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Thinking Upside Down – The Abiogenesis Paradigm

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Not too many months ago I ran across Richard Dawkins’ statement that life got its start when, somehow, on the early Earth a self-replicating molecule formed.  I nearly fell out of my chair laughing.  I had read the quote before, and he has repeated the idea in various writings and interviews, but after having studied the issues with abiogenesis in a bit more detail, in particular the concept of a self-replicating molecule to kick off the origin of life, the idea struck me as particularly preposterous.

In this post, I want to follow up on the other recent thread regarding abiogenesis.  This time, however, I want to focus on the matter of self-replication.

The Abiogenesis Paradigm

As mentioned, the idea of a self-replicating molecule is central to most abiogenesis storylines.  Dawkins is not unique in this view, but I offer one of his quotes so that the reader can understand the general thrust.  In a 2012 COSMOS interview, Dawkins said:

Heather Catchpole: Have you put any thought into the beginning of life and into what kicked that off?

Dawkins: Not personally.  I mean, it’s increasingly clear that the big step that had to be taken – and it was probably a step that involved a large element of luck – was the origin of the first accurately self-replicating molecule.  Colloquially, you could say the first gene.  Which probably was not DNA, it might have been RNA.

That’s the step that must have been taken in the origin of life, and that’s what people are working on all around the world.  It’s hard to work on it because it happened a very long time ago under very different conditions, and it is a problem in chemistry rather than biology, it is pre-biology.

But the event in chemistry that must have taken place was the spontaneous arising of a self-replicating molecule.  That’s how I stated it in The Selfish Gene and that hasn’t changed, but people are now actively working on various theories of how that might have happened.  I’m not working on that.

Dawkins is of course not alone.  The search for a self-replicating molecule is the Holy Grail of origin of life research.  Indeed, you can take it to the bank that if a simple self-replicating molecule is ever discovered materialists will all but proclaim that the problem of life’s origin has been essentially solved.

The reason the elusive self-replicating molecule is so critical is that all honest researchers, even those committed to a materialist paradigm who dare not consider the possibility of design, acknowledge that there can be no evolution without a self-replicating entity.*  Once a self-replicating entity appears on the scene, however, the magic of natural selection can take over and then . . . watch out! . . . anything is possible.

Not that there is any good evidence, mind you, that natural selection can produce the kinds of systems we see in living organisms, much less the coding, protocols, and information-rich aspects.  But the vision of natural selection having near-mystical powers of creation has taken such hold on the evolutionary imagination that many individuals mistakenly believe with the magic wand of natural selection, “all things are possible.”  Stated another way, it is not that there is good evidence a self-replicating molecule can give rise to complex life; it is just that once natural selection kicks in, the idea becomes more believable to many people.

But back to those first steps of life’s origin . . .

Most criticisms of abiogenesis have focused on specific evidentiary details: the reducing atmosphere, energy sources, the difficulty of forming polymers in the primordial soup, the existence of the necessary nucleotides or amino acids at the right place and time, homochiralty, interfering cross reactions, the rise of coding and information-rich molecules, and so on.  Together these constitute a devastating indictment of the abiogenesis paradigm and give us ample reason to doubt the materialistic creation story.

However, much less time has been spent – and I want to focus on this today – on the issue of self-replication.  Indeed, even many critics of abiogenesis have skirted the issue or seem to have implicitly bought into the idea that a self-replicating molecule may indeed arise early on in the process.

In short, under the abiogenesis paradigm, the process is as follows:

chemical reactions -> self-replicating molecule -> natural selection kicks in -> eons pass -> life as we know it

This approach puts self-replication at the beginning of the creative story, the opening curtain if you will, in the long and complicated drama that is the history of life on Earth.  Under this paradigm, self-replication is viewed as the very first stage, the kicking-off point, the starting rung of the ladder of life.  Rather than having a living organism and then endowing that organism with an additional ability of self-replication, the materialistic paradigm makes self-replication the first ability.  Self-replication becomes the initial characteristic of an organism, the characteristic from which all others flow.

Let me say that again: Under the materialistic abiogenesis story, self-replication is the first characteristic of an organism to arise, the characteristic from which all additional characteristics then arise.  Characteristics like homeostasis, the genetic code, molecular machines, control mechanisms, the ability to locate, process and utilize materials from the environment, and so on.

The First Step of Life

This view of self-replication as the starting point, the initiator, the first step toward all other biological characteristics is not only questionable, it is completely backwards.  The abiogenesis story is upside-down.  Unfortunately, a failure to think through what is actually required for self-replication, the engineering and programming realities, gives rise to muddled thinking.  But for the magic wand of natural selection to kick in, self-replication must have been the first key step, the thinking goes.  This is why Dawkins would say: “it’s increasingly clear that the big step that had to be taken . . . was the origin of the first accurately self-replicating molecule.”

This insistence on a materialistic origin of life, coupled with the hypnotic trance of the limitless power of natural selection, thus leads the materialist to draw a conclusion that is not only unsupported, but that is diametrically opposed to the physical, chemical and engineering realities we see in the world around us.

The Realities of Self-Replication

A number of researchers have considered what might be involved in getting a self-replicating organism.  I have developed a tentative list of my own, but rather than lengthening this already too-lengthy essay, I will instead refer readers to the thought-provoking materials provided by InVivoVeritas.

In order to help us understand what is involved in self-replication, let us step back for a moment from the dizzying complexity of the living cell and consider what would be involved in building the simplest self-replicating machine possible with our existing technological understanding.

Self-replication has been the topic of much discussion in science fiction literature and movies, ranging from the large and powerful Terminator-style robots to small but deadly nanites.  However, in actual practice, creating a self-replicating machine is not so simple.

Some might be tempted to point to a software program that can copy itself, but such programs are not self-replicating in any substantive sense.  The software program only exists and runs on a carefully-designed and functional piece of hardware that is certainly not replicated in the process.  Furthermore, there is generally an operating system, as well as several additional pieces of software in the form of drivers, compilers, interfaces, middleware programs, and so on.  The most that can be said for such “self-replicating” programs is that a carefully-designed combination of hardware and software can produce a copy of a portion of the software.

No, true self-replication is a more onerous task.  Once we consider the task of actually instantiating a self-replicating machine in physical, three-dimensional space, the challenges become a bit more obvious.

Let’s take a real-world example of attempts to create a self-replicating machine.  To help us get a concrete idea of what is involved let’s look at the relatively-simple consumer-level 3D printers.

3D Printing

A considerable amount of effort has been dedicated toward the goal of self-replication and some modest gains have been made.  One of the most exciting technologies to emerge in recent years is 3D printing.  The ability of a machine to create various parts in three-dimensional space has set us on the path to the first realistic opportunity in human history to create a self-replicating machine.

I became interested in 3D printing years ago and have followed the development of the industry off and on ever since.  Recently the technology has become cheap enough that 3D printers have moved, if not into the world of the everyday consumer, then certainly into the world of the hobbyist and the technology enthusiast.  Popular consumer-level makers include MakerBot, FlashForge, 3DSystems, and others.

Today 3D printers range from personal machines costing a few hundred dollars that do rough prints in a single material to high-end professional printers costing many thousands of dollars boasting tolerances of less than one-tenth of a millimeter and printing in multiple materials.  Numerous 3D technologies also exist, from material extrusion (the most common technology for consumer and prosumer printers), light photopolymerization, powder bed fusion, ultrasonic additive, laser-induced, electron beam melting, and more.

Despite my interest in this area, I have not yet taken the plunge to buy my own printer.  I am guessing that within the next 12-18 months I will probably be willing to lay down some silver to acquire my own printer.  However, in the meantime our local library received a grant last year to educate patrons on the technology of 3D printers, so I took advantage of the opportunity to design and print a simple stand for one of my 5x5x5 cubes.

Printed - 2013-10-15 15.13.54_001

 

Printed-2013-10-15 15.13.03_001

 

This is an exciting and explosive technology that promises to fundamentally alter the landscape of design and prototyping activities, and, to a lesser though still meaningful extent, actual manufacturing processes.

A Self-Replicating 3D Printer?

One of the more interesting projects in the 3D printing world is the RepRap Project, an open-source project that seeks to create a self-replicating 3D printer.  A number of people have been involved in this project and have done tremendous work in moving it forward, with significant strides made.  As of this writing, many of the parts for a RepRap printer can be printed on the printer itself to reasonable tolerances, enabling a hobbyist to use those parts in the construction of a new printer.

RepRap 1.0 - Darwin
RepRap 1.0 – Darwin

As is often the case with groundbreaking new technologies, however, the excitement of future high-flying potential tends to intrude on assessments of the present on-the-ground realities.  For example, the RepRap website touts the machine as “humanity’s first general-purpose self-replicating manufacturing machine.”

At first blush, the uninitiated may look at projects like RepRap and think, “Wow!  We are almost there in terms of creating a self-replicating machine.”  But a closer look is warranted.

Another very interesting printer, the Kickstarter-backed BI V2.0, received breathless attention in late 2013, with myriad headlines touting “The World’s First Self-Replicating 3D Printer!”  This isn’t just sloppy newswire enthusiasm; even the official project website touts BI V2.0 as “A self-replicating, high precision 3D Printer.”

However, notwithstanding my enthusiasm for 3D printing technology and the long-term potential, such statements are overly-optimistic to the point of deception.  Neither RepRap nor BI V2.0 are self-replicating.

Not in theory or in practice.

Not even close.

Not even in the ballpark.

Don’t get me wrong.  I love this technology.  I’ve followed RepRap closely and consider it a fantastic idea and an excellent open-source project.  I also seriously considered contributing funds to the BI V2.0 Kickstarter project last year.

But despite the efforts that have been made to date, a human-designed self-replicating machine is a long way off.  We’re just scratching the surface.

So Close and Yet So Far

Although these printers do an impressive job of printing some of the parts needed for their construction, even a cursory look at the printer reveals that it is not even close to being able to print all its parts.

The printer itself must initially be set up and programmed with the right parameters, it must be fed the material for extrusion.  Even after parts are printed, they must be carefully removed from the bed by the user and, in many cases, cleaned up and sanded in order to finalize the usable parts.

In addition, notwithstanding the considerable effort expended to make as many parts as possible printable on the self-same machine, many other parts are simply not able to be printed by the printer.  The metal support rods that provide critical rigidity to the frame must be purchased separately.  More daunting still, the printer requires a circuit board, cabling, control switches and the like in order to function.  The printer at this stage is not even close to being able to produce all those parts.

BI V2.0
BI V2.0 (Click for closer look)

Yet there is another aspect that goes beyond the parts themselves.  Even if the printer had the capability of printing in multiple materials at the sub-micron level – even if the printer could print virtually every single part used in the construction of the printer, something which at this stage is but a distant dream – it would still not have the ability to assemble itself at all.

As we delve into the issue more deeply and more carefully, we realize that in order for a machine to be truly self-replicating, it must not only be able to produce all the necessary parts, but it must have a means to assemble those parts – in actual, physical, three-dimensional space.  In order to do that, the printer would not only have to be a printer of parts, but would need to have carefully-controlled and sophisticated robotic assembly systems.  For example, it would need an assembly arm to pick up the printed pieces, analyze them for completeness and quality, rotate them into the right position, and place them in the correct location.  In reality, this would likely require more than one assembly arm/mechanism.

And as soon as we introduce this new assembly arm/mechanism into the printer, then we have a whole additional set of machine parts that themselves have to be incorporated into the printer design, specified, coded, printed and assembled.  Indeed, the entire printer would need to be radically re-engineered in order for it to successfully assemble itself.

Furthermore, it is unclear how this printer could even accomplish this task without some significant re-engineering.  Remember, the printer is occupying a physical three-dimensional space.  The best it can do is assemble a copy right next to itself, with the far side of the copy some 12-24 inches away.  Thus any assembly mechanism would have to be able to reach outside of the box – outside of itself – in order to reproduce itself.

