Intelligent Design

The origin of abiotic species: Seven epic fails

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A team of researchers led by Professor Sijbren Otto of the University of Groningen, in the Netherlands, has announced that it has observed not only self-replication, but also mutants and even new “species,” in a bunch of molecules in the lab. Does this research show how life might have arisen spontaneously, or is it nothing more than a case of intelligent design by clever chemists?

In today’s post, I’m going to argue that the claims made by Professor Otto and his team are flawed, on no less than seven counts. But before I examine their press release and their paper in Nature Chemistry, I’d like to discuss a Science LinX video that was posted on Youtube last year (March 17, 2015), titled, “Chemical evolution: creating life?”, which explains the work being carried out Otto and his group:

The text of the video reads as follows (note: all bold emphases shown in this post are mine – VJT):

This is Sijbren Otto, a chemistry researcher from Groningen. A while ago, he and his research group discovered molecules that can reproduce. Start out with a handful, and after a while, you’ve got twice as many. A bit later, there are four times as many, and so on. There are even different kinds of reproducing molecules that compete for building blocks. “That looks exactly like animals competing for food,” Otto thought. Now, he wants to trick molecules into real evolution – you know, the Charles Darwin kind of evolution that all living organisms have been going through for some four billion years. Who knows? His research might one day result in some kind of chemical life form.

It all started with a pot of pretty simple molecules able to couple on two sides. Also, they have a little tail that exactly fits the tail of the other molecules. The idea was that this would help create some structure. And so it did. The molecules hook up and form rings, counting six, seven or eight molecules each. And as the tails fit onto each other, so do the rings. A six-ring fits a six-ring, a seven-ring fits a seven-ring, and so on. Stacks of rings become towers. Towers become long threads. If you stir the pot, the threads will break apart. But each piece will start to grow again – from both ends. Soon, Otto’s pots were teeming with small threads of molecules.

However, in real evolution, species also change when they reproduce every once in a while. A mutation causes a child to be slightly different from its parents. So, Otto’s students started working with several different tails that might sometimes not fit together so well. When the molecules stack, mistakes happen. These errors may cause the thread to grow faster, or to stop growing, or to grow into complicated shapes, or to do something else yet. In fact, Otto doesn’t know, because this is what his students are finding out now. In any case, Otto’s pots are brewing. The question is: when can it be considered life? Otto thinks there is a gray area between “really alive” and “really dead.” But when it waves at us and says, “Hello,” you can be pretty sure it’s alive.

The latest press release: “The origin of abiotic species”

On January 4, 2016, a press release titled, The origins of abiotic species, was put out by the University of Groningen. The key part reads as follows:

Otto has been working on chemical evolution for several years now. ‘It started with a chance discovery’, he explains. ‘We found some small peptides that could arrange themselves into rings, which could then form stacks.’ Once a stack began to form, it would continue to grow and would then multiply by breaking into two smaller stacks. These would both grow and break again, and so on. The stacks also stimulated the formation of the rings from which they are composed. The stacks and rings are called ‘replicators‘, as they are able to make copies of themselves.

Jan Sadownik, a postdoc in the Otto group, discovered that if you offer the replicators two different types (A and B) of building blocks (‘food’) they will make copies of themselves. He observed the emergence of a set of replicator mutants that specialized in food A, but also incorporated some B. The rings mainly comprised the A building blocks, with just a few B’s.

Some days later Sadownik saw a second set of mutants emerge that specialized in food B, but also tolerated some A. This second set proved to be a descendant of the first set, which meant there was an ancestral relationship between the sets. This is very similar to how new species form from existing ones during biological evolution, except that this process of species formation does not involve full-fledged biological organisms, but occurs instead at the molecular level.

Molecular speciation

Looking at the molecular ‘speciation’ process in more detail allowed the researchers to identify specific mutants within the first set of replicators that were responsible for the generation of the second set. They had therefore established the mechanism by which replicator ‘species’ form with unprecedented molecular-level detail….

This shows how new ‘species’ can emerge through chemical evolution. Otto explains, ‘Of course, the term speciation should only be used when referring to sexually reproducing organisms, but our work shows much the same patterns.‘ The exciting part, says Otto, is that ‘we start with no replicators, but see first one type emerge and then after a while, another. That is certainly most significant!’

One physicist’s take on the new research

Physicist Rob Sheldon made a pithy observation regarding the University of Groningen’s latest press release and the new paper by Sandownik, Mattia, Nowak and Otto: “If this paper were about anything but ‘peptides’, it would be called ‘crystallization’.”

Indeed. Crystals have been shown to exhibit many of the properties displayed by Professor Otto’s peptide structures. I would invite skeptical readers to have a look at a 2013 article titled, It’s almost alive! Scientists create a near-living crystal by Brandon Keim (Wired, January 31, 2013). Written in a tone of breathless anticipation, the article exudes the same kind of starry-eyed optimism as the University of Groningen press release, as it reports on how particles of a mineral called hematite (pictured above, image courtesy of Wikipedia) can be coaxed into forming “living crystals”:

Three billion years after inanimate chemistry first became animate life, a newly synthesized laboratory compound is behaving in uncannily lifelike ways.

The particles aren’t truly alive — but they’re not far off, either. Exposed to light and fed by chemicals, they form crystals that move, break apart and form again.

“There is a blurry frontier between active and alive,” said biophysicist Jérémie Palacci of New York University….

Palacci and fellow NYU physicist Paul Chaikin led a group of researchers in developing the particles, which are described Jan. 31 in Science as forming “living crystals” in the right chemical conditions….

Chaikin notes that life is difficult to define, but can be said to possess metabolism, mobility, and the ability to self-replicate. His crystals have the first two, but not the last.

As for what’s happening now in Palacci and Chaikin’s lab, a particle currently under development isn’t mobile, but it has a metabolism and is self-replicating.

We’re working on it,” Chaikin said.

The abstract of Palacci and Chaikin’s paper can be found here.

Now, to be fair, I should point out that the structures created by the University of Groningen team are capable of a kind of self-replication – that is, if you’re willing to call breaking in two “replication.” But that’s about the only thing they can do, that Palacci and Chaikin couldn’t – and in any case, they state towards the end of the article that they have now created a self-replicating particle which has a metabolism. So on the whole, I think Rob Sheldon’s remarks are pretty accurate. These peptide structures are no more alive than some crystals are.

The dogs that didn’t bark

Silver Blaze,” one of the most popular Sherlock Holmes stories written by Sir Arthur Conan Doyle, is a tale about the mysterious kidnapping of a prize race horse on the eve of an important race, and the apparent murder of its trainer. At one point in the story, the Scotland Yard detective, Inspector Gregory, asks Holmes: “Is there any other point to which you would wish to draw my attention?” “To the curious incident of the dog in the night-time,” answers Holmes. Inspector Gregory objects: “The dog did nothing in the night-time.” “That was the curious incident,” remarks Holmes.

This telling exchange inspired The Curious Incident of the Dog in the Night-Time, a 2003 best-selling novel by Mark Haddon.

The reason why I bring this up is that although the January 4 press release, “The origins of abiotic life,” was featured in Phys.org and Science Daily, it seems to have attracted remarkably little comment. Professor Jerry Coyne hasn’t mentioned it over at his Website, Why Evolution Is True. Nor has Professor Larry Moran said anything about it on his Sandwalk blog. Professor P.Z. Myers hasn’t said a word about it on his Pharyngula blog, either. This is quite remarkable, considering that three whole days have elapsed since the University of Groningen’s press release.

Why this deafening silence from North America’s leading evolution advocates? The only reason I can think of is that they don’t think that the new paper by Professor Otto and his team has any real relevance to the origin of life on Earth. What does that tell you about the paper?

But it would be churlish of me to dismiss a paper simply because no-one else had bothered to comment on it. So without further ado, I’d like to enumerate seven reasons why I think the paper fails to shed light on the origin of life on Earth, and of new species.

Seven reasons why the new paper fails to shed light on the origin of life and of new species

1. The peptide structures were the product of intelligent design

The Methods section of the paper (by Sandownik, Mattia, Nowak and Otto) describes how the peptide library was prepared: “Peptide building blocks 1 and 2 were synthesized by Cambridge Peptides Ltd from 3,5-bis(tritylthio)benzoic acid, which was prepared via a previously reported procedure…”. Building blocks 1 and 2 consisted of “an aromatic core functionalized with two thiol groups and a peptide chain”. The paper’s authors produced a dynamic combinatorial library from “building blocks that can react with each other through reversible covalent chemistry combine and recombine to give rise to a diverse set of products”.

The paper also states:

“Each building block is equipped with two thiol groups which, when oxidized to disulfides, form macrocyclic species of different ring sizes. The peptide sequence is designed to have alternating hydrophilic and hydrophobic residues to promote self-assembly into parallel β-sheets.”

(The following very brief explanation is intended for the benefit of readers who don’t have a strong background in chemistry. 3,5-Bis(tritylthio)benzoic acid looks like this and has the chemical formula C45H34O2S2. The term “aromatic” may be used to refer informally to any chemicals derived from the hexagonal, ring-shaped hydrocarbon, benzene, although it can also broadly refer to any flat, cyclic molecule that’s highly stable: for instance, the double-ringed bases in RNA and DNA are also described as aromatic. A thiol group is simply an -SH group, where S represents a sulfur atom and H represents a hydrogen atom. A disulfide refers to a functional group with the general structure R–S–S–R: the two sulfur atoms in the middle are bonded to one another, and the two R’s are groups of atoms containing carbon and/or hydrogen. A peptide is a sequence of amino acid molecules which are bonded together in a short chain. Finally, a molecule which is attracted to water is called hydrophilic, while one which is not attracted to water is called hydrophobic.)

An anonymous biochemist whom I contacted has forwarded his comments to me. The following is a brief summary of his remarks:

This is a very well-designed and skillfully performed piece of chemical engineering (based on some very nicely done research), in which peptide building blocks (as distinct from pure natural peptides) were made by a chemist, not via a natural process. Hopwever, its significance in relation to the origin of biological replication is highly questionable.

Additionally:

The description of the study shows how strong the design component was in these experiments. The carefully ordered formation of covalent bonds was guided by the designed structure of the building blocks, and the alternating hydrophobicity and hydrophilicity was designed to promote the formation of higher order structures.

I have to ask: since when does evidence of Intelligent Design count as evidence for unguided evolution?

2. The reactions would never occur under realistic conditions – and if they did, they’d rapidly come to a halt

The biochemist whom I contacted didn’t think that the conditions in the experiment were very realistic, either. He also pointed out that the reactions described in the paper would soon grind to a halt, under natural conditions. The following two paragraphs are intended to convey the gist of his comments.

This experiment is far removed from OOL [origin of life] conditions, where the reactions and structures would occur at random, and where a very large number of “undesirable” reactions would inevitably occur, drastically reducing the chances of obtaining the “correct” reactions under the assumed OOL conditions.

Under natural OOL conditions, a large number of unwanted reactions could (and probably would) occur, in a solution containing a multitude of different chemical components. Instead of obtaining a functioning system with life-like properties, the end result would be chaotic and unpredictable. Additionally, under natural conditions, the chemical reactions could lead to a dead end, and they would probably not be very useful for generating a replication system from nucleic acids. If this kind of self-organization were common in nature, then we could end up with a very large number of competing systems, which would rapidly deplete the chemical raw materials being used to build nucleic acids. In practice, however, hydrolysis and decomposition, as well as the formation of large amounts of “unwanted” chemical products, would seem to be the dominant trends.

Despite these criticisms, the biochemist whom I contacted wished to compliment the authors of the paper, on the quality of their scientific work. He added that it would indeed be possible for intelligent chemists to build systems that were capable of undergoing intelligently guided molecular evolution, as Otto et al. have done, and he expressed his opinion that they had actually generated a very interesting “evolutionary molecular system.”

3. The structures observed could not possibly have been precursors to the first living organisms on Earth

Another reason why the new paper by Sandownik, Mattia, Nowak and Otto fails to shed light on the origin of life on Earth is that the structures which they created are totally unrelated to those found in living things today. Want proof? I would invite readers to have a look at the article, Diversification of self-replicating molecules in Nature Chemistry, and scroll down and click on Figure 1: Library synthesis and the mechanism of self-replication. Have a look at the ring-structures created by the team of researchers. You’ll notice the six-rings and seven-rings described in the Youtube video at the top of this post. That’s what Professor Otto’s team created.

