Page 2 of 13

Re: Biology of life and 3D spatial positioning

Posted: Fri Jun 29, 2012 3:20 pm
by KBCid
sandy_mcd wrote: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?
"engineers/programmers/other specialists" have been dealing with spatial positioning of matter for quite some time. What paper needs to be written to prove that matter (which doesn't already have a natural positional control) cannot be reproduced into specific functional forms without 3D spatial control? That would be tantamount to asking for a paper to prove water exists or a paper to specify why a car doesn't naturally form on its own.
Should I write a paper to explain to you why a broom doesn't clean your floor by itself?

Tell me how many biologists are experts in spatial positioning of matter? From what I have read this part of reality is just barely beginning to dawn within their minds so they aren't yet experts when it involves spatial positioning apart from natural mechanism. I on the other hand am an expert on the subject and I already know the foundational understanding they will someday learn about and no I will not publish a paper on the specifics of how bricks become spatially positioned into the form of a house since for the majority of the world it is common sense that it requires a system of control.
This control minimally requires 3 points of reference relative to a specific origin point.

For me the funniest part of this eventual discovery by biologist will be the standard retort " it evolved" followed by the sheep agreeing that it must have.

Spatial Positioning
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

Re: Biology of life and 3D spatial positioning

Posted: Fri Jun 29, 2012 10:42 pm
by sandy_mcd
KBCid wrote:"engineers/programmers/other specialists" have been dealing with spatial positioning of matter for quite some time. ...
how many biologists are experts in spatial positioning of matter? From what I have read this part of reality is just barely beginning to dawn within their minds
So are the spatial positioning experts helping the inexperienced biologists? Wouldn't this be a fruitful area for collaboration? Are there any such papers?

Re: Biology of life and 3D spatial positioning

Posted: Fri Jun 29, 2012 11:32 pm
by KBCid
sandy_mcd wrote:So are the spatial positioning experts helping the inexperienced biologists? Wouldn't this be a fruitful area for collaboration? Are there any such papers?
As I noted this concept is just dawning in the minds of biologists and I also already said there are few papers that mention this great mystery of biology. So do you think that some new papers are going to magically evolve within a few days or do you think that repeating the same questions over and over will suddenly change what I have already stated?

I am an expert if you have questions about the subject of the thread fire away. If you have questions I've already answered then i'll simply cut and paste past answers.

Re: Evidence for ID
by KBCid » Tue Jun 26, 2012 7:39 pm
The concept is only just dawning on the minds of those who study biology. There are at least 6 papers that I have read that are concluding a need to explain the mechanism of how replication can occur and form precision formations of matter. Try looking up references to spatial organisation or 3d structure or something along that line and you will find papers that talk about its necessity but none that know exactly how it occurs. they just know that it is a requirement in order to explain how 3 dimensional formations can be made from coding.
Here is a must see for you to possibly get a grasp of the concept.

Time-lapse Tuesday: A frog's electric face
17:50 19 July 2011
How does an embryo know where its face should grow? This amazing time-lapse video reveals a surprising mechanism at work: electricity.
The footage shows a frog embryo early on its development. Watch carefully and around nine seconds into the video you'll see a flash of light and dark patterns that looks like a template for where the face will subsequently develop.
These patterns are called bioelectric signals - fluxes of charged particles shooting across cells - that are already known to be involved in the formation of organs which rely heavily on electrical signals to function, such as the heart. This is the first time that they've been spotted in the formation of such a complex embryonic structure.

"We believe this bioelectrical signal is a 'pre-pattern' - marking areas on the embryo that will become certain craniofacial structures," says Adam's colleague Laura Vandenberg. "What was most amazing was that this bioelectrical information is used to 'instruct' most if not all of the facial structures - the jaw, eye, nose, and otolith [a kind of ear bone]."
http://www.newscientist.com/blogs/nstv/ ... -face.html

I am also adding papers that involve the subject to the first post as I find them. So if you don't see what you're looking for there then you should try searching for yourself and if you find something of value post it and we can discuss it.

Again I will ask;
What paper needs to be written to prove that matter (which doesn't already have a natural positional control) cannot be reproduced into specific functional forms without 3D spatial control?

