Biology of life and 3D spatial positioning

[Ivellious]

Also, it should be pointed out that replicating is not considered the only factor in defining life. Viruses are not considered "living" by most standards of biology but can still replicate biologically. There are many different requirements for being defined as a living organism, and while reproduction is one, it is not necessarily a requirement nor is it the only requirement.

[KBCid]

Also, it should be pointed out that replicating is not considered the only factor in defining life. Viruses are not considered "living" by most standards of biology but can still replicate biologically. There are many different requirements for being defined as a living organism, and while reproduction is one, it is not necessarily a requirement nor is it the only requirement.

a virus needs a host to exist. Replication is the first factor and requirement in defining life. no replication, no life, no evolution.

[KBCid]

Consider finding an organism we will call Synthia. It exhibits most of the same things as other organisms do. Designed or natural cause?

Pile of sand - designed or naturally caused? Some things we just can't tell the difference.

you still don't get that a simple pile of sand doesn't exhibit "the types of information produced when intelligent agents act." which means that the pile of sand doesn't require the design inference. Intelligence can mimic the types of information produced when chance acts but chance hasn't mimic'd the types of information produced when intelligence acts. This is how we can discern when intelligent agency has acted, it exhibits a type of information unknown in the natural world.

"The resulting "synthetic cell" was then "rebooted" and it started to replicate. The ability to reproduce or replicate is considered the basic definition of life."

So is this cell alive? What if Venter had used a human's genome? Would that be alive? Would it be human?

I will let the scientist explain it to you.
Craig Venter creates synthetic life form
Craig Venter and his team have built the genome of a bacterium from scratch and incorporated it into a cell to make what they call the world's first synthetic life form
Scientists have created the world's first synthetic life form in a landmark experiment that paves the way for designer organisms that are built rather than evolved. "We were ecstatic when the cells booted up with all the watermarks in place," Dr Venter told the Guardian.

......... "It's a living species now, part of our planet's inventory of life."......

You see if you actually read the references instead of trying to avoid them you would have had the answer from the horses mouth but apparently a bit of handholding is necessary beyond a link. Now you tell me is this cell alive?
What would be the difference if a human genome was used? are the bases the same? would the structure be the same? if it boots up just like the other organism would it be what it was designed to be? all very wonderful questions with easy logical answers.

Consider finding an organism we will call Synthia. It exhibits most of the same things as other organisms do. Designed or natural cause?

Is the following the same answer to the question I posed? can you dismiss a life form that was designed with the same tired old watch arguement?

This is a very good example. It isolates the key components without introducing extraneous complications.
I would conclude it is not naturalistically formed:
1) The mechanical part as you say.
2) Complete lack of anything remotely similar observed today.
1) The mechanical part is the key part, which cannot be over-emphasized. Consider a watch found on a beach - you don't even have to see a picture, the very word tells you it is designed. And in the examples of design used, there is always this human/non-naturally occurring contribution which gives the answer even before design is considered.
2) People have a reasonable grasp of the basics of physics/chemistry/biology. No scientist is going to believe that such a robot popped up on its own. Unoxidized metals, silicon or other electronic chips, don't just spontaneously form into working robots. Likewise, no scientists believes a fully functioning cell just popped up on its own out of a brew of molecules. But the chemistry of carbon is incredibly complex. Scientists see no reason to not believe in an incremental process. Molecules can undergo lots of reactions to make new molecules; metal does not machine itself into forms.

[Ivellious]

a virus needs a host to exist. Replication is the first factor and requirement in defining life. no replication, no life, no evolution.

Lots of insects and bacteria also require a host to live and reproduce. Are they not alive by your definition as well?

Also, if replicating and reproduction must exist for life to work, then what about Artificial Intelligence? What if we were to create a form of program that was "living"? Would it not be alive because it didn't have biological reproduction?

[KBCid]

a virus needs a host to exist. Replication is the first factor and requirement in defining life. no replication, no life, no evolution.

Lots of insects and bacteria also require a host to live and reproduce. Are they not alive by your definition as well?