And now have a look at the diagram below, which depicts three possible representations of the three-dimensional structure of the protein triose phosphate isomerase. Hideously complicated, isn’t it? That’s what life is like. I don’t see any nice little rings of six, seven or eight molecules each. Do you?

I have focused on proteins here, because they’re the next step up from polypeptides. A protein consists of one or more long chains of amino acid units (or residues, in chemical jargon). A protein contains at least one long polypeptide. Short polypeptides, containing less than 20-30 amino acid units (or residues), aren’t usually considered by biochemists to be proteins. Instead, they’re just called peptides, or oligopeptides.

Now my point is that if the peptide structures created by Professor Otto and his team don’t look anything like proteins (much less anyother biological molecule found in living things), then we can safely assume that their relevance to the origin of life on Earth is: nil, nada, nothing, zip, zilch. Zero.

4. There are good reasons to believe that life didn’t begin with a self-replicating molecule

In any case, there are solid scientific reasons for rejecting the idea that life on Earth began with a self-replicating molecule – in which case, the claim by Professor Otto and his team to have created such a molecule is neither here nor there.

The late Professor Robert Shapiro (1935-2011) explained what’s wrong with the replicator-first theory in an interview with Vlad Tarko of Softpedia (Life Did Not Appear with A Self-Replicating Molecule, May 17, 2006):

A scientist proposes an alternative theory to the “replicator” theories of the origin of life – the idea that a self-replicating molecule, such as RNA, has spontaneously appeared and then spread and diversified.

Robert Shapiro from New York University calls such a possibility a “stupendously improbable accident”, although chemists managed to create “prebiotic” syntheses in the lab – syntheses of various building blocks of life such as amino acids. Shapiro says that the use of modern apparatuses and purified reagents is very unlikely to mimic the actual conditions on early Earth.

He says that one of the problems of replicator theories is that a high diversity of molecules of all sorts seems to hamper and endanger the replicator. The mere complexity of the assumed original replicator makes it to be unstable. He argues that what probably happened was the exact opposite – chemical variety was probably beneficial and increased the probability of life. The issue is how this chemical diversity eventually turned into self-replicating chemicals – i.e. life…

The appearance of a molecule that can self-replicate was not the first step, because this requires the combination of diverse chemicals in a long sequence of reactions in a specific order.

Of course, Professor Robert Shapiro’s “metabolism first” theory of the origin of life on Earth faces its own problems, as Leslie Orgel pointed out in an article titled, The Implausibility of Metabolic Cycles on the Prebiotic Earth (PLoS Biology 6(1): e18. doi:10.1371/journal.pbio.0060018 – see here for a non-technical overview by microbiologist Rich Deem). But the point I wish to make is that the “replicator-first” theory espoused by Professor Otto and his team is a very fragile one. It cannot work without just the right sequence of reactions occurring in just the right order, in just the right environment (to ensure that no decomposition occurred, along the way) – in other words, a miracle.

5. The new structures are not alive, in any meaningful sense of the term

Former “Science” editor-in-chief Daniel Koshland Jr. attempted to define “life” in a widely-cited article titled, “Seven pillars of life” (Science 22 March 2002: Vol. 295 no. 5563 pp. 2215-2216, DOI: 10.1126/science.1068489). Koshland listed what he saw as the seven defining features of life:

(1) a program, i.e. “an organized plan that describes both the ingredients themselves and the kinetics of the interactions among ingredients as the living system persists through time” (Koshland, 2002, p. 2215);

(2) improvisation, or a way of changing its master program (achieved on Earth through mutation);

(3) compartmentalization (a surface membrane or skin, and for large organisms, a subdivision into cells, in order to preserve the ingredients required for chemical reactions at their required concentrations);

(4) energy (which on Earth comes from the Sun or the Earth’s internal heat), to keep living systems metabolizing;

(5) regeneration (this includes reproduction), to compensate for the wear and tear on a living system;

(6) behavioral adaptability to environmental hazards; and

(7) seclusion, or some way of preventing one set of chemical reactions from interfering with another, in a cell.

When we look at the peptide structures created by Professor Otto and his team, what do we find? Which conditions are satisfied?

First, the structures lack a master program. Second, lacking a master program, they also lack the ability to modify their master program. Third, the structures possess no internal compartments whatsoever. While they have access to a source of energy (heat), they don’t metabolize, so Koshland’s fourth condition isn’t satisfied, either. (That’s why Professor Otto’s reference to “food” in the press release is misleading.) However, the fifth and sixth conditions are met, in some fashion: the structures can replicate, and they adapt to changes in the availability of different kinds of building blocks. Finally, the structures possess no mechanism for preventing one set of chemical reactions from interfering with another.

Overall Score: 2 out of 7. That’s a pretty long way from what I’d call “life.”

Of course, if you’re intellectually lazy, and you want to define the term “life” to mean anything that can replicate, then don’t let me stop you. But by the same token, many other things would also qualify as alive. As Dr. Steve Wolfram points out in his book, A New Kind of Science (Wolfram Research, 2002, p. 824, it has been known since the 1950s that abstract computational systems possess this capacity as well. Computer viruses would also qualify as alive, on the definition proposed, and there are mechanical devices (such as the “RepRap” machine shown below) that can make copies of themselves, too. How many readers would want to call these devices “alive”?

6. The term “mutant” is an inappropriate way of describing the variants that arose

In their press release, Professor Otto and his team use the term “mutant” to refer to a replicating molecule which is slightly different from the original version, because it tends to specialize in different building blocks, when assembling itself. However, as we have seen from Daniel Koshland’s article, “The Seven Pillars of Life“, which I cited above, the word “mutation” properly refers to an organism’s ability to change its master program. Since the structures described in the University of Groningen press release don’t possess anything analogous to a master program, or a genetic code, it follows that they can’t properly be said to mutate.

7. The processes observed in the lab shed no light on speciation, whatsoever

Finally, the processes described in the press release by Professor Otto and his team have absolutely nothing to do with speciation in living things. How can I be so sure of that? There are two things that give the game away.

The first is a very damaging admission in the last paragraph of the press release:

The next step is to introduce death. This can be done by feeding the system a constant flow of building blocks, while draining the contents of the reaction vessel. Replicators can only survive in this system when their growth rate exceeds the removal rate. ‘We could then seed such a system with one set of replicator mutants, and then change the environment, for example by adding another solvent. This would change the fitness of the various replicator mutants and shift the population of mutants towards those that are best at replicating in the new environment.’ The result would be a form of natural selection that Darwin would recognize. ‘We’re not the only ones to be really excited about these experiments – the evolutionary biologist I’ve consulted is too.’

Stop right there. The structures created by Professor Otto and his team don’t die. Consequently, they don’t undergo natural selection. The term, “survival of the fittest,” simply doesn’t apply to them, because they don’t even possess the property of “fitness.”

Without natural selection, speciation which results from a population becoming reproductively isolated from a founder population as it enters and colonizes a new niche, would never get off the ground. Such a model assumes that the new population becomes “fitter,” in relation to its new environment, over the course of time – which means that natural selection has to occur. But as we’ve seen, Professor Otto and his team haven’t achieved natural selection yet. Their excitement is, to say the very least, premature.

The other give-away is that the press release makes no mention whatsoever of a genetic code. And without a genetic code, there can be no genes – and hence, no genetic drift. That rules out other mechanisms of speciation, which rely on the occurrence of genetic drift in a population, in order to achieve reproductive isolation.

No natural selection, no genetic drift: no speciation. Of course, there are also species which are created through hybridization, but that presupposes the existence of genes and sexual reproduction – neither of which are found in the peptide structures created by Professor Otto and his team.

I conclude that the January 4 press release by the University of Groningen on the research conducted by Professor Otto and his team has very little relevance for the origin of life on Earth via an unguided process, much less the origin of living species.

What do readers think?

168 Replies to “The origin of abiotic species: Seven epic fails

  1. 1
    Mung says:

    Because the order that living things display is of a special kind, commonly termed “organization”: that [Steller’s] jay’s patterns of order have purpose or function. This feature is seen only in living things and their artifacts…

    – Franklin M. Harold In Search of Cell History

  2. 2
    Mung says:

    Truly, “the cell is the microcosm of life, and in its origin, nature and continuity resides the entire problem of biology.” When we inquire into the genesis of life, the primary objective must be to understand the origin of cells and cellular organization.

    – Franklin M. Harold. In Search of Cell History

  3. 3
    Dionisio says:

    VJT, interesting. Thank you.

    Please, let me repeat something I have said before.

    When I worked on software development projects for engineering design systems, the functionality of most required programming tools (computers, operating systems, interactive development environments, databases, communication networks, debuggers, quality assurance procedures, etc) was ready from the beginning. Most analysts and programmers were available from the start and eager to work. Most working conditions were optimally fine-tuned!

    We had the conditions and capabilities to create many really cool programs. All the required ingredients were in place.

    However, all that combined would not have helped to move the project in the right direction in order to reach the desired goal, if the director and project leader wouldn’t have explained to the rest -in an understandable manner- his main ideas about the way he envisioned (imagined) the system would work and how he wanted to build it.

    Obviously he was an excellent engineer and also consulted some potential users and many other engineers to hear their suggestions. He had brilliant ideas about resolving difficult technical issues associated with the representation of graphical information for efficient access and other fundamental conceptual problems.

    He established the procedures to develop, test, implement and deliver the product. He established the relationship with the users, gave the keynote speeches at the users conferences and made sure that customer support was at the highest level. He set the pace of development and the discipline rules. Basically, his mind was at the center of the whole project.

    The main point is that at the center of it all is the directing information without which nothing else would make sense at all.

  4. 4
    tjguy says:

    While we are on the subject of the origin of life, here is a new article on a creationist website about autopoeisis and the challenge this presents to the creation story of Naturalism: http://creation.com/lifes-irre.....utopoiesis

    On this issue, creationists and IDers are on the exact same page I believe. I said “new”, but it actually looks like it was first published in 2007.

    Part II which deals with naturalistic objections to the argument is also available.

  5. 5
    Mung says:

    nil, nada, nothing, zip, zilch. Zero

    bupkis

  6. 6
    Mung says:

    (6) behavioral adaptability to environmental hazards;

    I would disagree that these are in any sense capable of adaptation. This is basically the claim that they are subject to natural selection. No alleles no natural selection.

  7. 7
    Eric Anderson says:

    Thanks, vjtorley, for the interesting article.

    It looks like Otto’s group carried out some interesting research. Too bad it is all hyped in the context of some alleged precursor to biological evolution. But, hey, that is where the money and the headlines are.

    I agree with Sheldon’s sentiment: not much going on here beyond what has been observed for centuries with crystals. Namely, given the right solubles in a solution, crystals grow, eventually break, grow some more, and so on.

    Growing crystals do not provide an example of “self-replication” in any meaningful sense of the word. Rather, they are simply an example of distilling molecules out of solution. It isn’t self-replication any more than a puddle growing larger from a rainstorm and spilling over into another depression in the ground to form another puddle can be called “self-replicating.” Or sand dunes on the seashore growing and splitting with the wind. Or any other number of repetitive-type natural processes or chemical reactions that proceed naturally downhill — continuing until the materials are exhausted or until the process bogs down due to interfering cross reactions.

    The new process engineered and carefully carried out by Otto and his team is a little more sophisticated, but essentially amounts to the same thing we see with crystals.

    Interesting? Yes. Relevant to the origin of life? Almost certainly not.

  8. 8
    Eric Anderson says:

    By the way, RepRap is not self-replicating.

    Not even close.

    I discussed it specifically in the context of abiogenesis here:

    http://www.uncommondescent.com.....-paradigm/

  9. 9
    vjtorley says:

    Hi Eric Anderson,

    I jut had a look at your post. I stand corrected. I hadn’t realized that the claim that RepRap could self-replicate was just hype. Thank you for drawing that to my attention.