Assembling outside of itself might work on a clean tabletop with no other interference, but is of course unworkable in the fluid and watery biological environment.  So the cell uses an ingenious approach whereby the new outside housing/membrane is the last thing to be completed.  The cell essentially constructs a copy of itself within itself, using its own cell membrane to form the protective environment for construction, and then divides by drawing the cell membrane inward between the original and the copy, eventually sealing off the gap and releasing the now-completed copy into the larger environment.  It would be as though our printer, seen as a cube-like structure, were to remove one wall, extend its own frame to encompass a space the size of two printers, construct the internal components in that open space, and then rebuild two walls between the identical sections in order to release the completed copy.

Let us not forget that a truly autonomous self-replicating entity would also need to be able to locate and make use of its own materials and would need to be able to generate its own power from raw resources.  No convenient electrical cord plugged into the wall, please, nor any careful feeding of the printer filament by a user.  And for long-term successful replication over more than just a few generations, it would be critical to have various feedback and quality control mechanisms, error correction and the like.

The above is but the barest outline of what would be involved in building a truly self-replicating entity.  But as we think through some of these details (an activity that is, unfortunately, too often skipped by abiogenesis enthusiasts), we begin to get an inkling as to the scale of the problem.

We must remember, too, that every time we include a new part or an additional mechanism to assist with the self-replication process, that part or mechanism must too be replicated, requiring additional instruction sets, perhaps a reworking of the machine’s physical layout, and additional information about this new part or mechanism – how it is to be constructed, how it is to be assembled, how it is to function.

Indeed, every single time we add a new part, or in the vernacular of the materialistic evolution story, every time the nascent organism “evolves” a new function, that new function requires not only a careful integration into the whole, but the instruction set to implement and reproduce that new part.

The same principle holds in the biochemical world.  Let’s assume, through some miracle, that we discover a self-replicating molecule.  When that molecule “evolves” something additional, say a side strand polymer or a molecular complex, the self-replication process that formerly faithfully reproduced the simple molecule may no longer be up to the task.  The self-replication ability has to be re-worked, re-gained, re-programmed with every meaningful additional change or improvement to the nascent life form.

Self-replication needs to be seen for what it is: an additional, added capability beyond what is necessary for an organism to carry out its daily life functions.  It is simply true, a basic logical fact, that it is more challenging and complicated and difficult and sophisticated to design a machine that does X and self-replicates, than to design a machine that just does X.

The Big Picture

Self-replication is not a one-time origin of life problem.  Nor is it an occasional challenge at important junctures of the long evolutionary history of life.  At every stage of the evolution from a simple self-replicating molecule up to the most detailed and complex organism of the Earth – at every stage of the process, the ability to properly self-replicate has to, in essence, be reacquired.  This is almost never discussed openly and is rarely recognized for the massive conceptual problem that it is.

Thus self-replication, rather than being a basic kick-starting point at the beginning of the long road of evolution, instead itself lies at the end of an extremely complicated, sophisticated and specified design process.  Furthermore, every time something is added to assist in the self-replication process, the very adding requires a re-working of the self-replication process itself.

Don’t misunderstand.  This is not an infinite regress.  The self-replication process can be engineered and can be overcome.  But we do start to sense the scale of the problem.

Implications for the Abiogenesis Story

The materialist creation story, which places self-replication at the beginning of the evolutionary process is little more than a naïve just-so story, one that flies in the face of what we understand, not only of chemistry and physics in getting to the self-replicating molecule in the first place, but in the face of our engineering understanding of what is required for self-replication to function in the real world.

As a result, it is not just that abiogenesis is incomplete, with details remaining to be filled in.  It is not just that abiogenesis relies on numerous disputable physical and chemical factors from the reducing atmosphere to the primordial soup to the right energy source to the formation of information-rich molecules.  It is not just that abiogenesis is incomplete knowledge.  The abiogenesis paradigm, with its placement of self-replication as the first stage of development, is not just wrong due to various evidentiary details.  It is fundamentally flawed at a conceptual level.

I keep repeating this, because I want to be clear that this is not simply another in the long line of evidentiary critiques of this-or-that chemical or natural obstacle to abiogenesis.  This is a fundamental, central, irretrievable, conceptual problem with the idea.  A conceptual problem which separates abiogenesis from the realities of the physical world by such a deep and abiding chasm, that the concept of abiogenesis becomes not just mistaken, but actually anathema to knowledge.  It functions as a kind of anti-knowledge.  It is not just that, in accepting abiogenesis, one has learned something inaccurate or incomplete.  Rather, an individual’s view of the world and understanding of the science is actually worse off for ever having taken it seriously.

Conclusion

The abiogenesis paradigm – with self-replication as the starting point, the initial characteristic, of life – stands in stark contrast to physical, chemical and engineering realities.  Self-replication – the ability to timely and faithfully and accurately reproduce one’s own kind – far from being the first step, in fact lies at the end of a complex, carefully-coordinated, precisely-modulated, exquisitely-orchestrated, functionally-specified, information-driven process.  Speaking more poetically, self-replication – this remarkable ability to multiply and fill the Earth – is a creative end, the culmination of an organism’s existence, not its beginning.

The abiogenesis paradigm, attempts to stand this edifice on its head.  And without a sure foundation to stand on, the materialistic creation story crumbles.  Abiogenesis is not simply an incomplete paradigm.  It is fundamentally flawed.  As long as we insist on clinging to the outdated abiogenesis paradigm, one that is diametrically opposed to both the evidence and our real-world experience, we will never come to understand the beautiful and deep mystery that is life’s origin.

—–

* This insistence on self-replication being a critical aspect of evolution is not, in fact, correct.  However, that is a detailed topic that will have to wait for another day.

73 Replies to “Thinking Upside Down – The Abiogenesis Paradigm

  1. 1
    Andre says:

    Thank you Eric. I would like to add something to this quite possibly not even relevant. I noticed in a discussion on a blog the other day a complaint about how many engineers are in support of intelligent design. On reflection I have to comment on that observation as an engineer.

    Engineers understand the requirements with the construction of a system. That is why the materialist story of self replication is so difficult to swallow. It is simply not possible for such an eloquent system to assemble itself.

    I wish I could explain it in a better way but looking at such a system as an engineer you absolutely recognize that it is designed.

  2. 2
    bornagain77 says:

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    https://vimeo.com/91322260

  3. 3
    Dionisio says:

    Andre @ 1
    Agree. Thanks.

  4. 4
    Andre says:

    I guess I need to force myself to explain. Engineers are first and foremost problem solvers, feel free to disagree with me if you’re an engineer :). I think at the heart of the problem for me is the realization that OOL is more than a time and material problem. Not only is the individual parts very precisely arranged but as a whole they have a specific function. These kind of systems can not build themselves in time with trial and error it is frankly impossible and anybody that thinks it can, did or could are kidding themselves.

    I think engineers recognize the design because we recognize the problem.

  5. 5
    gpuccio says:

    Eric:

    Wonderful post!

    I would like to suggest a few ideas about what could be really considered fundamental for abiogenesis, before self-replication may become an acquired and important result. The following points are indeed well known, but they are often overlooked, with self-replication becoming the “darwinism supporting start”.

    So, here is a short list of what, IMO, is truly essential for life, and therefore for its origin:

    a) Establishing a separation between an inner environment and an outer environment, and generating definite differences between the two.

    That can seem a little bit strange, as a first point, but I am convinced that it is really where life as we know and understand it really begins.

    Life is a microcosm in a macrocosm. The two need to be different, because life has its own rules, and they are very strange rules, as we will see in the other points.

    That’s why life always needs a membrane. Now, darwinists know that very well, and that’s why all kinds of “natural membranes” appear here and there in bizarre OOL theories. But that will not do.

    A membrane for life is not simply a mechanical barrier. It is a fundamental part (not the only part) of what creates the difference between what is inside and what is outside. And the difference is the really important point.

    So, in biological beings as we know them, membranes are very complex, and very active. They are a real gate to another world.

    There should be no need to remind the importance of ion composition differences in most living cells between inner and outer environment, and the role that very complex machines like the sodium-potassium pump have in that process. That’s how most cells spend great part of their energetic resources: drawing sodium out and potassium in. That is also how electric potentials between inside and outside are created.

    b) Acquiring energy from the environment

    This is extremely important. Living beings are strange things, but the most strange thing in them is that they are irredeemable energy consumers. After all, they apparently and constantly violate the second law, and even darwinists admit that the only way to explain that (if it can be really explained) is that they receive energy from outside. All organic macromolecules, for example, are high energy molecules, and their synthesis requires energy support.

    OK, but what energy? Simply bathing in the sun will not do 🙂

    Living beings as we know them have very complex systems to derive energy from outside. Those who can do that without the help of other living beings are called “autotrophs”. We who depend on organic food are the “heterothrophs”.

    It stands to reason, probably even to darwinists, that OOL should be with autotrophs. OK, let’s assume that point.

    Now, there are two kinds of autotrophs. Phtoautotrophs and chemoautotrophs. IOWs, those who drive energy from light, and those who drive energy from high energy inorganic compounds. Both processes require complex metabolic pathways.

    Light is probably a little more complex. We all know how miraculous the absorption of light energy in living being is, with all its complexity and quantum aspects. I am not aware of OOL theories which really suggest that kind of process at the beginning.

    Chemical energy seems more promising, at least to darwinists. Volcanoes and ocean vents have a fascination fo their own, and believe me, it’s really fascination that darwinists need here, because they have nothing else.

    IMO, the most intelligent among OOL researchers are well aware of the priority of the energy problem. That’s why they usually adhere to the party which is called “metabolism first”. If I were a non design OOL researcher, I would do that too. Metabolism first, obviously!

    Unfortunately, the metabolism first pathway is as fascinating as devoid of any substance. Indeed, the only metabolism we know is in living beings, and it requires proteins, DNA, RNA, and a lot of other things. So, I really appreciate the metabolism first approach, but I am not sure what they are speaking of.

    c) Living “far from equilibrium”. IOWs, living an adventurous and dangerous life!

    This is eqyually important, and equally strange. It is in some way connected to the previous point, but it goes well beyond that.

    Indeed, the reason why living beings need energy is not only that they build high energy molecules. Having a lot of complex high energy molecules, but static, would be completely useless for our task. A protein repertoire is not a living thing.

    Just to give a brief overview of what “far from equilibrium” means, I quote here from the Cornell University Library:

    “Isolated systems tend to evolve towards equilibrium, a special state that has been the focus of many-body research for a century. Yet much of the richness of the world around us arises from conditions far from equilibrium. Phenomena such as turbulence, earthquakes, fracture, and life itself occur only far from equilibrium. Subjecting materials to conditions far from equilibrium leads to otherwise unattainable properties. For example, rapid cooling is a key process in manufacturing the strongest metallic alloys and toughest plastics. Processes that occur far from equilibrium also create some of the most intricate structures known, from snowflakes to the highly organized structures of life. While much is understood about systems at or near equilibrium, we are just beginning to uncover the basic principles governing systems far from equilibrium.”

    http://arxiv.org/abs/1009.4874

    So, living things are more similar to turbulence and earthquakes than to other natural objects. They are a process, rather than an object. And still they retain admirable form and function for long periods of time (usually called “life”), something that cannot always be said of turbulence and earthquakes.

    This is the main reason why, as often discussed here, even if we take all the components of a bacterium, and try to put them together, you cannot generate a living bacterium. IOWs, life comes only from life. Still true, still never falsified.

    Or, as Sal says, a dead dog remains a dead dog. Well, it seems that some on the other side have tried to doubt that. It would be beautiful to revive our dead pets (I am more for cats 🙂 ), but at present darwinism and materialism seem not to be enough.

    So, I really suggest that these three points are important. And often overlooked.

    If I were an OOL designer, and if I had found a good solution to all of them, then I would hurriedly look for a good way to write everything down (DNA, whatever is available) and to ensure that the final outcome may survive.

    And here is the final problem: far from equilibrium things cannot survive indefinitely. Their natural condition is to lose, in time, that miracle which is life.

    So, there seems to be only one solution left so that the idea may go on in time: self-replication.

  6. 6
    Eric Anderson says:

    Andre @1 and 4:

    Good thoughts. Yes, much of the problem with evolutionary thinking generally, and abiogenesis specifically, is that the alleged creative events reside at the level of vague generalizations and unspecific discussion. As soon as you start trying to get things working in the real world (essentially an engineering problem), you have to face the realities.