Re: Biology of life and 3D spatial positioning

Posted: Sat Jun 30, 2012 2:30 am
by KBCid
It would appear that mechanical engineers are rapidly moving into biology... and the machines that make life run...

Cells Into Systems
ENGINEERING FRONTIERS
A new research center will work with the basics of life to build complex biological machines.
By Roger D. Kamm, Robert M. Nerem, and K. Jimmy Hsia

...Engineers have been instrumental in the development of biological “parts” that might eventually be used to construct a machine. From various cell sources, such as stem cells, multipotent cells extracted from bone marrow, or even fat, a variety of mature cell types, needed for higher-level functions, can be derived...
...Along with cell and molecular biologists, mechanical engineers will be essential players in advancing this new field. Biological machines of the future will encompass the complexities of nature, the intricacies of which we are just beginning to comprehend. Engineers have developed effective methods to deal with large complex manufactured systems (e.g. the modern automobile) and similar approaches will be needed for building the biological machines of the future. The resulting complexities, especially extending down to the genetic level, will no doubt require computational models that embody our growing understanding of these critical processes. Engineers in general and mechanical engineers in particular, among all scientific and engineering professions, are trained to build machines, and this expertise will be indispensible...... But the barriers to success are considerable and much basic research is still needed to lay the foundation for engineering successes in the future. A current program, the National Academies Keck Futures Initiative, has focused on a number of the key issues. Some of the questions they raise have direct bearing on the future of biological machines:
How can self-synchronizing cell populations that behave coherently be engineered despite cell-to-cell variability?
How do we achieve effective cell communication over distance and time?
How do we design cells to organize themselves into defined three-dimensional structures?
http://memagazine.asme.org/Articles/201 ... ystems.cfm

Center for the Mechanics and Engineering of Cellular Systems
About Us
Living systems interact with their environment in a tremendous diversity of ways. Mechanical signals are now recognized as a major mechanism of communication, which can influence cell migration, growth, and differentiation. The vision of the Center for the Mechanics and Engineering of Cellular Systems is that a comprehensive understanding of the input and output of mechanical signals inside living cells, and between cells and the environment is essential in numerous areas. http://www.cmu.edu/cmecs/about_us/index.html

Engineering the cell: Mechanical engineering goes biological
Department of Mechanical Engineering
The Department of Mechanical Engineering (ME), long the cradle of the automotive industry's leading engineers, is joining the life sciences revolution in a big way.
Nearly half of its 54 faculty members have a significant interest in biological systems, and two of the newest hires, associate Prof. Edgar Meyhöfer and assistant Prof. Robert Dennis, are leading the charge in something they call "bio-systems."
This term generally refers to a broad area of life from the molecular and cellular level to that of tissues and organisms that are either inherently mechanical in nature, or that may be addressed by classical mechanical engineering disciplines, such as thermal and fluid sciences, dynamics, and controls or materials.
"Look at a cell," Meyhöfer says. "It's actually a very complex nano-machine. It has about 10,000 different proteins, its size is of a few micrometers, yet it's capable of organizing all reactions, and having everything happen at the same time.

"Anything that can't be done by diffusion, which basically only works efficiently over a micrometer distance or soor anything where you need some asymmetric distribution of things, where you need to get something to a specific location needs to be done by the cell expending energy; by having the molecular machinery actually transport things around," Meyhöfer says. http://ur.umich.edu/0102/Oct28_02/13.shtml

Re: Biology of life and 3D spatial positioning

Posted: Sat Jun 30, 2012 11:14 pm
by bippy123
Kbci, this is amazing news. I just hope that ID advocates can really start to get the press out to the layman's and explain this in a way that would be accessible and understandable to everyone out there .
This is the exact type of thing that could cause a paradigm shift in biology that I had been hoping to see, but like you said this is a new area of research and it will take a bit of time.

This is exciting stuff.