  10. 10
    jerry says:

    There is a new Teaching Company course on Information. When discussing OOL the lecturer talks about natural selection of self replicating molecules.

    The environment will favor the selection of some of these self replicating molecules (some of which are rna molecules) and reject others. So there will be an increase of some and a process that eliminates others. This is his speculation on how life eventually began.

    I have not examined the details of the experiments but some are not covered in Signature in the Cell.

  11. 11
    Eric Anderson says:

    jerry @10:

    Ah, yes, unsupported speculations continue to abound.

    Unfortunately, the lecturer doesn’t know much about chemistry, about natural selection, or about living systems. Or all of the above.

    It isn’t just that we need an incredibly lucky event to produce the first self-replicating molecule (we all agree on that). The whole concept of reproduction being the start of the biological story is completely backwards. Not to mention that an alleged “self-replicating” molecule has never before been seen or heard from. Not even after decades of dedicated research in the lab.

    Finally, I couldn’t tell from your comment if the lecturer’s speculations on OOL had anything to do with how information came to exist in living systems, but if he is proposing that self-replication somehow leads to information-rich molecules and systems, then the lecturer is completely clueless about how information arises.

    Might be a good lecture otherwise, but lots of strikes on the OOL front.

    —–

    BTW, I know you already know all this. Just putting it down on paper, so to speak, for the lurkers.

  12. 12
    jerry says:

    Eric,

    Here is what I posted on another thread

    The Teaching Company or The Great Courses recently relaeased a course on Information, “The Science of Information: From Language to Black Holes”

    http://www.thegreatcourses.com.....#038;pos=5

    The author, Benjamin Schumacher, is a physicist who speciality is Quantum Information Theory and he invented the term qubit. He explores many of these same topics.

    He is a world authority on information.

    As far as OOL, he presents information on how self replicating molecules (including some RNA molecules) survive based on environmental conditions. It is the same idea as natural selection as certain molecules get to proliferate as others disappear while in another environment these particular molecules may disappear and another type increases. I am certainly not qualified to evaluate these findings.

  13. 13
    Eric Anderson says:

    jerry, you are far too modest.

    Three things:

    First of all, he almost certainly did not present information on how “self replicating molecules” do anything, as no-one has ever, to my knowledge, ever seen such a beast. Oh, there are speculations, to be sure. But nothing concrete.

    Second, he definitely did not present any information about how a self-replicating molecule (should such a thing exist) would develop additional attributes and still be able to self replicate. That is one of the foundational problems with naturalistic abiogensis ideas. They start with self-replication (which is exactly backwards) and then pretend that the magic of natural selection is going to do something (which you and I both know isn’t true, as natural selection doesn’t do anything).

    Finally, even if we had a self-replicating molecule that were able to get additional attributes and still keep self-replicating, it doesn’t tell us anything about how an information-rich molecule could arise (which is the real crux of the matter).

    Look, he is no doubt a smart guy who knows a lot about Quantum Information Theory.

    And he also apparently knows very little about OOL.

    You, and many others, are certainly qualified to evaluate that.

  14. 14
    Eric Anderson says:

    jerry:

    Incidentally, the statement that rna “survives” based on environmental conditions means what, exactly?

    A molecule “surviving” just means that the molecule will continue to exist in its present form, at least for the time being.

    An rna molecule “surviving” is about as exciting as me saying that the after I drew my bath and left for an hour and came back I observed that most of the water molecules had “survived.”

    People tend to wax very poetic and anthropomorphize molecules when they discuss OOL. As though the molecules were doing something beyond just being subject to normal chemical and physical reactions. The fun essay Vy linked to on the other thread is worth looking at. I didn’t read the whole thing, but the first half, while a bit tongue-in-cheek, is spot on in its indictment of the tendency to anthropomorphize molecules in the OOL context:

    http://www.evolutionnews.org/2.....02101.html

    —-

    So back to the point: an rna molecule exists and “survives” — meaning, we now understand, that it continues to exist. Great. So what? Now we have a molecule that exists and . . . wait for it . . . continues to exist.

    Until, of course, it doesn’t. Due to natural decay, interfering cross reactions, environmental changes, or otherwise. Which means it is is just like any other inanimate molecule in the universe and we have learned precisely nothing about abiogenesis from the observation that this inanimate molecule temporarily “survived” in a given environment.

  15. 15
    Alicia Cartelli says:

    An RNA molecule “surviving” is actually pretty important. Whether a single molecule is “surviving” the environment at a given point in time because of certain conditions, or (if it’s a self-replicating molecule) it is “surviving” over a period of time by making successive copies of itself. Either way it’s pretty important to current abiogenesis hypotheses.

  16. 16
    Eric Anderson says:

    Of course “surviving” is important. Because if it isn’t surviving then it isn’t existing.

    So, as I said, we have a molecule that . . . continues to exist. Congratulations. Now what?

    I am fully aware that current abiogenesis hypotheses fantasize about the never-before-seen, hypothetical self-replicating molecule and imagine that, should such a thing exist, it would somehow be “selected for” by the benevolent hand of natural selection. And then, allegedly it would undergo unspecified changes, all the while inexplicably (and contrary to known chemistry) retaining its ability to self-replicate. And then, some never-defined hypothetical version of this never-seen hypothetical molecule would be “selected for” because it is more . . . well, who knows? More something. And then it would accidentally change some more and . . . insert lots of time . . . Ta Da! We have our first living organism.

    The naturalistic creation myth is pretty well known. That it is a preposterous, laughable, fantasy is also well known by anyone who has looked into the details.

    Naturalistic abiogenesis ideas are supported not by actual chemistry or the science, but by vague generalizations, lots of what-if’s, and handwaving speculations.

    Modifying a maxim I have used with evolution more generally:

    The believability of abiogenesis is inversely proportional to the specificity of the discussion.

  17. 17
    Jonas Crump says:

    People talk about OOL being triggered by molecules that can self-replicate. But do they have to replicate in the manner that DNA does in order to get the ball rolling? Prions don’t “replicate” but they can turn (catalyze?) other proteins into structures identical to the prion. And crystals can be said the “replicate”.

    We don’t even agree on the definition of life. How are we going to agree on the origin of something that we can’t define?

  18. 18
    Alicia Cartelli says:

    ‘an rna molecule exists and “survives” — meaning, we now understand, that it continues to exist. Great. So what?’

    ‘Of course “surviving” is important.’

    You should try to limit how often you contradict yourself, EA. People start to worry about your mental health.

  19. 19
    Eric Anderson says:

    Alicia, please consider the difference between necessary and sufficient conditions before you opine on OOL or before you throw stones at those who have examined the issue in far more detail than you. There are myriad conditions that are important to the abiogenesis creation story, including, yes, that the alleged self-replicating molecules can “survive” in the particular environment long enough to replicate. Big deal. Even if we grant a dozen of these necessary conditions abiogenesis still doesn’t have any realistic chance of getting off the ground. Molecules being able to exist in an environment is “important” in the sense that it is one more in an exceedingly long list of necessary requirements for abiogenesis, yes. “Important” in the sense that it tells us much of anything about how abiogenesis could have occurred, no.

    So my comment and question is still fully on the table: Congratulations, you have rna molecules that can exist (read “survive” in the strained Darwinian-burdened terminology) in a particular environment. So what? It doesn’t address any of the key problems with abiogenesis.

    Yet we have people apparently thinking that the ability of certain hypothetical molecules to exist in a particular environment is some big accomplishment, some big step toward the formation of first life on the Earth.

    It isn’t.

    Instead, the responses we get to the serious questions are vague claims about some hypothetical self-replicating molecule, equally vague assertions about unspecified changes that would take place to such molecules, unsupported suggestions that self-replication would continue apace even with such changes, and silly references to natural selection stepping in to “select” the more “fit” molecules — fitness being, of course, left wholly undefined and as vague as everything else in the story.

    Yet again,

    The believability of abiogenesis is inversely proportional to the specificity of the discussion.

  20. 20
    Eric Anderson says:

    Jonas, you make some good points, and raise some good questions.

    Self-replication of molecules need not occur as we see it occur in organisms. Indeed, abiogensis posits that the first hypothetical self-replicating entities did not do so as it happens in organisms today. Though note Mung’s excellent point and my response on the other thread here:

    http://www.uncommondescent.com.....ent-594890

    Yet the proposals of self-replication to date generally posit the molecules at the very least doing something — performing some catalytic function, for example, that would not occur without that catalytic function of the replicator.

    It is worth contrasting how that compares to the formation of crystals, which essentially occurs as the result of a solute distilling or “falling out” of a solution. A crystal’s “growth” isn’t any more related to the growth of a living system than is rain falling out of the sky and creating a puddle. And a crystal breaking into fragments or splitting into a secondary crystal isn’t “self-replicating” any more than a puddle spilling over the edges and forming two puddles can be said to be “self-replicating.”

    There are all kinds of natural physical processes that involve solutes or accretion or physical breakage and so on. But none of these can be properly understood as self-replication in any meaningful sense that would be relevant to the origin of life. (And if we insist that they are examples of self-replication then we are playing a semantic game that just requires a redefinition of terms to get back to the real substantive issue at hand.)

  21. 21
    Alicia Cartelli says:

    How could you possibly know how much I have examined the issue, EA?

    And you are incorrect on pretty much everything.
    There is a relationship between stability and reactivity when talking about molecules. So finding that RNA is capable of both catalyzing reactions and holding information to be passed to daughter molecules, while also finding conditions that the molecule “survives” in is incredibly important and certainly does address some of the questions raised by abiogenesis.
    I guess “those who have examined the issue in far more detail than you,” didn’t include you, EA.

  22. 22
    EugeneS says:

    Producing life (symbolically controlled cell chemistry) out of non-life (abiogenesis) can only be possible via fine intelligent control.

  23. 23
    Virgil Cain says:

    Alicia Cartelli:

    Of course “surviving” is important.’

    Rocks survive. What is so important about that? RNA is not alive and does not seek to be alive. It could care less- actually it doesn’t care at all. It is happy being RNA or just its parts. It isn’t striving to be anything else.

  24. 24
    jerry says:

    Eric,

    I am still trying to digest what this lecturer is saying about OOL. It is one of two lectures on biology out of 24. He is a physicist with a speciality in quantum information theory so also knowledgeable on information theory.

    His emphasis during the lecture is on certain types of polymers that self replicate. It is confusing because it is not clear whether the RNA polymers he talks about which contain no functional information need another different RNA molecule that acts like an enzyme and facilitates replication of the RNA polymer ( these molecules are in the presence of nucleotides to build new RNA polymers.)

    After looking at the lecture a second time, it is more informative for what is not there than what he presents. He really has nothing but a suggestion that this process is just the start of a long lost sequence of steps that led to life. It is all speculation.

    He also uses the idea that RNA clings to clay and clay will expand in random way affecting the sequences of molecules that cling to the clay. All very iffy and I may not have described his presentation accurately.

    In no way does he admit that it cannot have happened by natural means but what he presents he says is the likely starting place. Because of what he has presented or what he has failed to present, it means there is no coherent theory for OOL because if there was it would have been part of the lecture. It is another case of the “dog barking in the night.” No bark, no dog that was upset or in this case no coherent idea or no clue as to how it happened.

  25. 25
    jerry says:

    Rocks survive. What is so important about that? RNA is not alive and does not seek to be alive. It could care less- actually it doesn’t care at all. It is happy being RNA or just its parts. It isn’t striving to be anything else.

    The issue is that the rocks are not replicating or if there were certain types of rocks that did replicate and survive while other rocks would not replicate but disappear.

    Certain polymers will duplicate while others will not. The environment in which the polymers exist affects whether one expands its presence while another disappears.

    That is the claim and it is not clear how prevalent this is or not.

  26. 26
    Virgil Cain says:

    Replicating RNA will never get you anything but that. You will have Spiegelman’s monster in no time but nothing more complex than what you started with.

  27. 27
    Virgil Cain says:

    Does anyone know the sequence specificity for replicating RNAs? The Joyce/ Lincoln self-sustained replication of RNAs” started with two designed RNAs and many smaller RNAs that just required one bond to be made in order to get the same sequence of the starting two. They were able to vary at some loci but never did they gain a new function. The only difference is some variants were able to replicate faster than the original.