Do they have the resources available to permit replication? Then they can't be excluded from being considered alive by the weak definition that science uses.
Scientists struggle to define life
WASHINGTON — Philosophers wrestling with the big questions of life are no longer alone. Now scientists are struggling to define life as they manipulate it, look for it on other planets, and even create it in test tubes.
So as scientists push the bounds of biology, astronomy and robotics, a big question looms: What exactly is life?
Broadly put, scientists like Deamer say life requires a cell with genetic material and the ability to reproduce, turn food into energy, and to evolve through natural selection.
http://www.usatoday.com/tech/science/20 ... life_N.htm

Also, if replicating and reproduction must exist for life to work, then what about Artificial Intelligence? What if we were to create a form of program that was "living"? Would it not be alive because it didn't have biological reproduction?

You will have to argue the specifics with every person who has an opinion since life has not yet been empirically defined. But of course the question of what absolutely defines life has nothing to do with this thread. This thread deals with what is minimally required for 3 dimensional life to exist and that it requires a replication system that can control the spatiotemporal occurance of matter. this system is required 'prior' to anything that would be considered life and anything that can exhibit the effect of evolution.
Since evolution is defined simply as the change in alleles in a population then it requires there to be a population that can replicate alleles. No replication, no evolution, no 3 dimensional life.

[sandy_mcd]

Now you tell me is this cell alive?
What would be the difference if a human genome was used? are the bases the same? would the structure be the same? if it boots up just like the other organism would it be what it was designed to be? all very wonderful questions with easy logical answers.

Consider finding an organism we will call Synthia. It exhibits most of the same things as other organisms do. Designed or natural cause?

Is the following the same answer to the question I posed? can you dismiss a life form that was designed with the same tired old watch arguement?

The watch is obviously designed because of the materials and form. The human-designed organism could be indistinguishable from a natural one. So designed or natural cause? Couldn't say. And so what is the conclusion?
Humans can now design simple organisms that are indistinguishable from natural ones, just as in the past they could design sand piles indistinguishable from natural ones.
Does this mean life was designed? I don't see how that follows.


Sidetrack: So you seem to accept that humans can design human cells. If they create a human, should that person be treated as a regular human or some subclass?

[FlawedIntellect]

Sidetrack: So you seem to accept that humans can design human cells. If they create a human, should that person be treated as a regular human or some subclass?

Wouldn't the default position being held is that, considering that the DNA is human, and being based off of humans, it is a human?
At least that's my idea on the matter.

[KBCid]

Is the following the same answer to the question I posed? can you dismiss a life form that was designed with the same tired old watch arguement?

The watch is obviously designed because of the materials and form.

This is where the old Paley's anti-watch argument fails. You are asserting that 'materials and form' are the indicator of intelligent design and essentially its limitation. This argument no longer holds any force.
Intelligence has harnessed the atom. Intelligent designers are now able to use the same materials that life is made of... Intelligent agency has caused to be 'formed' lifes 3 dimensional shape from 4 base chemicals... a living organism now exists as a testament to what intelligence can use for materials and the 3 dimensional form it can mechanically form.

So, If as you think 'materials and form' is how you can identify intelligent design then you have no choice but to agree that life was designed since I can prove that intelligent agency uses biological lifes base building blocks as material to make the 3 dimensional form consistent with an observable living organism.
Intelligent design has an empircally discernable effect on matter all the way down to the size of the atom. There is now virtually no matter in our environment that we cannot control. There are virtually no formations of matter beyond our ability to replicate or design.

The human-designed organism could be indistinguishable from a natural one. So designed or natural cause? Couldn't say. And so what is the conclusion?

Unfortunately you don't have the necessary observable evidence to form that dichotomy. You have never seen a 'naturally' formed organism to infer from. So, the conclusion is that you have no causal evidence for anything other than intelligent agency which has empirically proven it is capable of forming lifes 3 dimensional replicating form. Science is based on observable evidence.

Literacy in the Sciences: Activity No. 18
Science vs. Science Fiction
Science fiction is a type of fiction where the stories revolve around science...
...it's useful to remind your child that while science fiction may be based loosely on scientific truth, it is still fiction.
http://www.readingrockets.org/article/50445/

Science fiction is largely based on writing rationally about alternative possible worlds or futures.[2] It is similar to, but differs from fantasy in that, within the context of the story, its imaginary elements are largely possible within scientifically established or scientifically postulated laws of nature (though some elements in a story might still be pure imaginative speculation).
http://en.wikipedia.org/wiki/Science_fiction

Humans can now design simple organisms that are indistinguishable from natural ones, just as in the past they could design sand piles indistinguishable from natural ones. Does this mean life was designed? I don't see how that follows.

again the same false dichotomy... and design is distinguishable from natural unless it is mimicing which I already pointed out earlier. Intelligence can mimic natural where natural cannot mimic ID.

