, 2012 10:26 am

I believe a thread dealing specifically with 3D spatial positioning and the formation of living systems is now something we can begin to discuss.
I will post relevant scientific articles to this discussion in this initial post and we can then tackle the understandings about it. Bippy this thread was conceived after our discussion in another area. If you find any further papers dealing with the subject, post it and i'll add them to this first post to give us all a single reference post to work from.

Tissue-specific spatial organization of genomes
http://genomebiology.com/content/5/7/R44

Statistical Analysis of 3D Images Detects Regular Spatial Distributions of Centromeres and Chromocenters in Animal and Plant Nuclei
http://www.ploscompbiol.org/article/inf ... bi.1000853

Micro-environmental control of cell migration – myosin IIA is required for efficient migration in fibrillar environments through control of cell adhesion dynamics http://jcs.biologists.org/content/125/9/2244.abstract

Cancer Cell Migration in 3D https://aiche.confex.com/aiche/2012/web ... 71104.html

The trypanosome flagellum http://jcs.biologists.org/content/116/5/757.full.pdf

Analysis of spatial relationships in three dimensions: tools for the study of nerve cell patterning
http://www.biomedcentral.com/1471-2202/9/68/

Mechanosignaling to the Cell Nucleus and Gene Regulation http://www.annualreviews.org/doi/abs/10 ... de=biophys

Time-lapse Tuesday: A frog's electric face http://www.newscientist.com/blogs/nstv/ ... -face.html

Spatial Positioning
Abstract
The eukaryotic cell nucleus is a heterogeneous organelle. Chromosomes are nonrandomly positioned within the nuclear space, and individual gene loci experience distinct local environments due to the presence of chromatin domains and subnuclear compartments. Recent observations have highlighted the important yet still largely mysterious role of spatial positioning in genome activity and stability.
http://www.cell.com/abstract/S0092-8674(04)00944-4

Location, Location, Location http://www.sciencemag.org/content/326/5957/1205.short

Mypt1-mediated spatial positioning of Bmp2-producing cells is essential for liver organogenesis
http://dev.biologists.org/content/135/19/3209.abstract

Spatial Control of Cytokinesis by Cdr2 Kinase and Mid1/Anillin Nuclear Export
http://www.cell.com/current-biology/abs ... 09)00985-3

Three-dimensional organization of the mammalian nucleus in normal and tumor cells.
http://atlasgeneticsoncology.org/Deep/3 ... 20053.html

On emerging nuclear order
Increasing evidence suggests that the arrangement of chromosomes, gene loci, and nuclear bodies is nonrandom and exhibits features of self-organization in space and time...
Although mechanisms governing spatial positioning and how specific nuclear subcompartments at the periphery influence transcriptional state are not well understood, they appear to be important regulatory events in development.
http://jcb.rupress.org/content/192/5/711.full

Micropatterned environments in cell biology
http://www.seas.upenn.edu/~chenlab/pdf/ ... vMat04.pdf

LOL even the people from the wacko type sites are getting in the action....

Genetics: Does DNA also encode mathematical values of lengths, distances and angles?
Each organism eventually has a certain physical shape and in humans, this is inevitably 2 arms, 2 legs, a head, 2 ears, 2 eyes, hands, fingers, etc. Now these are obviously the external shape and appearance of the organism. But there are also internal 3 dimensional structures e.g. blood vessels, the brain, the heart, the liver, kidneys, stomach, etc, etc.
So where is the information stored that determines the "physical" 3 dimensional shape (internal and external) of the organism ? Presumably also somewhere within the DNA How is this information retrieved and used ?

