Biology of life and 3D spatial positioning

[bippy123]

I have been enthusiastically following this thread for a while and the more I read the more I'm convinced is that an intelligent agent has to logically have been there to start this all, especially since Kbcid has made it a bit easier for a layman like me to begin to understand why. Whatever reservations I had before are now gone.

This is beyond chance or chemicals to do.

[KBCid]

I have been enthusiastically following this thread for a while and the more I read the more I'm convinced is that an intelligent agent has to logically have been there to start this all, especially since Kbcid has made it a bit easier for a layman like me to begin to understand why. Whatever reservations I had before are now gone. This is beyond chance or chemicals to do.

Bippy sorry for not getting some newer material up in awhile. I had to take a break from research to handle a job I took on in another state. Everything is soooo critical about it and I had to provide multiple empirical tests for each point so lots of interaction between design and testing.
Buuut,
What a marvel it is to watch as the construction begins.... Looking down on the construction site we can see material being moved through space and time in the correct order to those places they are specifically needed at the proper time so that everything goes according to a schedule. The only other place you can watch this is within your own body.

Here is a reference to something new coming from the evo side. It appears that they are making some concessions toward the ID side since they are actually going to look for the informational controls which I have been asserting have to be there in order to control 3 dimensional structural formation.

ASU researchers propose new way to look at the dawn of life
...In a nutshell, the authors shift attention from the “hardware” – the chemical basis of life – to the “software” – its information content. To use a computer analogy, chemistry explains the material substance of the machine, but it won’t function without a program and data...

...“Chemical-based approaches,” Walker said, “have stalled at a very early stage of chemical complexity – very far from anything we would consider ‘alive.’ More seriously they suffer from conceptual shortcomings in that they fail to distinguish between chemistry and biology.”...

...“To a physicist or chemist, life seems like ‘magic matter,’” Davies explained. “It behaves in extraordinary ways that are unmatched in any other complex physical or chemical system. Such lifelike properties include autonomy, adaptability and goal-oriented behavior – the ability to harness chemical reactions to enact a pre-programmed agenda, rather than being a slave to those reactions.”...
https://asunews.asu.edu/20121212_dawnoflife

And lets not overlook this little gem of engineering;

Souped-Up Hyperdrive Flagellum Discovered
Get a load of this -- a bacterium that packs a gear-driven, seven-engine, magnetic-guided flagellar bundle that gets 0 to 300 micrometers in one second, ten times faster than E. coli.

If you thought the standard bacterial flagellum made the case for intelligent design, wait till you hear the specs on MO-1, a marine bacterium described by Japanese researchers in the Proceedings of the National Academy of Sciences. Edited by Howard Berg, Harvard's mastermind of flagellum reverse engineering, this paper describes the Ferrari of flagella.
Instead of being a simple helically wound propeller driven by a rotary motor, it is a complex organelle consisting of 7 flagella and 24 fibrils that form a tight bundle enveloped by a glycoprotein sheath.... the flagella of MO-1 must rotate individually, and yet the entire bundle functions as a unit to comprise a motility organelle.
To feel the Wow! factor, jump ahead to Figure 6 in the paper. It shows seven engines in one, arranged in a hexagonal array, stylized by the authors in a cross-sectional model that shows them all as gears interacting with 24 smaller gears between them. The flagella rotate one way, and the smaller gears rotate the opposite way to maximize torque while minimizing friction. Download the movie from the Supplemental Information page to see the gears in action.
http://www.evolutionnews.org/2012/12/so ... 66921.html

Make sure to look at the support pdf that is refered to in the article it should be here;

http://www.pnas.org/content/suppl/2012/ ... 5274SI.pdf

Here is a bit of engineering perspective in biology for transporting various substrates through 3 dimensional space and it has a clutch......
The Molecular "Clutch" of the Dynein Motor Protein
http://www.evolutionnews.org/2012/10/th ... 65241.html

And...
Video: Amazing Molecular Machines, and Still So Much to Learn
http://www.evolutionnews.org/2012/07/vi ... 62631.html

[bippy123]

Kbcid I'm very thankfull for all of the info u left us here, but I'm glad that your also taking care of business in the workplace too .
Thank you for the new info.
To me it's like being a kid in a candy store. If this thread was a candy store I'd have gum disease by now
To me this info points to the limits of chemistry and backs the intuition we've had all along with an incredible wealth of new information . It's also good that biologists are finally conceeding to the informational aspects that life possesses. Hopefully they can keep proceeding forward. For me this is like being there at the birth of a new paradigm , and they've only scratched the surface here.