Sidetrack: So you seem to accept that humans can design human cells. If they create a human, should that person be treated as a regular human or some subclass?

And you seem to not accept that humans have designed the structure of a synthetic cell that is alive. Since ultimately the point was that ID uses the same materials to form life then the rest of your text only serves as a sidetrack to the point that was made.

Red herring – a speaker attempts to distract an audience by deviating from the topic at hand by introducing a separate argument which the speaker believes will be easier to speak to.

[KBCid]

Sidetrack: So you seem to accept that humans can design human cells. If they create a human, should that person be treated as a regular human or some subclass?

Wouldn't the default position being held is that, considering that the DNA is human, and being based off of humans, it is a human? At least that's my idea on the matter.

By what rationale is a human cell discerned from any other living cell? Is it made from different base materials? Does it use totally different mechanisms? The human designation is applied to an end result of a replication event. Biological life is biological life. It exhibits the;

"types of information produced when intelligent agents act. Scientists then seek to find objects which have those same types of informational properties which we commonly know come from intelligence.". http://www.intelligentdesign.org/whatisid.php

Intelligent design produces types of information not found by natural causes. Natural causes have never been observed to produce the type of information that intelligent action produces. Empirical observable evidence

[KBCid]

Emerging paradigms of regulated microRNA processing
The exquisite spatio–temporal control of miRNA abundance is made possible, in part, by regulation of the miRNA biogenesis pathway...
...Thus, miRNAs themselves must be post-transcriptionally regulated. In fact, regulation at multiple biogenesis steps and at turnover of the mature miRNA has now been established...
...it is clear that miRNA processing is regulated in a complex manner, and we are only beginning to understand its true nature. http://genesdev.cshlp.org/content/24/11/1086.full

Transcriptional control of mitochondrial biogenesis: the central role of PGC-1a
Mitochondrial biogenesis
Mitochondrial proteins are encoded by the nuclear and the mitochondrial genomes. The double-strand circular mitochondrial DNA (mtDNA) is
16.5 kb in vertebrates and contains 37 genes encoding 13 subunits of the electron transport chain (ETC) complexes I,III, IV, and V, 22 transfer RNAs, and 2 ribosomal RNAs necessary for the translation.
Correct mitochondrial biogenesis relies on the spatiotemporally coordinated synthesis and import of 1000 proteins encoded by the nuclear genome, of which some are assembled with proteins encoded by mitochondrial DNA within newly synthesized phospholipid
membranes of the inner and outer mitochondrial membranes. In addition, mitochondrial DNA replication and mitochondrial fusion and fission mechanisms must also be coordinated (Figure 1). All of these processes have to be tightly regulated in order to meet the tissue requirements.

...Mitochondrial biogenesis thus involves an intricate, complicated network of transcription factors NRFs/PPARs/ERRs that activate target genes encoding enzymes of FAO, oxidative phosphorylation, and antioxidant defences (Figure 2). PGC-1a, by co-activating, and controlling the expression of this network, directly links external physiological stimuli to the regulation of mitochondrial biogenesis
and function. Additionally, mitochondrial biogenesis involves fusion/fission and requires protein import and processing and cardiolipin biosynthesis. http://cardiovascres.oxfordjournals.org ... 8.full.pdf

MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis
In yeast Saccharomyces cerevisiae (S. cerevisiae), the coordinated association of more than 800 proteins (mostly encoded by the nuclear genome) are required to assemble a functional organelle (8,9).
http://nar.oxfordjournals.org/content/e ... lowres.pdf

[KBCid]

Signalling ballet in space and time
Abstract.
Although we have amassed extensive catalogues of signalling network components, our understanding of the spatiotemporal control of emergent network structures has lagged behind. Dynamic behaviour is starting to be explored throughout the genome, but analysis of spatial behaviours is still confined to individual proteins. The challenge is to reveal how cells integrate temporal and spatial information to determine specific biological functions. Key findings are the discovery of molecular signalling machines such as Ras nanoclusters, spatial activity gradients and flexible network circuitries that involve transcriptional feedback.
...findings from genome projects have revealed a new problem: there are fewer genes than biological processes. Hence, the concept that the specificity of biological processes is generated on the gene or even protein level erodes.