    I doubt any sequence of RNAs will do the trick so there must be some sequence specificity required. If we could determine that we could at least determine the probability of it happening by chance.

  28. 28
    Mung says:

    Of course surviving is important. You can’t have survival of the fittest without it! It’s just Alicia playing games again.

    What is the fittest of the elements? Is it the most fit because it has survived the longest or because it is the most fecund?

  29. 29
    Mung says:

    RNA is “important” because of it’s potential function as a carrier of information.

    Thus it would appear that purpose and meaning are fundamental to the concept of life and the abiogenesis myth is absurd when used by certain religious sects to dispute purpose and meaning in the universe.

  30. 30
    Eric Anderson says:

    jerry @24:

    Because of what he has presented or what he has failed to present, it means there is no coherent theory for OOL because if there was it would have been part of the lecture. It is another case of the “dog barking in the night.” No bark, no dog that was upset or in this case no coherent idea or no clue as to how it happened.

    Precisely.

    Furthermore, I suspect the “polymers that self replicate” he refers to, on closer inspection, will turn out to not be polymers that self replicate. Does he provide any references for the claim?

    OOl isn’t his speciality, and isn’t the main thrust of his lectures apparently. So what would someone in his position do? Well, just do a little research, adopt the party line from some other “expert” he ran across, and present that. That is why what he is presenting isn’t any more or less than a summary of the same old vague assertions we see time and again from the promoters of the materialist creation story. Understandable approach, and one for which he can perhaps be forgiven, but not helpful if someone wants to understand OOL or the origin of information in biology.

  31. 31
    Eric Anderson says:

    Let’s be very clear:

    To my knowledge, no-one has ever seen a self-replicating string of RNA that has any chance of functioning in the real world.

    Someone please let me know if they are aware of such a thing. (And BTW, the Joyce experiment is not an example.)

    Again, I fully agree with most commenters here that even if such a beast existed it wouldn’t get us very far toward OOL. But I keep harping on this because for some reason people keep referring to these self-replicating strands of RNA as though they actually existed, instead of as the hypothetical beasts that they are.

  32. 32
    Eric Anderson says:

    jerry @25:

    Certain polymers will duplicate while others will not.

    By “duplicate” I presume you mean new polymers will “form” as a result of the natural chemical reactions between smaller molecules in the solution? And will presumably continue to form until the small molecules are used up.

    Or are you suggesting that the existing polymer is doing something to “duplicate” itself?

  33. 33
    Virgil Cain says:

    Eric Anderson- Have you read Nick Lane’s “Life Ascending: Ten Greatest Inventions of Evolution”? The OoL is one of them and he gives the best account I have ever read or heard of. The rocks lining white smokers in the oceans seem to offer the right materials and disequilibrium to not only the create macromolecules but also start the Krebs cycle. The rocks have many tiny cell-size pores that can trap the materials and allow them to coalesce and become part of a system.

  34. 34
    Alicia Cartelli says:

    Not responding to me again EA?
    How come you never responded to my answer to your “abiogenesis challenge” a while back?

  35. 35
    Eric Anderson says:

    virgil @33:

    I haven’t had the opportunity to read Lane’s book, though it looks interesting.

    But start the Krebs Cycle — really!? That is quite a claim, especially since getting something close to the Krebs Cycle is far beyond anything that anyone has ever demonstrated to be possible for inanimate molecules even under carefully controlled lab conditions.

    Would you be able to provide a brief summary of Lane’s claim on this front? It is probably worthy of a head post for discussion.

    Or perhaps by “start” the Krebs Cycle he doesn’t actually mean get the cycle going, but instead just that one or two of the reactions involved in the Krebs Cycle are also found under abiotic conditions? In that case it would be an interesting observation, but not really much help for OOL.

  36. 36
    Eric Anderson says:

    Alicia @34:

    Not responding to me again EA?

    Let’s see, it has been a whole 7 hours and I am accused of ignoring you?

    Like you, I have limited time and use that time to respond to the issues and points that seem most interesting to me. You didn’t say anything @21 beyond just repeating how important this “surviving” is, to which I have already responded in detail. You think this is a terribly important observation that is somehow highly meaningful for OOL. I think it is trivial and doesn’t tell us anything meaningful about OOL.

    There we have it. I’ll leave it to the reader to decide which of us has provided more detail and support for their position.

    —-

    As for the abiogenesis post, I appreciate you writing up a short description for the OP and do apologize for not being involved in that as I had hoped to be. I trust you were able to get some feedback and input from others. My engagement with UD tends to be in fits and spurts as my work and other circumstances allow. You’ll notice that I didn’t just ignore your abiogenesis thread, I ignored UD entirely for several weeks. In just the past couple of days I’ve had a bit of time to re-engage. I haven’t even checked your abiogenesis post in recent weeks, but I’ll try to take a look at it to see where things left off. Unfortunately, it is exceedingly difficult to restart old threads, but maybe there is something else of value we can discuss there . . .

  37. 37
    Virgil Cain says:

    Lanes states the source of energy needed to get started comes from the vents themselves. They produce acetyl thioesters. These are significant as they are in an ancient branch point in metabolism and still found in organisms today. When CO2 reacts with an acetyl thioester more complex organic molecules form. The reaction is spontaneous, releases energy and produces pyruvate, which is the entry point to the Krebs cycle. Now for the energy for the Krebs cycle acetyl phosphate is also formed from the reactions of acetyl thioesters and CO2. Acetyl phosphate is, you guessed it, a simpler form of ATP.

    The grand part in all of this is it can drive the Krebs in reverse and spit out the complex molecules that are normally required as an input.

    Pulling all this together, alkaline hydrothermal vents continuously generate acetyl thioesters, providing both a starting point for forming more complex organic molecules and the energy needed to make them, packaged in a format essentially the same as that used by cells today. The mineral cells that riddle the chimneys provide at once the means of concentrating the products, favoring such reactions, and catalysts needed to speed up the process, without any requirement for complex proteins at this stage. And finally, the bubbling of hydrogen and other gases into the labyrinth of mineral cells means that all the raw materials are replenished continually and thoroughly mixed.pg 29 “Life Ascending”

  38. 38
    Mung says:

    Who needs a membrane. Right Alicia?

  39. 39
    Eric Anderson says:

    Alicia:

    I looked at my UD dashboard just now, which I haven’t worked on since late November and there is a post in the system labeled “Alicia Cartelli on Abiogenesis”, but it is marked “Draft”.

    I’m wondering if I didn’t publish it before I went away for a couple of months. Have you never seen the post? If that is the case, I sincerely apologize for the lengthy delay. Let me know and I’ll get it posted right away.

  40. 40
    Eric Anderson says:

    virgil @37:

    Thanks for the additional information. Interesting.

    What is your take on it?

    Where do you think it gets us on the path to OOL?

    Also, I’m not assuming you were suggesting such, but it doesn’t look like we have anything that is “self-replicating” in his proposed scenario, correct?

  41. 41
    Virgil Cain says:

    Eric, There is still a big leap from those mineral cells to a living cell. ATP synthase is one huge obstacle that Lane feels is easy-peasy although he never gets down to explaining it. Without ATP synthase mineral cells are stuck as they need a portable energy source.

    I think it’s interesting in that it goes to show that life depends on normal, everyday chemical reactions. But depending on them isn’t the same as being reducible to them.

  42. 42
    jerry says:

    Eric,

    By “duplicate” I presume you mean new polymers will “form” as a result of the natural chemical reactions between smaller molecules in the solution? And will presumably continue to form until the small molecules are used up.

    Or are you suggesting that the existing polymer is doing something to “duplicate” itself?

    I haven’t had time to listen closely to every part of the lecture or look at the references but the more I do, the more it is intellectually dishonest. Which leads me to then question the other lectures. It could be that he has little insight into the OOL issue or that he must take whatever straw is out there.

    I am starting to understand the premise of the RNA world and it is really grasping at straws which is why anyone endorsing it is intellectually dishonest. From what I understand of the RNA world, they can concoct solutions of some RNA strands and add to that other RNA molecules that act like as a replicase enzyme for duplicating the RNA strands. The duplication will not work without the replicase enzyme so it begs the question where did this type of RNA polymer come from.

    They assume it just arose somehow. But even with this, the ability to replicate is limited. The enzyme would only replicate smaller strands of RNA. Then a few years ago they developed a strand by taking a variant of a previous enzyme that would replicate a slightly longer strand. The new molecule is 202 bases long but can replicate a RNA strand of 206 bases long.

    That is the RNA world they are touting. As I said grasping at straws.

    Also the use of the term information is bogus because it is so vague but apparently within much of Shannon’s version of information theory. Any sequence is information whether it has meaning or not. So the duplication of a meaningless segment that has no value to anyone is replication of information and any error in the replication is new information. A lot of what the RNA world is about is about meaningless information.

    The lecturer touts clay crystals duplicating with these crystals splitting sometimes into imperfect forms of the original crystal and forcing other molecules attached to it to vary as they cling to the clay crystals. It seems that the clay crystal formation becomes a way of forming new molecules and that maybe some day one of these new molecules will have interesting properties.

    It seems to be searching for ways that complicated molecules could form and that some of these complicated molecules could be magic in the formation of life. Grasping at straws or grasping at clay.

    I have never paid much attention to the RNA world hypothesis so all of this is new to me and maybe not totally an accurate understanding.

  43. 43
    Mung says:

    jerry, “meaningless information” is an oxymoron.

  44. 44
    Mung says:

    VC: Eric, There is still a big leap from those mineral cells to a living cell.

    Let’s not call them cells then.

  45. 45
    jerry says:

    jerry, “meaningless information” is an oxymoron.

    I may be wrong but any random string of letters, bases, amino acids, symbols etc. is information in the Shannon sense. So what is wrong? Is is that the term information is meaningless or that anything is information? Unless you already are familiar with it then it is no longer information.

    From the lecture on Information theory

    In the same way, the idea of information is not about the value or significance of a message. Meaning, value, and significance are obviously important qualities, but they are not the keys to understanding what information is.

    Shannon’s definition of information is as follows: “Information is the ability to distinguish reliably among possible alternatives.”

    Meaning or purpose have no part in a discussion of this type of information. But obviously the normal conversation is about meaning or purpose when discussing information. This is just showing that bringing in Shannon only confuses a discussion.

    So the lecturer is going back and forth between various understandings of what information is and this is typical of many discussions of the topic.

  46. 46
    Virgil Cain says:

    Shannon didn’t care about meaning because the equipment that transmits and receives it doesn’t care. It is supposed to send what it is told to send. His concept was all about the proper transmission, reception and storage of some sequence.

    But that doesn’t mean that information can be meaningless.

  47. 47
    Virgil Cain says:

    Mung:

    Let’s not call them cells then.

    Too late as Nick Lane refers to them as such in his book.

  48. 48
    jerry says:

    His concept was all about the proper transmission, reception and storage of some sequence.

    Sounds like the song, Do, Re Mi from Sound of Music. The children ask but what does it mean. And Maria answers you have to put in words for each note. Until then, is it a song? Maybe yes, but one without meaning.

    But that doesn’t mean that information can be meaningless.

    But according to Shannon, it doesn’t have to have meaning. We are using the term in more than one way which is common on this site for a lot of concepts (e.g. evolution, life, science, evil). And we end us with not very much meaning or understanding.

    But back to the original issue. The RNA world is just random sequences with have no specific meaning or value. A few RNA sequences (replicase enzymes) help replicate the random sequences. So there is some purpose in these enzyme sequences but not necessarily in the strands being duplicated. There is just hope or better, a faith that this is how it happened.

    I am not trying to be contentious but trying to understand what people are claiming. My reading of those who propose anything of significance to the RNA world is that they are being disingenuous at best. They should admit they have nothing but wild speculation. It should not be presented as gospel or even likely in any scientific discussion.

  49. 49
    Virgil Cain says:

    Functionality is meaning as it is a specification of sorts.

    Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. In virtue of their function, these systems embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the same sense required by the complexity-specification criterion (see sections 1.3 and 2.5). The specification of organisms can be crashed out in any number of ways. Arno Wouters cashes it out globally in terms of the viability of whole organisms. Michael Behe cashes it out in terms of minimal function of biochemical systems.- Wm. Dembski page 148 of NFL

  50. 50
    Eric Anderson says:

    Mung @43:

    Exactly. Which is why we should stop calling the Shannon carrying capacity measurement “Shannon Information.” After all, Shannon himself said his theory didn’t deal with “meaning”. 🙂

    —–

    jerry @45:

    This is just showing that bringing in Shannon only confuses a discussion.

    Indeed. As it almost always does. Including, quite often, confusing the very lecturer who is talking about it.

  51. 51
    jerry says:

    Eric,

    Just read your comment from yesterday on Shannon Information on the other thread. I am starting to learn what this is all about.

  52. 52
    Eric Anderson says:

    jerry @42:

    Thanks for the additional detail and for taking time to share it.

    I don’t know that you should toss out the lectures generally, maybe just keep a close eye out for where he goes astray.

    What I have often seen happen is that an expert in one area (information theory in this case) will run across something that is interesting or related in a somewhat different area that they would like to share (OOL in this case). But not being well-versed in that area, they just do a few brief searches, rely on the usual voices, and present their quick findings as though they were fact — after all, the “experts” in that other area said so.

    An understandable approach and one that doesn’t cause too many problems in most areas that are non-controversial: the date of Lincoln’s birth, the text of the Gettysburg Address, etc. But when it comes to highly controversial areas (such as OOL), it is very easy to be misled by the usual voices, and so the unsuspecting lecturer, however expert they may be in their own field, quickly gets led down the garden path when examining a new field. The reality is that they aren’t meaningfully more capable of understanding a new field than anyone else. It takes a lot of time, energy, and careful thought — like what you have been investing — to really understand a controversial area and appreciate the pitfalls and nuances.

    —–

    I definitely agree with you that the RNA world is grasping at straws.

  53. 53
    Mung says:

    Eric: Exactly. Which is why we should stop calling the Shannon carrying capacity measurement “Shannon Information.”

    I’m completely on board with that. I’ve taken to calling it the Shannon Measure of Information (SMI).

    The mistake people commonly make, as is apparently the case in the lecture jerry cites, is in thinking that the Shannon Measure tells us what information is. It does not.

    The Shannon Measure is always relative to a probability distribution. If you don’t know the distribution you don’t have a quantity for your measure.

    You can of course assume all symbols are equiprobable, the maximum entropy principle, and amazingly the Boltzmann distribution can be derived from that.

  54. 54
    Eric Anderson says:

    Mung:

    I’m not sure that is much better. Shannon’s measurement isn’t measuring information — at least not in any normal sense of the word information (that which has meaning or informs, as you rightly keep pointing out), nor in the sense that is relevant to the design inference.

    It is measuring capacity of the pipeline (whether we want to look at it in terms of packaging or rate, both of which are inexorably linked).

  55. 55
    kairosfocus says:

    F/N: The shannon metric is a measure of info carrying capacity. Cf 101 here. KF

  56. 56
    Zachriel says:

    jerry: Sounds like the song, Do, Re Mi from Sound of Music. The children ask but what does it mean. And Maria answers you have to put in words for each note. Until then, is it a song? Maybe yes, but one without meaning.

    What Maria actually says:

    Let’s start at the very beginning
    A very good place to start
    When you read you begin with A B C
    When you sing you begin with Do Re Me

    When you know the notes to sing
    You can sing most anything

    jerry: The RNA world is just random sequences with have no specific meaning or value.

    In RNA World, the sequences include the capability of self-replication, so they are not without meaning or value in terms of their continuance through time.

  57. 57
    Eric Anderson says:

    “In RNA World, the sequences include the capability of self-replication . . .”

    Referring, we must presume, to the hypothetical, never-before-seen sequences that are allegedly capable of self-replication.

    Furthermore, you are conflating the word “meaning” in this context, and I suspect you know it. A random RNA sequence has no meaning, codes no information, represents nothing outside of itself.

    jerry’s assessment is spot on.

  58. 58
    jerry says:

    In RNA World, the sequences include the capability of self-replication, so they are not without meaning or value in terms of their continuance through time.

    Thank you for making my point. You agree that their only value is meaningless in that all they do is continue. The RNA world is a world of make believe so has a lot in common with Disney’s many movies.

    The RNA are not actually self replicating though. There is a separate mechanism that does the copying. So self replicating is a misnomer for what actually goes on.

  59. 59
    Zachriel says:

    Eric Anderson: Referring, we must presume, to the hypothetical, never-before-seen sequences that are allegedly capable of self-replication.

    Yes, the hypothetical RNA World was the premise of jerry’s question.

    Eric Anderson: Furthermore, you are conflating the word “meaning” in this context

    Clearly not, as we explicitly qualified the statement.

    jerry: You agree that their only value is meaningless in that all they do is continue.

    Continuing your family line, your children, may be meaningful to you. Meaning, in your sense, is in the eye of the beholder.

    jerry: The RNA are not actually self replicating though.

    RNA World posits self-replicators, though the mechanism may involve more than one molecule.

  60. 60
    Virgil Cain says:

    Zachriel:

    RNA World posits self-replicators,

    Of course it does. However there isn’t any evidence for a RNA world so it might as well be Disney World, where imagination rules.

  61. 61
    Mung says:

    It is my understanding that RNA has a natural tendency to fold on itself. What is the longest known sequence of bases in a molecule of RNA that does not fold on itself?

    What prevents messenger RNA from folding on itself?

  62. 62
    Eric Anderson says:

    Not just the hypothetical “RNA World” but the hypothetical self-replicators as well. And the hypothetical “mechanism.” The whole thing is fantasy.

    —–

    Is there any substantive difference in meaning between what you wrote in your comment and a string of gibberish? Both continue to exist. That is not the issue.

    If you don’t acknowledge a substantive difference then discussion on the issue is pointless.

  63. 63
    Virgil Cain says:

    Mung:

    What prevents messenger RNA from folding on itself?

    You need complementary pairs to effect folding and perhaps mRNAs sequences are just too random for that. That’s what I infer from looking at the sequences of RNAs that do fold.

    But what do I know, I just break toasters. 🙂

  64. 64
    Virgil Cain says:

    Oh my, is Eric really trying to reason with Zachriel?

  65. 65
    Mung says:

    Eric: Shannon’s measurement isn’t measuring information — at least not in any normal sense of the word information (that which has meaning or informs, as you rightly keep pointing out), nor in the sense that is relevant to the design inference.

    I guess I take sort of a middle position. I say that the Shannon Measure of Information (SMI) actually does measure information, that it is information that has meaning or does inform, but probably not in the sense relevant to ID.

    So by saying that “Shannon Info” is actually about something and is meaningful I am not contradicting myself.

    So what is it about? It’s about what is expected given the probability distribution of the source and the reduction in uncertainty that takes place given receipt of a symbol. Or as kf likes to point out, we’re talking averages here. In this way of understanding SMI it still involves our knowledge (or lack thereof) and reducing our uncertainty.

    Seems to me this is still within what people think of when they think of information.

  66. 66
    Arthur Hunt says:

    It is my understanding that RNA has a natural tendency to fold on itself. What is the longest known sequence of bases in a molecule of RNA that does not fold on itself?

    What prevents messenger RNA from folding on itself?

    One can experimentally find mRNAs that do form secondary structures. And one can find mRNAs that associate with any of a number of RNA-binding proteins (that may interfere with, or stabilize, secondary structures).

  67. 67
    kairosfocus says:

    Folks, I have to note how we are straining at gnats while swallowing camels. Or should I be saying that there is eager speculation on RNA worlds and whatnot — EA is right to use the word fantasy while VC and Jerry hint at Disney’s Fantasia; meanwhile, there is a herd of elephants standing and trumpeting in the middle of the room but they are stubbornly relegated to the fringes of the secularist Overton window: http://www.uncommondescent.com.....lly-issue/ KF

  68. 68
    Eric Anderson says:

    Mung @65:

    So by saying that “Shannon Info” is actually about something and is meaningful I am not contradicting myself.

    I agree that the Shannon measure is about something. I suspect we also agree essentially on what it is about.

    Here is the key, though:

    The Shannon measure is precisely that: a way to measure something.

    Let’s say I have a physical object, maybe a box.

    Using my tools of measurement (such as a ruler), my intellectual capabilities, and an agreed-upon set of numerals and terminology, I can measure the box and pronounce that the box is, say, 1 meter in length.

    That statement “the box is 1 meter in length” is indeed information. It is information produced, as information always is, by an intelligent agent, using the tools of investigation and articulated in an agreed-upon symbolic system (in this case English, coupled with numerals and a particular system of weights and measures).

    So yes, now an intelligent agent has produced a new piece of information. And it is information about something, namely the box; more precisely, about one particular aspect of the box. So we now have information about something. But it is nonsensical to say that we were measuring this “information.” No. We were measuring the box, and we produced information about the box.

    There are lots of different measurements we could make about a box: its height, width, volume, color, material, and on and on. And in every case we would not be measuring information in the box. Rather, we would be producing information about the box through our tools of investigation and our intellectual effort.

    —–

    The same exact situation holds true with a string of symbols. There are lots of ways we can measure that string. One specific, agreed-upon system for measuring that string, for investigating something about that string, is the Shannon approach.

    So we can use our intellectual capabilities and Shannon’s approach, this tool of investigation, plug in the string (along with all the other relevant parameters) and it will spit out some result, say, “100 bits.”

    This resulting measurement “100 bits” is indeed information and it is about something. It is about the string; more precisely, about one particular aspect of the string. But it is nonsensical to say we were measuring that information. No, we were measuring a particular aspect of the string. And in doing so we produced information about the string.

    —–

    I fully appreciate that people are sloppy when they speak and that there is much inertia in terminology and we probably won’t be able to get people to clear up their terminology to the point of avoiding confusion.

    But it is simply incorrect to say that a string “contains” Shannon information or that we are measuring Shannon information in a string. No. We are measuring a particular characteristic of the string and then producing (with our agreed-upon system of measurement that Shannon proposed) a result.

    We would all be better off if that result were called something like the “Shannon Metric” or the “Shannon Measure,” rather than “Shannon Information,” as the latter causes no end of confusion.

    But even if we insist on calling the result of our measurement “Shannon Information” we need to recognize that this “information” was not measured, it was produced by us with our tools of investigation and our intellectual effort.

    The Shannon approach does not measure information. It measures a particular characteristic of a string. And the result of that measurement has meaning and informs and is about something — the result is indeed information.

  69. 69
    Zachriel says:

    Eric Anderson: We would all be better off if that result were called something like the “Shannon Metric” or the “Shannon Measure,” rather than “Shannon Information,” as the latter causes no end of confusion.

    Shannon Entropy.

  70. 70
    Virgil Cain says:

    As Meyer and others have pointed out Shannon measured information carrying capacity.

  71. 71
    Eric Anderson says:

    Zachriel:

    Yes, that term is sometimes used as well. Is it referring to the result or the thing measured? 🙂

  72. 72
    Mung says:

    Shannon Entropy doesn’t help at all. Entropy about what? You may as well say Shannon Uncertainty. Uncertainty about what?

  73. 73
    Mung says:

    Eric:

    There are lots of different measurements we could make about a box: its height, width, volume, color, material, and on and on. And in every case we would not be measuring information in the box. Rather, we would be producing information about the box through our tools of investigation and our intellectual effort.

    And if we wanted to quantify how much information about the box we had obtained? We would not talk about the information carrying capacity of the box, I hope. 🙂

  74. 74
    Mung says:

    The Shannon approach does not measure information.

    I disagree. But over at TSZ they complain that we never disagree with each other here at UD. LoL.

    It measures a particular characteristic of a string.

    I disagree. 🙂

  75. 75
    Eric Anderson says:

    And if we wanted to quantify how much information about the box we had obtained?

    What does that even mean?

    If I measure the length I now know the length and I can express that information the same way it always is expressed: by instantiating it in some symbolic coded system.

    Can we then quantify “how much information about the box” we have obtained through our measurement?

    What does that even mean? I’m struggling to see how such a question even makes sense . . .

  76. 76
    Zachriel says:

    Eric Anderson: that term is sometimes used as well.

