Information Intelligent Design Origin Of Life

Writing Biosemiosis.org

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In September of 2009 I started a new document on my computer entitled “A System of Symbols”, where I was going to write about the part of design theory that interested me the most – that is, the representations that are required for self-replication (von Neumann, Pattee). My goal was to inventory all the physical conditions necessary for one thing to represent another thing in a material universe. I wrote and rewrote that essay for more than four years — reading, learning, and sharing along the way. As it turns out, writing that essay was my way of coming to understand the issues, and I spent a great deal of that time trying to articulate things I had come to understand conceptually, but could not yet put into words. Eventually I came into contact with the types of scientists and researchers who had substantial experience with these issues, up to and including those who had spent their entire careers on the subject. It was a humbling experience to share my thoughts with people of that caliber, and have them respond by sending me papers of their own that reflected the same concepts.

Then In 2014, I retired that essay and began writing Biosemiosis.org in its place. Since that work is available to any reader, I won’t recapitulate it here, but there are a couple of concepts I’d like to highlight – particularly the discontinuity found in the translation of recorded information. Read More

[I’d like to thank Barry and Uncommon Descent for allowing me to publish this introduction to my two projects]

464 Replies to “Writing Biosemiosis.org

  1. 1
    Mung says:

    Awesome!

    Congratulations!

  2. 2
    Upright BiPed says:

    Thank You, Mung.

    (why aren’t you out Trick or Treating? or something).

    🙂

  3. 3
  4. 4
    Mung says:

    It’s cold and wet. I was going to go as a Boy and His Cat and the cat is not cooperating.

  5. 5
    Eugen says:

    Great website. This is our candy for Halloween 🙂 (beside what I’ll steal from my kids)

  6. 6

    Thank You BA, and Thank You Eugen.

    (Leave some candy for your kidz)

  7. 7
    Andre says:

    Upright Biped

    Wonderful information and right at the heart of the issue.

    About Halloween, we recently moved and my boys have been spoilt on Halloween in our previous neighbourhood. So here in the new one my wife and I made some sweet packets and took it to the neighbours just in case. The boys were not really optimistic but with our encouragement they went trick or treating. After an hour when they got back James full of smiles said to us….

    “That went better than expected”.

    Priceless, because not only did they get the sweets we handed out everybody had some for the occasion.

  8. 8
    gpuccio says:

    UB:

    Please accept my most heartfelt compliments!

    Now I hope that serious and constructive discussion about your work may begin. 🙂

  9. 9
    EugeneS says:

    UB

    That’s great. A lot of hard work. Excellent stuff.

  10. 10
    kairosfocus says:

    UB, well done, again. I join with GP in the hope that serious, constructive and open-minded discussion of your work (and of our wider work in and around UD) will now follow. In particular, I trust that those who have been spreading messages such as that we refuse to offer any evidence of ID, will have the grace to withdraw such rhetoric. KF

  11. 11

    At long last!! Big time congratulations!!

  12. 12
    Box says:

    Congratulations UB! I will do my utmost to understand your argument.

  13. 13
    Virgil Cain says:

    Moreover, this system is not the product of Darwinian evolution.

    You have to do more than just baldly declare that as there are Darwinists who baldly declare the opposite- Nick lane, for example and larry Moran, although he doesn’t consider himself a Darwinist because he didn’t read “On the Origins of Species…”

  14. 14
    EugeneS says:

    KF,

    Unfortrunately, there will be people who will object no matter what. That is the mystery of free will. But that does not mean one should stop laying out his scientific argument for the sake of the unbiased.

  15. 15
    Dionisio says:

    UB,

    It’s good to see the introduction to your projects published here. Excellent topic! Very timely!
    I look forward to enjoy reading this thread in the days ahead (D m). Thank you.

  16. 16

    Hello All, GP, KF, ES, WJM, Andre, Dio…

    Thank you all for the kind words. It is truly appreciated.

  17. 17

    I’d like to say a special “Thank You” to GPuccio.

    Early on, it was GP who made me understand how the issues of semiosis applied to genetic translation. He was the person who turned the light on. After that, I could find my way to the relevant literature by the relevant researchers.

    Thank you GP.

  18. 18

    KF,

    There are a lot of different kinds of arguments and conversations that take place here at UD (evolution, fossil record, descent, genetics, etc). And then there are the arguments specifically about information. There is a whole class of these objections regarding information that are simply (and very rationally) emptied by the observations of semiosis. For some, the information on Biosemiosis.org will clarify the issues, and it will actually matter to them. But unfortunately, there are many who will simply continue on as if nothing had ever been presented. Not much can be done about that. People do what profits them.

  19. 19

    Box,

    Thank You.

    I remember our first meeting here on UD. I was in the middle of a raging argument, and you were asking questions, attempting (as I saw it) to relate what I was saying to your own conceptions of the issues. I remember this because the distance between our conceptions interested me, as we both stand on the same side of the argument. You (in many ways like GPuccio) are very tuned to the realities of consciousness and purpose and intentionality, while I was interested in the material nuts and bolts of information in the natural world.

    I hope you will find the meeting of our two views in the writing I have presented. There is nothing at all difficult about the argument I am making. I do not know how the mind interacts with matter, but I cannot even type this sentence without knowing that it does. I do not know where the “I” is, or the soul. But I do know that effects of information aren’t determined by the dynamic properties of the representations that evoke and constrain those effects — thus, the reason to inventory the material conditions that allow that constraint to occur.

    The distance between our interests and conceptions is short. Again, thanks.

  20. 20
    Mung says:

    Virgil Cain:

    You have to do more than just baldly declare that [this system is not the product of Darwinian evolution.] as there are Darwinists who baldly declare the opposite-

    The system is what is required for open-ended evolution to even occur. So claiming it is the product of Darwin evolution doesn’t help.

