Biomolecular machines

[Phronesis]

As expected, "basic chemistry" accounts for events that you try to explain by mystical means.

Again, please elaborate how "basic chemistry" explanations explain away purpose?
Basic physics explain how a computer works. Or do you really believe electrons and circuit boards designed themselves and we just happened to use them. No. While physics explains how a computer works, it was still made with a purpose, and by gosh self-assembling methodologies can be used to design e.g.
Nanoparticles self-assemble through chemical lithography

Not quite old chap. As Hawking has said:



Not too relevant at the levels of ordinary chemistry we are talking about. Unless, of course, basic chemical reactions are completely random and uncertain, like your car's number 3 cylinder turning petrol-and-air into Caesium-137 every so often LOL!

I think you again miss the point. Chemical reactions are statistically predictable but not deterministic. And then you should know observers can also interfere.
Here is a simple video for you to understand .

 

[rwenzori]

Again, please elaborate how "basic chemistry" explanations explain away purpose?



I think you again miss the point. Chemical reactions are statistically predictable but not deterministic. And then you should know observers can also interfere.

1. Basic chemistry concerns itself with atoms and molecules and how they react, which they do predictably and consistently. I cannot see any "purpose" at work. Where is this "purpose" to be found when an atom of oxygen combines with one of carbon to form a carbon monoxide molecule?

2. Atoms and molecules, under the same conditions, react in the same way, as I have said several times. Yes, down at the subatomic level quantum indeterminacy is something to fuss about. But chemistry starts with atoms, and chemical reactions do not change atomic nuclei, only the interrelationships of the atomic electron clouds, and the determination of, for example, the location or momentum of particular electrons is irrelevant to chemical reactions. So, again, atoms and molecules, under the same conditions, react in the same way.

No doubt it is possible to describe chemical reactions in terms of quantum theory, but such descriptions are going to be rather long and complex, and practically unnecessary. If your "point" had relevance, scientists would have to do so though.

Maybe you would like to demonstrate your "point" about statistical predictability in chemical reactions by showing a good many cases where chemical reactions produce substances that are not predicted by basic chemistry. It would be interesting to see a SASOL churning out gold or cheeseburgers, and I'd suggest pulling out of any investments in places like the Dow Chemical Company, or DuPont, since you don't know what the heck their plants will produce from day to day!

 

[Phronesis]

1. Basic chemistry concerns itself with atoms and molecules and how they react, which they do predictably and consistently. I cannot see any "purpose" at work. Where is this "purpose" to be found when an atom of oxygen combines with one of carbon to form a carbon monoxide molecule?

The purpose can be in the motives of an agent for catalyzing that reaction for a purpose. Like humans purposefully creating internal combustion machines and making use of chemistry and physics to create energy for a purpose.

And as you know by now, machines don't just reorganize from a mess. Only when the constituents needed for the machine do some structures self-organize.

2. Atoms and molecules, under the same conditions, react in the same way, as I have said several times. Yes, down at the subatomic level quantum indeterminacy is something to fuss about.

So that is all you need to understand . No need to misrepresent me by implying that I think gold will turn into cheeseburgers.

 

[Phronesis]

New Models Question Old Assumptions About How Many Molecules It Takes To Control Cell Division

ScienceDaily (Feb. 24, 2009) — A single cell – whether a yeast cell or one of your cells – is exquisitely sensitive to its surroundings. It receives input signals, processes the information, makes decisions, and issues commands for making the proper response. As with any control system, noise – errors, slip-ups, mis-reads – can get in the way of correct decision making. Virginia Tech biologists and engineers have created a mathematical model to explore the roles of noise in controlling the basic events of the cell cycle – DNA replication and cell division.

Their work will appear the week of February 23 in the Online Early Edition of the Proceedings of the National Academy of Sciences (PNAS) and later in the print version of the special feature issue on complex systems. The article, "Exploring the Roles of Noise in the Eukaryotic Cell Cycle," is by postdoctoral associate Sandip Kar; William Baumann, professor of electrical and computer engineering; Mark Paul, professor of mechanical engineering; and John Tyson, University Distinguished Professor of biological sciences.