    Shannon Entropy is the proper term, so it’s worth mentioning.

    Eric Anderson: Entropy about what?

    Shannon Entropy is explicitly defined. See Shannon, A Mathematical Theory of Communication, Bell System Technical Journal 1948.
    http://languagelog.ldc.upenn.e.....ntropy.gif

    Shannon Theory of Communication has both nothing and everything to do with common notions of information. It forms the basis of all electronic communications, including transmission of this blog, but doesn’t say whether your communications are meaningful to others or meaningless gibberish.

  77. 77
    Eric Anderson says:

    Shannon Entropy is the proper term . . .

    Again, is it referring to the thing measured or the result of the measurement?

  78. 78
    Zachriel says:

    Eric Anderson: is it referring to the thing measured or the result of the measurement?

    When you measure a stick with a ruler, is it referring to the thing measured or the result of the measurement?

  79. 79
    Eric Anderson says:

    Just answer the question:

    You said the proper term is “Shannon Entropy.” The proper term for what — the thing measured or the resulting information from the measurement?

    This is not a trick question. I am not trying to catch you in some mistake. What do you think your “Shannon Entropy” is referring to? The thing measured or the information resulting from the measurement?

    —-

    P.S. Don’t confuse the discussion. We haven’t even talked about the ruler yet. I’m confident you aren’t suggesting “Shannon Entropy” might be the term to describe the tool of measurement . . .

  80. 80
    Zachriel says:

    Zachriel: When you measure a stick with a ruler, is it referring to the thing measured or the result of the measurement?

    Eric Anderson: Don’t confuse the discussion. We haven’t even talked about the ruler yet.

    By answering the question, we can better understand what you are trying to ask. If you say the stick is 10″ long, you are making a claim about the measured property of the stick. Similarly for Shannon Entropy: it is a claim about a measured property of a communication.

  81. 81
    Mung says:

    Shannon Entropy works for any probability distribution.

  82. 82
    Eric Anderson says:

    So we have three components. As we always do when investigating anything:

    1. Some property of the thing being measured.
    2. Some tool to do the measuring.
    3. Some output of the tool.

    #3 is clearly information. Produced, as always, by an intelligent being through intellectual effort — in this case our work of investigation and the tool we have created. When we say that “Shannon Information” means something, or informs us about something, we are talking about this information that we have produced in our investigation of the thing being measured. It informs, it describes, it has meaning, it can be encoded in an agreed-upon language and system of weights and measures (such as when we say “100 bits”), it can be translated into different languages, etc. It is “information” in every sense of the word.

    #2 is not information in and of itself (although the tool may of course contain or utilize information in its operation).

    #1 is the confusing case for many people. If we produce information as part of our investigation (#3), does that mean we are measuring information? No. It does not. It means simply that we are measuring some property of the thing being measured. If I measure the length of a box, it does not mean I am measuring information. I am measuring a physical property of the box and producing information as the output of my intellectual endeavor. It is no different with a string of characters or anything else we are measuring.

    —–

    All that said, I again repeat: I recognize that history and inertia will probably never allow us to clean up the terminology confusion associated with this issue. But regardless of terminology we should be careful not to fall into the trap of thinking that because we have produced real, meaningful information as a result of our investigation that such real, meaningful information was somehow contained in the thing measured or that the information was itself the thing being measured.

  83. 83
    Zachriel says:

    Eric Anderson: But regardless of terminology we should be careful not to fall into the trap of thinking that because we have produced real, meaningful information as a result of our investigation that such real, meaningful information was somehow contained in the thing measured or that the information was itself the thing being measured.

    Shannon’s Theory of Communication is the basis of modern communications, including the Internet. Whether you consider most of what is posted on the Internet to be “real, meaningful information” is subjective.

  84. 84
    Eric Anderson says:

    Zachriel, do you even understand the point at issue, or are you just arguing for argument’s sake? If you cannot, or will not, acknowledge a meaningful difference between a coherent sentence in, say, the English language and a string of random gibberish, then there is no point in having a discussion with you.

    You don’t need to battle just because you think you must battle against everything an ID proponent says, lest (heaven forbid) you should find yourself actually agreeing on some point.

    I’m not battling you on your suggestion that we refer to “Shannon Entropy”. I’m taking that suggestion and running with it. Fine. Give it whatever label we want. What does it mean in substance, what is it referring to? It isn’t helpful to come back with some vague assertion about information on the internet being subjective.

  85. 85
    Virgil Cain says:

    Zachriel is just a bloviating equivocator, and that is being nice.

  86. 86
    Zachriel says:

    Eric Anderson: If you cannot, or will not, acknowledge a meaningful difference between a coherent sentence in, say, the English language and a string of random gibberish, then there is no point in having a discussion with you.

    We can make the distinction, but the meaningfulness of a sentence is often subjective.

    Eric Anderson: It isn’t helpful to come back with some vague assertion about information on the internet being subjective.

    Is data on the Internet information?

    Eric Anderson: Give it whatever label we want. What does it mean in substance, what is it referring to?

    Shannon Entropy measures the uncertainty in a random variable, that is, the expected quantity of data to be communicated in a data-stream. That data is usually called information in the modern sense of the word.

  87. 87
    Eric Anderson says:

    Do you believe it is possible to have information that does not inform, that contains no meaning?

    —–

    . . . that is, the expected quantity of data to be communicated in a data-stream.

    I presume you mean “data that could be communicated in a data-stream,” not necessarily is communicated?

    And by “data” it sounds like you mean “information. Fine for present purposes.

    So to reword slightly, you are saying that Shannon Entropy is a measure of the quantity of information that could be communicated in a given string. Am I understanding you correctly?

  88. 88
    Zachriel says:

    Zachriel: Is data on the Internet information?

    Eric Anderson: Do you believe it is possible to have information that does not inform, that contains no meaning?

    It depends on the sense of the word information. A computer stores information. A router routes information. We say that even if we have no idea of the content of the data-stream. It may be Shakespeare. It may be doggerel. It may be gibberish. However, one can also use the word information to refer to data about something.

    Eric Anderson: And by “data” it sounds like you mean “information.

    We’re looking for a term with a neutral sense to represent the stream of communication. As to whether anyone cares about the data, or finds it meaningful, that is largely subjective.

    Eric Anderson: you are saying that Shannon Entropy is a measure of the quantity of information that could be communicated in a given string.

    Yes. And that depends on the structure of the data being transmitted. For instance, knowing that a data-stream is a text in the English language, Shannon showed that the entropy is only about one bit per letter.

    You can discover this yourself by playing the Shannon Game. Given a bit of text, try to guess the next lette_. If you can guess the next letter, then transmitting the letter gives you no additional knowledge.

  89. 89
    Mung says:

    A computer stores information. A router routes information.

    And a nut cracker cracks nuts, and we still call it a nut cracker when it’s not actually cracking any nuts. We could also us it to squeeze grapes.

  90. 90
    Mung says:

    If you can guess the next letter, then transmitting the letter gives you no additional knowledge.

    What if I guessed wrong? What if I did not read English?

  91. 91
    Zachriel says:

    Mung: And a nut cracker cracks nuts

    The bits and bytes which pass through the Internet are called information. There may be other uses for the word, but that is certainly one of them.

  92. 92
    Zachriel says:

    Mung: What if I did not read English?

    Understanding the meaning of the symbols isn’t required to determine the Shannon Entropy, just letter and letter-combination frequency.

  93. 93
    Virgil Cain says:

    A router routes information.

    Only if provided the proper information. 🙂

    According to Meyer in SitC ID’s use of the word is:
    b : the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects

    So we can determine the Shannon Entropy/ information carrying capacity, and observe any special effects, as in the transcription of DNA into mRNA, the processing of that mRNA and then the translation into functioning protein.

  94. 94
    Virgil Cain says:

    We can make the distinction, but the meaningfulness of a sentence is often subjective.

    That may be but all words are defined, ie they have meaning.

  95. 95
    Mung says:

    Zachriel: The bits and bytes which pass through the Internet are called information.

    The bits and bytes which pass through the Internet are called bits and bytes. Routers don’t know what they are routing and nut crackers don’t know what they are squeezing. Routers no more tell us what information is than do nut crackers tell us what nuts are. But do carry on Zachriel. I’m sure someone finds your claims convincing.

    Zachriel: Understanding the meaning of the symbols isn’t required to determine the Shannon Entropy, just letter and letter-combination frequency.

    IOW, your puzzle was misguided. At least you admit it. What is needed is knowledge of [information about] the probability distribution. How does Shannon Entropy tell us what the probability distribution is? It doesn’t.

    That’s why I disagree with Eric about this statement:

    It measures a particular characteristic of a string.

    It [Shannon Entropy / Shannon Information / Shannon Measure] doesn’t measure anything absent a known or assumed probability distribution. We can’t look at a string of symbols and from that string of symbols, by means of Shannon’s formulae, discover the probability distribution.

    Feel free to show me why I am wrong.

  96. 96
    Mung says:

    Zachriel:

    Shannon Entropy measures the uncertainty in a random variable, that is, the expected quantity of data to be communicated in a data-stream. That data is usually called information in the modern sense of the word.

    Do you have any clue what you’re talking about?

  97. 97
    Eric Anderson says:

    Mung @95:

    Any measuring tool needs parameters to operate. And an investigator typically needs to know something about the object in question and the parameters that can be applied to perform a proper measurement. (Don’t ask me to pull out my Imperial scale in pounds to measure the distance from Los Angeles to New York in kilometers — wrong tool, wrong unit of measure.)

    You keep harping on the fact that we have to plug some parameters into your Shannon tool in order for the tool to kick out a coherent measurement. Yes, of course. We have to know something about what we are measuring in order to measure it correctly.

    All of that most certainly does not mean that we aren’t measuring a property of the string. Just as when we measure anything we are measuring some property of the thing measured. Surely you aren’t suggesting that (i) we are pulling the measurement out of thin air, or (ii) we are fully imposing the measurement from without.

    Unquestionably it is a property of the object in question that we are measuring. Otherwise, there is nothing to measure and no need to do the measurement.

    This is so self evident, that I highly doubt we have a substantive dispute on the issue. Maybe just using different terminology?

  98. 98
    Zachriel says:

    Mung: The bits and bytes which pass through the Internet are called bits and bytes.

    Cisco: “A router acts as a dispatcher, choosing the best path for information to travel so it’s received quickly.”

    Wikipedia: “A hard disk drive (HDD), hard disk, hard drive or fixed disk[b] is a data storage device used for storing and retrieving digital information”

    WordReference: information: “(in information theory) an indication of the number of possible choices of messages, expressible as the value of some monotonic function of the number of choices, usually the logarithm to the base 2.”

    Not sure the usefulness of arguing semantics. Information is clearly used in more than one sense. If you want to use a different sense, just say so, but don’t falsely claim other senses don’t exist.

    Mung: How does Shannon Entropy tell us what the probability distribution is?

    By looking at the data-stream. You don’t have to know the English language to notice that most telegrams have lots of E’s and A’s.

  99. 99
    EugeneS says:

    “In RNA World, the sequences include the capability of self-replication, so they are not without meaning or value in terms of their continuance through time.”

    And for that, you need guess what? Control, which is inherently telic. Especially in cases of algorithmic control.

    The more you delve into detail, the more you become convinced that this can really only be intelligently guided, probably as complex as in today’s chemical factories. There is a big gap here, ever growing in time, that needs bridging. Being a naturalist, it takes a leap of faith to get over it.

  100. 100
    Zachriel says:

    EugeneS: And for that, you need guess what? Control, which is inherently telic.

    RNA World posits that self-replication arose through natural means, though whether it is RNA-first or not is still an open question.

  101. 101
    Mung says:

    Zachriel: You don’t have to know the English language to notice that most telegrams have lots of E’s and A’s.

    Counting E’s and A’s in a telegram isn’t going to give you the probability distribution of the source.

    https://en.wikipedia.org/wiki/Gadsby_%28novel%29

  102. 102
    Zachriel says:

    Mung: Counting E’s and A’s in a telegram isn’t going to give you the probability distribution of the source.