  21. 21
    Virgil Cain says:

    Mung:

    The system is what is required for open-ended evolution to even occur.

    Even if it is, and that is debateable, that alone doesn’t mean Darwinian evolution could not have produced it.

    So claiming it is the product of Darwin evolution doesn’t help.

    Doesn’t help what? It helps Darwinism and neo-Darwinism.

    Look, all I am saying is that it isn’t enough to just declare things. Doing so makes us as guilty as the position we oppose.

  22. 22

    VC,

    The sentence you quote is from the opening text of the site. I do not merely “declare” it, but go into substantial detail.

    Darwinian evolution require a genome. The site describes the material conditions that allow the genome to exist. If A requires B for A to exist, A cannot be the source of B.

    Will people argue anyway? Of course they will.

  23. 23
    Virgil Cain says:

    The sentence you quote is from the opening text of the site. I do not merely “declare” it, but go into substantial detail.

    Then the proper thing to do is add a footnote at the end of that sentence that references the evidentiary support.

    The point is I agree with what you say. I also know that opening statements can capture an audience or lose one. Reference your statement so that you capture more than you lose.

    And even if Darwinian evolution had a genome all it could do is degrade it-> Spiegelman’s Monster is what darwinian evolution can produce. 😉

  24. 24

    DEAD ARGUMENTS:

    It’s just chemistry

    It’s only a metaphor

    There is nothing symbolic in the cell

    There is no way to test for intelligence

    There is no evidence of design in biology

    There is no way to objectively detect ID

    ID can’t define what it means by intelligence

    ID proponents never offer evidence

    Evolution did it

    DEFLECTIONS/DISTRACTIONS:

    What is information?

    What is arbitrary?

    What is a code?

    What is intelligence?

    – – – – – – – – – –

    In common parlance we refer to these sites as containing “information” in the form of specific nucleotide sequence. It’s a very useful analogy and I think everyone knows what we mean when we use it. Nobody expects it to conform to the meanings of “information” in other disciplines. Nobody, that is, except some IDiots who like to play semantic word games instead of addressing real science. I hope you’re not one of those people. — Larry Moran

    Yes, I’m afraid I am.

    🙂

  25. 25
    Virgil Cain says:

    Should read – DEAD ARGUMENTS still used by our opponents

    and

    DEFLECTIONS/DISTRACTIONS still used by our opponents

    That puts it in context

  26. 26
    Mapou says:

    UB,

    I will be following your work closely because it is directly relevant to my work in artificial intelligence. Knowledge representation is the biggest unsolved problem in AI. The goal in AI is to come up with a universal knowledge representation scheme that can potentially model any kind of real world phenomena.

    The two big questions in my mind right now are: When does a structure become a representation? Can it be an intrinsic or self-supporting representation or is it a representation only in the conscious mind of an observer?

    I ask these questions because the conscious mind can only sense an internal representation of the environment constructed from sensory data. We never sense the world directly regardless of how “real” everything seems to us. Everything we see is in our visual cortex.

    But it gets very confusing from this point on because, for example, the colors that we see are neither in the environment nor the brain. Our consciousness somehow attaches color sensations to certain neuronal activities in the visual cortex. One cannot claim that colors are abstract symbols because they are directly known by our minds. At the same time, color sensations are triggered by the environment and can be said to represent environmental phenomena.

    It’s complicated.

    Edit: But then again, maybe colors are abstract (non-physical) entities after all. Maybe they are not of this world. Maybe, they are spiritual entities.

  27. 27
    Mapou says:

    U.B.

    After briefly surfing through the material at the links provided, something in your ideas immediately struck me as odd. You seem to think of a representation as a causal agent. I say it’s odd because my long held understanding calls for a representation to be entirely passive. The only active thing that I can see is the decoder.

    A representation is a passive symbol, IMO. A symbol written on a 2000 year-old papyrus is a representation, not a causal agent.

    PS. It’s very possible that I am misreading your ideas. So correct me if I’m wrong.

  28. 28
    kairosfocus says:

    Mapou, the code gets used in controlling machinery which is causal. KF

  29. 29
    Mung says:

    Think of the music box analogy. There are different levels of causation. That which causes the tine to vibrate is not the same as what causes this song to play rather than some other song.

    My .02

  30. 30

    Hi Mapou,

    I think we are on the same page. I have tried to pick out what I might have said to make you think that I see a representation as “causal agent”, and I think I know what it is…

    The pattern itself becomes the causal object in the system, and the primacy of the pattern over the medium results in a representational system with two distinct properties. These two properties are fundamental to an open-ended self-replicating system.

    I am here pointing out the pattern becomes the very thing that the system (the decoder in your vernacular) recognizes and responds to. This point is being presented in the context of the pattern being independent of the minimum total potential energy state of the medium.

    I have gone to great lengths to show just how “passive” a representation is (in regard to determining what effect is produced by its recognition), and it was not my intent to reverse all that work with that one sentence. That pattern must still be recognized by the system (the decoder) and that recognition must still be acted upon by the organization of the system.

    Read in context, I don’t see a reason that our individual understandings differ.

    Edit: Representations evoke effects, but they do not determine what those effects will be.

  31. 31
    Dionisio says:

    One can learn very interesting things from reading this discussion.
    🙂

  32. 32
    Mung says:

    And this is important because at root we are not talking about the effect of a nucleotide, we are talking about the effect of a sequence.

    It wasn’t called “the sequence hypothesis” for nothing.

  33. 33
    Steve says:

    UB,

    your site has a donation page. but looks like the donation is set at 18 bucks.

    But what if someone like me thought 18 bucks was too little to give?

    How about unlocking the donation amount?

    This is a limited offer and will self-destruct if the secret password in not decoded in time.

    Tick-tock.

    🙂

  34. 34

    Hi Steve,

    Right below the “Contribution” button, there is a link that allows someone to up their contribution if they’d like.