    I’ve said this before, but your thoughts reminded me of it, so I’ll say it again:

    The perception of evolution’s explanatory power is inversely proportional to the specificity of the discussion.

  7. 7
    Eric Anderson says:

    gpuccio:

    Fantastic comments, thanks!

    All three issues you highlighted are critical. I was going to talk a bit more about acquiring and using energy, but the post was already too long, so thank you for covering that.

    I particularly liked your description of the membrane creating “the difference between what is inside and what is outside,” with careful control mechanisms to maintain that state. The simple vesicles or bubbles or mud globules proposed as part of abiogenesis scenarios don’t represent a functional membrane in any meaningful sense.

  8. 8
    rna says:

    ” … The search for a self-replicating molecule is the Holy Grail of origin of life research. Indeed, you can take it to the bank that if a simple self-replicating molecule is ever discovered materialists will all but proclaim that the problem of life’s origin has been essentially solved.

    The reason the elusive self-replicating molecule is so critical … ”

    Günter von Kiedrowski, Angewandte Chemie International Edition, 1986, Vol 25, page 932 …
    “A self-replicating hexadeoxynucleotide”

    Quayle, J. M., Slawin, A. M. Z. & Philp, D. 2002, Tetrahedron Letters. 43, p. 7229-7233 “A structurally simple minimal self-replicating system” and reference cited therein

    So simple self-replicating molecules have been found already a long time ago.
    I don’t understand the statement cited above from your post. Please explain.

  9. 9
    groovamos says:

    What makes Dawkins so ridiculous with the comment is that the first replicatED molecule would have to search for or absorb nourishment, and process the energy input for this purpose. Meaning somehow to take in materials and metabolize, leading to another replication, which was somehow timed to occur with everything in place, requiring monitoring and regulating systems. Since the replicated molecule is a copy, then the first replicatING molecule could do all this too. Meaning the first replicating molecule was required to do a whole lot more than replicate. But it all came together by chance, made believable in an infinity of universes, none of them causal of course. But believable as part of the Landscape so I’m told, by dwellers thereof.

  10. 10
    gpuccio says:

    rna:

    The examples you quote are technically “self-replicating” molecules, but bear no relationship to the problem of OOL.

    What is really needed, the “Holy Grail”, is an information bearing molecule which can have catalytic action to self-replicate its information from non information bearing simpler molecules, so that it can undergo variation and selection.

    IOWs, what you need is a ribozyme which can self-replicate from simple nucleotides.

    As far as I know, that has not been found yet. I am not saying that it will not be found, such a molecule can exist in principle. But, if and when it is found, it will be the result of complex human engineering, it will be complex, and it will be well beyond any chance of random origin.

    As I quoted in a previous post, the best examples of that are at present ribozymes of almost 200 nts, still extremely inefficient, and they are the product of long and painful human engineering..

  11. 11
    Eric Anderson says:

    rna @8:

    Good question, thanks.

    I think what we’ll see in these cases, is that the enthusiastic titles and headlines are a bit ahead of the actual reality, though not as bad as in our 3D printer examples.

    Take the first article you mention, for example. I don’t have access to the full article, but the abstract says, in part:

    . . . in a system consisting of three oligonucleotides. A simple form of self-replication occurs, albeit only to a small extent: the template T organizes the building blocks Å and B in such a way that condensation can occur, leading to a second template molecule.

    In other words, if we take a molecule whose function is to fuse two molecules together, and then we split a copy of that molecule in half at the right place, the original molecule can, yes, perform its original function of fusing the two halves together. Very interesting work, to be sure, but we have to ask ourselves what exactly has been accomplished. In this case the chemist intelligently creates the constituent molecules, places them in proximity with the template molecule, and places it all in an environment that assiduously avoids interfering cross reactions. Even in this case, the authors do not claim to have produced a stable self-replicating molecular structure that would have any chance of working in the real world. Their claim is, appropriately, more modest: “a simple form of self-replication occurs, albeit only to a small extent.”

    What could that small extent be? A 2006 paper by Zhang and Yurke, A DNA Superstructure-based replicator without product inhibition

    http://www.dna.caltech.edu/Pap.....icator.pdf

    says, with respect to the Kiedrowski paper you cited, his subsequent work, and several similar template-based replication attempts:

    A characteristic problem of these systems is that the product remains bound to the template or competes with monomers for binding with the template. Such systems exhibit sublinear parabolic growth rather than exponential growth. The replication process tends to stall as the concentration of product increases.

    —–

    In a more recent and more well-known paper relating to the RNA-world approach to abiogenesis, Lincoln and Joyce onstensibly established the ability of RNA to self-replicate.

    However, Stephen Meyer notes:

    Instead, in Lincoln and Joyce’s experiment, a pre-synthesized specifically sequenced RNA molecule merely catalyzes the formation of a single chemical bond, thus fusing two other pre-synthesized partial RNA chains. In other words, their version of “self-replication” amounts to nothing more than joining two sequence specific pre-made halves together. More significantly, Lincoln and Joyce themselves intelligently arranged the matching base sequences in these RNA chains. They did the work of replication.”

    —-

    If I get a chance in the next day or two, I’ll try to look up the Quayle article you mentioned.

  12. 12
    Eric Anderson says:

    groovamos @9:

    It might, at some future point, be the case that a simple legitimately self-replicating molecule is discovered or designed. However, for anything to function in the real world, particularly as it evolves and becomes more complex, the things you cite are absolutely right: ability to take in materials, metabolize, monitoring, regulation. And of course all of those systems then have to be replicated as well! It quickly compounds into an unbelievably challenging engineering problem.

    —–

    By the way, I mentioned Dawkins because his happened to be the quote I ran across recently, but maybe I shouldn’t be so hard on him. In fairness, he acknowledges that origin of life isn’t his specialty, so he is probably just parroting the party line.

    On the other hand . . .

    I heard Dawkins on NPR not too long ago making the absolutely outrageous statement that “we have a pretty good idea” how life started. An intellectually irresponsible thing to say, particularly to a public audience. That kind of statement can only be borne of either incompetence or deception. So he probably deserves any ridicule that comes his way.

  13. 13

    Eric,

    This is an excellent post.

    As usual your writing is very clear, easy to follow and a pleasure to read.

    I found significant value for the reader in the way you conduct the developing analysis of what a true self-replicating 3D printer would do (or would mean). And this developing analysis reveals step by step the layered complexity lying at the core of a true, concrete and autonomous self-replicator.

    It is a royal way of presenting to the reader the portrait of a self-replicator and also, a little bit of the consequences introduced by a hypothetical evolution paradigm on top of a self-replication foundation.

    One more detail to your analysis is that probable the most demanding parts of a true self-replicating 3D printer will be the electronic components , actually the semiconductor components in – I suppose – the printer controller, maybe a highly integrated circuit or a low level microprocessor.

    This means that our wonder self-replicating 3D printer must have a semiconductor fabrication facility , maybe a “clean room” with controlled climate and air purity. This extension of the story makes even clearer the difficulties of implementing a real self replicator. And the electronic components (the highly integrated circuits and/or microprocessors) will be needed not only for the printing controller but also for:

    – All robotic arms /manipulator/assemblers

    – For the computers that run the software that animates such robots/manipulators/assemblers.

    – For the fabricator components that fabricate the metal parts of the robots, the wires, etc.

    Another dimension of the inherent complexity of an autonomous 3D self-replicator is the availability of all the raw materials and substances (iron, carbon, silicon, primary raw materials for fabricating plastics, various chemicals needed in electronics manufacturing) in the environment where the 3D printer “resides” and its ability to extract such materials from its environment and to process them into “ready-for-fabrication” substances.

    As you already emphasized the complete autonomy of the self-replicating 3D printer (and in general of any real self-replicator) is extremely demanding and unimaginable difficult to accomplish in real-life.

    I want to make a speculative claim also: a hypothetical self-replicating molecule is a logical impossibility.
    (I guess this is my homework to see if I can prove this claim).

    Also a single self-replicating molecule is not a genuine self-replicator since the “original thing” must have at least 3 parts: an enclosure, one gateway on the enclosure and (at least) one interior element. (the intuition here is that one single original element cannot be at the same time: 1. Enclosure, 2. Self-replicating thing.)

    Now I want to tell that I do not really understand your thinking when you say:

    The abiogenesis paradigm – with self-replication as the starting point, the initial characteristic, of life – stands in stark contrast to physical, chemical and engineering realities. Self-replication – the ability to timely and faithfully and accurately reproduce one’s own kind – far from being the first step, in fact lies at the end of a complex, carefully-coordinated, precisely-modulated, exquisitely-orchestrated, functionally-specified, information-driven process

    If a the Hypothetical First Cell passed through – what it appears you say – some preliminary “developing” stages of increased complexity – it is a paradigm that does not fit a blind sequence of random natural happenings. It can be empirically and logically stated that in order that abiogenesis to succeed it must pass (at the 1st attempt or at the bazillion attempt) through a “real self-replication ability state”. And this being the most demanding state that is implied for a successful abiogenesis is natural to study it, its logical derivations and demands in order to reason about the possibility that such a state can be achieved by pure chance. So I don’t see here what is what you call the “inverted order” or something like that. Briefly stated: the self-replication is the sine qua non passing test for abiogenesis.

    As I afirmed in the Minimum Cell Model the real challenge for abiogenesis is to – miraculously “collect” all needed pieces of the mechanism in the same place (inside an enclosure) at the same time, to have these pieces engaged with each other in the proper way and together to function as if designed for a productive purpose: the production of an exact replica.

    Self-replication – the ability to timely and faithfully and accurately reproduce one’s own kind – far from being the first step, in fact lies at the end of a complex, carefully-coordinated, precisely-modulated,…..

    I am not sure what is your point here.

    Maybe you can explain this. If there were some preliminary steps to achieve only functions F1, F2, F3 from the total Series of functions: F1, F2, F3, …, F100, those preliminary steps are irelevant for the success of the abiogenesis and will be forever lost (they have no consequence) in the mist of mythical history of abiogenesis.

    What is IMPORTANT is that ALL F1, F2, ….. , F100 functions (to use a simplifying scheme where Fk may mean either a needed component or a needed relationship between components) MUST be ALL present at the “testing” time.

    This is the single element of your post that I would like to understand. Maybe I am not reading it correctly.

  14. 14
    Eric Anderson says:

    InVivoVeritas @13:

    I want to make a speculative claim also: a hypothetical self-replicating molecule is a logical impossibility.

    Well, that is why I literally laughed out loud when I read Dawkins’ statement. This self-replicating molecule is a key part of the abiogenesis idea, of the materialist creation story. Yet no-one has ever, to my knowledge, seen or even engineered such a thing. I also suspect such a thing has never existed.

    In theory I think a self-replicating molecule might be technically possible, but it would be a single “molecule” only by dint of having multiple functional parts linked together to make it a “single” molecule. In other words it would really be a molecular complex, but could perhaps technically be called a “single” molecule if it is all bound together. Even then, however, such an entity would have little chance of functioning very long in the real world (certainly not in a chaotic primordial soup) without a protective membrane and the other capabilities you mention.

    Thus, I would say that although a self-replicating molecule might be theoretically possible, it would be a rather complicated beast and would be limited to functioning only in the protective lab environment, with no chance of functioning in the real world.

    My view is that the hypothetical self-replicating molecule required by the abiogenesis story is just that — a hypothetical. Something that has existed only in the minds of theorists. As a result, the abiogenesis story itself is just that — a story.

    This is a large part of what I am trying to point out. Most critiques of abiogenesis focus on the reducing atmosphere, or the difficulty of forming particular polymers, or the homochiralty problem, or the need to infuse information. Many critics either grant or assume that it is possible to have a self-replicating molecule, but point out other problems with the abiogenesis paradigm.

    These critiques are all true and constitute a devastating indictment of the abiogenesis paradigm, particularly the need for infusion of information. Yet the abiogenesis proponent keeps falling back on the idea that if they can just get a simple self-replicating molecule going, then natural selection will take care of all the rest, including the information infusion. (This is precisely the tactic used by AVS, for example, in his recent exchanges on the other thread).