The idea of isolated pathways has given way to the concept of signalling networks, which allow a limited number of components to generate an exponentially larger number of outcomes owing to combinatorial interactions. Although we now can describe parts of these complex network topologies in detail, we still do not understand how they operate to generate biological specificity. It is like trying to plan a journey with an incomplete railway network map lacking train time schedules. However, biological networks not only transport, but also process and integrate signals. Crucial cell decisions, including whether to undergo proliferation, apoptosis and differentiation, are governed by the temporal dynamics and spatial distribution of key signalling effectors1–4. This realization provides a strong impetus to explore the emergent properties of signalling networks that are encoded by spatial and temporal dynamics.

Spatiotemporal control of information.
In addition to the temporal kinetic specification of network function, spatial control plays a major and complementary part. Our trains may leave at the same time but go to different destinations, or leave at different times heading for the same destination. Although the spatial component is less studied than the temporal one, its importance is highlighted by new findings.

Importantly, the transmission of spatial information is controlled by feedback and feed-forward network motifs and cell shape104,109,110

Scaffolds: managers of spatiotemporal organization
The marriage of spatial and temporal orchestration is embodied in scaffolding proteins. Scaffolds are hallmarked by their ability to simultaneously bind two or more signalling proteins that typically have an enzyme–substrate relationship. The physical colocalization generates interesting properties, such as insulating signalling modules by physically tying them together, reducing reaction kinetics to zero order, enabling immediate feedback and anchoring protein complexes to distinct subcellular sites. Importantly, scaffolds allow the re-use of enzymes for different functions in a highly context-dependent manner, providing a simple solution to the dilemma of possessing fewer genes than processes.

The function of scaffolds in other systems, such as the MAPK pathway, is increasingly being appreciated and was also recently reviewed45–47. Here, we focus on open questions and try to delineate the design principles of how scaffolds contribute to spatiotemporal organization of signalling networks. To illustrate this, we use two examples (FIG. 3).

Given the similarity between the Ras and GPI-anchored nanocluster systems, it is tempting to speculate that this type of analogue–digital–analogue circuitry may represent a general mechanism for high fidelity signal transmission by lipid-anchored signalling proteins. Similarly to Ras, GPI-anchored proteins also show a fixed monomer to cluster distribution that violates simple mass action kinetics. Recent work has shown that this distribution is actively maintained and crucially dependent on cortical actin dynamics84. More broadly, the role of the unique architecture of the plasma membrane in supporting the assembly of analogue–digital–analogue converters brings into focus membrane spatiotemporal dynamics as a new regulator of signal transmission.

Conclusions.
We have changed our perception of signalling pathways from linear pipelines to networks. We also have begun to rationalize how these network structures can determine the kinetics of distinct biochemical processes with high fidelity to translate them into specific biological responses. Along this way we have realized that specificity is generated by combinatorial assemblies and spatiotemporal dynamics rather than by a large number of genes with specific functions. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2977972/

[KBCid]

I should check my email more often... This email reply was recieved several days ago. Its nice to see that my concept has gotten an initial acceptance by one of the places I sent it out to. Of course this doesn't mean much until they get some feed back from those people they sent it on to but, at least it is getting further than it would get if I had sent it to an evo site.


Dear xxxxxx,

We have reviewed your letter to us about the "3D spatiotemporal control system" and we have passed it on to several of our fellows who are more knowledgeable about mechanical engineering. Our initial reading of your letter makes us feel that your logic about the existence and necessity of such a designed system has merit and will be reviewed.
Incidentally, we recently released a commentary in Evolution News and Views that may have some connection with with the system in your letter. You can find it here: http://www.evolutionnews.org/2012/07/a_ ... 62601.html.