    Many Many Many Thanks!

  35. 35
    Mung says:

    How do I get my donation back?

    😉

  36. 36
    Mapou says:

    UB @30,

    Thanks for the clarification. I was obviously mistaken. I prefer to use the term “decoder” because I believe that a representational system consists of 3 things: the code creator, the code (representation or pattern) and the decoder. All 3 are part of the same system. Furthermore, the code creator must think of both the pattern and the decoder at the time of creation.

    While it is obvious that a code is an intelligent artifact, it is possible to use strict rules in order to automate code creation in an AI program during learning. For example, I have implemented a spiking neural network that can automatically discover and create internal patterns from signals (spikes) arriving at a set of input sensors. The discovered patterns can still be called representations (or codes) even though they were not directly made by an intelligent coder.

  37. 37
    gpuccio says:

    Mapou and UB:

    Very interesting thoughts about representations.

    I will try to add some personal reflections, to keep the discussion going.

    Mapou says:

    “I ask these questions because the conscious mind can only sense an internal representation of the environment constructed from sensory data.”

    That’s absolutely true. We could say that the whole sensory system is a “machine” whose purpose is to generate a physically ordered representation of physical events, in a form which can be “perceived” by our consciousness.

    Let’s imagine that our consciousness is a subject which can only see what is on a specific monitor. And the monitor is fed by a complex recording system, which takes different shots of different things by some set of sensors, and transforms the information into the correct physical stimuli which can build an image on that monitor.

    The point is: the conscious representation (in the sense of perception) exists only when our consciousness “sees” what is in the monitor, but we can also say that the recording system generates a “representation” (in the sense of an ordered physical system which “takes on” the form of other physical events) which is then “passed” to the subject to be “represented” (in the sense of “perceived”) in the consciousness.

    So, maybe we should distinguish between two different meanings of “representation”:

    1) A passive physical ordering of some physical substrate whose purpose is to catch some specific information and retain it in a specific form.

    2) The conscious event which transforms representation of that first type into conscious events.

    Now, the important point IMO is that the conscious events which take place in 2) are not representations in the sense of 1).

    So, just to say, the experience of red is not the same thing as the physically coded impulse which corresponds to the experience of red in my consciousness.

    I would not necessarily say that it is a “spiritual entity”, because that would bring the discussion to the ontologic philosophical level, but we can certainly say that it is a “conscious event”, an event where an I represents something as a conscious perception.

    Another point is that representations of the first kind do not imply conscious events in the actual process of their generation (a video camera can work without any conscious contribution), but the systems which generate them do require an act of design to come into existence.

    Why? Because they are functionally complex.

    In particular, to go back to UB’s main argument, all the systems which generate and use representations (in the first sense) which are symbolic and use a code to transmit their information and generate a specific semiotic and functional outcome are always, always, always the result of conscious design.

    IOWs, their origin is traceable to representations of the second type.

  38. 38
    Steve says:

    Thanks UB for the info.

    FYI, the ghost of ben franklin just dropped by biosemiosis.org for tea.

    Great work, indeed! Look forward to lots more!

  39. 39
    Steve says:

    Where are the TSZ regulars to congratulate UB?

    If I am not mistaken, they were so sure UB’s website would never materialize.

    So keiths, Sir Richard, Liz, petrushka, the 2 als, et all??

    No comments? none??

  40. 40
    Virgil Cain says:

    The septic zone is still in code denialism and they are also in science denialism. And to top it all off they could be awarded 3.1 million dollars if they could just support their claim tat the genetic code can be accounted for via physicochemical processes- but they won’t even attempt to collect it!

    Talk about cowardice…

  41. 41
    Dionisio says:

    UB

    Where is the information on how to form the morphogen gradients for morphogenesis (important part of organogenesis) stored in?

    Does the morphogen gradient formation have to be done according to the protocols used by the cells for morphogen gradient interpretation?

    Does all this somehow relate to the semiotic concepts?

    Where is all that information stored in?

  42. 42
    Dionisio says:

    Steve @ 39

    Sorry to disappoint you, but those folks are probably very busy trying to answer the “where’s the beef?” questions for the evo-devo pseudoscientific nonsense that is published out there.

    🙂

  43. 43
    gpuccio says:

    Dionisio:

    Very good questions! And I would be really happy if we could have some answers, even partial.

    The problem of what controls the epigenetic procedures, as you well know, is still completely unsolved.

    We have a number of different layers of control (at least: DNA methylation, Histone modifications, Chromatin remodeling, 3D chromatin structure, Transcription Factors, Post transcriptional regulations, Post-translational modifications), which seem to act in a redundant and strictly intertwined pattern.

    As you always say, that is complex complexity indeed!

    Do those layers configure semiotic codes? Absolutely! Unfortunately, those codes are so complex that we scarcely understand them.

    For example, take the Histone code. Histone modifications have a recognizable, repetitive meaning. The most universally known meanings are the activating effect of H3K4me3 and the inhibitory effect of H3K27me3, and the double pattern (activation + inhibition) in many stem cell genes.

    I quote from the Wikipedia page:

    Unlike this simplified model, any real histone code has the potential to be massively complex; each of the four standard histones can be simultaneously modified at multiple different sites with multiple different modifications. To give an idea of this complexity, histone H3 contains nineteen lysines known to be methylated — each can be un-, mono-, di- or tri-methylated. If modifications are independent, this allows a potential 419 or 280 billion different lysine methylation patterns, far more than the maximum number of histones in a human genome (6.4 Gb / ~150 bp = ~44 million histones if they are very tightly packed). And this does not include lysine acetylation (known for H3 at nine residues), arginine methylation (known for H3 at three residues) or threonine/serine/tyrosine phosphorylation (known for H3 at eight residues), not to mention modifications of other histones.