    So I am going a step further in my critique and taking away this last refuge of the materialist creation story. I argue that the very idea of a self-replicating molecule is nonsense. The very notion of self-replication being the first step (or even an early step) in the creation process is fundamentally flawed at the deepest level. That being the case, then the materialistic creation story never gets to the point where the magic of natural selection can be called upon. The whole enterprise never gets off the ground.

  15. 15
    Eric Anderson says:

    InVivoVeritas @13:

    This is the single element of your post that I would like to understand. Maybe I am not reading it correctly.

    I think we’re on the same page.

    Maybe I can describe it this way. Abiogenesis stories typically work something like this:

    random chemical reactions -> simple self-replicating molecule -> infusion of information -> generation of complex molecular apparatus, sophisticated membrane, control mechanisms, etc.

    However, in the real world, from a fundamental engineering standpoint, in order to have stable self replication, we need those molecular apparatus and mechanisms. Thus, the real path to self-replication is:

    careful planning and design* -> infusion of information -> generation of complex molecular apparatus, sophisticated membrane, control mechanisms, etc. -> self replication

    Thus, the abiogenesis story has it exactly backwards. It posits the idea that self-replication can be a simple, first step in the evolutionary process — the step from which all others, including information infusion, arise. But self-replication is not a simple process; it is not something that can function properly without all those other systems and all that information already in place. As you say, self-replication requires all those other things in order function properly. So we can’t start with self-replication, we have to start with those other things.

    So the idea of self-replication being the starting point is precisely backwards. It is fundamentally flawed. The only reason the idea lives on is because people don’t carefully think through what is required for self-replication. If they did they would realize we can’t start with self-replication. Rather, self replication is the result of having information, a sophisticated membrane, energy acquisition apparatus, copying and construction mechanisms, controls and so on.

    —–

    * Note: This step, at least in theory, could be replaced with “random chemical reactions.” There is of course no evidence that such reactions could produce information and sophisticated molecular machines. So there is an evidentiary problem with that approach. But at least it would be a logically coherent approach, in that it would recognize the fact that self-replication cannot function without information and the various molecular apparatus in place.

  16. 16
    rna says:

    Eric Anderson @11:

    I quoted the Kiedrowski paper from 1986 on purpose because it is the first “proof of principle” description for a simple self replicating molecule and since your post explicitly mentioned a simple self-replicating molecule.

    “… Indeed, you can take it to the bank that if a simple self-replicating molecule is ever discovered …” – Remember?

    Of course research has not stopped there. For instance the problem with product inhibition observed in this early example which you mentioned has been overcome in other systems:

    e.g.

    Wang and Sutherland, Chem. Comm., 1997, 1495

    Kindermann et al. Angewandte Chemie Int. Ed., 1991, Vol. 41, 6908
    “Systems Chemistry: Kinetic and Computational Analysis of a Nearly Exponential Organic Replicator”

    Kassianidis and Philp, Angewandte Chemie Int. Edition, 2006, vol. 45, 6344 …

    In addition, self-replicating systems with more than three building blocks have been developed. There are systems were self-replication functions faithfully in the presence of competing reactions and in the presence of other molecules and inhibitors (not yet the chaotic primordial soup you mention but still …).

    So stable self-replicating molecules are not just a theoretical possibility as you state in @14 but a practical experimental reality.

    It is also interesting to note that a number of different classes of molecules are capable of self-replication. So the ability to self-replicate is apparently nothing exotic in the world of chemistry or somehow restricted to biomolecules.

  17. 17
    rna says:

    gpuccio @10

    “The examples you quote are technically “self-replicating” molecules, …”

    So what is the difference between technically “self-replicating” molecules and really self-replicating molecules?

    “… What is really needed, the “Holy Grail”, is an information bearing molecule which can have catalytic action to self-replicate its information from non information bearing simpler molecules …”

    So some of the building blocks used for the construction of self-replicating molecules by chemists for instance have the ability to form 3 hydrogen bonds in a spatially defined manner, undergo stacking interactions etc. … Thus, their “information content” is very similar to the “information content” of a nucleotide as the building block of dna/rna. The organic self-replicators contain exactly the amount of information needed to make copies of themselves even in the presence of competing reaction pathways, inhibitors etc. …

    Or do you think that nucleotides do not contain information and only rna/dna does?

    “… As I quoted in a previous post, the best examples of that are at present ribozymes of almost 200 nts, still extremely inefficient, and they are the product of long and painful human engineering…”

    That is in my opinion a slightly twisted description of what happens in the selection experiments from where these ribozymes come.
    The selection starts with a random pool of sequences, normally 10Exp14-15 molecules. For the experiment it is desirable to have the sequences in the pool as random as possible. The “engineering” part as you call it goes into the methods to fish out those sequences from the pool that have the desired function from this random pool.
    It is a bit as saying that the jupiter moons are engineered because galileo designed the telescope he used to observe them.

  18. 18
    gpuccio says:

    rna:

    Very simple answers:

    a) “Technically” just meant that they are self-replicating, but not in the sense that could help an OOL rna based theory. Nothing more. Those systems are too simple, and in no way can help explain the generation of complex informational molecules, like a ribozyme.

    b) Nucleotides do not contain the kind of information we usually refer to in ID, for example, using my terminology, dFSCI. That kind of digital information is linked to a sequence of nucleotides or AAs, and is exactly the information that is passed in cell reproduction. You certainly understand very well that RNA has been chosen for a faschionable OOL scenario exactly because it has two properties: digital information content that can be transmitted in reproduction, and catalytic activity. So, it sums up some of the qualities of DNA and of proteins. The informational content is linked to the nucleotide sequence, which is then related to chemical prpoperties of the final molecule. It is something completely different from the chemical information that every molecule has for the simple fact that it exists. Life is based on digital information expressed as a sequence of basic molecules (an alphabet). If we are trying to explain OOL, that’s the kind of information that we must explain. That’s the kind of information that must be self-reproduced.

    c) Here, you seem not to understand a fundamental difference that has been debated many times here. Those molecules are the result of human engineering. It is that kind of bottom up engineering that uses random variation as part of the algorithm, and intelligent selection. It is design in every sense. It is completely different from the supposed algorithm in neo darwinisn theoy, which depends on random variation and natural selection.

    The fundamental difference between NS and IS, and in their abilities and powers, has been debated many times here. IS is always design, and it confers huge advantages to the system. IS is very powerful. NS is not. I will not go into detail now, but if you want we can deepen that discussion.

    Your final example with Galileo is pointless. Galileo observed the jupiter moons, but did not select them out of many other things for any further intervention in an experiment. That has nothing to do with what we are debating, as should be obvious to you too.

  19. 19
    Eric Anderson says:

    rna:

    The Kiedrowski paper from 1986 was not an example of a self-replicating molecule, as I’ve already discussed above, notwithstanding the title of the paper or the headlines.

    If you’ll permit me to retain my skepticism for a while longer, I suspect the other papers you cited are also not examples of a self-replicating molecule. There have been too many claims and headlines over the past 30 years for me to buy in without further review and a healthy dose of skepticism. Nevertheless, thanks for the papers you mentioned. Hopefully I can get a chance to look at them soon.

    Please note, I have no doubt that a self-replicating system can be developed. But a single self-replicating molecule, I doubt it.

    I would be very interested in a truly, legitimate self-replicating molecule. Then I would be interested to know whether such molecule has any realistic chance of forming on its own, rather than being carefully constructed with specific procedures in the lab. Then I would want to know whether it could exist outside of the lab in real-world conditions.

    Think what is required for a self-replicating molecule, as proposed by abiogenesis. At a minimum:

    – The molecule has to form under natural conditions, without help from a lab technician.

    – The molecule then has to be able to make copies of itself by locating and ordering specific atoms or small molecules, not by simply catalyzing a reaction between previously-prepared sections of itself (like the original Kiedrowski paper you cited, or the more recent RNA example by Lincoln and Joyce).

    – The molecule has to be stable enough to exist in real-world conditions (the proverbial primordial soup) without breaking down too quickly and without getting bogged down with interfering cross reactions.

    – The molecule, at least to be a precursor for evolution, must have the capacity to mutate, while still retaining the ability to faithfully replicate its now-mutated self.

    Let me know if you are aware of anything that meets these basic requirements.

    As far as I am aware, there is nothing like this that has been discovered. This of course also does not address the additional challenge of the self-replication process needing to be reacquired on a nearly constant basis as the alleged proto-organism increases in complexity and capability, but that is a separate issue.

  20. 20
    bornagain77 says:

    rna, What is your definition of ‘life’? As far as I can tell, the most basic definition of life for an atheist/materialist is defined as the capacity of a set of molecules to self replicate and undergo Natural Selection:

    WHAT DID FIRST LIFE LOOK LIKE?

    “I really think that the crucial step, where I would say that these molecules became lifelike, is when two types of polymers cooperated with each other.”
    —Nicolas Hud, Georgia Tech

    “I think you don’t really have life until you’ve got natural selection operating, and I don’t see it as operating on anything less than something like RNA.”
    —Nick Lane, University College London

    “A self-sustaining chemical system capable of evolution. If I’m in a dark alley with a gun to my head, that’s the definition I’m going to give.”
    —Niles Lehman, Portland State University

    “It’s hard to define life, a satisfying definition for life, but basically all of them, I think, would have the word evolution in them. If you don’t have a system that is capable of Darwinian evolution, then it’s hard to make an argument that it’s a living system.”
    —Michael Robertson, Scripps Research Institute
    http://www.the-scientist.com/?.....World-2-0/

    In my personal opinion, something has been severely ‘lost in translation’ with the materialists definition of life.,,, The Bible has a far different, and more clear, definition of what is dead and what is alive:

    Biblical Definition of Death as separation
    Excerpt: 1. Physical Death
    The separation of the body and soul

    2. Spiritual Death
    The separation of the man from God

    3. Hell as the second spiritual separation from God
    http://www.bible.ca/d-death=separation.htm

    But in order for the Theistic claim to be true, that life comes from God (and that life does not end with the death of our temporal bodies), there must be something beyond space in time present within life. Do we evidence of such a beyond space and time, i.e. transcendent, entity within molecular biology? Yes! There is evidence of ‘non-local’, beyond space and time quantum information/entanglement in the molecular biology of living organisms on a massive scale:

    Quantum Information/Entanglement In DNA – short video
    http://www.metacafe.com/watch/5936605/

    It is very interesting to note that ‘non-local’ quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (Bell, A. Aspect, A. Zeilinger) Appealing to the probability of various configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!

    Also of note, this ‘quantum information’ that is found in molecular biology on a massive scale is also found to be ‘conserved’:

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

    Quantum no-deleting theorem
    Excerpt: A stronger version of the no-cloning theorem and the no-deleting theorem provide permanence to quantum information. To create a copy one must import the information from some part of the universe and to delete a state one needs to export it to another part of the universe where it will continue to exist.
    http://en.wikipedia.org/wiki/Q.....onsequence

    also of note, matter and energy both reduce to ‘non-local’ quantum information. Quantum information does not reduce to matter and energy as the Materialists/Atheists presuppose:

    Quantum Teleportation of a Human? – video
    https://vimeo.com/75163272

    Moreover,

    The Unbearable Wholeness of Beings – Steve Talbott
    Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.
    ,,,Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity.
    http://www.thenewatlantis.com/.....-of-beings

    So where does this quantum information go upon the death of an organism if it cannot be destroyed? i.e. Do all dogs go to heaven?

    In regards to materialism being unable to explain any of this quantum stuff coherently, it is interesting to note that Theism has always postulated a transcendent component to man that is not constrained by time and space. i.e. Theism has always postulated a ‘living soul’ for man that lives past the death of the body!

    Genesis 2:7
    “And the LORD God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.”