Re: Biology of life and 3D spatial positioning

Posted: Sun Jul 01, 2012 12:33 pm
by KBCid
bippy123 wrote:Kbci, this is amazing news. I just hope that ID advocates can really start to get the press out to the layman's and explain this in a way that would be accessible and understandable to everyone out there . This is the exact type of thing that could cause a paradigm shift in biology that I had been hoping to see, but like you said this is a new area of research and it will take a bit of time. This is exciting stuff.
Our maker new when he first began to create, that complex specified order doesn't arise without a cause. He placed man in the garden... Gen 2:15 ... of Eden to dress it and to keep it. because he new that the garden would only keep a "natural" order he had imbued it with.
Man was given some understanding from the beginning that even this type of orderliness was not natural / normal. This was a form of order that was arranged that we might have power over it since we did not have God's power to control form, fit and function. However, since our first choice against our father the entire creation has ceased to be kept in the order God created, it groans for the control it was once under and the understanding man once had has also been degrading.
The once beatiful and elegant concept of man to scientifically investigate this orderliness within the nature that God formed has degraded over time until it no longer honors the former of the complexity it continues to investigate. Nature is a creation of God the father, God almighty... and man now worships the creation in ways similar to how our ancestors worshipped the simple creations of our hands. Nature is nothing more than any other created thing. The difference now is that we have put the silliness of worshipping things we create aside and have chosen something we can't create to woship, Nature.
I know for sure that mankind will never return enmasse to worship the Father. No single concept will ever be powerful enough to change convinced minds. The term of mans existence was to complete the separation of good from bad. God's second act in forming the orderliness he envisioned was to separate light from dark. Much of this initial work involved separation of physical disorder into physical order. The last work he performs is to separate spiritual disorder from spiritual order. Only those who can choose correctly will eventually be rewarded. The rest will return to non-existence.

My hope lies in this phrase, "1Cor 1:27 But God hath chosen the foolish things of the world to confound the wise..." I will simply tell the truth from the 'simple' understanding I was given. Replication of 3 dimensional formations of matter cannot occur without control, thus it had to exist from the beginning of living formations of matter. If others in ID and other sciences come to understand this correctly then I am sure that they will have a tool to help convey the truth. The sad fact is that there will always be the convinced that will try to convince others that even this fact was overcome and evolved by the power of nature.

It is nice to know Bippy that you have already chosen wisely.

Re: Biology of life and 3D spatial positioning

Posted: Sun Jul 01, 2012 4:03 pm
by sandy_mcd
KBCid wrote:It would appear that mechanical engineers are rapidly moving into biology... and the machines that make life run...
Ok, I pulled up the CMU and UM websites and spent some time looking around.

How many of these of these people are ID advocates? [I couldn't find any evidence.]
I'll accept your statement that biologists don't recognize design when they see it. But these engineers most certainly must.

So where is the scientific backing for ID? Included are some recent publications from their labs. Which of these proclaim the engineers' recognition of design?

CMU
Rape, A.D., W.H. Guo, and Y.L. Wang. (2011 Mar) The regulation of traction force in relation to cell shape and focal adhesions. Biomaterials 32(8):2043-51. Epub 2010 Dec 15.
Ruder, W.C. and P.R. LeDuc. (2011) Bioinspirations: Cell-Inspired Small-Scale Systems for Enabling Studies in Experimental Biomechanics. Integrative and Comparative Biology (Former journal name: American Zoologist) 51(1):128-132.
Weinger J., M. Qiu, G. Yang, and T. Kapoor. (2011) A nonmotor microtubule binding site in kinesin-5 is required for filament crosslinking and sliding, Current Biology, 21:1-7.
Zhou, M-N, E. Kunttas-Tatli, S. Zimmerman, F. Zhouzheng, and B.M. McCartney. (2011) Cortical localization of APC2 plays a role in actin organization but not in Wnt signaling in Drosophila. Journal of Cell Science, 124(Pt 9): p. 1589-600.
Goodman B., W. Channels, M. Qiu, P. Iglesias, G Yang, and Y. Zheng. (2010) Lamin B counteracts the kinesin Eg5 to restrain spindle pole separation during spindle assembly, Journal of Biological Chemistry, 285:35238-35244.
Holt, B.D., P.A. Short, A.D. Rape, Y.L. Wang, M.F. Islam, and K.N. Dahl. (2010 Aug 24) Carbon nanotubes reorganize actin structures in cells and ex vivo. ACS Nano 4(8):4872-8.
Lin, Y.W., R.M. Bellin, C.M. Cheng, R. Steward, Y.R. Cheng, P.R. LeDuc, and C.C. Chen. (2010) Probing Localized Neural Mechanotransduction through Surface-Modified Elastomeric Matrices and Electrophysiology. Nature Protocols 714, 5(4): 714-724.
Zimmerman, S.G., L. M. Thorpe, V. R. Medrano, C. A. Mallozzi, and B. M. McCartney. (2010) Apical constriction and invagination downstream of the canonical Wnt signaling pathway requires Rho1 and Myosin II. Developmental Biology 340:54-66.
Domian, I.J., M. Chiravuri, P. van der Meer, A.W. Feinberg, X. Shi, Y. Shao, S.M. Wu, K.K. Parker, and K.R. Chien. (2009 Oct 16) Generation of functional ventricular heart muscle from mouse ventricular progenitor cells. Science 326(5951):426-9.
Frey, M.T. and Y.L. Wang. (2009) A photo-modulatable material for probing cellular responses to substrate rigidity. Soft Matter 5:1918-1924.
Webb, R.L., O. Rozov, S. Watkins, and B.M. McCartney. (2009) Using Total Internal Reflection Fluorescence (TIRF) microscopy to visualize cortical microtubules in the Drosophila syncytial embryo. Developmental Dynamics 238(10): 2622-2632.