Their efforts to accurately calculate the effects of noise in a yeast cell revealed flaws in two accepted notions about information processing in single cells: about the numbers of messenger RNA (mRNA) molecules in a cell, and about how long they live.

A fundamental challenge of systems biology is trying to understand the molecular basis of decision making in a single cell. "Information processing is done by a molecular network consisting of interacting genes and proteins," Tyson said. "You could compare it to a computer that is based on integrated circuits or to a mechanical control system based on sensors, wires and servomotors -- except that information processing in cells is unique in two ways. First, the cell is a sloppy, liquid environment, with molecules bouncing around and reacting with one another. Second, cells are extremely tiny; therefore sensitive to random fluctuations in the number of molecules being created or destroyed at any given moment."

Even though cells are small and they have a sloppy, randomly fluctuating liquid environment, biomolecular machines make use of these random fluctuations.
Consider the following:
Fluctuation as a tool of biological molecular machines
Abstract:

The mechanism for biological molecular machines is different from that of man-made ones. Recently single molecule measurements and other
experiments have revealed unique operations where biological molecular machines exploit thermal fluctuation in response to small inputs of energy
or signals to achieve their function. Understanding and applying this mechanism to engineering offers new artificial machine designs.

From the article:

Biological machines are different from man-made artificial ones in many ways. One primary difference is the amount of energy supplied. For example, a supercomputer playing chess with a champion uses much larger amounts of energy than its adversary. A computer unit element, or IC chip, uses energy much larger than thermal energy (500 times greater) to avoid the disturbance caused from thermal noises whereas biological machines use the energy released from the hydrolysis of ATP, which is only approximately 10 times greater than thermal energy. Large excess energy inputs in computers result in far less efficiency at converting their energy inputs although they are more precise at their task than biological machines. Computers err once per 1060 trials, while basic biochemical reactions underlying biological machines err as often as once per 103 trials. For this reason, computers are in some respects superior to one of nature’s greatest machines, the human brain. Computers make calculations much faster as IC chips work on the order of nanoseconds (10−9 s), while the time scale for basic biochemical reactions in biological machines is milliseconds (10−3 s). They also have superior memory capacity and data transfer rate. The computer rate is on the order of 109 bites/s while in brain it is estimated to be only 400 bites/s. However, biological machines are more flexible, readily responding to changes in their environment. In contrast, man-made machines are designed to maintain their. function regardless of environmental changes. Therefore, the fundamental mechanisms between the two machines are different. Biomolecules and their assemblies, biomolecular machines, are in the order of nanometer in size meaning the effects of thermal noises are large. Nevertheless, biomolecules and molecular machines execute their roles despite these noises. But how? Recent experimental data suggest that biological molecular machines harness thermal fluctuation to achieve their functions. Thus, thermal fluctuation seems to play an important role from the molecular level to cellular and organism level. We have developed measurement systems that trace these thermal fluctuations in biomolecular machines when eliminating measurement noise.

Our model biomolecular machine of choice is the molecular motor. Molecular motors are composed of a motor protein, which move using the chemical energy of ATP, and protein tracks, which the motors move along. Molecular motors and protein tracks share unique characteristic properties such as enzymatic activity, molecular recognition, energy conversion and self-organization with other typical molecular machines. Thus the results obtained for molecular motors may be extended to other systems.

Lastly, in addition to the stochastic nature at the molecular and cellular levels, visual perception has shown stochastic dynamics. Visual perception processes are explained by equations similar to formulae that govern the behavior of biomolecules (Murata et al., 2003). Thus the mechanisms obtained at molecular and cellular levels likely apply at even higher levels. These mechanisms offer blueprints to engineer artificial machines that utilize fluctuations.

So, again highlighting design principles of biomolecular machines and showing the carbon based nanotechnology in cells can be utilized and adopted by our engineers for our own designs seeing that these machines are able to harness even thermal fluctuations.

To get back to the article about control oof cell division:

Nonetheless, the ebb and flow of molecules in a cell must reliably convey instructions for such essential processes as DNA replication and cell division.