  21. 21
    bornagain77 says:

    Of somewhat related note to the preceding Bible verse, ‘non-classical’ biophotonic emission from humans is greater in the facial area:

    Photocount distribution of photons emitted from three sites of a human body – 2006
    Excerpt: Signals from three representative sites of low, intermediate and high intensities are selected for further analysis. Fluctuations in these signals are measured by the probabilities of detecting different numbers of photons in a bin. The probabilities have non-classical features and are well described by the signal in a quantum squeezed state of photons. Measurements with bins of three sizes yield same values of three parameters of the squeezed state.
    http://www.ncbi.nlm.nih.gov/pubmed/16520060

    Strange! Humans Glow in Visible Light – Charles Q. Choi – July 22, 2009
    Schematic illustration of experimental setup that found the human body, especially the face, emits visible light in small quantities that vary during the day. B is one of the test subjects. The other images show the weak emissions of visible light during totally dark conditions. The chart corresponds to the images and shows how the emissions varied during the day. The last image (I) is an infrared image of the subject showing heat emissions.
    http://i.livescience.com/image.....1296086873

    ‘I was in a body and the only way that I can describe it was a body of energy, or of light. And this body had a form. It had a head. It had arms and it had legs. And it was like it was made out of light. And ‘it’ was everything that was me. All of my memories, my consciousness, everything.’ –
    Vicky Noratuk’s Near Death Experience (Blind From Birth) part 1 of 3 youtube

    Of somewhat related note, the facial area on the Shroud of Turin received a greater intensity of ‘non-classical’ light from the facial area in the formation of the image:

    Shroud of Turin – The Historical Trail
    2004: Another result of the restoration was the discovery of the Shroud’s double face image. Italian scientists, Giulio Fanti and Roberto Maggiolio of Padova University were able to analyze scans of the backside of the Shroud after it was removed from the backing cloth. This had never been done before. The previous backing cloth had been attached since 1534 as part of the restoration following the fire of 1532. Examining the scans revealed faint superficial images of the face and hands. The image occurs only on the top surface of the fibers, similar to the front side of the Shroud but there is no coloring of the threads in between.
    http://shroud2000.com/FastFacts.html

    The absorbed energy in the Shroud body image formation appears as contributed by discrete values – Giovanni Fazio, Giuseppe Mandaglio – 2008
    Excerpt: This result means that the optical density distribution,, can not be attributed at the absorbed energy described in the framework of the classical physics model. It is, in fact, necessary to hypothesize a absorption by discrete values of the energy where the ‘quantum’ is equal to the one necessary to yellow one fibril.
    http://cab.unime.it/journals/i.....802004/271

    Scientists say Turin Shroud is supernatural – December 2011
    Excerpt: After years of work trying to replicate the colouring on the shroud, a similar image has been created by the scientists.
    However, they only managed the effect by scorching equivalent linen material with high-intensity ultra violet lasers, undermining the arguments of other research, they say, which claims the Turin Shroud is a medieval hoax.
    Such technology, say researchers from the National Agency for New Technologies, Energy and Sustainable Economic Development (Enea), was far beyond the capability of medieval forgers, whom most experts have credited with making the famous relic.
    “The results show that a short and intense burst of UV directional radiation can colour a linen cloth so as to reproduce many of the peculiar characteristics of the body image on the Shroud of Turin,” they said.
    And in case there was any doubt about the preternatural degree of energy needed to make such distinct marks, the Enea report spells it out: “This degree of power cannot be reproduced by any normal UV source built to date.”
    http://www.independent.co.uk/n.....79512.html

    Moreover, ‘life’ is found to precede material reality. In fact, due to advances in quantum mechanics, the argument for God from consciousness can now be framed like this:

    1. Consciousness either preceded all of material reality or is a ‘epi-phenomena’ of material reality.
    2. If consciousness is a ‘epi-phenomena’ of material reality then consciousness will be found to have no special position within material reality. Whereas conversely, if consciousness precedes material reality then consciousness will be found to have a special position within material reality.
    3. Consciousness is found to have a special, even central, position within material reality.
    4. Therefore, consciousness is found to precede material reality.

    Four intersecting lines of experimental evidence from quantum mechanics that shows that consciousness precedes material reality (Wigner’s Quantum Symmetries, Wheeler’s Delayed Choice, Leggett’s Inequalities, Quantum Zeno effect):
    https://docs.google.com/document/d/1G_Fi50ljF5w_XyJHfmSIZsOcPFhgoAZ3PRc_ktY8cFo/edit

    That pretty much blows a hole in your definition of life as merely self-replication doesn’t it rna? But why would you look for the living among the dead in the first place?

    Verse and Music:

    In their fright the women bowed down with their faces to the ground, but the men said to them, “Why do you look for the living among the dead?

    Lucie Silvas – Nothing Else Matters
    http://www.youtube.com/watch?v=QohUdrgbD2k

  22. 22
    Mung says:

    From the OP:

    Heather Catchpole: Have you put any thought into the beginning of life and into what kicked that off?

    Dawkins: Not personally.

    ‘Nuff said.

  23. 23
    Mung says:

    gpuccio:

    So, here is a short list of what, IMO, is truly essential for life, and therefore for its origin:

    a) Establishing a separation between an inner environment and an outer environment, and generating definite differences between the two.

    That’s the really short list!

    b) Acquiring energy from the [outer] environment

    Across the membrane. See a).

    c) Living “far from equilibrium”.

    See a).

  24. 24
    Eric Anderson says:

    rna:

    Tentatively, it looks like my suspicions have been borne out.

    I’ve now looked at a summary of the 2006 Philip paper you mentioned (as well as the later 2008 study. Interesting work, to be sure, and Prof. Philip and his colleagues should be commended for their efforts.

    Again, however, this is essentially a situation in which the researcher builds component parts of a molecule that can bind to each other.

    At most, this kind of situation might be called “guided replication”, but it is not a situation in which a molecule is actually self-replicating from basic elements.

    Again, if a replication requires the hand of the researcher to help get the replication going (to build the subcomponents, for example), then it is, by definition, not “self” replication.

    —–

    I’m just thinking out loud here, but maybe we need to distinguish between simple chemical reactions in which A automatically binds to B from a replication process in which the replicating system actually controls the process in some manner.

    For example, there is no question that we can inject two types of atoms/molecules that have binding affinity into a beaker and they will begin to bind together to form a new product. But we wouldn’t refer to that as any kind of self-replication. The reaction will simply continue by pure biochemical necessity until the components are exhausted or until an equilibrium is reached in the solution. It is pretty clear that this is not of any help in getting the abiogenesis process off the ground.

    How much farther along are we if we do the same thing, but this time instead of, say, an inert product, we use components of a catalyst for that particular reaction? As the components come together in the mixture they form a catalyst, which in turn speeds the formation of similar catalysts. Yes, it goes faster in an exponential fashion. Yes, at first blush it seems like we might be witnessing some form of “self-replication.” But the catalyst wasn’t really performing a replicative function. All it was doing is its normal catalytic job which — due to the researcher’s prior careful selection of component molecules — just happened to result in production of more catalyst.

    Substantively, we end up at the exact same result as we did with our first example. Namely, the reaction continues until either the reaction takes over the solution or, if applicable to the particular situation, equilibrium is reached.

    In either case all we have witnessed is a basic downhill chemical reaction, one that just continues until it runs out. I’m not sure there is anything here that could be called self-replication in any meaningful sense.

    It doesn’t seem to represent any self-replication situations that we see in the living world. Certainly not anything that exhibits control over the process, that has the ability to create anything that is not a pure driven-by-necessity chemical process, nothing that is able to build strings that aren’t linked by chemical necessity (nucleotide strings, for example), nothing that is able to create and maintain a far-from-equilibrium environment like living cells do.

  25. 25
    scordova says:

    Great discussion Eric, sorry I couldn’t participate this round, I’m tied up on my own threads. I’m glad you talking about 3D printing, people need to appreciate how difficult it is to make a 3D copy!

  26. 26
    gpuccio says:

    Mung:

    Thank you for the simplification! 🙂

  27. 27
    Eric Anderson says:

    BA77 @20:

    It is an intellectual travesty that some people have gotten so enamored with the concept of evolution, indeed the specific Darwinian version of evolution, that they think life should be defined in terms of Darwinian evolution.

    I fully recognize that life is an enigma at some level and that defining it to satisfy every corner case is exceedingly difficult, perhaps impossible. But using Darwinian evolution as though it were the sine non qua of life demonstrates a thoroughly unwholesome worship of evolution. Unfortunately, to the materialist mindset all reality is a process of evolution, so they tend to think it underscores everything and “explains” everything.

    It is a trivial matter to think of a living organism that would not undergo Darwinian evolution. For example, let’s suppose there were a single-celled organism that replicated faithfully without fail. No mistakes or mutations or deletions or insertions. Generation B is identical to A, and C is identical to B. Would we say that such an organism is not a form of “life” because it cannot undergo evolution? Of course not. Furthermore, most forms of life on Earth have never been known to undergo Darwinian evolution (assumed, yes; but not demonstrated), so it doesn’t make sense to define them in terms of an unknown, hypothetical event that may or may not have occurred.

  28. 28
    gpuccio says:

    Eric:

    I think that the only problem here is of words.

    rna is using “self-replicating molecule” in a very literal chemical sense, and that can be correct, but it is not of any use in the discussion about OOL.

    We are using the concept in a different perspective. That’s why I have tried to clarify that what is needed is “a self replicating molecule which can be an useful first actor in an OOL scenario”, in the sense that it bears digital information which can be replicated by itself and passed to daughter cells. IOWs, at least a ribozyme which can self-replicate from simple nucleotides.

    I have also clarified that in principle such a molecule can exist, but long and painful years of human engineering have not yet been able to design it.

    rna has tried to argue that human engineering is not engineering, giving us a new example of an intelligent person who has to use explicitly wrong arguments when he has to defend what cannot be defended.

    Obviously, even if and when a self-replicating ribozyme is engineered, the following little problems remain:

    a) Could it arise in a non design way? The answer will be: no! (this is a prediction 🙂 ). And please, don’t tell me that RV + NS can do it! They can’t, but that is not the point here.

    The point here is that NS, whatever it can or can’t do, is simply not there unless and until we have at least a self-replicating ribozyme. Otherwise, we go back to AVS fairy tales about “selection” acting on inorganic molecules which have inadvertently been trapped in some “membrane”.

    b) What is the environment needed? Almost certainly, the human ribozyme will need extremely favorable lab conditions, first of all high concentrations of available nucleotides. None of that can be explained by any reasonable theory.

    c) Where did the energy come from? Polymerization requires energy.

    d) How did the membrane divide regularly, without simply destroyng the “protocell”?

    And so on, and so on…

  29. 29
    gpuccio says:

    Eric:

    It is an intellectual travesty that some people have gotten so enamored with the concept of evolution, indeed the specific Darwinian version of evolution, that they think life should be defined in terms of Darwinian evolution.

    You are being very generous here!

    I would define it one of the most infamous examples of cognitive dishonesty and arrogance in the history of human cognitive activity. And that’s just because I am in a compassionate mood 🙂

    Its only rightful companion, in that sense, is the infamous “statistical” argument which comes in many forms (hand of cards, lottery, etc.) and which states that unlikely events happen all the time.

    Well, no, that one is simply stupid. So, the darwin-centered definition of life is still the most infamous.

  30. 30
    Eric Anderson says:

    gpuccio @28:

    Thanks for your comments.

    I understand you are willing to grant, for purposes of discussion, that the examples rna has referred to are “self-replicating.”

    It is also true, that the most challenging issues for abiogenesis have to do with information content and control. I like your phrase: “a self replicating molecule which can be an useful first actor in an OOL scenario.”

    That said, the examples rna has given (and every example I have seen thus far to date) are not self-replicating. They are simple downhill chemical reactions that were set up and made possible by an intelligent lab technician. We should not call them self-replicating molecules, because they aren’t. Not in any meaningful sense of the word. It doesn’t matter what the paper titles or headlines say. We should not concede that self-replicating molecules can and do exist until we are actually shown such a thing.

    There are numerous, insurmountable problems with abiogenesis. My primary thrust in the OP was to focus on what is required for self-replication in the real world, and the fact that such a characteristic has to be essentially re-acquired at every step along the way.

    However, as a secondary point, I also want to put some pressure on the abiogenesis story by challenging the most basic and foundational assertion about how life came about: the formation of a simple self-replicating molecule in early Earth conditions. Many people (like you have done on this thread) are willing to grant the existence of self-replicating molecules. I am not. Not until I actually see one. Until someone can give us an example of a molecule that meets at least the 4 criteria I outlined @19 above, we should continue to put pressure on this part of the abiogenesis story. Independent of information infusion and molecular machines and the like.