Bellin, R.M., J.D. Kubicek, M.J. Frigault, A.J. Kamien, R. Steward, H.M. Barnes, M.B. DiGiacomo, L.J. Duncan, C.K. Edgerly, E.M. Morse, C.Y. Park, J.J. Fredberg, C.M. Cheng, and P.R. LeDuc. (2009) Defining the Role of Syndecan-4 in Mechanotransduction using Surface-Modification Approaches. Proceedings of the National Academy of Sciences 106(52): 22102-22107.
Webb, R.L., M-N Zhou, and B.M. McCartney. (2009) An APC2-Diaphanous complex organizes actin in the Drosophila syncytial embryo. Development 136(8):1283-1293.




dennis at um
1. Borer K.T. and Dennis R.G. Activity disc and cage for continuous measurement of running activity and core temperature in hamsters. Physiology and Behavior 50:2-6, 1991.

2. Miller S.W. and Dennis R.G. A parametric model of muscle moment arm as a function of joint angle: Application to the dorsiflexor muscle group in mice. J Biomechanics 29(12): 1621-24, 1996. (view PDF)

3. Macpherson P.C.D., Dennis R.G. and Faulkner J.A. Sarcomere dynamics and contraction-induced injury to maximally activated single muscle fibers from soleus muscles of the rat. J Physiol 500.2: 523-33, 1997. (view PDF)

4. Dennis R.G. Bipolar implantable stimulator for long-term denervated muscle experiments. Med & Biol Eng & Comput Med & Biol Eng & Comput, March, 36: 225-28, 1998. (view PDF)

5. Putnam A.J., Cunningham, J.J., Dennis R.G., Linderman J.J., Mooney D.J., Microtubule assembly is regulated by externally-applied strain in cultured smooth muscle cells. J. Cell Sci., 111: 3379-3387, 1998. (view PDF)

6. Dennis R.G., Kosnik P. Excitability and isometric contractile properties of mammalian skeletal muscle constructs engineered in vitro. In Vitro Cell. Dev. Biol. Anim. 36(5): 327-335, 2000. (view PDF)

7. Dennis, R.G., Paul E. Kosnik, II, Mark E. Gilbert, and John A. Faulkner. Excitability and contractility of skeletal muscle engineered from primary cultures and cell lines. Am J Physiol Cell Physiol 2001 280: C288-C295. (view PDF)

8. Haase, S., Cederna, P., Dennis, R.G., Kuzon, W. Peripheral Nerve Reconstruction Using Acellular Nerve Grafts. Surgical Forum. 51: 607-609, 2000. (view PDF)

9. Kosnik P. Jr., Dennis R.G., Faulkner J.A. Functional Development of engineered skeletal muscle from adult and neonatal rats. Tissue Engineering 7(5) 573-584, 2001. (view PDF)