How big are the molecular fluctuations expected in a single yeast cell? Physicists estimate molecular fluctuation using a rule-of-thumb that the size of typical fluctuations is the square root of the average number of molecules. "If there are on average 900 molecules of a particular protein in a cell, then we can expect fluctuations of plus or minus 30 molecules, or 3.3 percent," said Tyson. "That is not too bad."

For DNA there might be a severe problem, Tyson noted, "because there is only one copy of every gene in a yeast cell. But cells are equipped with an elaborate and expensive mechanism to replicate DNA molecules and not allow the random fluctuations predicted by statistical physics."

The weak link in the is mRNA: the molecule that carries information from the gene to the cell's ribosomes, where proteins are made.

The literature reports that there is on average only 1 mRNA molecule per gene per cell, in yeast, and that each mRNA molecule lives, on average, for 15 to 20 minutes before it is degraded. "This is intriguing," said Tyson, "because the physicist's rule-of-thumb would predict very large fluctuations in mRNA abundance – sometimes 1, sometimes 0, sometimes 2 or 3 or 4 -- which means the noise among mRNA molecules is huge, and it propagates to the level of the encoded protein."

The noisy fluctuations in protein level may be 50 percent instead of 3 percent. "There is no way the control system can work in the face of such large fluctuations," Tyson said. "It would be completely unreliable."

Progression through the cell cycle is indeed a noisy process, with typical flucutations of 15 to 20 percent for the time taken to complete the process. To achieve this level of control, the Virginia Tech researchers conclude, in their PNAS paper, that 1) the average number of specific mRNA molecules must be 5 to 10 times larger than the generally accepted value, or 2) the half-life of mRNA molecules must be 10 to 20 times shorter than the reported value, or 3) the cell must have specific mechanisms for noise reduction in its mRNA populations. Or some combination of these strategies.

Anyone want to venture a prediction which one of these explanations are most likely seeing how exquisitely controlled the cell cycle of even simple single eukaryotic cells are?

 

[rwenzori]

Basic Chemistry - 10 : I.D. - 0

The purpose can be in the motives of an agent for catalyzing that reaction for a purpose. Like humans purposefully creating internal combustion machines and making use of chemistry and physics to create energy for a purpose.

"Catalyzing" - big word for you TelePhrone, and with a specific meaning in chemistry. Let's look at the research on the ribosome you quoted - no sign of any catalysts required for the reactions.

So let's again refer to the ribosome. Sergey says basic chemistry. Are you trying to say that there is a mind, with a motive, purposefully putting all those long carbon chains together?

LOL! I know who I'll believe!

So that is all you need to understand . No need to misrepresent me by implying that I think gold will turn into cheeseburgers.

So when you said "because of quantum indeterminancy you will never be able to create two conditions thast react exactly the same" ( spelling errors and all ), you were misunderstanding chemistry, as well as Sergey Steinberg's point about "basic chemical principles". I read one amusing ID quote along the lines of:

God does not play dice; he IS the dice.

Clearly no dice at play - just basic chemistry, so I repeat: as expected, "basic chemistry" accounts for events that you try to explain by mystical means. And that includes ALL the stuff you quote mined in the next post. Ain't basic chemistry wonderful!

 

[Phronesis]

"Catalyzing" - big word for you TelePhrone,

ROFL, you little old trash talker you.

and with a specific meaning in chemistry. Let's look at the research on the ribosome you quoted - no sign of any catalysts required for the reactions.

Uhm, do you know how the ribosome is assembled? By gosh, are you really saying catalysts are irrelevant? Catalysts, ribosome assembly, polycistronic precursor rRNA, covalent modification and pre-processing of the mature rRNA, assembling processed rRNA to ribosomal proteins... basic chemistry.

You really want to go into a bit of detail here Mr trash-talker? Mmm, let's do that and once and for all settle YOUR ACTUAL acumen regarding basic chemistry .

Always quick to sneer, but even quicker at evasion when the detail gets a little tough for you. Don't worry, alloytoo, you and cyghost are the same. Two-bit trash-talkers. No doubt you are going to continue with the trash-talk, but let's try to keep the discussion ABOUT ribosome assembly and how it is controlled.