The completed arm will have a physical shape thats recognizable as an arm which means that during the entire process of creating the arm, millions of cells will become involved and will require knowledge of their position in space and their position relative to all the other cells busily working away at creating their part of the arm. Otherwise if cells were allowed to simply divide and position themselves randomly, the foetus would most likely end up with a blob or some other weird shape for an arm.
The fact that an arm most times develops in the right place and looks like an arm, must mean that every cell that played a part in the construction of that arm must have also been supplied or had access to spatial positioning information and some kind of coordination system ... information that would say "get x number of cells to divide but only in THIS direction only and then stop ... then get y number of cells to divide but only in THIS different direction, then stop." http://www.abovetopsecret.com/forum/thread518463/pg1

Maybe they aren't so wacko after all....

Spatially dependent activation of the patterning protease, Easter
Easter is the final protease in a serine protease cascade in which initial reaction steps appear not to be ventrally restricted, but where Easter activity is promoted ventrally through the action of a spatial cue at an unknown step in the pathway. Here, biochemical studies demonstrate that this spatial control occurs at or above the level of Easter zymogen activation, rather than through direct promotion of Easter's catalytic activity against the signaling ligand. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644372/
Last edited by KBCid on Thu Jun 28, 2012 3:58 pm, edited 4 times in total.
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Re: Biology of life and 3D spatial positioning

#2

Post by Byblos » Wed Jun 27, 2012 10:55 am

I watched some videos yesterday on 3D printing of organs, that is some freaky (as in amazing) stuff right there. Can you imagine a printer actually printing any organ which is then used for transplantation? Although it will be years until human trials but the technology is here today. Really incredible.
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Re: Biology of life and 3D spatial positioning

#3

Post by bippy123 » Wed Jun 27, 2012 11:31 am

Yea Byblos this is fascinating stuff. Maybe ill get addicted to studying this from now on. :mrgreen:

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Re: Biology of life and 3D spatial positioning

#4

Post by sandy_mcd » Wed Jun 27, 2012 12:05 pm

I've skimmed the first few references and don't understand what they are talking about - too many unfamiliar words and phrases. Can you summarize in plain English? Thanks

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Re: Biology of life and 3D spatial positioning

#5

Post by KBCid » Wed Jun 27, 2012 4:29 pm

sandy_mcd wrote:I've skimmed the first few references and don't understand what they are talking about - too many unfamiliar words and phrases. Can you summarize in plain English? Thanks
Yes mam I can.

The simplest way to get a grasp on this subject is by analogy to coding. In DNA there are 4 bases that can be arranged in any order because there is no mechanical / chemical preference for their attachment. In the same way this is also true of cells and much of the components within cells. When there are multiple cells they can attach to each other in any orientation they want to unless their positioning is controlled. Scientists are now finding by observation that almost everything is being spatially (3 dimensionally) controlled. Thus to be controlled requires a controller in the absence of a mechanical / chemical positional preference.
What this means as a bottom line is that the 3 dimensional structures of living organisms had to have a system of spatial control from the beginning. Such a system has so many requirements to function that it cannot be formed in a stepwise manner. You either have positional control or you don't there is no intermediary to such a functionality. This is the simplest way I can conceive to explain this. I hope I made some headway.
It is as if some Christians sit there and wait for the smallest thing that they can dispute and then jump onto it...
The Bible says that we were each given an interpretation – this gift of interpretation is not there so we can run each other into the ground. It is there for our MUTUAL edification.
//www.allaboutgod.net/profiles/blogs/chri ... each-other

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Re: Biology of life and 3D spatial positioning

#6

Post by KBCid » Wed Jun 27, 2012 4:36 pm

Bippy and Byblos what did you think about the electric frog face?

To actually observe the foundational 'PRE' planning of future structures is very humbling to me.
It is as if some Christians sit there and wait for the smallest thing that they can dispute and then jump onto it...
The Bible says that we were each given an interpretation – this gift of interpretation is not there so we can run each other into the ground. It is there for our MUTUAL edification.
//www.allaboutgod.net/profiles/blogs/chri ... each-other

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Re: Biology of life and 3D spatial positioning

#7

Post by bippy123 » Wed Jun 27, 2012 4:37 pm

KBCid wrote:
sandy_mcd wrote:I've skimmed the first few references and don't understand what they are talking about - too many unfamiliar words and phrases. Can you summarize in plain English? Thanks
Yes mam I can.