    Every nucleosome in a cell can therefore have a different set of modifications, raising the question of whether common patterns of histone modifications exist. A recent study of about 40 histone modifications across human gene promoters found over 4000 different combinations used, over 3000 occurring at only a single promoter. However, patterns were discovered including a set of 17 histone modifications that are present together at over 3000 genes.[10] Therefore, patterns of histone modifications do occur but they are very intricate, and we currently have detailed biochemical understanding of the importance of a relatively small number of modifications.

    Structural determinants of histone recognition by readers, writers and erasers of the histone code are revealed by a growing body of experimental data.[11]

    Transcription factors act in a very complex combinatorial patterns. Complexes made by transcription factors and other proteins, which may include even 10-15 different molecules, connect enhancers to promoter regions, and modify dynamically 3d chromatin structure.

    So, do those layers configure semiotic codes? Absolutely!

    Where is the information which controls those layers? We really don’t understand that, at present.

    But, wherever it is, it is extremely complex and very functional.

  44. 44
    gpuccio says:

    Well, it seems that there is some problem with the update of the “recent comments” section.

  45. 45
    Dionisio says:

    gpuccio @37 & @43

    Excellent points! Very insightful comments!
    Thank you.

    PS. RE: @44 yes, noticed the same update problem.

  46. 46
    Virgil Cain says:

    Why is the following so difficult to follow?

    1- Experiences and observations say that all codes come from intelligent agencies

    2- No one even knows how to model physicochemical processes producing a code. Such a thing flies in the face of our experiences and observations

    3- And because of that it is safe to infer that an intelligent agency designed the code even though we did not observe it happening, as is the case with the genetic code.

    Science 101. And yes that inference, as with all scientific inferences, can be refuted by demonstrating that physicochemical processes can produce the genetic code. Again, science 101

    Our opponents whine about that because they know they could never demonstrate such a thing.

  47. 47
    Carpathian says:

    Mapou:

    The discovered patterns can still be called representations (or codes) even though they were not directly made by an intelligent coder.

    Exactly!

    We call DNA “code”, but it was not directly made by an intelligent coder.

    Will you now try to prove to me that your statement was wrong?

  48. 48
    Carpathian says:

    Virgil Cain:

    3- And because of that it is safe to infer that an intelligent agency designed the code even though we did not observe it happening, as is the case with the genetic code.

    You are assuming that the genetic “code”, was the result of an intelligent designer, but that is the very thing you and ID are trying to prove.

    See Mapou’s comment above.

    Science 101. And yes that inference, as with all scientific inferences, can be refuted by demonstrating that physicochemical processes can produce the genetic code. Again, science 101

    So as I read it, you can infer but we have to demonstrate .

    That’s not science 101.

    You and ID should have to prove the point you are trying to make.

    Show that an intelligent designer is a probable cause of life.

  49. 49

    Carp,

    Mapou gave a simple example were he, as an intelligent agent, arranged a system that can create representations to be interpreted as patterns within the system. In order to function, the system requires both the arrangement of the representations as well as the means to interpret them. You lifted his example out of its context, and are now daring him to prove to you that his statement was wrong — as if he is to demonstrate that the system that he arranged could have appeared on his test bench without his input.

    You didn’t think things through. And you most assuredly have not conceptualized the issues yet. Just once, take your blinders off and deal with the observations as they are presented, without carelessly jumping at the chance to deny them.

    Can you do that Carp? Actually do it? Can you?

  50. 50
    gpuccio says:

    To all:

    Just a few words about how the code is implemented.

    The true key to the code is recorded in a set of 20 very complex proteins, the aminoacyl t-RNA synthetases.

    For those interested, I suggest reading this page from the PDB (Protein Data Bank):

    http://www.rcsb.org/pdb/101/motm.do?momID=16

    A few simple quotes:

    When a ribosome pairs a “CGC” tRNA with “GCG” codon, it expects to find an alanine carried by the tRNA. It has no way of checking; each tRNA is matched with its amino acid long before it reaches the ribosome. The match is made by a collection of remarkable enzymes, the aminoacyl-tRNA synthetases. These enzymes charge each tRNA with the proper amino acid, thus allowing each tRNA to make the proper translation from the genetic code of DNA into the amino acid code of proteins.

    As you might expect, many of these enzymes recognize their tRNA molecules using the anticodon. But this may not be possible in some cases. Take serine, for instance. Six different codons specify serine, so seryl-tRNA synthetase must recognize six tRNA molecules with six different anticodons, including AGA and GCU, which are entirely different from one another. So, tRNA molecules are also recognized using segments on the acceptor end and bases elsewhere in the molecule. One base in particular, number 73 in the sequence, seems to play a pivotal role in many cases, and has been termed the discriminator base. In other cases, however, it is completely ignored. Note also that each enzyme must recognize its own tRNA molecules, but at the same time, it must not bind to any of the other ones. So, each tRNA has a set of positive interactions that match up the proper tRNA with the proper enzyme, and a set of negative interactions that block binding of improper pairs.

    Aminoacyl-tRNA synthetases must perform their tasks with high accuracy. Every mistake they make will result in a misplaced amino acid when new proteins are constructed. These enzymes make about one mistake in 10,000. For most amino acids, this level of accuracy is not too difficult to achieve. Most of the amino acids are quite different from one another, and, as mentioned before, many parts of the different tRNA are used for accurate recognition. But in a few cases, it is difficult to choose just the right amino acids and these enzymes must resort to special techniques.

    These enzymes are not gentle with tRNA molecules. The structure of glutaminyl-tRNA synthetase with its tRNA (entry 1gtr) is a good example. The enzyme firmly grips the anticodon, spreading the three bases widely apart for better recognition. At the other end, the enzyme unpairs one base at the beginning of the chain, seen curving upward here, and kinks the long acceptor end of the chain into a tight hairpin, seen here curving downward. This places the 2′ hydroxyl on the last nucleotide in the active site, where ATP and the amino acid (not present in this structure) are bound.