10. Murphy, W.L., Dennis, R.G., Kileny, J., Mooney, D.J., Salt fusion: a method to improve pore interconnectivity within tissue engineering scaffolds. Tissue Engineering. 8(1) 43-52, 2002. (view PDF)

11. Dennis, R.G., Dow, D.E., Faulkner, J.A.; "An Implantable Device for Stimulation of Denervated Muscles in Rats", Medical Engineering & Physics, 25(3), 2003, pp. 239-253. (view PDF)

12. Cederna, Kuzon, Dennis, Borschel, ... Recovery of Muscle Contractile Function Following Nerve Gap Repair With Chemically Acellularized Peripheral Nerve Grafts" Journal of Reconstructive Microsurgery. May 2003 (Volume 19, Number 4).

13. Borschel G.H., Kia, K.F., Kuzon, W.M., Dennis, R.G., Mechanical properties of acellular peripheral nerve. J Surg Res 114:133-39 (2003) (view PDF).

14. Borschel G.H., Dennis, R.G., Kuzon, W.M., Contractile skeletal muscle tissue-engineered on an acellular scaffold. (Manuscript submitted to Plast Reconstr Surg).



myehofer from um

1. Kim T, Meyhofer E. Nanofluidic Concentration of Selectively Extracted Biomolecule Analytes by Microtubules. Anal Chem. (2008, advanced publication available). PDF
.
2. Lin CT, Kao MT, Kurabayashi K, Meyhofer E. Self-Contained, Biomolecular Motor-Driven Protein Sorting and Concentrating in an Ultrasensitive Microfluidic Chip. Nano Lett. 8 (4): 1041-1046 (2008). PDF
.
3. Kim T, Kao MT, Hasselbrink EF, Meyhofer E. Nanomechanical model of microtubule translocation in the presence of electric fields. Biophys J. 94(10): 3880-92 (2008). PDF
.
4. Goyal S, Lillian T, Blumberg S, Meiners JC, Meyhofer E, Perkins NC. Intrinsic curvature of DNA influences LacR-mediated looping. Biophys J. 93(12): 4342-59 (2007). PDF
.
5. Tracking single Kinesin molecules in the cytoplasm of mammalian cells. Biophys J. 92(12): 4137-44 (2007). PDF
.
6. Kim T, Kao MT, Hasselbrink EF, Meyhofer E. Active alignment of microtubules with electric fields. Nano Lett. 7(1): 211-7 (2007). PDF
.
7. Fan CY, Kurabayashi K, Meyhofer E. Protein pattern assembly by active control of a triblock copolymer monolayer. Nano Lett. 6(12): 2763-7 (2006). PDF
.
8. Reed NA, Cai DW, Blasius TL, Jih GT, Meyhofer E, Gaertig J, Verhey KJ. Microtubule acetylation promotes kinesin-1 binding and transport. Curr Biol. 16 (21): 2166-2172 (2006). PDF
.
9. Lin CT, Kao MT, Kurabayashi K, Meyhofer E. Efficient designs for powering microscale devices with nanoscale biomolecular motors. Small 2 (2): 281-287 (2006). PDF
.
10. Lakamper S, Meyhofer E. Back on track - On the role of the microtubule for kinesin motility and cellular function. J Muscle Res Cell Motil. 27 (2): 161-171 (2006). PDF
.
11. Cheng LJ, Kao MT, Meyhofer E, Guo LJ. Highly efficient guiding of microtubule transport with imprinted CYTOP nanotracks. Small 1 (4): 409-414 (2005). PDF
.
12. Joglekar AP, Liu HH, Meyhofer E, Mourou G, Hunt AJ. Optics at critical intensity: Applications to nanomorphing. Proc Natl Acad Sci USA. 101 (16): 5856-5861 (2004). PDF
.
13. Hoff JD, Cheng LJ, Meyhofer E, Guo LJ, Hunt AJ. Nanoscale protein patterning by imprint lithography. Nano Lett. 4 (5): 853-857 (2004). PDF
.
14. Lakamper S, Meyhofer E. The E-hook of tubulin interacts with kinesin's head to increase processivity and speed. Biophys J. 89 (5): 3223-3234 (2005). PDF
.
15. Lakamper S, Kallipolitou A, Woehlke G, Schliwa M, Meyhofer E. Single fungal kinesin motor molecules move processively along Microtubules. Biophys J. 84 (3): 1833-1843 (2003). PDF