The simplest way to get a grasp on this subject is by analogy to coding. In DNA there are 4 bases that can be arranged in any order because there is no mechanical / chemical preference for their attachment. In the same way this is also true of cells and much of the components within cells. When there are multiple cells they can attach to each other in any orientation they want to unless their positioning is controlled. Scientists are now finding by observation that almost everything is being spatially (3 dimensionally) controlled. Thus to be controlled requires a controller in the absence of a mechanical / chemical positional preference.
What this means as a bottom line is that the 3 dimensional structures of living organisms had to have a system of spatial control from the beginning. Such a system has so many requirements to function that it cannot be formed in a stepwise manner. You either have positional control or you don't there is no intermediary to such a functionality. This is the simplest way I can conceive to explain this. I hope I made some headway.
Wow, I finally understand this a bit better Kbci, thanks for having the patience to explain it better to us. This leaves no wiggle room at all for the naturalist to posit that it could have happened by chance or through chemical processes alone.
Now I'm having real fun, and when it gets fun for me I want to learn more :mrgreen:

I was so excited in writing this response that I had to go back and fix my typos hehehe
Simply amazing!!!
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Re: Biology of life and 3D spatial positioning

#8

Post by bippy123 » Wed Jun 27, 2012 4:43 pm

KBCid wrote:Bippy and Byblos what did you think about the electric frog face?

To actually observe the foundational 'PRE' planning of future structures is very humbling to me.
Hey KBCI, I was about to get to that link so I skipped the last few to check it out :mrgreen:
Im in awe, My jaw just dropped to the ground.
The kind of detail needed to create something like this is unbelievable.
Methodological Naturalists, eat your hearts out
Our God truely is an awesome God isnt he:)

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Re: Biology of life and 3D spatial positioning

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Post by KBCid » Wed Jun 27, 2012 5:42 pm

bippy123 wrote:Our God truely is an awesome God isnt he:)
In a cataclysmically understated way ;)

Gen 2:7 And the LORD God formed man of the dust of the ground...

What isn't noted in the genesis account is that when God formed the material body from the earthly components he gave it the encoding system to reform itself in 3 dimensions. God was the first to spatially position matter into functional formations. Man who was created in his image is only now becoming aware of just what that means.

I added a bunch more papers to my original post... It would appear that science is moving a bit faster than I expaected to the realization of how important spatial positioning is in the formation of functional structures. Maybe if there were more mechanical engineers and less evolutionary biologists involved we could get to the truth that never changes.
It is as if some Christians sit there and wait for the smallest thing that they can dispute and then jump onto it...
The Bible says that we were each given an interpretation – this gift of interpretation is not there so we can run each other into the ground. It is there for our MUTUAL edification.
//www.allaboutgod.net/profiles/blogs/chri ... each-other

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Re: Biology of life and 3D spatial positioning

#10

Post by bippy123 » Wed Jun 27, 2012 10:47 pm

KBCid wrote:
bippy123 wrote:Our God truely is an awesome God isnt he:)
In a cataclysmically understated way ;)

Gen 2:7 And the LORD God formed man of the dust of the ground...

What isn't noted in the genesis account is that when God formed the material body from the earthly components he gave it the encoding system to reform itself in 3 dimensions. God was the first to spatially position matter into functional formations. Man who was created in his image is only now becoming aware of just what that means.