    So, not only the genetic code is in itself an impossibility for non conscious causes (a symbolic correspondence between 64 combinations of three letter words in a four symbol alphabet to an output space of twenty aminoacids, including start and stop symbols); but also, the implementation of the code is extremely complex, and requires long and big proteins which can only be synthetized by the code itself.

    Just for reference, here is tha AA length of the 20 AA tRNA synthetases in humans:

    Class I:

    Arginine: 660 AAs
    Cysteine: 726 AAs
    Glutamate: 523 AAs
    Glutamine: 775 AAs
    Isoleucine: 764 AAs
    Leucine: 1176 AAs
    Methionine: 593 AAs
    Tyrosine: 528 AAs
    Tryptophan. 471 AAs
    Valine: 1264 AAs

    Class II:

    Alanine: 968 AAs
    Aspartic acid. 500 AAs
    Asparagine: 548 AAs
    Glycine: 739 AAs
    Histidine: 509 AAs
    Lysine: 597 AAs
    Phenylalanine: 508 + 589
    Proline: 475 AAs
    Serine: 514 AAs
    Threonine: 433 AAs

    This is just to give you the flavor of what is at stake here. The point is, these complex proteins do recognize with high fidelity both the aminoacid and the anticodon (or, more in general, the tRNA) separately, each protein recognizes the appropriate couple of molecules, and there is no other biochemical connection between the correct aminoacid and the correct tRNA (or tRNAs): the only connection is established by the existence of the right protein in the system.

    In UB’s terms: that’s discontinuity at its best!

  51. 51
    gpuccio says:

    Carpathian:

    Codes can be generated by intelligent agents, both directly and indirectly. But they are always generated by intelligent agents, in all empirical observations.

    That is a sound basis for inference.

    If your theory is that codes can be generated by non conscious systems, while that has never been observed, it’s up to you to show that your theory has some reason to be entertained.

    Can you understand this?

  52. 52

    Hi GP,

    Thank you for all your input. I want to address the topic between you and Mapou, but it would take me some time to gather up my thoughts, and time is limited just now. So I am jumping past it for now, but I hope to return to it later.

    The RCSB page you quoted above is in the bibliography on the site.

  53. 53

    I am wondering if any critics are going to address the content of the article in the OP – that is, that there are three individual yet interdependent instances of arbitrariness that are required to organize the heterogeneous cell?

    The combination of these three instances of arbitrariness result in an arrangement of matter that serves as a representation for a thing it otherwise has no systematic relationship with. Furthermore, the arrangement of this representation is independent of the physical properties of the matter it’s made of, and only serves as a representation because it’s organized in a system by a set of contingent regularities that have no basis in thermodynamic law. And all of this is required to encode the amount of information that the system needs to record itself into an open-ended transcribable memory. This memory is actually the fourth and most widely-known example of arbitrariness in the system — the order of the individual representations in that memory (the information it contains) is indifferent to inexorable law.

    – – – – – – – – – – –

    Thus, when we observe the particulars of the genetic translation system, we are not merely looking at features that happen to be coincidental to the system’s function – instead, each individual feature we observe imparts a very specific capacity on the system, and each of these capacities are collectively necessary in making the organization of a heterogeneous cell possible. They are necessary because they make the translation of information possible. They make memory and heredity possible. And to whatever extent the origin of life required any additional information to organize the first living cell, we can know by virtue of life’s self-replicating nature that the original informational content of the heterogeneous cell contained at least enough information to replicate and organize the elements of the system described above.

    Link

  54. 54
    Mapou says:

    U.B. @49,

    Carpathian knows very well that he/she is lying. It’s what he does. He’s a weaver of lies and deception, just like Zachriel, Moran, Dawkins, Matzke and all the others. And not very bright either.

  55. 55
    Carpathian says:

    Mapou:

    Carpathian knows very well that he/she is lying. It’s what he does. He’s a weaver of lies and deception, just like Zachriel, Moran, Dawkins, Matzke and all the others. And not very bright either.

    I take it you didn’t have a response that was actually better than a personal attack.

    If you had, you would have used it.

  56. 56

    Oh well, scratch my post at #53.

    The critics don’t even get that far. I just did a quick glance at the IDosphere, and the daily critics refuse to even address the details of semiosis itself.

    Apparently when you are confronted with the necessary physical conditions of the genetic code (von Neumann, Pattee, Crick, Zamecnik, Nirenberg, etc), the proper response is to ignore the material observations and argue over what a “code” is. How much easier it is to stand your ground when your remarks are not constrained by any observations.

  57. 57
    EugeneS says:

    Carpathian,

    A comment in passing… In terms of personal attack, the laurels of the winner belong to Prof Moran. He calls all of us idiots. What can be more generic?!

    Even in the case of macros generating malicious code, the code causally depends on there being conscious intelligence behind the design and implementation of the code processing system. The same is true in the case of natural languages, cultural codes, mathematics and art.

    Evidence is undeniable. As soon as you produce a single trustworthy and repeatable demonstration of a naturalistic mechanism giving rise to symbolic control in material systems, you win.

  58. 58
    Mapou says:

    Jackasses should be attacked personally and forcefully each and every time they act like jackasses. It’s called classical conditioning. LOL.

  59. 59
    Carpathian says:

    Upright BiPed:

    Mapou gave a simple example were he, as an intelligent agent, arranged a system that can create representations to be interpreted as patterns within the system.

    The intelligent designer could have designed a means by which coding and decoding systems could have arisen without the need of any intelligence guiding it.

    Just like Mapou could design a system that generated or decoded codes, the ID designer could have done the same.

    This system that the ID designer designed, might have not been possible without the designer’s hands on guidance.