1) The simplest ribosomal complex: The bacterial 30S subunit
A) Transcription of pre-rRNA (needs transcription machinery)
B) Pre-rRNA processing (needs rRNA processing machinery to process from polycistronic precursor rRNA)
These include:
I) Covalent modification
II) Processing of the pre-rRNA to the mature rRNAs
III) Assembly of the rRNAs with the ribosomal proteins

There are about 6 assembly proteins needed to assemble the structure (but proteins need ribosomes in the first place) e.g. RimM, RbfA, RimJ etc.

Right, so you need transcription and pre-rRNA processing machinery. Once they have done their job, the S16 folds into place through self-assembly. Once folded, ribosomal proteins (yes those little structures that need ribosomes in the first place) are needed to stabilize the structure. These proteins ALSO function to suppress misfolding.

But, the rRNA is not done yet, it still needs to be assembled to ribosomal proteins. But by gosh, there is evidence for co-folding of ribosomal proteins (yes those structures that rely on themselves for assembly) and rRNA. But this is not the last detail, even after assembly, there are proteins that monitor the assembly process and guide the structure into place. Ah wait, it gets better, RbfA even forces certain self-assembled helices out of their original position and refolds them into their correct formation. And the final step: Well sometimes things do go wrong, but like a well oiled machine, yep there is a quality control mechanism present even for the last step. Defective ribosomes get assigned for destruction and don't just float around willy-nilly.

So you see, catalyzing does play an important role in guiding reactions and "stuffs" don't just magically self-organize from goo. Self-organization is just one of the players .
But, if self-organizing principles are used in the long run (aka evolution), it essentially means our existence was inevitable in a lonely universe. For some, the teleological implications are clear to see, so I am surprised you accept self-organizing principles.

 

[rwenzori]

ROFL, you little old trash talker you.
...
Always quick to sneer, but even quicker at evasion when the detail gets a little tough for you. Don't worry, alloytoo, you and cyghost are the same. Two-bit trash-talkers. No doubt you are going to continue with the trash-talk, but let's try to keep the discussion ABOUT ribosome assembly and how it is controlled.
...
But, if self-organizing principles are used in the long run (aka evolution), it essentially means our existence was inevitable in a lonely universe. For some, the teleological implications are clear to see, so I am surprised you accept self-organizing principles.

I must admit to being wrong here. It looks like biocatalysis is a big thing.

Have a cookie for the error. Ooops, no, too many insults - Bad TelePhrone! No cookie!

No quantum indeterminacy at play though - just basic chemistry. As ALWAYS in these biological reactions. No intentionality, no nano-intentionality either.

I can't see no teleological implications myself - **** happens. Tell me, what is the teleological purpose of earthly evolution? To make humans? Are we the pinnacle, or is there more to come?

 

[alloytoo]

I must admit to being wrong here. It looks like biocatalysis is a big thing.

Have a cookie for the error. Ooops, no, too many insults - Bad TelePhrone! No cookie!

No quantum indeterminacy at play though - just basic chemistry. As ALWAYS in these biological reactions. No intentionality, no nano-intentionality either.

I can't see no teleological implications myself - **** happens. Tell me, what is the teleological purpose of earthly evolution? To make humans? Are we the pinnacle, or is there more to come?

I don't think he watched the movie that far, he can't seem to get beyond "Run Forest Run."

 

[Phronesis]

I must admit to being wrong here. It looks like biocatalysis is a big thing.

If you can't even get to grips with biocatalysts and their function, what was all this about?

Not too relevant at the levels of ordinary chemistry we are talking about. Unless, of course, basic chemical reactions are completely random and uncertain, like your car's number 3 cylinder turning petrol-and-air into Caesium-137 every so often LOL!

Looks like you are not "any good in understanding chemistry" yourself!

You joking around?

More about catalysis and the selectivity of enzymes.
Consider the following:

RNA

RNA constituents
​

Say you have the following soup of chemicals and they magically react with each other (note, they don't, they need catalysts but assume they do)

Phosphodiester bond formation​

Note, there are thousands of possibilities. Specific enzymes (generated through the ribosome machinery) direct the biosynthesis of RNA and not the other molecules. Only when RNA is synthesized can it participate in self-organzational process if the sequences permit it.