I added a bunch more papers to my original post... It would appear that science is moving a bit faster than I expaected to the realization of how important spatial positioning is in the formation of functional structures. Maybe if there were more mechanical engineers and less evolutionary biologists involved we could get to the truth that never changes.
Thanks again for the added links KBC. This is great reading.
It's gonna be a while before the grip that these evolutionary biologists have on our educational institutions is finally loosened, but when that happens it's will be a major paradigm shift.
It will happen eventually and I hope it happens in my lifetime.:)

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Re: Biology of life and 3D spatial positioning

#11

Post by sandy_mcd » Thu Jun 28, 2012 12:08 am

Developmental Biology http://www.sciencedirect.com/science/journal/00121606 has been going since 1959. The aims and scope http://www.journals.elsevier.com/developmental-biology/ are :
Developmental Biology publishes original research on mechanisms of development, differentiation, and growth in animals and plants at the molecular, cellular, and genetic levels. Areas of particular emphasis include transcriptional control mechanisms, embryonic patterning, cell-cell interactions, growth factors and signal transduction, and regulatory hierarchies.

Research Areas Include:

• Molecular genetics of development
• Control of gene expression
• Cell interactions and cell-matrix interactions
• Mechanisms of differentiation
• Growth factors and oncogenes
• Regulation of stem cell populations
• Gametogenesis and fertilization
• Developmental endocrinology
• Plant development
• Evolution of developmental control
What's been the impact of recent developments on spatial control on articles and thoughts published in this magazine? It seems the ideal place to publish.

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Re: Biology of life and 3D spatial positioning

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Post by KBCid » Thu Jun 28, 2012 3:42 pm

sandy_mcd wrote:What's been the impact of recent developments on spatial control on articles and thoughts published in this magazine? It seems the ideal place to publish.
Is someone here looking to publish something?
It is as if some Christians sit there and wait for the smallest thing that they can dispute and then jump onto it...
The Bible says that we were each given an interpretation – this gift of interpretation is not there so we can run each other into the ground. It is there for our MUTUAL edification.
//www.allaboutgod.net/profiles/blogs/chri ... each-other

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Re: Biology of life and 3D spatial positioning

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Post by sandy_mcd » Thu Jun 28, 2012 3:54 pm

KBCid wrote:
sandy_mcd wrote:What's been the impact of recent developments on spatial control on articles and thoughts published in this magazine? It seems the ideal place to publish.
Is someone here looking to publish something?
That's normally the way science works. I was wondering if there are/will be any papers published on the recent discoveries by engineers/programmers of the significance of 3d spatial positioning as opposed to what biologists have been doing.

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Re: Biology of life and 3D spatial positioning

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Post by KBCid » Thu Jun 28, 2012 4:09 pm

sandy_mcd wrote:That's normally the way science works. I was wondering if there are/will be any papers published on the recent discoveries by engineers/programmers of the significance of 3d spatial positioning as opposed to what biologists have been doing.
3D spatial control to form structures of matter is not a recent discovery. Intelligent designers have been performing this feat daily as far back as recorded history. If you need a peer reviewed paper to confirm this then you are seriously out of touch.
Since biologists currently don't understand exactly how spatial positioning occurs then there is no opposition. Note that science has determined that there are some definable components necessary for a system to implement spatial positioning but so far there is no understanding of how or where the control begins.
It is as if some Christians sit there and wait for the smallest thing that they can dispute and then jump onto it...
The Bible says that we were each given an interpretation – this gift of interpretation is not there so we can run each other into the ground. It is there for our MUTUAL edification.
//www.allaboutgod.net/profiles/blogs/chri ... each-other

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Re: Biology of life and 3D spatial positioning

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Post by sandy_mcd » Thu Jun 28, 2012 7:11 pm

KBCid wrote:Since biologists currently don't understand exactly how spatial positioning occurs then there is no opposition. Note that science has determined that there are some definable components necessary for a system to implement spatial positioning but so far there is no understanding of how or where the control begins.
Let me rephrase: What contributions have been made by engineers/programmers/other specialists in spatial positioning to the role of spatial positioning in biology? Biologists have been studying this topic for many years; i pointed you to the journal of developmental biology. What papers/insights/research areas have been opened up by non-biologists who are spatial positioning experts?

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