    So I have “agreed” with Mapou and I have “agreed” with you.

    To sum up, the ID designer designed a system that generated codes without his help.

    Just like we see in “Darwinism”.

  60. 60

    Carp, please deal with the actual observations.

    What is required for a representation to be a representation?

  61. 61
    Carpathian says:

    Mapou:

    Jackasses should be attacked personally and forcefully each and every time they act like jackasses. It’s called classical conditioning. LOL.

    This is exactly what I see happening if ID ever gets into schools.

    Teachers like you call students jackasses in front of class.

    This will show the other students that science is all about being more powerful than the other guy.

    “If you don’t have a good argument just shout louder”, will be the lesson.

    You’ll generate some great scientists that way.

    Keep up the good work.

  62. 62

    Now that the “jackasses” comment has followed the deliberate misrepresentation, we have that out of our systems.

    Stay on topic.

  63. 63
    Carpathian says:

    Upright BiPed:

    What is required for a representation to be a representation?

    In your view, a representation must have been generated by intelligent intent.

    In my view, it doesn’t.

    Waveforms from an AM radio transmitter have a certain period and amplitude and an intelligence intended that.

    Waves in an ocean have a certain period and amplitude, but no intelligence intended that.

    That is the argument.

    Were the “codes” we see intended or not?

    That is the question to address, not a definition of what a “code” is.

    Tie your genetic “code” to the intent of a designer.

    Without that connection, the genetic “code” is simply a pattern we observe.

    How it came about is the issue.

  64. 64
    Carpathian says:

    Upright BiPed:

    Now that the “jackasses” comment has followed the deliberate misrepresentation, we have that out of our systems.

    There was no misrepresentation by me, deliberate or otherwise.

    Designed systems can generate code without further input from the designer.

    God could have created such a system.

    Does anyone want to dispute that?

  65. 65

    In your view, a representation must have been generated by intelligent intent.

    In my view, it doesn’t.

    An Easy Understanding of Semiosis –and– The Information Tetrahedron

    Waveforms from an AM radio transmitter have a certain period and amplitude and an intelligence intended that.

    Waves in an ocean have a certain period and amplitude, but no intelligence intended that.

    That is the argument.

    Waves are not translated into physical effects that I am aware of. If you know differently, then explain.

  66. 66
    gpuccio says:

    Carpathian at #59:

    ???? What do you mean?

    “The intelligent designer could have designed a means by which coding and decoding systems could have arisen without the need of any intelligence guiding it.”

    Then, you must observe an intelligently designed, complex system which generates codes. Where is this system in nature? And it would always be the intelligence of the designer which generates the code, indirectly, through the designed system. What is your point?

    “Just like Mapou could design a system that generated or decoded codes, the ID designer could have done the same.”

    OK, and where is that system? In your imagination?

    “To sum up, the ID designer designed a system that generated codes without his help.”

    Is that a sum up? You just said that a designer could have designed such a system. Please, clarify of what system you are speaking, where we can observe it, how it works. And it is not true that the system works “without the designer’s help”. The system works because of the designer’s help (the intelligent complex functions implemented in it by the designer), even if no reintervention is needed.

    “Just like we see in “Darwinism”.”

    ???? Again, what do you mean? What do you see in darwinism? A designer? A complex designed system? Please, share with us your sightings.

    (A final clue to you: this post is not a personal attack).

  67. 67
    gpuccio says:

    Carpathian:

    “Without that connection, the genetic “code” is simply a pattern we observe.”

    Ah, something resembling an argument. Well, that’s an improvement.

    The point is, a pattern is not a code. A code is a pattern which represents symbolically something else.

    The sequence of nucleotides in DNA is not just a pattern, like the waves of the ocean. It is a pattern which obeys strict symbolic rules, so that each word of 3 nucleotides, when interacting with the translation system, generates a specific aminoacid, and the resulting protein is the functional proteins. So, it is similar to the radiowave patterns which transmit language, or a piece of music.

    Could you please answer that, instead of confounding patterns with codes? Thank you.

  68. 68
    Dionisio says:

    gpuccio @50

    […] the implementation of the code is extremely complex, and requires long and big proteins which can only be synthetized by the code itself.?

    Did you just describe a case of chicken-egg dilemma?

    Or maybe I misunderstood what you wrote?

  69. 69
    Mapou says:

    U.B.

    I’m rather busy with more mundane but pressing issues at this time. But, as soon as I get some free time to think, I do plan to look deeper into your ideas and react to them accordingly.

  70. 70
    computerist says:

    The way I see it and have always argued, code alone is not what is so interesting, what is interesting is universal code flexible enough to be used for building and maintaining higher order functional systems. The binary system (1’s and 0’s representing electrical states) was chosen for its simplicity in implementation and potential. So the code is derived from its potential, top-down, that is the primary reason I would infer design as opposed to merely arbitrary symbolic labeling (object->symbol mapping).

  71. 71

    computerist,

    That is the meat of the OP with regard to the additional utility of spatially-oriented representations, (dimensional semiosis) and the material requirements to implement them into a physical system.

    Dimensional semiosis enables combinatorial utility and efficient transcribability, but can only be enabled by additional organization.

  72. 72
    Carpathian says:

    Upright BiPed:

    Waves are not translated into physical effects that I am aware of. If you know differently, then explain.

    An AM radio converts waves into audio that drives a speaker.

    A very physical effect.

  73. 73
    gpuccio says:

    Dionisio:

    Chicken-egg, absolutely! 🙂

  74. 74
    Carpathian says:

    gpuccio:

    Then, you must observe an intelligently designed, complex system which generates codes. Where is this system in nature?

    The system is nature.

    1) God designs nature.

    2) Nature designs life.

    Do you think God is not powerful enough to do what I have just suggested?