Re: Biology of life and 3D spatial positioning

Posted: Sun Jul 01, 2012 9:56 pm
by KBCid
sandy_mcd wrote:Ok, I pulled up the CMU and UM websites and spent some time looking around. How many of these of these people are ID advocates? [I couldn't find any evidence.]
Did anyone say any of these references were?
sandy_mcd wrote: I'll accept your statement that biologists don't recognize design when they see it.
Not true. in fact most see it that way the thing for them is that they have been told to see it as a natural occurence. Without evidence of course.
sandy_mcd wrote:But these engineers most certainly must.
Many people are lulled into the belief that the as yet unseen ability of nature could make the reality they see. I could probably finds thousands who believe such a thing. however, the majority of engineers are studying biology to make better machines for human use. they focus on existing cellular technology in order to make money. Origins is not where you will find them studying.
sandy_mcd wrote:So where is the scientific backing for ID?
everywhere. every object that exhibits specified complexity is existing evidence for ID and everything that exhibits such attributes as ID leaves behind can have ID posited as its cause.
sandy_mcd wrote: Included are some recent publications from their labs. Which of these proclaim the engineers' recognition of design?
How many of them are studying origins? As I stated there are not many papers even recognising this part of the origins question and I also noted that you won't find sites dedicated to it yet. So there is no instant gratification nor is there sites against it. the closest you will find deals with information theory.

There are engineers who are looking at the origin of life and making conclusions based on their understandings and my concept is inclusive with all of them as it is part of the required "information" needed to form matter into 3 dimensional formations. This simple concept of 3D formation is part of what must be specified by the information needed to replicate a form.

"Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure." Leslie Orgel, 1973. The Origins of Life, New York: John Wiley & Sons, p. 190.

Origin of Life: The 5th Option
by Bryant M. Shiller
...Life portrayed as an intelligent system based on a “primary design platform (PdP)” that is immune from evolution and that epitomizes the basic building block of biology – the biological cell - as the product of nanotechnology.
http://the5thoption.com/

Re: Biology of life and 3D spatial positioning

Posted: Sun Jul 01, 2012 10:57 pm
by bippy123
Kbci thanks a bunch for that 5th option link. I wonder if they have an ebook download.
Absolutely fascinating stuff :)

Re: Biology of life and 3D spatial positioning

Posted: Sun Jul 01, 2012 11:01 pm
by sandy_mcd
bippy123 wrote:Kbci thanks a bunch for that 5th option link. I wonder if they have an ebook download.
Absolutely fascinating stuff :)
Wouldn't have thought that would be up your alley (from the 5th option):
The undeniable existence of biological evolution

Re: Biology of life and 3D spatial positioning

Posted: Mon Jul 02, 2012 12:55 am
by bippy123
sandy_mcd wrote:
bippy123 wrote:Kbci thanks a bunch for that 5th option link. I wonder if they have an ebook download.
Absolutely fascinating stuff :)
Wouldn't have thought that would be up your alley (from the 5th option):
The undeniable existence of biological evolution
I'm interested more in the reverse engineered aspects he talks about in his book.

I think something that should be more up your alley sandy is the fruit fly experiment that shows macro-evolution to be a complete flop, but then again you can always resort to the evolution of the gaps theory that makes a claim that evolution can happen within the blink of an eye and would explain why we can never observe it happening now or in the fossil record.
Sounds like blind faith to me, but then again I used to be a believer in evolution. Maybe I have a problem falling in line with the rest of the wannabe methodological naturalists. If your ok with that then that's cool. ;)

Re: Biology of life and 3D spatial positioning

Posted: Mon Jul 02, 2012 8:59 am
by KBCid
sandy_mcd wrote:Wouldn't have thought that would be up your alley (from the 5th option):
The undeniable existence of biological evolution
This is an engineer looking at the complexity of life and making conclusions. His analysis may not be matched by mine at various points but, the fact is that engineers are beginning to look. that was the point. The basis of my point is that no engineer can deny the need for control to reproduce 3d forms. If he asserts that a control for something came by evolution he would then have to provide empirical data to back it. This is how mechanical engineers operate. Hopefully more engineers will analyse the origin of life question and focus on that specific point.