No quantum indeterminacy at play though - just basic chemistry. As ALWAYS in these biological reactions. No intentionality, no nano-intentionality either.

Once again I think you are missing the the point about nano-intentionality. I am not implying that compounds are able to intentionally choose between say an exothermic or endothermic reaction. They are governed by law. The level of nano-intentionality lies at the organismal level where an organism is able to choose between conditions. For example, bacteria are able to interpret information and act on it. Say a glucose gradient is formed at a higher temperature. Bacteria are able to do do work and assemble machinery and swim towards the higher glucose content or swim away from the higher temperature, some are stationery. Now, technology is not yet advanced enough to fully determine the exact atomic make-up of each bacteria in order to determine why some react differently. But no two organisms are exactly the same so there is no way of telling how two exact same organisms will react in exactly duplicated scenarios.

I can't see no teleological implications myself - **** happens. Tell me, what is the teleological purpose of earthly evolution? To make humans? Are we the pinnacle, or is there more to come?

We have free will, it seems plausible our purpose is to exercise our free will.

More machines
(please note alloytoo, the thread is about biomolecular machines, you are welcome to discuss Forrest Gump in your own thread and even insult me there if you feel the need arises ).



'Switch Off, Light On': Molecular Biologist Discovers New Control Mechanism In Cell Signaling

ScienceDaily (Feb. 26, 2009) — The MAP Kinase signal transduction pathway plays an important role in embryonic development as well as in differentiation, growth and programmed cell death of human cells. “The enzymes Raf/MEK/ERK are important for cell division and therefore also play a role in uncontrolled cell growth leading to cancer.

 

[rwenzori]

<drivel snipped>

Once again I think you are missing the the point about nano-intentionality. I am not implying that compounds are able to intentionally choose between say an exothermic or endothermic reaction. They are governed by law. The level of nano-intentionality lies at the organismal level where an organism is able to choose between conditions. For example, bacteria are able to interpret information and act on it. Say a glucose gradient is formed at a higher temperature. Bacteria are able to do do work and assemble machinery and swim towards the higher glucose content or swim away from the higher temperature, some are stationery. Now, technology is not yet advanced enough to fully determine the exact atomic make-up of each bacteria in order to determine why some react differently. But no two organisms are exactly the same so there is no way of telling how two exact same organisms will react in exactly duplicated scenarios.

You see TelePhrone, one difference between you and me is that if I make an error, I admit it, while you try to cover up and dissimulate LOL!

You said "because of quantum indeterminancy you will never be able to create two conditions thast react exactly the same", thereby putting your foot into the poo in terms of basic chemistry as repeatedly stated by me:

As I have tried to explain to you before, the same atoms and molecules under the same conditions react in the same way.

If you can't even get to grips with basic chemistry, what are you on about?

All this lovely stuff you are on about is just basic chemistry as usual.

If you wish to posit any form of "intentionality" or purpose, you need to show mind and brain in these situations, as, by your own definition, intentionality requires mind. Or is Baby Jesus supplying that part LOL?

Is it really necessary for you to repeat these examples of basic chemistry at work ad nauseam, just to be blown out the water on your own definitions? Can we try something new maybe, as repetition has zero effect on the substance and truth of your claims?

We have free will, it seems plausible our purpose is to exercise our free will.

To clarify - the purpose of teleological evolution is to create man so that he can exercise free will - is that your position?

 

[Phronesis]

You see TelePhrone, one difference between you and me is that if I make an error, I admit it, while you try to cover up and dissimulate LOL!

Ad hominem much?

You said "because of quantum indeterminancy you will never be able to create two conditions thast react exactly the same", thereby putting your foot into the poo in terms of basic chemistry as repeatedly stated by me:

Please read up on Brownian motion and see if it is possible to create two conditions that are exactly the same.

All this lovely stuff you are on about is just basic chemistry as usual.