  75. 75
    gpuccio says:

    Carpathian:

    “An AM radio converts waves into audio that drives a speaker.”

    An AM radio is designed, I suppose. As the radio transmitter. Translation systems are complex and designed.

  76. 76

    #72

    Ocean waves Carp, ocean waves.

    Your own counter-example, remember?

    – – – – – – – – – –

    My previous question to you: What is required for a representation to be a representation?

    Have you clarified this in your mind yet? I am trying to get you to focus on actual material observations.

  77. 77
    Carpathian says:

    gpuccio:

    And it is not true that the system works “without the designer’s help”. The system works because of the designer’s help (the intelligent complex functions implemented in it by the designer), even if no reintervention is needed.

    I’ll give you that for the sake of argument.

    1) The ID designer designs nature.

    2) Nature, without the reintervention of the ID designer, designs life.

  78. 78
    computerist says:

    BTW, great work UBP. It will be interesting to see where ID research such as this will influence science for the foreseeable future.

  79. 79

    Carp, please try to focus on the actual argument.

  80. 80
    Carpathian says:

    Upright BiPed:

    Ocean waves Carp, ocean waves.

    No, UB, waves and the patterns groups of waves make.

    In the case of ocean waves, period and amplitude.

    In the case of AM radio waves, period and amplitude.

    One has intent, the other doesn’t.

  81. 81
    gpuccio says:

    Carpathian:

    Ah, OK, are you a Theistic Evolutionist? That would explain much.

    Going to your point. If the system is nature, then you must show that nature has the power to generate symbolic codes. Please, do that.

    You ask:

    “Do you think God is not powerful enough to do what I have just suggested?”

    I do not think anything like that. I just observe that nature cannot generate symbolic codes. that’s it. Observation, not thinking.

    Regarding God, I could well answer:

    “Do you think God is not powerful enough to intervene and design biological objects in time and space?”

    But, frankly, I am not interested to discussions about how powerful God should be according to our narrow ideas about Him.

  82. 82

    Thank you computerist. Please help me the foster dialogue when you can.

  83. 83

    Carp,

    In the case of ocean waves, period and amplitude.

    In the case of AM radio waves, period and amplitude.

    One has intent, the other doesn’t.

    Please focus on the actual argument Carp.

  84. 84
    Carpathian says:

    Upright BiPed:

    My previous question: What is required for a representation to be a representation?

    Have you clarified this in your mind yet?

    Yes and I thought I explained it.

    A representation is dependent on the observer.

    AM radio waves intentionally encode a song.

    Ocean waves unintentionally encode local weather or distant seismic activity.

    Your task is to prove intelligent intent for your representations.

    You haven’t tried to do that.

    Connect life with the intent of an ID designer.

  85. 85

    Ocean waves unintentionally encode local weather or distant seismic activity.

    Okay. I’ll play along. What is required for an ocean wave to serve as a representation of the weather beyond the horizon?

  86. 86
    kairosfocus says:

    Folks, ocean waves are a dynamic system, not symbolic discrete state codes, they are not even a case of analogue modulation. The objections are being stretched to the point of reductio, inadvertently underscoring the force of the point. KF

  87. 87
    gpuccio says:

    KF:

    Thank you for bringing other important points to the discussion. Equivocating between deterministic patterns, which are only the result of the forces which create them, and symbolic representations, like modulated radio waves expressing language or music, or, even more evidently, digital codes where definite numeric states correspond to symbolic meanings, is really a poor argument.

  88. 88
    Virgil Cain says:

    Carpathian- You ignored the argument- try again:

    1- Experiences and observations say that all codes come from intelligent agencies

    2- No one even knows how to model physicochemical processes producing a code. Such a thing flies in the face of our experiences and observations

    3- And because of that it is safe to infer that an intelligent agency designed the code even though we did not observe it happening, as is the case with the genetic code.

    Science 101. And yes that inference, as with all scientific inferences, can be refuted by demonstrating that physicochemical processes can produce the genetic code. Again, science 101

    Our opponents whine about that because they know they could never demonstrate such a thing.

    The only thing assumed is that our knowledge, based on our experiences and observations, is correct.

  89. 89
    Virgil Cain says:

    Carpathian:

    1) The ID designer designs nature.

    2) Nature, without the reintervention of the ID designer, designs life.

    Great, find a way to test it.

  90. 90

    C’mon Carp, don’t quit. We can drive this bus together right to the font door. You are not hitting on anything that hasn’t been thrown up and worked through thousands upon tens of thousands of times in the history of thought on this subject. You’ll end up right were the evidence universally takes you. All this nonsense about ocean waves could have been avoided if you would just quiet yourself long enough to uptake the observations, but you don’t seem to be that kind of person. So, we can go through all your counter-examples if you wish. They will all fade away unless you demand them against evidence to the contrary, but if that is your goal, nothing can be done for you anyway. After all, we are not discussing how to be a better dancer or how much spice to add in a recipe, we are discussing universal material facts.

  91. 91
    Barry Arrington says:

    Based on several exchanges with Carp, I will answer UB’s question to Carp at 49:

    Can you do that Carp?

    No.

    Actually do it?

    No.

    Can you?

    No.

    Which is not to say that exchanges with Carp do not serve a purpose. He is a valuable resource for us here at UD. He supplies us with an apparently inexhaustible fount of Darwinist talking points that we take apart at our leisure. Thanks Carp. And thanks to those, like UB, who have the patience to deal with him.

  92. 92
    Zachriel says:

    From the diagram at the top of the post, with the indication of a “necessary discontinuity”, this seems to simply be a flavor of irreducible complexity.

  93. 93
    Barry Arrington says:

    Irony: Carp almost certainly sniggers, smirks and mocks the religious fundies who, in his view, clinch their teeth and dig in their heels in the face of evidence and logic.