    Take the first line of Gadsby. If we randomly delete every tenth character or so,

    If Youth, thr-u-hout all h-story, had -ad a champion to stan- u- f-r it; to show a doub-in- worl- th-t a child ca- th-nk;-and- possibl-, do it practically;-you wo-ldn’t constantly run ac-oss fol-s today who claim that “a child don’t-know anyt-ing.”

    you should be able to guess most of the remaining letters. As noted above, Shannon showed that the entropy of English is about 1 bit per character. There is substantial redundancy in English, which can be a good thing, as even if the error rate is high, the message can still be transmitted intact.

  103. 103
    Virgil Cain says:

    Zachriel:

    RNA World posits that self-replication arose through natural means,

    1- Define “natural means”
    2- Provide the evidence for such a thing

    Prediction- Zachriel will not do so

  104. 104
    Mung says:

    Zachriel: you should be able to guess most of the remaining letters

    I see were back to playing games. Not interested in playing your games Zachriel. This is ground already covered.

    What if I do not read English?

    And around and around we go.

    Do you have any clue what you’re talking about?

  105. 105
    Eric Anderson says:

    RNA World posits that self-replication arose through natural means. . .

    We know what it posits. You don’t need to keep endlessly repeating the speculative theory as though it were an answer. Evidence, please.

  106. 106
    Zachriel says:

    Mung: What if I do not read English?

    Again, one doesn’t have to read English, just notice patterns. Even an isolated snippet of English text will usually have lower entropy than a random sequence. Taking the first line of Gadsby again, there are 29 symbols, so would normally require 4.86 bits per symbol to encode. However, due to the uneven distribution of symbols in the text (lots of A’s, O’s and T’s), the Shannon entropy is only 4.20 bits per symbol.
    http://languagelog.ldc.upenn.e.....ntropy.gif

    A much longer transmission of English text will generally have even lower entropy.

  107. 107
    EugeneS says:

    Zachriel can’t even see the issue: the text and the processor must arise at the same time! An irreducibly complex structure at its worst is at stake here. But it is apparently beyond Zachriel.

    It is indeed word games. The moment he says “meaning”, there must be an appropriate definition for it in the context of pragmatic utility in the system. He does not understand (or makes believe he doesn’t) that nature does not care if anything maintains its own state.

    Pragmatic utility is about quality. Nature is indifferent to quality (accuracy, tenacity, buoyancy, minimax type of criteria such as chemical stability AND reactivity where chemicals react only ‘as needed’). That is why naturally produced regularities are not dynamically stable. Consequently, fine control is necessary in order to maximize utility.

    Algorithmic control is an absolute killer of RNA-world and other rubbish of the same sort.

  108. 108
    Zachriel says:

    EugeneS: the text and the processor must arise at the same time!

    In the case of a posited self-replicating RNA molecule, the text and the processor are the same thing.

  109. 109
    Mung says:

    Zachriel: In the case of a posited self-replicating RNA molecule, the text and the processor are the same thing.

    And yet in living organisms they are not the same thing. So now you must suppose two miraculous events instead of just one. Isn’t it more parsimonious to believe in just one miraculous event over some unknown and probably unknowable series of miraculous events?

  110. 110
    Zachriel says:

    Mung: And yet in living organisms they are not the same thing.

    No, however, ribosomes provide evidence of the primordial state.

    Mung: So now you must suppose two miraculous events instead of just one.

    The transition to DNA-world is posited to have occurred through darwinian evolution.

  111. 111
    Virgil Cain says:

    The transition to DNA-world is posited to have occurred through darwinian evolution.

    And until that can be tested no one cares.

  112. 112
    Eric Anderson says:

    The transition to DNA-world is posited to have occurred through darwinian evolution.

    As Mung said, another serious of miraculous events.

    This is getting too funny. Yes, we know what is posited. Please, for the love of all that is good and holy, please stop repeating ad nauseam the theory. The theory is a joke. What we need is evidence.

  113. 113
    Zachriel says:

    Eric Anderson: we know what is posited.

    If you reject evolution, then any discussion of abiogenesis lacks foundation.

  114. 114
    Mung says:

    Zachriel: …ribosomes provide evidence of the primordial state.

    Can we stick to the science please?

    You may as well claim ribosomes provide evidence of the intelligent designer.

    So you are now pushing the RNA+Protein world?

  115. 115
    Zachriel says:

    Mung: Can we stick to the science please?

    Given evolution, extant life provides clues to ancient life. If you reject evolution, then any discussion of abiogenesis lacks foundation.

  116. 116
    Mung says:

    Zachriel, look up the details on the ribosomal subunits.

    You’re off in la la land.

  117. 117
    EugeneS says:

    Zachriel,

    “The text and the processor are the same thing”

    No, you don’t understand the issue. Otherwise you would not have posted this nonsense.

    Nowhere in the world is a text the same thing as its processor. This dichotomy is inherent in self-replicating heterogenous systems.

    In what kind of world do evolutionists live?! In one where they can posit anything they like!

  118. 118
    EugeneS says:

    ‘then any discussion of abiogenesis lacks foundation.’

    There is no foundation at all. Abiogenesis is an attempt to explain life exclusively in terms of chemistry. This is simply wrong and is therefore bound to fail. Life is inherently algorithmic, which is disregarded by abiogenesis.

  119. 119
    Zachriel says:

    Mung: look up the details on the ribosomal subunits.

    Okay. Now what? Did you have an argument to make, or are you just waving your hands in the general direction?

    EugeneS: Nowhere in the world is a text the same thing as its processor.

    The evidence for self-replicating molecules undermines that generalization.

    EugeneS: This dichotomy is inherent in self-replicating heterogenous systems.

    Um, no. A self-replicating molecule is a coherent concept even if you reject its physical existence.

    EugeneS: Abiogenesis is an attempt to explain life exclusively in terms of chemistry.

    The origin of life, not its diversification, which is due to evolutionary mechanisms.

  120. 120
    Mung says:

    Zachriel: Okay. Now what?

    Now count the number of proteins in each subunit and explain the presence of those proteins in an RNA world.

    See @114.

  121. 121
    Zachriel says:

    Mung: Now count the number of proteins in each subunit and explain the presence of those proteins in an RNA world.

    RNA can catalyze the production of proteins, so there’s no reason why RNA World couldn’t have evolved to use proteins. Not sure if you are making a coherent point.

  122. 122
    Mung says:

    Zachriel, please list the proteins in the ribosomal subunits then kindly explain their presence in an RNA world.

    Zachriel: RNA can catalyze the production of proteins

    Not sure if you are making a coherent point.

    ETA (@114): So you are now pushing the RNA+Protein world?

  123. 123
    EugeneS says:

    Zachriel,

    “A self-replicating molecule is a coherent concept even if you reject its physical existence.”

    They exist, so what? Molecular gates do exist, so what?

    Even if you don’t realize you are writing nonsense, it is still nonsense.

    ‘Can catalyse’ and ‘will catalyse’ are different concepts. For such a complex thing as life, control is necessary. Nature does not control anything because it is indifferent. It can at best make sure control is a physical possibility.

    Life is not reducible to chemistry. Life is algorithm-based. It is symbolically controlled chemistry. Welcome to the 21 century.

  124. 124
    Virgil Cain says:

    Zachriel:

    The evidence for self-replicating molecules undermines that generalization.

    What evidence? Your bluff has been exposed and yet you still persist with it.

  125. 125
    Zachriel says:

    EugeneS: They exist, so what?

    It undermines the claim that the text and the processor must be distinct entities.

  126. 126
    jerry says:

    I left this discussion a ways back. Is there evidence for self replicating molecules anywhere? I understand that certain RNA polymers can help replicate other RNA polymers but this is not self replicating. This is a system of replicating.

    If I put some polymers in a place which also contains individual molecules such as amino acids or nucleotides, will they produce more of the same polymer? I realize the original polymer had to come from somewhere but is there a process that once a polymer is formed, the environment will enhance the production of the same polymer?

  127. 127
    Zachriel says:

    jerry: I understand that certain RNA polymers can help replicate other RNA polymers but this is not self replicating. This is a system of replicating.

    If molecules replicate one another, then that is, for all intents and purposes, self-replication. There is some success with transcription, but not yet of the length necessary to replicate the replicator. Highly contrived molecular systems are capable of self-replication and darwinian evolution.

    You asked for evidence. This is evidence, even if not conclusive.

  128. 128
    EugeneS says:

    No, it does not Zachriel. Physically there is an SSD in your computer, which is one ‘thing’. It may have several different logical partitions. It is a different concept. Is it so difficult to grasp? You are conflating (probably, knowingly) the notion of logical entity with the notion of physical entity.

    Nowhere in the world is there a text which processes itself. That is a nonsense. A processor is necessarily a different logical entity.

    All you are saying really, is that the text and the processor may coexist within the same molecule. I don’t know whether it is true. What does it change in principle? Absolutely nothing.

    Even if it is true, it does not change the fact that there must be a logical division of functions between different parts of the same molecule.

    You have not made it any simpler (in fact, possibly even more complex).

  129. 129
    Zachriel says:

    EugeneS: Nowhere in the world is there a text which processes itself.

    You said the claim was “inherent”, which would not require an appeal to generalization.

    EugeneS: A processor is necessarily a different logical entity.

    Thank you for rewording the claim, so we can be sure of your claim by “necessity”.

    EugeneS: All you are saying really, is that the text and the processor may coexist within the same molecule.

    Not merely side-by-side, but one and the same thing. Template reproduction is the obvious counterexample. But we’ll allow that the same molecule would probably act as processor to another’s text. This returns us to your previous claim.

    EugeneS: the text and the processor must arise at the same time! An irreducibly complex structure at its worst is at stake here.

    As they are the same molecule, you aren’t pointing to a problem of irreducibility.

  130. 130
    jerry says:

    You asked for evidence. This is evidence, even if not conclusive.

    Thank you.

    You have answered my question. There is no evidence or else you would have presented it. When a molecule needs some other outside entity to produce duplicates, it is not self replicating.

    It seems what is happening by this rhetorical approach is to protect the use of the term “self replicating” as a valid concept. It is playing games. Notice the use of the term “replicator.”

  131. 131
    Zachriel says:

    jerry: There is no evidence or else you would have presented it.

    That’s exactly contrary to what we stated. You might respond to the points raised. Perhaps you don’t understand the nature of scientific evidence: If A entails B; then if B, A is supported; or if not B, A is falsified.

    If RNA World, RNA should be able to act as both genetic memory and enzyme. If RNA World and RNA replicated by transcription, then RNA molecules should be able to transcribe. If RNA World and RNA replicated by assembly of smaller assemblages, then RNA molecules should be able to copy itself by assembling smaller assemblages. These entailments have been demonstrated, so they offer support, albeit not conclusive support, for the hypothesis.

    Among researchers the question isn’t so much whether RNA World existed, but whether RNA World was the most primitive state.

  132. 132
    jerry says:

    Perhaps you don’t understand the nature of scientific evidence:

    Oh, I understand scientific evidence. I also understand nonsense. You have admitted there is no such thing as self replicating. I suggest you refrain from using the concept of self-replicating. Discussing the RNA world has nothing to do with self-replicating. Transcription is not a self-replicating event for an individual molecule.

    If RNA World and RNA replicated by assembly of smaller assemblages, then RNA molecules should be able to copy itself by assembling smaller assemblages.

    You use the word “should.” So you are saying that the RNA replicator should replicates itself from smaller assemblages? (There certainly is no information that each RNA molecule acts as a replicator.) And that there is no evidence that the replicator does replicate itself but maybe this will be shown some day. Replicating other RNA molecules is not an example of self-replication.

  133. 133
    Zachriel says:

    jerry: You have admitted there is no such thing as self replicating.

    Replication in highly contrived situations has been demonstrated, such as where two enzymes catalyze each other’s synthesis from a total of four oligonucleotide substrates. See Lincoln & Joyce, Self-Sustained Replication of an RNA Enzyme, Science 2009.

    jerry: Transcription is not a self-replicating event for an individual molecule.

    RNA can transcribe another molecule. This process is currently limited in length insufficient for self-replication, but it is certainly evidence that self-replication is possible.

    jerry: You use the word “should.”