    Maybe it is just a question of degree, and I take your point about definitions. But I think there is value in requiring abiogenesis proponents to actually demonstrate that the very first step of abiogenesis, the basic foundational entity at the start of the great tree of life, is not just a figment of our imagination.

  31. 31
    Eric Anderson says:

    Sal, thanks for the kind comments. Lots of good discussion on various threads the last few days!

    Eric

  32. 32
    johnp says:

    “If you don’t have a system that is capable of Darwinian evolution, then it’s hard to make an argument that it’s a living system.”

    Does that mean that Coelacanths (and other “living fossils” are not living systems?

  33. 33
    Mung says:

    gpuccio@26:

    You are most welcome sir!

    The greatest barrier to the origin of life is, well, the barrier. 🙂

    If it’s outside the barrier, how does it get in?

    If it’s inside the barrier, how does it get out?

    If we have RNA or some other medium that might serve as a repository for the stored representation of information inside the membrane, where do the materials come from?

    What is the simplest scheme under which particles might move cross a membrane (in either direction) and what are the limits upon which particles may or may not pass across the barrier by such means?

    How do we assemble those materials into RNA/DNA?

    How do we get from diffusion, etc, to transport and pumps!?

    Diffusion, Osmosis, and Movement Across a Membrane

    In my humble opinion, this is a great untapped resource of ID exploration.

    But you are so right dear friend:

    Establishing a separation between an inner environment and an outer environment, and generating definite differences between the two.

    But I think the problem is so much greater than most people realize. They have no idea of the complexity of cell membranes, nor what it would take to get from some “primitive” membrane to what we have today.

    cheers

  34. 34
    Mung says:

    Eric:

    I also want to put some pressure on the abiogenesis story by challenging the most basic and foundational assertion about how life came about: the formation of a simple self-replicating molecule in early Earth conditions. Many people (like you have done on this thread) are willing to grant the existence of self-replicating molecules. I am not. Not until I actually see one.

    Oh my, you must have missed this thread, in which numerous examples of self-replicating molecules were presented for our inspection.

  35. 35
    Mung says:

    not really

  36. 36
    Eric Anderson says:

    Mung:

    That is a great page you linked to regarding diffusion, osmosis and movement across a membrane. Great stuff to think about.

    A bit of reflection is adequate to realize that even “simple” stuff like a passive membrane letting materials in by diffusion/osmosis, is not a “simple” matter.

    For example:

    Movement of water into a cell can put pressure on plasma membrane. Animal cells will expand and may burst. Some cells, such as Paramecium have organelles called contractile vacuoles which are basically little pumps which pump excess water out of cell.

    Sheesh, now we need pumps too, just to keep from blowing ourselves up!

    Lots to think about.

  37. 37
    gpuccio says:

    Eric:

    I am always willing to concede, when I know that I win anyway! That makes me look more openminded 🙂

  38. 38
    Eric Anderson says:

    Question for anyone who might know:

    How many “functions” does a single molecule typically have? For example, a molecule might assist with binding, it might be a catalyst, it might be a receptor, it might be a transporter, etc. Other molecules might be relatively inert on their own.

    In other words, is it common for a single molecule to perform more than one activity/function? Do we know of any specific examples, or perhaps any wild guesses as to how many molecules can perform more than one function?

    Thanks,

  39. 39
    scordova says:

    Self replication isn’t in and of itself the most important distinction for life. There are many self-replicators in nature, like crystals.

    The sort of self-replication in life isn’t spontaneous, and isn’t the expected outcome — that’s what makes life special.

    When I first studied the question in detail, I have to admit I thought there was a chance the problem was getting solved by things like the ghadiri peptide, which was an autocatylic reaction. Even the arguments for self-ordered crystals was compelling for a few minutes.

    Robert Hazen, Harold Morowitz and others advocate self-ordering properties of chemicals. But those explanations fail because the chemical properties of the molecules of life actually have slightly self-disordering and self-disorganizing qualities outside of organisms.

    Perhaps to illustrate with a house of cards. Cards left to themselves on a table subject to perturbation (wind, earthquakes, or other distrubances) will tend to remain un-organized. However they can be made to become a delicate structure of interdependent parts (cards) that make the whole (house of cards) possible.

    The OOL question is how parts that would normally not organize when left to themselves end up in an organized state where they are interdependent and are able to replicate similar interdependent structures.

  40. 40
    franklin says:

    In other words, is it common for a single molecule to perform more than one activity/function?

    well, yes it is common.

    Do we know of any specific examples, or perhaps any wild guesses as to how many molecules can perform more than one function?

    yes, there is no need to make any wild guesses when a bit of study of biochemistry (some very basic at that) provides the answer.

    For example: Hemoglobin, nitric oxide, sodium, and epinephrine as a four quick examples.

    Funny that you ask such a question.

  41. 41
    gpuccio says:

    Eric:

    The answer is yes, but there are different aspects that must be considered.

    For example, complex multi-domain proteins have many functions (each domain has usually one or more different biochemical function), which usually are part of a global meta-function.

    Enzymes have usually the main function of catalyzing a specific reaction, but they can have other functions too.

    A special case is that of molecules which act as transmitters of signals, for example peptidic hormones like insulin, and intracellular signal pathways. Hormones which bind to membrane receptors activate a signal which is in many ways transmitted to the nucleus. That signal can have different meanings in different cells, and activate different responses, even if the hormone is the same. The same is true of the pathways which transmit the signal from the membrane to the nucleus. The same pathway can generate different responses in different cells, or even according to the modulation of other signals and pathways. It is a system which is very similar to a neural system.

  42. 42
    Eric Anderson says:

    Sal:

    There are many self-replicators in nature, like crystals.

    Nonsense. 🙂

    Crystals do not self-replicate. Crystals form when a precipitate distills out of a solution. And it occurs by pure dint of elemental chemistry plus gravity.

    An existing crystal, by getting larger when more precipitate distills onto the existing crystal, is not replicating itself.

    It makes no more sense to say that a crystal is self-replicating because more precipitate adheres to it, than it does to say that a puddle is “self-replicating” when it rains and the puddle grows larger, or to claim that a sand dune is “self-replicating” when more sand falls out of the blowing wind and makes the dune larger. Or the dust on my bookshelf is “self-replicating” because more of it has settled there over time.

    None of these processes — processes, yes, by which a mass of collective particles can grow in size — have anything to do with self-replication.

    Furthermore, all naturally occurring chemicals are “self-ordering” at the basic level. That does not mean they are self-replicating.

    —-

    I of course agree with your larger point about the distinction between what we see in life and elsewhere in the natural world. Your question is excellent:

    . . . how parts that would normally not organize when left to themselves end up in an organized state where they are interdependent and are able to replicate similar interdependent structures.

  43. 43
    Eric Anderson says:

    franklin and gpuccio:

    Terribly-worded question. My bad. Thanks for your thoughts.

    Of course there are many molecules that can perform different functions in organic systems (with the function depending on the particular organized system it is involved with).

    What I was really trying to drive at is whether a simple molecule outside of the organic context — by itself, without being involved in a particular system — can have multiple functions. Maybe “function” isn’t even the right word; it is really just a question of which chemical act it can perform.

    For example, molecules can be sometimes classed as to whether they have the ability to bind, to catalyze, or to split some other molecule or reaction. What I was wondering is whether, at that very basic level, there are very many molecules that do more than one of these tasks. Can a molecule be both a binder and a cleaver, for example? If so, how common is this?

    I’m still not describing this very well, and maybe there isn’t a clean distinction or way to view it. Maybe it just depends on the actual physical/chemical context the molecule is in? In which case we’re back to having to look at particular cases.

  44. 44
    scordova says:

    Nonsense. 🙂

    Crystals do not self-replicate.

    Some people view crystals as self-replicators. I try to avoid use of terminology that can be argued away and become a red herring. “Natural duplication” does exist, and that might be the phrase I’ll use in the future to avoid confusion.

    What makes life special is that it that duplication in life is NOT the expected outcome of the chemicals involved starting from a random state like a pre biotic soup.

    This is in contrast to self-ordering systems where the expectation is to find duplicates. Hazen and Morowitz amazingly swear by self-ordering.

    There is moderate self-ordering in life. Michael Denton really likes self-ordering. His paper on platonic forms explores self-ordering. It was hailed as a pro-ID paper because it was anti-Darwinian, but it wasn’t exactly a pro-ID paper because of its advocacy of self-ordering. He gave credible evidence of some self-ordering.

    He’s not quite in agreement with most IDists on the matter of self ordering and self organization. He actually thinks physics is the driving factor to assembling life, whereas most IDists think physics makes life possible but highly improbable. Denton is an anti-Darwinian, but he is a mix of IDists and Self-Organization theorist.

    The ID case is strengthened by showing that the chemicals of life are slightly anti-ordering and anti-organizing by themselves, but will work when they are assembled into those rare configurations that allow for interdependence and self-replication.

    I thought the best treatment of the topic was by Jack Trevors (an atheist). It was fair and especially potent because Jack is not an IDist. He was willing to say, “science might not solve OOL”.

    I don’t agree with Denton on self-ordering, but neither do I think his views are totally without merit.

  45. 45
    franklin says:

    eric, your post #43 is still terribly worded and expressed. it makes so little sense that I doubt anyone could provide any answers since what you are asking is so unclear. try thinking on it a bit.

    For example why do you seek to constrain multi-functionality of a molecule to an ‘organic’ system?

    What is ‘organic context?

    What is a ‘particular system’? (any molecule anywhere is constrained within that a ‘system’ of sorts)

    Can a molecule be both a binder and a cleaver, for example? If so, how common is this?

    Of course they can. Why do you think they can’t? (the only reason I can think of is lack of knowledge of inorganic and organic chemistry let alone biochemistry)

    Maybe it just depends on the actual physical/chemical context the molecule is in? In which case we’re back to having to look at particular cases.

    Well of course chemistry depends on the environment that the chemistry is going on in, e.g., many molecules behave differently at different pH, e.g., inorganic phosphate, bicarbonate, or hemoglobin. Absolutely, you have to look at specific cases otherwise you can’t make any sense out of any chemistry.

  46. 46
    gpuccio says:

    Eric:

    I think franklin’s answer is correct. I would add that, in the case of biologically active molecules like proteins, it is useful to distinguish between what I call “the local function”, IOWs the strict biochemical action, and the meta-function, IOWs the outcome of that chemical activity in the biological context.

    For example, in the case of insulin, the “local function” could be defined as the ability to bind to the insulin receptor in the cell membrane, but after that a lot of complex things happen, and they are different in different cells, so the meta-functions of insulin are many and very complex.

    But it is the local function that is directly related to the biochemical properties of the molecule. The meta-functions are more an informational consequence, which depends critically on the whole biological system and on its organization.

    Hemoglobin has the main local function of binding oxygen, but it binds also other ligands, which regulate its affinity for oxygen, and therefore contribute to the wider meta-function (binding oxygen in the lungs, releasing it in the peripheral tissues).

    A molecule can have many local functions. Multidomain proteins, typically, have different active sites which do different things. Aminoacyl tRNA synthetases, for example, have a catalytic domain, which phosphorilates the aminoacid and transfers it to the tRNA molecule, and an an anticodon binding domain, which recognizes the correct anticodon region of the tRNA. Some of them also have a proofreading reaction to ensure fidelity of the whole process. In this case, binding the correct aminoacid and recognizing the correct anticodon are two different “local functions”, performed by two different domains, while the meta function is to couple the correct aminoacid to the correct tRNA, ensuring the right translation of the genetic code in the mRNA molecule.

    In general, any object can have many functions. That is an important point that has to be considered when defining functional information. I am preparing a post on that subject, where i hope I can go into greater detail about that.

  47. 47
    Mung says:

    “Natural duplication” does exist, and that might be the phrase I’ll use in the future to avoid confusion.

    Hello Salvador,

    What is the difference between “Natural duplication” and it’s alternative (presumably non-natural duplication)?