Sincerely,

xxxxxxxxxxxxxxx
Center for Science and Culture
Discovery Institute


That commentary is interesting for sure;

Through a light microscope, students and scientists have long noticed the paired chromosomes oscillating back and forth before they split apart. Those movements don't just happen; there are machines (dynein and kinesin) pulling them toward the pole (P) and away from the pole (AP) to jostle them into place along the central axis until the signal is given to divide. Upon that signal, the spindle poles winch the separated chromosomes into the daughter cells by controlling the assembly and disassembly of microtubule building blocks.

...Kinetochores, as Berry explains, have been under intense study for over 100 years, and "we're still just beginning to discover what it's all about." Like the authors of the Science paper, he also did not offer an evolutionary explanation for these structures with their "signal broadcasting system" and all.

Machines with moving parts that obey the laws of physics while performing goal-oriented functions -- our uniform experience with such systems insistently proposes that the best explanation is intelligent design.
http://www.evolutionnews.org/2012/07/a_ ... 62601.html

It is very interesting to see that someone else saw the connection of my 3D spatiotemporal control system concept to a current scientific paper.

[Proinsias]

Just a thought but do crystals not provide an example of 3d spacial positioning control and replication that appears to be naturally occurring? I'm sure there's a few hypothesis based around the idea of life or proto-life generating around crystalline type structures. I don't have the knowledge to argue for such a position but more just to show that the idea of naturally occurring precisely organised 3d frameworks are know to exist above, on and below the cellular level.

[bippy123]

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:)

[KBCid]

Just a thought but do crystals not provide an example of 3d spacial positioning control and replication that appears to be naturally occurring?

Yes they do. In fact there are a great number of atomic structures that display natural affinities which cause an orderly repetetive structuring. However, this is not considered controlled replication. Snow flakes and crystals of many varieties naturally order their structures in very specific patterns which are reducible to mathematical modeling.

I'm sure there's a few hypothesis based around the idea of life or proto-life generating around crystalline type structures. I don't have the knowledge to argue for such a position but more just to show that the idea of naturally occurring precisely organised 3d frameworks are know to exist above, on and below the cellular level.

you are quite correct that there are attempts to show theoretically that crystaline structuring could be the start of living structuring. Unfortunately living structures don't follow the natural structuring exhibited by crystaline formations. Our structure is not one contiguous repetetive set of building block arrangements.
The structure of a cell has its own particular 3 dimensional structural control and then the arrangement of the cells themselves have another 3 dimensional structure control. So, in fact an account must be made for both types of structural ordering one that orders the building components that make a cells structure and one that makes the positioning of the cells themselves.

Here is a simple analogy;
Man makes bricks in specific shapes by way of chemical interactions of the substrates using a mold. Then, those structurally formed building blocks are arranged into what would be considered a superstructure. Neither of these 3 dimensional structurings can be accounted for by crystaline types of affinity structuring as science can attest to. Since, structure cannot be accounted for by atomic force controls then it requires another answer scientifically. In the absence of a natural control the most logical answer is that it must be systematically controlled. Thus, a system of 3 dimensional positional control must exist.
One other point that should not be lost among this discussion is the temporal side of the equation. Temporal or timing control is a necessity in 3 dimensional formation. In the analogy I gave above we considered the construction of a superstructure being formed from the building blocks called bricks however, I never mentioned the orderly method that such a construction requires. Suppose you wish to build a brick wall. You begin by placing one brick at a 'time' in a very specific pattern right? well suppose the individual bricks were not there all at the same time for you to repetetively make your ordering from. Suppose they only appear one at a time 12 hours apart... not very condusive to helping you form the wall right? living systems require organisation events to haappen in a time constrained orderly fashion. Thus, there must be 2 systems of control active during a formation event, one that precisely positions the building block itself and one that controls 'when' the blocks appear to be placed. In fact there are several more controls in living systems but we can touch on them as the need arises.

Edit;
There is one more point that I think should also be made here. The evolutionary mechanism cannot function on affinity structuring since changes would need to be heritable. Think about it showflakes don't evolve nor do crystaline structures whichis why they can be mathematically modeled.
The entire problem with affinity structures is that they posess an inherent control for their structuring wich would continually overide any ordering that does not conform to this natural order. Evolution is dependant on heritable change.