[KBCid]

Here is a bit of newness about the origin of life perspective. Although not specifically defined the point comes down to the irreducible complexity required to begin replicating life.

More from Thomas Nagel on Neo-Darwinian Evolution and the Chemical Origin of Life
Thomas Nagel's new Oxford University Press book Mind & Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False includes so many compelling statements about the scientific weaknesses in neo-Darwinian evolution and chemical evolution that it would surely violate copyright to reproduce them all for you.

My skepticism is not based on religious belief or on a belief in any definite alternative. It is just a belief that the available scientific evidence, in spite of the consensus of scientific opinion, does not in this matter rationally require us to subordinate the incredulity of common sense. (p. 7)

[D]oubts about the reductionist account of life go against the dominant scientific consensus, but that consensus faces problems of probability that I believe are not taken seriously enough, both with respect to the evolution of life forms through accidental mutation and natural selection and with respect to the formation from dead matter of physical systems capable of such evolution. (p. 9)

Also, with regard to the origin of life, he observes that "the coming into existence of the genetic code -- an arbitrary mapping of nucleotide sequences into amino acids, together with mechanisms that can read the code and carry out its instructions -- seems particularly resistant to being revealed as probable given physical law alone." (p. 10)
http://www.evolutionnews.org/2012/10/mo ... 65131.html

Note that the page 10 point specifically points to the physical laws of nature being the focus for why it can't happen just as I have focused on the same physical laws to back my position. So far no one that has responded to this thread has even attempted to deal with these physical laws as I have applied them in my theory.
All 3 dimensional construction methods must have a physically definable way to move substrates from where they are to where they need to go and to do it requires that a system be in place to apply force in all 3 planes of reality. On top of that the system must also account for the fourth dimension of time. This in and of itself is irreducibly complex.
All 3 dimensional constructions are ultimately effects that have definable causes and if you can't define the cause then you don't understand how the effect occurs. Evolution has no explanation for how anything is constructed other than to say its in the genes and when asked they can't define how the genes cause it either.
Nature has her methods of constructing things for sure and we can observe cause and effect almost anywhere but when it comes to living formations we cannot tie the effect to any natural cause, since we have never observed any natural cause making that effect. It truly appears that living forms are unnatural just as a car or washing machine are unnatural. all of these things beg for a cause capable of arranging the irreducibly complex foundations that the structures arise from.

[bippy123]

KBCID, great article link. I wish there were more scientists like Nagel out there that aren't afraid to point out the massive problems associated with life arising in this fashion, and his views are based not on his religiius beliefs as he says, but on the available evidence.

Can't wait to see the time time when the engineers enter into the fray fullblast as they are in my opinion the most qualified to recognize and explain the obvious design that is found in life

[KBCid]

Miniature Molecular Power Plant: ATP Synthase
http://www.youtube.com/watch?v=XI8m6o0g ... e=youtu.be

A rotor, a stator, a drive shaft etc. all within a foundational mechanism / machine that provides the main power source ATP for the very cell itself. without this machine you would cease to exist. There would be no replication and thus no evolution and this is just the power plant that powers every other mechanism to perform its function.
Chemicals stop acting like reaction components when they start performing as mechanical parts that come together as machines. Machines after all are just consituents of matter arranged in a 3 dimensional pattern that allows for mechanistic function right?

Of course we cannot forget the almost useless parts of DNA right. You know, the "majority" of DNA that evo's said were byproducts of evolutionary action...

‘Junk’ DNA hides assembly instructions
UNC-CHAPEL HILL (US) — Snippets of information contained in dark matter, or “junk DNA,” can alter the way a gene gets put together, according to new research.