    Some people view crystals as self-replicators.

    Do you?

    Self replication isn’t in and of itself the most important distinction for life. There are many self-replicators in nature, like crystals.

    Or not. Did you change you minds?

    Now that you’ve removed crystals from the collection of “many self-replicators in nature” what’s left? Anything?

    Are all these other self-replicators really nothing more than natural duplicators?

    Are living cells natural duplicators or self-replicators? What’s the difference? Are self-replicators a subset of natural duplicators, or are natural duplicators a subset of self-replicators, or are the two completely separate, or is there some overlap between the two? How do you tell?

    Eric:

    Nonsense.

    Like.

  48. 48
    Mung says:

    eric @38 @43

    I understand completely, and the answer is yes/no/maybe – it depends, or not.

    Hope that helps!

  49. 49
    Mung says:

    …there is a second, and absolutely indispensable criterion for selection – namely that the element must fulfill a function which is both an absolute requirement for life as it existed at that moment in time, and which cannot, or may not, be fulfilled by some other element.

    – Biological Inorganic Chemistry

    Now this is in the Section Why Do We Need Anything Other Than C, H, N, and O (Together With Some P And S)?

    Obviously, the topic is essential elements. But I think if we read further we can find that the same element can be used for differing ends.

    And absent further evidence we might even infer that molecules are analogous to the elements in this respect, and further that as some artifacts can be put to use to serve different purposes so also we should not be surprised to find a particular molecule serving different purposes in living organisms.

    How prevalent this is and whether it is evidence for design or purposeless happenstance is another topic.

    If you are interested in the same molecule serving different ends in the cell I could point you to, perhaps:

    Ribose forms part of the backbone of RNA. It is related to deoxyribose, which is found in DNA. Phosphorylated derivatives of ribose such as ATP and NADH play central roles in metabolism. cAMP and cGMP, formed from ATP and GTP, serve as secondary messengers in some signalling pathways.

    .

    What do you think?

    But in the end, it comes down to ends. and Darwinian Materialism has no purpose for ends 🙂

    Any “end” or “purpose” is just yet another nail in the lid of that coffin.

    Eric:

    What I was really trying to drive at is whether a simple molecule outside of the organic context — by itself, without being involved in a particular system — can have multiple functions. Maybe “function” isn’t even the right word; it is really just a question of which chemical act it can perform.

    Interesting question. Once I have recovered from patting myself on the back for the so excellent answer to the question you did not ask, I shall perhaps address myself to it!

  50. 50
    Eric Anderson says:

    Sal @44:

    I don’t agree with Denton on self-ordering, but neither do I think his views are totally without merit.

    Well said.

    In my view Denton has done a lot of good in raising awareness of deficiencies in the standard evolutionary storyline, as well as proposing some affirmative ideas worth considering.

    Self-ordering, however, whatever merit it may have in certain instances, is not going to take us very far in explaining either life’s emergence or how it got to its current state of complexity and diversity. Self-ordering is anathema to many of the things that are required for life, including that most important item of all: information.

  51. 51
    Eric Anderson says:

    All, thanks for your comments.

    gpuccio, I appreciate your careful thoughts about biologically active molecules and look forward to your post about functional information. Again, though, I apologize for the initial vague question. I am not talking about what happens in biochemistry. This thread relates to abiogenesis, which is what got me thinking about the issue, so I am interested in the non-biological context, the pre-biological context, if you will.

    —–

    franklin, I have apologized for the vague nature of the initial question, so it would be helpful if you would tone down the insults and accusations if we are to have a fruitful exchange. I note the irony in the fact that you said my question was so unclear as to not be amendable to any answers, but then asserted that the answer to my question was so obvious that any simpleton who had even the slightest knowledge of chemistry would know the answer.

    Also:

    For example why do you seek to constrain multi-functionality of a molecule to an ‘organic’ system?

    I don’t and I haven’t. I haven’t made such an argument. I haven’t proposed any theory. I am just exploring and brainstorming at this point. In fact I would be a little surprised if multi-functionality were limited to biological systems, but I am willing to explore the issue a bit.

    Can a molecule be both a binder and a cleaver, for example? If so, how common is this?

    Of course they can. Why do you think they can’t? (the only reason I can think of is lack of knowledge of inorganic and organic chemistry let alone biochemistry)

    I never said they couldn’t. And given this is such a simple issue, you should be able to (i) give me several examples off the top of your head of molecules in the non-biological context that act as binders and cleavers, and (ii) tell me how common this is among molecules generally.

    —–

    Mung, thanks for your thoughts.

    Interesting question. Once I have recovered from patting myself on the back for the so excellent answer to the question you did not ask, I shall perhaps address myself to it!

    No problem. 🙂

  52. 52
    Eric Anderson says:

    Allow me to now to continue to brainstorm a bit . . .

    If I have a very simple molecule in the non-biological context, what is its basic function – what does it do? Let’s take a concrete example. I have a simple molecule made up of 3 atoms, say, a water molecule. What does it do? And I don’t mean what mass quantities of water can do, like rivers carving a canyon or the ocean serving as the aqueous medium of transport for other molecules. A single water molecule. What does it do? Given its properties, what can it do?

    Let’s set aside for a moment all the many wonderful macro things that water can do or the larger effects it causes. If you are in a dark alley at gunpoint with a demand that you describe the basic, most foundational, essential activity of a water molecule, what would you say?

    Maybe this is too elementary a way to think about it, but we do need to think about some very basic properties in the abiogenesis context.

    Consider the smallest and simplest hypothetical self-replicating molecule: a two-atom molecule (SR) made up of atoms A and B, where the basic function of SR is to bind A and B together into the form SR. In this case we can see that SR, once formed, will be self-replicating in the sense that its basic function is to take naturally-occurring elementary parts and join them into a copy of itself. As far as I know, such a simple self-replicating molecule has never been discovered or created, but that is the hypothetical starting point.

    Note that A and B must not come together on their own, by dint of basic chemical reactions. In that case we would not be dealing with self-replication, but rather with a basic chemical reaction of atoms A and B forming a molecule. For example, if I mix hydrogen and oxygen together I get water. If I then add more hydrogen and oxygen to the mix I get more water. But the water that was already there is not “self-replicating.” We have just added more oxygen and hydrogen to the mix, which themselves, come together to form more of the product.

    So a true self-replicating molecule must be one in which the function of the self-replicating molecule – what it does – is cause the formation of itself and which in the absence of such function, more copies of itself would not form.

    Given that such a simple two-atom self-replicator currently seems to be outside the realm of possibility and that something slightly larger, more complex and more specified is required, as in the lab-designed examples rna cited earlier in this thread, we can then ask what is required (meaning, what functions must be performed) for basic self-replication.

    We need some kind of binding function certainly. But we also need something to help with the ordering of the constituent parts if a molecule of even modest specificity is required (again, as the examples rna cited seem to demonstrate). In theory such ordering/specificity could also be caused by simple binding, but it is not clear that a single molecule could perform both tasks. Consider a slightly more complex and ordered molecule, say, made up of a small chain of 4 atoms A-B-C-D. Could such a molecule perform the functions of, in this case, binding A to B, and B to C, and C to D? The binding requirements may be different for the different atoms. Is there good experimental reason to think a single molecule could do this?

    In true self-replication, at least in all examples that we know of, there are different functions carried out by multiple different molecules. Can this process be simplified? Perhaps. But (i) what is the minimal set of basic functions that need to be performed to carry out self-replication in the pre-biotic context, and (ii) is it possible, even in theory, that a single molecule could perform all the necessary functions?

    Again, I am not proposing any theory or making any claim at this point. But these are perfectly valid and important questions to ask.

  53. 53
    franklin says:

    And given this is such a simple issue, you should be able to (i) give me several examples off the top of your head of molecules in the non-biological context that act as binders and cleavers, and (ii) tell me how common this is among molecules generally.

    I would expect someone, like yourself, who is quick to declare what chemistry and biochemistry cannot do to have at least a basic enough understanding of the subject to not ask such mundane questions.

    as for your request for examples: epoxide hydrolase, glutathione, acetylcholinesterase, anything that binds ATP, anything that binds NADH, rnase, iron, water, ect., ect. These examples work in an organism or in a beaker on a bench top.

    As for your #52 why don’t you use real examples from bio/chemistry? without any knowledge of charge environment and the physical/chemical properties of your hypothetical molecules it would be impossible to determine what they could or could not do. It would seem a more fruitful course of action then playing pretend bio/chemistry.

  54. 54
    gpuccio says:

    Eric:

    As I will discuss more in detail in my next OP (when I find the time), the idea is that anything can do something, and probably anything can do many things.

    Function is defined by us, but it depends on the properties of the object. We define a function for an object that can be used to obtain a certain result. The same object can be used to obtain many different results.

    The error, IMO, is in thinking that the function is in the object itself. The function is rather a way in which the object itself, given its properties, can be used to give a certain result.

    That’s why the existence of potential function in any object would be of no use, in itself, to detect design. We can find function, even many different functions, for many non designed objects.

    It’s only the existence of a complex potential function in an object which is really interesting. Complex functional information is the real thing. It is the tool to detect design.

    So, it’s only when the form which allows us to use the object to obtain a result is really complex (a concept that I will try to define better and in greater detail as soon as possible), it’s only when no simpler, more probable form could achieve the result, that we have a tool for design detection.

  55. 55
    Mung says:

    Eric, we’ll be waiting forever for gpuccio’s next OP. 😉

    It would seem that you are speaking of what is known as Inorganic Chemistry.

    http://en.wikipedia.org/wiki/Inorganic_chemistry

    http://chemwiki.ucdavis.edu/Inorganic_Chemistry

    http://www.chemguide.co.uk/inorgmenu.html

    http://pubs.acs.org/journal/inocaj

    Somewhere around here I have a book Natural Selection of the Chemical Elements

    It should be interesting to see what it says about the various “uses” of the inorganic elements. If they are not “useful,” if they serve no “function,” upon what basis could they be “selected”?

  56. 56
    Mung says:

    Abstract:

    Evolution is treated here in a novel way. DNA or any other code is considered to be conservative and therefore, once life began, it would prevent change. Change was imposed upon the DNA code as a stress resulting in vulnerability to “advantageous” DNA damage and mutation. In this respect it is the stress, the changing environment, that opened up a possibility of evolution once an early life form had optimised itself in primitive circumstances. Here I examine the initial slow-coming-to-terms with the environment of primitive life, and then its evolution as the environment forced the DNA into novel development by introducing chemical elements in new forms. The situation today is no different. Environmental change is hostile to present day life and will lead to further evolution.

    http://www.ncbi.nlm.nih.gov/pubmed/9432285

  57. 57
    Eric Anderson says:

    franklin @53:

    I would expect someone, like yourself, who is quick to declare what chemistry and biochemistry cannot do to have at least a basic enough understanding of the subject to not ask such mundane questions.

    I presume you are only referring to my discussions regarding abiogenesis, rather than the question about multi-functionality for simple molecules in the non-biological context? The former you have not commented on. Regarding the latter I have certainly not been “quick to declare” anything.

    as for your request for examples: epoxide hydrolase, glutathione, acetylcholinesterase, anything that binds ATP, anything that binds NADH, rnase . . .

    Good grief man. I have explicitly said the question relates to non-biological situations.

    iron, water, ect., ect.

    Yes, yes. You keep saying — while evidently missing the question — that everything is multi-functional. It may be the case. But, ironically, with all your assertions about what an obvious and “mundane” question this is, you have not yet deigned to tell me what, at the most basic level, a water molecule does, nor what its “multiple” functions are. One might be forgiven for suspecting that you have not ever before thought about the issue at the relevant level of detail.

    without any knowledge of charge environment and the physical/chemical properties of your hypothetical molecules it would be impossible to determine what they could or could not do. It would seem a more fruitful course of action then playing pretend bio/chemistry.

    No-one is playing pretend chemistry. I have thrown out some early nascent thoughts for consideration and brainstorming. I agree that some specific situations may be helpful, which is why I outlined the water molecule example, and I will continue to think through the issue in the future.