Re: Biology of life and 3D spatial positioning

Posted: Mon Jul 02, 2012 6:15 pm
by KBCid
OK Bippy it is now time for phase 2 of my roll out on the subject of 3D spatial positioning. Hang onto something... if you liked the concept I am introducing then you will love this additional observable evidence that would appear to have a direct tie in to the positioning subject.

As you should know by now 3d positioning of replicating structure requires 4 points of reference in order to "calculate" a position. This previous sentence should make you want to ask a simple question "what exactly is doing the calculation"?.
Indeed this is important. Let us take a investigative walk throught a recent technology that most everyone now enjoys.

GPS... As all should know GPS means global positioning system. This system originally designed for military use has come into full application by civilians. This system holds very important truths for my subject and you will need to read about it to gain further understanding. This is the point where the horse is led to the water...

How GPS Works
A GPS receiver must acquire signals from at least four satellites to reliably calculate a three-dimensional position.
http://www.esri.com/news/arcuser/0103/d ... l1of2.html

Position Determination with GPS
For the determination of its position on earth, the GPS receiver compares the time when the signal was sent by the satellite with the time the signal was received. From this time difference the distance between receiver and satellite can be calculated.

the present position can be calculated by trilateration (meaning the determination of a distance from three points). This means that at least three satellites are required to determine the position of the GPS receiver on the earth surface. The calculation of a position from 3 satellite signals is called 2D-position fix (two-dimensional position determination). It is only two dimensional because the receiver has to assume that it is located on the earth surface (on a plane two-dimensional surface). By means of four or more satellites, an absolute position in a three dimensional space can be determined. A 3D-position fix also gives the height above the earth surface as a result.

Depending on the accuracy of the clock in the GPS receiver, the determined position will be more or less wrong. For the practice of GPS based navigation this would mean that no determined position can ever be of any use, as the runtimes of the signals are so short, that any clock error has an overwhelming influence on the result.
A clock error of 1/100 second, which is difficult to imagine but quite common from car races or skiing races, would in GPS navigation lead to a mistake in the position of about 3000 km. To achieve an accuracy of 10 m of the position, the runtime of the signal must be precise to 0.00000003 seconds. http://www.kowoma.de/en/gps/positioning.htm

You should now have a bit of understanding about GPS and how it calculates 3 dimensional position. Buuuuuttt.... There is one element of that study that should be carefully noticed. In order to calculate position it requires a clock. Not just any clock either. It requires a very precise clock. Here I leave you with this information to peruse.

Cells Have a Circadian Clock
...According to lead author of the study Akhilesh Reddy, "We know that clocks exist in all our cells; they're hard-wired into the cell. Imagine what we'd be like without a clock to guide us through our days. The cell would be in the same position if it didn't have a clock to coordinate its daily activities." http://biology.about.com/b/2011/01/27/c ... -clock.htm

Study of cell 'clocks' looks at what makes us tick
Our internal timepieces are more complicated than scientists previously thought
http://www.msnbc.msn.com/id/41277802/ns ... s-us-tick/

New research shows how proteins make biological clock tick
January 11, 2006 | Science News
They discovered that, rather than randomly colliding, the two proteins bind together in the cytoplasm almost immediately and create what Young and Meyer refer to as an “interval timer.” Then, six hours after coming together, the complexes rapidly break apart and the proteins move into the nucleus singly, all of them within minutes of each other. “Some switch is thrown at six hours that lets the complex explode. The proteins pop apart and roll into the nucleus,” Young says. “Somehow, implanted within the system is a timer, formed by Period and Timeless, that counts off six hours. You have a clock within a clock.” He notes that this precise timer shows how carefully orchestrated interactions between proteins really are.
http://newswire.rockefeller.edu/2006/01 ... lock-tick/

Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication
The chromosomal origin and terminus of replication are precisely localized in bacterial cells.We examined the cellular position of 112 individual loci that are dispersed over the circular Caulobacter crescentus chromosome and found that in living cells each locus has a specific subcellular address and that these loci are arrayed in linear order along the long axis of the cell. Time-lapse microscopy of the location of the chromosomal origin and 10 selected loci in the origin-proximal half of the chromosome showed that during DNA replication, as the replisome sequentially copies each locus, the newly replicated DNA segments are moved in chronological order to their final subcellular destination in the nascent half of the
predivisional cell. Thus, the remarkable organization of the chromosome is being established while DNA replication is still in progress. The fact that the movement of these 10 loci is, like that of the origin, directed and rapid, and occurs at a similar rate, suggests that the same molecular machinery serves to partition and place many, if not most, chromosomal loci at defined subcellular sites. http://www.pnas.org/content/101/25/9257.full.pdf

Now a few words from our sponsor;
Gen 1:4 And God saw the light, that it was good: and God divided the light from the darkness.
Gen 1:5 And God called the light Day, and the darkness he called Night. And the evening and the morning were the first day.

The second thing God ordered after the creation of light was the reference to time for his creation. ALL of his creations use time within their structures to order their existence within the 3 dimensional realm. God felt that time was important enough that he;

Gen 2:3 ...blessed the seventh day, and sanctified it: because that in it he had rested from all his work which God created and made.

God blessed and sanctified a period of time.

I submit that everything in a living organism is controlled including precise 3 dimensional spatial positioning of all the components that make up all the structures which provide function to the organism. I further assert that there is sufficient cellular components within every cell for a type of GPS function that uses time as part of each individuals "calculation" of position.

So essentially I have made a hypothesis based on known understandings about positioning of matter in conjunction with known components in cellular mechanisms whose only analogy lies in those things that intelligence has formed... and only intelligence has formed. I infer that 'when' this hypothesis is confirmed that it will be apparent that no living form could have arisen without a minimal complexity including all the components necessary to repeat 3 dimensional form. Such an assembly is beyond any logical chance of random formation and is indeed the most basic irreducibly complex formation 'required' to allow for replication success. Such a system requires intelligent design.

Re: Biology of life and 3D spatial positioning

Posted: Mon Jul 02, 2012 8:20 pm
by bippy123
Thanks again KBCi for the information :mrgreen:
Ok so far I am on the Cells Having a Circadian Clock which I will finish tomorrow (on my 45th birthday :clap: ).
Now I have a little better understanding of GPS tracking.
I feel like im getting a free course here :mrgreen:

God bless

Re: Biology of life and 3D spatial positioning

Posted: Tue Jul 03, 2012 9:24 am
by KBCid
bippy123 wrote:Thanks again KBCi for the information :mrgreen:
Ok so far I am on the Cells Having a Circadian Clock which I will finish tomorrow (on my 45th birthday :clap: ).
Now I have a little better understanding of GPS tracking. I feel like im getting a free course here :mrgreen: God bless
You can save your thanks for the one who who gave the understanding ;)

Happy Bday! mine is the 24th of this month and I will be 49

I have been studying the aspect I am proposing for nearly 3 years now when I first began to model cells and their components in virtual 3d. I have consulted with a biologist friend I know to see what they know about how components are arranged in the cell. I found it quite interesting that they feel they have a good understanding of positioning based on various proteins and such but when pressed for where the order originates to control the proteins themselves it becomes clear that it is still a huge black box to them.
The simplicity for rational thought here is to look at reality. How could crystals form a shape if their molecular structures were not attracted to each other in a specifiable way? or how might a snowflake get its form without those same understandings? Things that don't have an easily understood mechanism of control inherently must have some form of control impressed on them from outside. This requires a system. Systems typically have multiple parts that work together in concert to perform a function. Rationale follows rationale till an inevitable conclusion can be realised.
Once realised it became clear that the proteins pointed to by my biologist friend are simply part of a greater system and when they perform knockout experiments they can affect formation but they are not the control of form within themselves as it is understood that it takes a variety of them occuring at specific times and places. Thus they are controlled in time and space just as the components that they convey information to.
The electric frog face video really begins to elucidate how complex the control is as it also uses electrical energy as part of the system.