"So it turns out that the sequencing element in both exons and introns can regulate the splicing process," says senior author Zefeng Wang. "We call it the splicing code, which is the information that tells the cell to splice one way or the other. And now we can look at these variant DNA sequences in the intron to see if they really affect splicing, or change the coding pattern of the exon and, as a result, protein function."

In a process called alternative splicing, a single gene could code for multiple proteins with different biological functions. In this way, alternative splicing allows the human genome to direct the synthesis of many more proteins than would be expected from its 20,000 protein-coding genes.
http://www.futurity.org/science-technol ... tructions/

More code that drive the construction process... who would have guessed? The further we are able to peer the more complex becomes the mechanism of replication... The one thing required by evolution in order to even begin functioning.

Power plants...
controlled spatial movements....
Codes....
Machines driven by power molecules...

Amazing how the chemical world is looking more and more like just another type of substrate to form designed machines. Machines we never see natural forces forming on its own. Without a doubt I will have much more to reference as time and observable evidence accumulates.

[KBCid]

Here is another article that deals with how substrates are moved in time and 3 dimensional space.... apparently without chaos...

How Cellular Motors Prevent Traffic Jams
Living cells have superhighways of microtubules, crowded with molecular machines that "walk" along them delivering cargo. Sometimes things get a bit crowded, but deliveries arrive on time -- thanks to a unique strategy.

In short, the machines hand off their cargo, one to the next, till it reaches the end of the traffic jam, something like the kid's relay race game of passing a beach ball overhead down the line.

Two recent papers explain how scientists are opening the black box of intracellular transport....

In one observation, they found the cargo could travel 4.5 micrometers while the kinesins stuck in traffic only moved one micrometer. The cargo appears to be handed down the line. It's like the motor stuck behind the bumper of the next motor hands off the cargo to the driver, and so on, till the cargo arrives in front faster than the rear driver could have gotten there. Wouldn't that be cool if truck drivers could do that!...

So while they ended by noting that more research will be required, the efficiency and effectiveness of intracellular transport appears to be a promising area for design-theoretic research. The proof of the pudding is in the eating. We can eat pudding, walk to the store to buy it, and do all the other things we do in life because of a coordinated system of molecular machines at work in each and every cell of our bodies.
So why waste research time looking for a stochastic, aimless process? When the overall picture is one of purposeful action dependent on multiple coordinated parts, each required for function, that's the green light to go hunting for intelligent design. Prediction: a traffic control system will be found. That's the heuristic model most likely to provide understanding.
http://www.evolutionnews.org/2013/01/ho ... 68121.html

They assert that "a traffic control system will be found" I assert that a 3D spatiotemporal control system will be defined....
Both assertions point to the same thing, control of substrates in time and space. Thus, this paper is absolutely inline with what I am asserting is necessary for the existence of life and the ability of any evolutionary mechanism to begin functioning. It all begins with being able to move substrates in 3 dimensional space in a coordinated and accurate manner within a timeframe. Life cannot begin to exist in our 4 dimensional reality until a system occurs that allows it to deal with all dimensions at once. This requires an irreducible organisation whose complexity cannot be logically realised by natural causes.

[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.
http://jcs.biologists.org/content/123/11/1841.full.pdf

So scientists are giving greater attention to the 4 dimensional aspect of reality and what do you know... They are seeing even complexity.
Note the specificity of the view with their new toys;

These approaches clearly show ....
.....complex spatio-temporal signaling programs that involve precise crosstalk...

Programs and precision communication between components acting within a system.
Just think... without computer it would be nearly impossible to visualise a proper understanding of the self replicating living system.
Not long ago the insides of cells were considered just simple 'plasm'... oooey goooey goodness that just pops new life into existence 'naturally'.

Strangely if you think about this in perspective, it took both an understanding of a computer and the use of one to observe how much a cells guts act like one. Almost every description of the inner workings of the cell can be defined in ways typically used to describe the various inner workings of the computer itself.
This is all quite a cool development in scientific inquiry to be sure... but we should also keep in mind that even with all the technology being designed and implemented we are not really much further along in understanding how it actually works in a blueprintable way.
And this is just for the functionality being exhibited within the clear 'plasm' within the cell itself. How much more complex does the system conceivably become when we look to explain how all of the cells that compose our 3 dimensional form can be constrained to collectively make it functional.
Have you considered what is actually meant by the wording "all of the cells"... glad you asked, lets explore;

How many cells are there in the human body?
“How many cells are there in a 9-year old tree, in a flower and in an elephant?” – I was asked this question recently by an elementary school teacher, and I, as a biologist, should naturally know this answer. The students found out, by research, that the adult human body contains an estimated 10 trillion cells. Fascinated by this number, they asked the teacher on the number of cells of all sorts of organisms.