    Sure. Demonstrating the contrived example is not in itself sufficient to demonstrate that it occurred in nature.

    This is at the heart of the difference between science and Intelligent Design. Scientists consider a hypothesis, and then devise tests, making discoveries along the way. Intelligent Design lacks this scientific fertility.

    It’s also amazing how many lucky guesses these scientists make: RNA can transcribe without proteins; RNA can assemble oligonucleotides into a copy of itself; whales with legs.

  134. 134

    RNA can transcribe without proteins

    The raison d’être is translation, formalized by memory. It’s fundamentally a product of organization, not of chemistry.

  135. 135
    jerry says:

    I think the most interesting part of these discussions is to see the contortions that the anit-ID people go through to defend their position. The other part of their behavior is their zeal for finding some minute detail wrong with those they criticize.

    Answering each contortion just begets more contortions. Maybe this is a self-replication example. One contortion leads to another contortion.

    Meanwhile, self-replication of a molecule is apparently a fantasy.

    And ID is about good science, not the junk science (relevant to the origin of complex capabilities) committed by many in the evolutionary science area.

  136. 136
    EugeneS says:

    Zachriel will never acknowledge playing word games.

    Organization is undeniably present everywhere where there is data processing. Organization is a logical concept.

    “As they are the same molecule, you aren’t pointing to a problem of irreducibility.”

    Zachriel, who is unable to tell between physical and logical, is insisting upon absurdities.

  137. 137
    Zachriel says:

    EugeneS: Organization is undeniably present everywhere where there is data processing.

    Sure. Self-organizing systems are found in non-biological nature.

    EugeneS: who is unable to tell between physical and logical, is insisting upon absurdities.

    You are not actually addressing the point.

    EugeneS: the text and the processor must arise at the same time! An irreducibly complex structure at its worst is at stake here.

    If the text and processor are the same sequence or structure, then the relationship between text and processor does not represent irreducible complexity.

  138. 138
    Virgil Cain says:

    Zachriel:

    If molecules replicate one another, then that is, for all intents and purposes, self-replication.

    Only a deluded moron would say that-> enter Zachriel. Self-replication means one molecule replicates itself.

    And there aren’t any whales with legs- just as there aren’t any evolutionists with integrity.

  139. 139
    Eric Anderson says:

    Sigh . . .

    Self-organizing systems are found in non-biological nature.

    Self-organization in non-biological systems, such as crystals and the like, are precisely what we do not need to explain life. Self-organization by pure physics and chemistry is anathema to the formation of information-rich systems.

    This process is currently limited in length insufficient for self-replication, but it is certainly evidence that self-replication is possible.

    It is certainly not evidence that self-replication is possible. That is false. The study showed the limits of what can be accomplished. Read the study. Self-replication doesn’t work without outside help and intervention. That is the key take-home message.

    And that is in the carefully-controlled and coddled lab environment. We haven’t even started talking about real-world situations . . .

  140. 140

    … and in the end, it doesn’t achieve translation, which is where the money is.

  141. 141
    Mung says:

    More nonsense from Zachriel.

    To organize – arrange or form into a living being or tissue.

    Latin root is organum – instrument, tool.

    We’re talking design.

  142. 142
    EugeneS says:

    “Sure. Self-organizing systems are found in non-biological nature.”

    More unscrupulous word games from Zachriel.

    Organization =/= order.

    Self-ordering phenomena (such as formation of crystals or sand dunes, Moir effect, convection patterns) are categorically different from organization in the sense of autonomous replicating heterogeneous multi-component systems with symbolic control and memory.

    Ordering is absolutely NOT sufficient to explain life.

    To explain life one absolutely need to explain the algorithmic telic nature of life. RNA-world is bankrupt.

  143. 143
    Zachriel says:

    Eric Anderson: Self-organization in non-biological systems, such as crystals and the like, are precisely what we do not need to explain life.

    Then pointing to organization is not an effective argument.

    Eric Anderson: It is certainly not evidence that self-replication is possible.

    Of course it’s evidence: It’s an entailment of the claim. Do you think they were just lucky, that they just guessed that RNA could transcribe RNA sequences? Other experiments show replication from oligonucleotide substrates.

    Eric Anderson: Organization =/= order.

    We weren’t referring to simple ordering, but organized systems, such as weather systems.

  144. 144

    Then pointing to organization is not an effective argument.

    It is a specific type of organization; one that brings representations into being, and establishes a reading-frame code formalized by memory.

    Of course it’s evidence: It’s an entailment of the claim.

    The claim has no teeth. It does not accomplish what is required to organize the cell.

  145. 145
    Phinehas says:

    Z:

    You might want to reconsider your approach. This is starting to look very much like the intellectual equivalent of sticking your fingers in your ears and yelling, “La-la-la-I can’t hear you!”

    😛

  146. 146
    Zachriel says:

    Upright BiPed: It is a specific type of organization; one that brings representations into being, and establishes a reading-frame code formalized by memory.

    Turns out that such “representations” can evolve. For instance, we can start with random peptides, and through iterative selection, end up with functional proteins.

    Upright BiPed: The claim has no teeth.

    Others have argued that RNA replication is *inherently* impossible.

    Upright BiPed: It does not accomplish what is required to organize the cell.

    No discussion of abiogenesis is reasonable without presupposing evolution. Without evolution, there’s no reason to suppose a common ancestor. Without evolution, it wouldn’t matter if primitive organisms sprang into life or not. It still wouldn’t explain kittens and kokopu.

  147. 147

    Turns out that such “representations” can evolve. For instance, we can start with random peptides, and through iterative selection, end up with functional proteins.

    And the representations are where?

    No discussion of abiogenesis is reasonable without presupposing evolution.

    I’ll write that down.

    By the way, since Darwinian evolution is a product of prior organization, what will we say is the source of that?

  148. 148
    Zachriel says:

    Upright BiPed: And the representations are where?

    The same type of “representations” found in natural proteins, the sequence that folds into a functional protein.

    Upright BiPed: By the way, since Darwinian evolution is a product of prior organization, what will we say is the source of that?

    Darwinian evolution is a natural consequence of reproduction.

  149. 149

    The same type of “representations” found in natural proteins, the sequence that folds into a functional protein.

    I won’t be equivocating on what is required for a representation.

    Darwinian evolution is a natural consequence of reproduction.

    I won’t be equivocating on what is required for Darwinian evolution either.

  150. 150

    It’s Friday. It’s the end of the day. Goodbye.

  151. 151
    Mung says:

    Zachriel, you should say hypothetical more often.

  152. 152
    Mung says:

    Zachriel:

    No discussion of abiogenesis is reasonable without presupposing evolution. Without evolution, there’s no reason to suppose a common ancestor. Without evolution, it wouldn’t matter if primitive organisms sprang into life or not. It still wouldn’t explain kittens and kokopu.

    Credit where credit is due. At least Zachriel willingly admits something we have all known for a long time about the relationship between abiogenesis and evolution.

    The two are inextricably inter-twined.

  153. 153
    Zachriel says:

    Upright BiPed: I won’t be equivocating on what is required for a representation.

    Nor are we. (Notice the scare-quotes above.)

    Mung: you should say hypothetical more often.

    Z @59: Yes, the hypothetical RNA World was the premise of jerry’s question.

    Z @108: In the case of a posited self-replicating RNA molecule, the text and the processor are the same thing.

    Z @110: The transition to DNA-world is posited to have occurred through darwinian evolution.

    Z @131: These entailments have been demonstrated, so they offer support, albeit not conclusive support, for the hypothesis.

    Z @133: Scientists consider a hypothesis, and then devise tests, making discoveries along the way. Intelligent Design lacks this scientific fertility.

    Mung: At least Zachriel willingly admits something we have all known for a long time about the relationship between abiogenesis and evolution.

    While the Theory of Evolution stands independently from the origin of life, what we know of primordial life is often a result of what we have learned from evolution. For instance, life is billions of years old; common descent points to a common origin, though the origin is probably not a singularity; the last universal common ancestor is not the first life; and once there are replicators, they will evolve and adapt by darwinian processes.

    Without these presuppositions, any discussion of abiogenesis is without foundation.

  154. 154
    Mung says:

    Ribosomes contain proteins. We’re still awaiting the discovery of a ribosome that has no protein component but which can nevertheless manufacture a protein and insert the protein into it’s own structure.

    Hypotheticals piled on top of hypotheticals, each less believable than the last. No evidence. No proof of concept. No demonstration of possibility. No demonstration of probability. Just lots of wishful thinking.

  155. 155
    Zachriel says:

    Mung: Ribosomes contain proteins.

    Sure, but the actual protein synthesis is done by RNA, so that doesn’t seem to be a barrier. Analysis of the network of relationships in the ribosome provide evidence that the proteins were added after the origin of the primordial ribosome.

  156. 156
    EugeneS says:

    Phinehas #145,

    It’s always been like that.

    Zachriel #155,

    “so that doesn’t seem to be a barrier.”

    Doesn’t seem to whom? Are you talking for yourself or for the entire humanity? Man can walk, therefore man can walk to the Moon. Invincible logic.

  157. 157
    Zachriel says:

    EugeneS: Doesn’t seem to whom?

    Based on the evidence.

  158. 158
    Mung says:

    Zachriel: …but the actual protein synthesis is done by RNA

    The ribosomal proteins are just there for decoration.

  159. 159
    Zachriel says:

    Mung: The ribosomal proteins are just there for decoration.

    Many proteins in the ribosome are structural, such as guides to the ribosomal tunnel. Modern ribosomes are dependent on proteins, but that doesn’t represent a problem for evolution, which can modify helpers to become essential components. It’s thought that the order of assembly of the ribosome provides an approximation of the history of evolution.

  160. 160
    EugeneS says:

    Zachriel,

    “It’s thought that…”

    Now I see.

  161. 161
    Zachriel says:

    Zachriel: It’s thought that the order of assembly of the ribosome provides an approximation of the history of evolution.

    As evolution is well-established, applying evolution to the ribosome follows. However, there is no certainty at this point as the evidence is still very limited.

  162. 162
    DillyGill says:

    Zac @161
    “there is no certainty at this point as the evidence is still very limited.”

    I guess you just need to add deep time, imagination and rhetoric to that to produce certainty rather than further evidence. That is how unguided evolution works after all.
    As more evidence is obtained it rather shows that life is to complicated to come around by chance and yet you concede nothing. Further evidence is unlikely to help you but will never stop you putting your spin on it.

    Still, most of mankind cares little for the detail, that combined with the assumed position of authority gets you much further than is good for humanity.

  163. 163
    Zachriel says:

    DillyGill: As more evidence is obtained …

    Large, seemingly insurmountable gaps become smaller gaps.

  164. 164
    Mung says:

    Zachriel: Modern ribosomes are dependent on proteins, but that doesn’t represent a problem for evolution, which can modify helpers to become essential components.

    Is anything a problem for evolution?

    Modern ribosomes are dependent on proteins. A ribosome not dependent on proteins seems nothing more than a fantasy. That these proteins were ever helper proteins seems like a fantasy.

    Evolution allows people to live a rich fantasy life.

  165. 165
    Zachriel says:

    Mung: Is anything a problem for evolution?

    There are all sorts of questions in evolutionary biology. However, the evidence for evolution generally encompasses many different fields, and is so strongly supported, that it would take considerable evidence to show it doesn’t apply in some way to the origin of ribosomes.

  166. 166
    rna says:

    Mung #164

    “… A ribosome not dependent on proteins seems nothing more than a fantasy. That these proteins were ever helper proteins seems like a fantasy. …”

    Noller and coworkers 1992 (!): “Unusual resistance of peptidyl transferase to protein extraction procedures.” Science, vol. 256(5062):1416-9
    So maybe it is not a fantasy but an extrapolation from well-established experimental facts?

  167. 167
    Mung says:

    Zachriel:

    There are all sorts of questions in evolutionary biology. However, the evidence for evolution generally encompasses many different fields, and is so strongly supported, that it would take considerable evidence to show it doesn’t apply in some way to the origin of ribosomes.

    Blind belief, handwaving, arguing from ignorance and wishful thinking are not scientific fields.

  168. 168
    mike1962 says:

    What do you know? What can you prove?

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