  58. 58
    Eric Anderson says:

    gpuccio @54:

    Function is defined by us, but it depends on the properties of the object. We define a function for an object that can be used to obtain a certain result. The same object can be used to obtain many different results.

    Well, we can look at something that is doing something and call it a function, true. And I agree that the same object can be used to obtain many different results — by design, by an intelligent agent that knows how to create environments in which a single object can perform multiple functions. But the object, in and of itself, is either capable of doing something in a particular situation or it isn’t – that should be an objectively observable property of the object.

    In the abiotic environment, for example, a molecule to kick start abiogenesis must have the ability to self-replicate. And that activity requires certain functions to be performed. There is no-one there to help out or to assign assign a function to the molecule or to “use it to obtain many different results.” It either can perform the task at hand — by pure dint of blunt chemistry — or it can’t.

    The error, IMO, is in thinking that the function is in the object itself. The function is rather a way in which the object itself, given its properties, can be used to give a certain result.

    I completely agree . . . in the context of a designed system. A designer can use an object many different ways to obtain certain desired results. Our primordial soup has no such ability. Either the basic chemical reactions do X or they don’t.

    —–

    Please don’t think I’m arguing. I realize you are talking about a different context (biology, designed systems, etc.), so I’m just trying to talk through out loud, so to speak, what I see as the differences between that and the basic prebiotic soup situation. Notwithstanding the different context, your thoughts about designed systems and functionality have been very helpful, and I certainly look forward to your OP!

  59. 59
    Eric Anderson says:

    Mung @55:

    Thanks for the comments — and for making the effort to follow my still-solidifying thought process on the topic. Yes, we are definitely in the inorganic realm.

    Given that self-replication, as far as I am aware (and no-one has yet provided any example to the contrary) is only known to occur in the biological context, it is perfectly reasonable to ask whether such a thing can — either in fact or even in principle — occur in the pre-biotic realm. Such questions, however, are apparently verboten to some people who consider such questions as too mundane to even think about.

    BTW, how many books do you have?! It seems you have a book for nearly every topic that comes up.

    . . .

    Except macroevolution. LOL!

  60. 60
    gpuccio says:

    Eric:

    I think we agree, only we say things slightly differently.

    The point is, function is always recognized by a conscious observer, and it is often set up by a conscious designer. That’s the only problem. We can recognize function even in things that were not designed. That’s why we need a tool to detect design, IOWs to discriminate between apparently functional things that were not designed, and functional things that were designed and whose function was set up by a conscious, intentional being.

    As observers of the mere object in its context, we cannot immediately discriminate between apparent function and designed function. Clouds may appear to be designed to look like a face, but they are not.

    In principle, we could observe some natural context where a simple molecule spontaneously self-replicates.

    In that case, would it be a clue to a design inference?

    No, if the system we observe is simple enough, or can be explained by known physical and chemical laws.

    Yes, if the system is complex and cannot be explained by known physical and chemical laws.

    Moreover, another question is: is an eventual self-replicating molecule a support to the RNA world OOL theory?

    As I have tried to argue here, the answer is yes only in the self-replicating molecule is a ribozyme, or something similar to it: IOWs, a molecule that at the same time bears digital information that can be passed on, and can replicate itself.

    The concept of digital information is fundamental here. A simple self-replicating molecule, if it exists, can only perpetuate itself. That does not help in an OOL theory.

    A self-replicating RNA molecule, instead, has digital information that can change by variation, and therefore potentially undergo a process of variation and selection.

    IOWs, if we had a self-replicating water molecule, the simple result would be the proliferation of water. The water molecule is constrained by chemical laws, and even if it can be considered as having some information, that is not the kind of sequential digital information that can change randomly in replication, as required by the neo darwinian model.

    IOWs, what we need is a self-replicating system whose properties are linked to some unconstrained digital information, like the sequence of nucleotides, which can assume different forms by random events (or by design).

    I hope that clarifies better what I think.

  61. 61
    Eric Anderson says:

    gpuccio:

    Thanks for the thoughts.

    As I have tried to argue here, the answer is yes only in the self-replicating molecule is a ribozyme, or something similar to it: IOWs, a molecule that at the same time bears digital information that can be passed on, and can replicate itself.

    The concept of digital information is fundamental here. A simple self-replicating molecule, if it exists, can only perpetuate itself. That does not help in an OOL theory.

    Quite true. However . . .

    OOL research today (at least many versions of it) does not start with an information-rich molecule. The thought is that once self-replication exists, the self-replicator can perpetuate itself and sometimes mistakes/mutations will be made. Through the magic of natural selection, that mutating self-replicating molecule will eventually be modified to contain information.

    In other words, the materialist sees no more difficulty in generating new information at the abiogenesis stage (if we have a self-replicating molecule to work with), than generating new information in the genome today. Both are eminently possible through the magic of natural selection, so the thinking goes.

    Indeed, this was precisely the tactic taken by AVS on the other thread. He refused to address how information would arise (actually, in practice, in the real world), instead clinging to the idea that once a self-replicator appears, the hard work is done.

    So while I agree with you that information is critical to having a workable OOL, the concept doesn’t phase the committed materialist. After all, information arises by purely natural processes all the time — just look, everything we see around us is the result of natural processes!

    But if the alleged self-replicating molecule — that elusive first step that even the hardened materialist admits is essential to abiogenesis — never existed under natural conditions, then hopefully (just perhaps) the materialist will have enough intellectual honesty to reconsider his position.

    A self-replicating molecule for OOL purposes must have, at a minimum, the four characteristics I outlined in #19 above. Personally, I do not think such a thing can exist without information and carefully coordinated control mechanisms. That is where the information comes into play.

    But I want to press the materialist into giving us some rational reason for thinking that such a self-replicator could exist — in the pre-biotic context, in the pre-information context. If the materialist cannot do so, as thus far no-one has been able to do, it then underscores the need for information, right up front, at the very beginning of the origin of life.

  62. 62
    scordova says:

    Eric,

    Just as a heads up, I found the following last night while doing some research to respond to PZ Myers. It’s something I anticipate will be thrown at me so I wanted to find stuff like this before I get hit with it in debate.

    we have shown that even within the simple helical structure, a peptide replicator can contain a rich degree of information that enables it to display, at the molecular level, some of the basic characteristics of living systems, such as self-replication, homochirality, and resistance toward accumulation of errors (stereochemical mutations). The link between these traits allows the replicator to selectively amplify homochiral sequences. Therefore, chiroselectivity in peptide self-replication is a direct result of complementary noncovalent interactions that pass on both binding and stereochemical information simultaneously. That such a prototypical peptide system is able to amplify homochiral products through self-replication suggests that this and similar mechanisms may have affected the origin of homochirality on Earth.

    http://www.nature.com/nature/j.....797a0.html

    But, it won’t evolve.

  63. 63
    scordova says:

    The self-replication is rigged, but I need a chemist to explain it. I sort of understand how it’s done, but it’s not my field.

    Sal

  64. 64
    Eric Anderson says:

    Thanks, Sal.

    Shall I make a preliminary guess (even without reading the paper) as to whether their “self-replication” is really self-replication or assisted replication? 🙂

  65. 65
    Mung says:

    Follow Sal’s link and look for “design” or “designed.” 😀

  66. 66
    Mung says:

    BTW, how many books do you have?! It seems you have a book for nearly every topic that comes up.

    Far too many. More than I can read. I’d love to make a deal with the DI where they take them off my hands and just give me access, lol.

    Except macroevolution. LOL!

    lol. true. I think I now have one:

    Macroevolution: Diversity, Disparity, Contingency: Essays in Honor of Stephen Jay Gould

  67. 67
    gpuccio says:

    Eric:

    You say: “OOL research today (at least many versions of it) does not start with an information-rich molecule.”

    But that is not exactly my point. My point is that the self-replicating molecules must bear that kind of information that can be subject to variation during replication, otherwise it cannot undergo the process of RV, which is essential for “evolution”.

    It could be just a little of that information, it is not
    necessary that the molecule be “rich” of it. So, even a ribozyme made of three nucleotides would suffice. Unfortunately, such a simple ribozyme does not exist. Ribozymes with even a little of self-replicative activity are made of hundreds of nucleotides.

    What I am saying is that a self-replicating molecule which can be used as an actor in any OOL theory must not only self-replicate, but also be a polymer bearing information in the sequence of the monomers. IOWs, we need “configurable switches” in the molecules for tranmittable information potentially subject to variation to exist.

    A complex self-replicating molecule, completely determined by chemical laws, would not do, because it would only replicate its own information, without any chance at evolution. That’s why I made the example of the water molecule: it is simple, but its problem is that it cannot vary, because it is fully determined in its chemical configuration. A more complex molecule of the same kind would have the same limitation.

    Instead, a polymer which can vary in the sequence of its monomers has a digital information which can be copied and which can undergo variation. And it must also be catalytic, to provide self-replication.

    Only RNA, as far as I know, can have all those qualities. That’s why they have developed the RNA world hypothesis.

    That’s why they need a ribozyme: only a ribozyme would work.

  68. 68
    Mung says:

    Even a ribozyme would not work.

    gpuccio:

    So, here is a short list of what, IMO, is truly essential for life, and therefore for its origin:

    a) Establishing a separation between an inner environment and an outer environment, and generating definite differences between the two.

    I agree. But how would the presence of a ribozyme establish this separation? It would not. The ribozyme could perhaps exist outside the membrane, but how would it establish the necessary separation?

  69. 69
    Eric Anderson says:

    gpuccio @67:

    My point is that the self-replicating molecules must bear that kind of information that can be subject to variation during replication, otherwise it cannot undergo the process of RV, which is essential for “evolution”.

    Well, you are probably right, as far as the ultimate process goes. I think a number of abiogenesis researchers recognize the need for information-bearing molecules.* Yet at an even more basic level, there seems to be this idea, among some researchers and certainly among the lay materialist (AVS, for example), that the self-replication can come before the information, that the self-replication can be the source of the information.

    That is why I talked about the self-replicating molecule being the first step on the road to life as being upside down. Their idea is, unfortunately, little more than vague, unspecified (no pun intended) assertions, but it relies heavily on the oft-heard and extremely intoxicating idea that once a self-replicator is available (no matter how simple, no matter whether it contains any meaningful information or not), then natural selection can take over. And we all know what that means — with natural selection “all things are possible.”

    —–

    * Sorry, Mung, I couldn’t bear to write the longer and more convoluted “molecules that contain representations of information” — well, rats, I just took the time to write it. 🙂

  70. 70
    Mung says:

    lol!

    All is well.

    The more I look into biological membranes the more unlikely it seems that “it just happened, that’s all” can suffice as a a reasonable explanation.

  71. 71
    gpuccio says:

    Mung:

    Even a ribozyme would not work.

    Obviously! I just meant that only a ribozyme would work to start a just so story about an RNA world. All the other insurmountable difficulties remain 🙂

    The more I look into biological membranes the more unlikely it seems that “it just happened, that’s all” can suffice as a a reasonable explanation.

    It can’t.

  72. 72
    Zachriel says:

    gpuccio: After all, they apparently and constantly violate the second law, and even darwinists admit that the only way to explain that (if it can be really explained) is that they receive energy from outside.

    Really wish you wouldn’t say that. Life does not violate the the laws of thermodynamics. It’s like saying window frost violates the laws of thermodynamics.

    gpuccio: As far as I know, that has not been found yet. I am not saying that it will not be found, such a molecule can exist in principle. But, if and when it is found, it will be the result of complex human engineering, it will be complex, and it will be well beyond any chance of random origin.

    The claim in the original post was that a molecular replicator can’t exist.

    Eric Anderson: A bit of reflection is adequate to realize that even “simple” stuff like a passive membrane letting materials in by diffusion/osmosis, is not a “simple” matter.

    Actually, a simple single-chain amphiphiles are permeable to the small molecules, but would contain and segregate the larger product molecules. They also lend themselves to competitive growth. See Chen & Walde, From Self-Assembled Vesicles to Protocells, Cold Spring Harbor Laboratory Press 2010.

  73. 73
    Virgil Cain says:

    Zachriel:

    Life does not violate the the laws of thermodynamics.

    Life arising from matter and energy via blind and undirected physicochemical processes does.

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