Apply this to electronics and specifically a chess playing computer. Lovely basic electronics and physics explaining why electrons flow along a copper wire, or how a transistor works. Lovely, basic stuff. However, the machine represents the intentions of its creator. I.e. to play chess. The machine has no mind, but it has derived intentionality. Do molecular machines represent the intentionality of an engineer? I don't know. Now remember this request (and a few others mind you ). Please at least attempt to give an answer.

Is it really necessary for you to repeat these examples of basic chemistry at work ad nauseam

Why such an aversion for molecular machines? I think they are fascinating.

Here is more:
Self-regulating Molecular 'Transformers' Control Intracellular Protein Delivery

ScienceDaily (Feb. 19, 2009) — Scientists from the California Institute of Technology (Caltech) have uncovered the Transformer-like properties of molecules responsible for carrying and depositing proteins to their correct locations within cells. The research could eventually lead to novel treatments for diseases that result from flaws in protein delivery as well as the development of new types of antibiotics.

To clarify - the purpose of teleological evolution is to create man so that he can exercise free will - is that your position?

I think that is a reasonable place to start developing a sound theodicy. Feel free to add to this .

 

[Phronesis]

Oh snap.. more loverlies....

Molecular Motors In Cells Work Together, Study Shows

ScienceDaily (Feb. 25, 2009) — Even within cells, the left hand knows what the right hand is doing.

Molecular motors, the little engines that power cell mobility and the ability of cells to transport internal cargo, work together and in close coordination, according to a new finding by researchers at the University of Virginia. The work could have implications for the treatment of neurodegenerative disorders.

"We found that molecular motors operate in an amazingly coordinated manner when moving an algal cell one way or the other," said Jeneva Laib, the lead author and an undergraduate biomedical engineering student at the University of Virginia. "This provides a new understanding of the ways cells move."

Now if only we can reverse engineer that .

 

[rwenzori]

Ad hominem much?

Just stating facts, and in any event not as often as you by a long way.

Please read up on Brownian motion and see if it is possible to create two conditions that are exactly the same.

ROFL! "Quantum Indeterminacy" let you down, now you're on to "Brownian Motion". Call me back when Dow's sulphuric acid plant starts producing cheeseburgers! Remember - BASIC CHEMISTRY!

Do molecular machines represent the intentionality of an engineer? I don't know.

You'r coming along nicely I see - beginning to doubt the non-existent "engineer". Good Yeti, TelePhrone!

Why such an aversion for molecular machines? I think they are fascinating.

I have an aversion for non-existent "engineers" and imaginary "intent".

PS - on your link - I don't accept your terms.

 

[Phronesis]

ROFL! "Quantum Indeterminacy" let you down, now you're on to "Brownian Motion". Call me back when Dow's sulphuric acid plant starts producing cheeseburgers! Remember - BASIC CHEMISTRY!

Misrepresentation much? Are you saying Brownian motion and quantum mechanics are not related? Mmmm?

PS - on your link - I don't accept your terms.

Of course you don't. Whenever you are faced with a question, it becomes a battle of definitions, you never being satisfied, but don't attempt to resolve it. Strange isn't it.

 

[rwenzori]

Misrepresentation much? Are you saying Brownian motion and quantum mechanics are not related? Mmmm?

What I am saying is that neither is particularly relevant to the "machines" you describe, as pointed out in this lovely article you brought to our attention LOL.

Remember these bits?

While the ribosome is a complex structure it features a clear hierarchy that emerged based on basic chemical principles

In the absence of such explanations, some people could imagine unseen forces at work when such complex structures emerge in nature.

Of course you don't. Whenever you are faced with a question, it becomes a battle of definitions, you never being satisfied, but don't attempt to resolve it. Strange isn't it.

Tough, ain't it.

 

[Phronesis]

What I am saying is that neither is particularly relevant to the "machines" you describe, as pointed out in this lovely article you brought to our attention LOL.

Remember these bits?

Yes, you also forget he is describing self-organizing principles. Something you seem imply has no evidence.

And you are also forgetting how self-organizational processes are being used by cells in the first place.

 

[rwenzori]

Yes, you also forget he is describing self-organizing principles. Something you seem imply has no evidence.