Estimating the number of cells should, mathematically, not be too difficult: We assume that an average eukaryotic cell is about 10 micro meters across. Further, we assume that a human cell is a cube. We calculate the volume, and then assume that the density of the cell is about like the density of water. This way we can compute the mass of a cell. You then simply weigh the organism, and multiply this mass by the number of cells in one kg, and voila: you have the number of cells in the body.

•Diameter of a cell: 10 micro meters (microns)
•Volume of a cell: 10x10x10 cubic microns = 1000 cubic microns
•If there are a billion (10⁹) cubic microns in a cubic mm, then this means that there are a million cells in a cubic mm.
•Consequently, there are a million million (10¹²) cells in a cubic decimeter (1dm³ = one liter). This happens to be one trillion cells in one liter of volume.
•We assume that 1 liter is about 1kg, assuming the density of water. There are therefore 10¹² cells in one kg.
•If we assume that the person has a mass of 80kg, then we obtain: 80×10¹² cells, this is 80 trillion cells.
http://www.microbehunter.com/2010/12/17 ... uman-body/

Hmmm the number is estimated to be somewhere between 10 trillion and 80 trillion individual complex cells that all act in accord to support the super structural system. How might one envision this 'organisation' of extremely complex individuals working collectively when the collective is expressed in the trilions of individuals and the 3 dimensional space they occupy is not a cube or a flat plane.

controlled 3 dimensional structuring being repeated or reproduced precisely is not something that rationally comes into existence by chance. To really understand the implications here you have to be minimally able to rationalise how it can occur at all. What would it take minimally to make such a system work in such a way? I have spent a considereable part of my career finding the best physical methods for reproducing 3 dimensional structures and after all this time there are some very definable parts of reproduction that cannot be eliminated. As applied physics is showing there is a definite minimal complexity 'required' to allow for reproduction to even begin and without replication evolution has no functionality.

[KBCid]

Human Hearing Outsmarts Physical Limits

...Mike Lewicki, a computational neuroscientist at Case Western Reserve University in Ohio, says the research is "a nice demonstration that our perceptual system is doing complex things - which, of course, people have always known - but this is a nice quantitative demonstration by which, even at the most basic level, using the most straightforward stimuli, you can demonstrate that the auditory system is doing something quite remarkable".

The ability of the human auditory system to beat the Gabor limit was first discovered in 1970, but was "not picked up by the broader scientific community, partly because cochlear processes were not then understood." As scientists have learned more in the interim, they are beginning to piece together the mechanisms by which the ear and brain achieve such "hyper acuity."

The researchers think that this superior human listening ability is partly due to the spiral structure and nonlinearities in the cochlea. Previously, scientists have proven that linear systems cannot exceed the time-frequency uncertainty limit. Although most nonlinear systems do not perform any better, any system that exceeds the uncertainty limit must be nonlinear. For this reason, the nonlinearities in the cochlea are likely integral to the precision of human auditory processing.

What's the implication for intelligent design? It's another example of "over-design" in nature -- an ability that exceeds the requirement for mere survival. Evolutionists might be able to concoct a story that animals and humans needed precision in the timing and pitch of sounds to escape predators, but such a story would not provide a cause for generating the random mutations that resulted in a finely tuned system. It would only imply that without the equipment, the animal would probably not survive. But that's the issue: how could a blind, purposeless process come up with it in the first place?
http://www.evolutionnews.org/2013/02/hu ... 68941.html

Here is another irreducibly complex arrangement. On one side there is all the mechanical parts that have the ability to sense and on the other side there is the ability to give meaning to it. Hardware and software working in a coordinated manner. Imagine that you were not supplied a driver for your video card or you were supplied a driver without the video card... both are useless without the other and each of them individually is highly complex and irreducible in order to even begin their individual functionality.