And you are also forgetting how self-organizational processes are being used by cells in the first place.

I have no clue what you are on about in your first claim.

Regarding the second - be careful of your terms, TelePhrone - I do hope that the words "being used" are not meant to imply mind and intent LOL!

Basic chemistry ( and **** ) happens!

 

[Phronesis]

I have no clue what you are on about in your first claim.

It would help if you read some of the posts in the thread .

Regarding the second - be careful of your terms, TelePhrone - I do hope that the words "being used" are not meant to imply mind and intent LOL!

Basic chemistry ( and **** ) happens!

Basic chemistry and molecular autonomous agents as described here:
On emergence, agency, and organization

such a system should be able to
1) Reproduce with heritable variation.
2) Perform at least one work cycle.
3) Have boundaries such that it can be individuated naturally.
4) Engage in self-propagating work and constraint construction.
5) Be able to choose between at least two alternatives.

Mmmm, how about we talk about agency and intentionality in this thread, and limit this thread to biomolecular machines .

 

[rwenzori]

Basic chemistry and molecular autonomous agents as described here:
On emergence, agency, and organization

Hmmmm... Old Tecumseh not good enough for you?

What do we have there from Mr. Kauffman and his mate? Some serious kite flying, I'd say.

Firstly, they introduce a seriously dumbed down definition of "agency", then they proceed with a whole lot of speculation, after which they admit that there is no scientific foundation for their speculative claims. Their definition is suspect: their conclusion bogus.

By your own definition ( mine is different ) intentionality implies mind. Mind implies brain. The "choices" these boys talk about are not through conscious thought or purpose - in all likelihood good old basic chemistry working. Does the Venus Flytrap snap shut on the fly with intent? I think not.

Mmmm, how about we talk about agency and intentionality in this thread, and limit this thread to biomolecular machines .

No, let's stay here, so that you do not get carte blanche to peddle your ID wares.

 

[Phronesis]

Chemists Create Two-armed Nanorobotic Device To Maneuver World's Tiniest Particles

ScienceDaily (Mar. 6, 2009) — Chemists at New York University and China's Nanjing University have developed a two-armed nanorobotic device that can manipulate molecules within a device built from DNA. The device was described recently in the journal Nature Nanotechnology.

The aim of nanotechnology is to put specific atomic and molecular species where we want them and when we want them there," said NYU Chemistry Professor Nadrian Seeman, one of the co-authors. "This is a programmable unit that allows researchers to capture and maneuver patterns on a scale that is unprecedented."

The device is approximately 150 x 50 x 8 nanometers. A nanometer is one billionth of a meter. Put another way, if a nanometer were the size of a normal apple, measuring approximately 10 centimeters in diameter, a normal apple, enlarged proportionally, would be roughly the size of the earth.

The creation enhances Seeman's earlier work—a single nanorobotic arm, completed in 2006, marking the first time scientists had been able to employ a functional nanotechnology device within a DNA array.

The new, two-armed device employs DNA origami, a method unveiled in 2006 that uses a few hundred short DNA strands to direct a very long DNA strand to form structures that adopt any desired shape. These shapes, approximately 100 nanometers in diameter, are eight times larger and three times more complex than what could be created within a simple crystalline DNA array.

As with Seeman's previous creation, the two-armed nanorobotic device enables the creation of new DNA structures, thereby potentially serving as a factory for assembling the building blocks of new materials. With this capability, it has the potential to develop new synthetic fibers, advance the encryption of information, and improve DNA-scaffolded computer assembly.

This type of technology is already present in cells.
Develop fibers? Check out microtuble dynamics, actin polymerization. The necessary subunits needed for self-organization is produced on site so it can organize into formation. No accident. Another nice video

Encryption of information? Three codes present in cells, e.g. histone, ribosomal and the highly optimal genetic code as well as the necessary machinery to code and decode information.

Scaffolded assembly? Scaffolding proteins play crucial roles in the assembly of multiprotein units. E.g.
Scaffold proteins and assembly of multiprotein signaling complexes

We are just beginning to mimic this for our own technological gains...