[KBCid]

Some Perspective on the "Mechanical Prowess" of DNA Replication
...Synthesis of all genomic DNA involves the highly coordinated action of multiple polypeptides. These proteins assemble two new DNA chains at a remarkable pace, approaching 1000 nucleotides (nt) per second in E. coli. If the DNA duplex were 1 m in diameter, then the following statements would roughly describe E. coli replication. The fork would move at approximately 600km/hr (375 mph), and the replication machinery would be about the size of a FedEx delivery truck. Replicating the E. coli genome would be a 40 min, 400 km (250 mile) trip for two such machines, which would, on average make an error only once every 170 km (106 miles). The mechanical prowess of this complex is even more impressive given that it synthesizes two chains simultaneously as it moves. Although one strand is synthesized in the same direction as the fork is moving, the other chain (the lagging strand) is synthesized in a piecemeal fashion (as Okazaki fragments) and in the opposite direction of overall fork movement. As a result, about once a second one delivery person (i.e. polymerase active site) associated with the truck must take a detour, coming off and then rejoining its template DNA strand, to synthesize the 0.2km (0.13 mile) fragments.
http://www.evolutionnews.org/2013/02/so ... 68951.html

This perspective elucidates what is minimally needed to replicate... reliably. If you can't replicate reliably then it is impossible for the conceptual mechanics of evolution to function. So the question being begged here is how did evolution function before or while the system of reliable replication was being formed? and second how could such a system form in a stepwise fashion without the evolutionary conceptual controls being functional?

[bippy123]

Miniature Molecular Power Plant: ATP Synthase
http://www.youtube.com/watch?v=XI8m6o0g ... e=youtu.be

A rotor, a stator, a drive shaft etc. all within a foundational mechanism / machine that provides the main power source ATP for the very cell itself. without this machine you would cease to exist. There would be no replication and thus no evolution and this is just the power plant that powers every other mechanism to perform its function.
Chemicals stop acting like reaction components when they start performing as mechanical parts that come together as machines. Machines after all are just consituents of matter arranged in a 3 dimensional pattern that allows for mechanistic function right?

Of course we cannot forget the almost useless parts of DNA right. You know, the "majority" of DNA that evo's said were byproducts of evolutionary action...

‘Junk’ DNA hides assembly instructions
UNC-CHAPEL HILL (US) — Snippets of information contained in dark matter, or “junk DNA,” can alter the way a gene gets put together, according to new research.

"So it turns out that the sequencing element in both exons and introns can regulate the splicing process," says senior author Zefeng Wang. "We call it the splicing code, which is the information that tells the cell to splice one way or the other. And now we can look at these variant DNA sequences in the intron to see if they really affect splicing, or change the coding pattern of the exon and, as a result, protein function."

In a process called alternative splicing, a single gene could code for multiple proteins with different biological functions. In this way, alternative splicing allows the human genome to direct the synthesis of many more proteins than would be expected from its 20,000 protein-coding genes.
http://www.futurity.org/science-technol ... tructions/

More code that drive the construction process... who would have guessed? The further we are able to peer the more complex becomes the mechanism of replication... The one thing required by evolution in order to even begin functioning.

Power plants...
controlled spatial movements....
Codes....
Machines driven by power molecules...

Amazing how the chemical world is looking more and more like just another type of substrate to form designed machines. Machines we never see natural forces forming on its own. Without a doubt I will have much more to reference as time and observable evidence accumulates.

This is incredible KBC. I knew that biologists are finding more and more function for junk DNA , but I never knew the depth of their importance as far as carrying design instructions.
Wow
Keep em coming KBC

[Neige]

I just want to bump this thread. When I get lost in the secular comings and goings of my daily routine, I sometimes feel great need for something solid, something convincing to bolster my confidence in God's existence.

And then there's this. And it just hits me and leaves me thinking of how simple it is. Our DNA controls the position of every single cell (and its components within it) in our bodies - that's now a scientific fact. Which automatically leads to a conclusion that DNA cannot have an inorganic origin, since the system that would require its formation is within the DNA itself... How simple and beautiful is that?