  94. 94
    Barry Arrington says:

    Zachriel @ 92:

    Interesting observation. Any programmer here will tell you that “bugs” are bad things; if they have any effect at all, the effect is universally deleterious.

    What about the bugs that have been introduced into genomes (mostly of the fruit fly) over the last 100 years? Same thing. If they have any effect at all, the effect has been universally deleterious. Think about that Z. 100 years of zapping fruit flies with radiation to scramble their genome and not a improvement.

    Does that suggest that DNA is like or unlike human designed code?

  95. 95
    mike1962 says:

    Barry: 100 years of zapping fruit flies with radiation to scramble their genome and not a improvement.

    Yeah, but a million years of zapping it would produce astonishing effects. O ye of little faith! 😀

  96. 96

    I missed an earlier post at 69.

    Mapou, we can have that discussion when the time is right. Hopefully GP will be available to chime in.

  97. 97
    Dionisio says:

    KF @86

    Excellent point. Thank you.

    Problem is that some of your interlocutors won’t get it, simply because don’t want to. No matter how clear you explain it or how many times you repeat it.
    Pathetic reality we can’t ignore.

  98. 98
    Mung says:

    I’m rather busy with more mundane but pressing issues at this time.

    The story of my life.

  99. 99
    Mung says:

    Zachriel:

    From the diagram at the top of the post, with the indication of a “necessary discontinuity”, this seems to simply be a flavor of irreducible complexity.

    Indeed. That was also the conclusion reached by John von Neumann when he investigated the logic of self-replicating systems.

  100. 100
    Zachriel says:

    Mung: That was also the conclusion reached by John von Neumann when he investigated the logic of self-replicating systems.

    A von Neumann machine is not the simplest possible self-replicator, e.g. template replication.

  101. 101

    Don’t fret Zachriel, no one can take away your faith. But the physical realities remain.

  102. 102
    Mung says:

    Upright BiPed @ 101. So true.

    Neither are living organisms the simplest possible self-replicator, which ought to tell Zachriel something.

    And von Neumann wasn’t trying to model the simplest possible self-replicator, he was attempting to model a particular sort of self-replicator.

    So once again, Zachriel speaks a nugget of truth that tells us nothing at all interesting. It certainly isn’t a refutation of anything. What is of interest is what was left unsaid.

  103. 103
    Virgil Cain says:

    Upright Biped, sir, I found a transcription error in your explanation of DNA. You say:

    In order to encode this information, four different types of nucleic acids (adenine, thymine, guanine, and cytosine – A,T,G,C) are used to form individual representations called “codons”. A codon can be thought of as a “code word” inside the cell. Each of these code words is made up of three nucleic acids (triplets) which are read together as a single representation. For instance, the triplet TAC is translated by the cell to add an amino acid called tyrosine to a new protein being created. CTA means add leucine, GTC means add valine, CCG means add proline, GAC means add aspartic acid, and so on. This is how the cell builds every protein in the living world – it uses a code.

    You are using DNA codons. Those are transcribed into mRNA anti-codons. That means the DNA triplet TAC would code for the mRNA codon AUG, which represents the amino acid methionine. CTA in DNA = GAU in mRNA which means add aspartate. You need to redo your list.

  104. 104

    Thanks Joe. I am using the sense strand DNA table, as noted on my site.

    sense–> anti-sense–> mRNA–> tRNA

    CTA–> GAT–> CUA–> GAU–> tyrosine

  105. 105
    Virgil Cain says:

    OK, my bad, I forgot that you are trying to impress someone but don’t get carried away with the correlation being causation sloppiness just because you read it in a textbook.

    The strand that isn’t the template has nothing to do with the code. The CTA doesn’t get exposed so that the GAT can be a template. The CTA gets exposed just because it was paired with the required GAT. That is the tag for the proper tRNA.

    I didn’t finish reading your website, do you go over the fact that either strand can be the sense/ anti-sense strand?

  106. 106
    kairosfocus says:

    Z, a communication system from source to encoder/modulator, transmission, channel, receiving, demod/decode, sink, is inherently irreducibly complex by virtue of the implied process logic; a set of necessary, correctly organised and coupled components to achieve core function in a given system. Of course I left out the other element, the one we would love to but cannot get rid of, noise. Which has to be compensated for. In many systems, there is a feedback path, but that is simply the same set up going the other way. Once modulation and/or coding are incorporated, there further has to be a protocol match between the two as say the ISO OSI layercake model shows (and as is relevant to the Internet). The discontinuity UB discusses is in this context. Kindly cf: http://www.uncommondescent.com.....formation/ KF

  107. 107
    kairosfocus says:

    Z, template copying is not materially relevant to what is to be explained, the living cell and its replication of an encapsulated, smart gated, metabolic network implementing entity (huge FSCO/I in itself) with code using subsystems and von Neumann kinematic Self-Replication. Even in the case of using unzipped DNA to create mRNA, one has to account for editing and for the management process. Just the indexing and handling of in effect a long twisted string is a major headache as any sports angler can tell you: bird’s nest is the apt description, though it is nowhere near as organised as an actual bird’s nest. KF

  108. 108
    EugeneS says:

    Some of our interlocutors will never recognize that naturalism is a complete bankrupt as regards the origin of life. To actually see and recognize a failure one needs sufficient knowledge, personal courage and intellectual honesty.

  109. 109
    Zachriel says:

    Mung: Neither are living organisms the simplest possible self-replicator

    That’s right. So reproduction doesn’t require a “necessary discontinuity”.

    kairosfocus: a communication system from source to encoder/modulator, transmission, channel, receiving, demod/decode, sink, is inherently irreducibly complex

    Perhaps, but evolution can result in irreducibly complex structures.

    Hermann Joseph Muller (1918): “… thus a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former.

  110. 110
    Virgil Cain says:

    Zachriel:

    So reproduction doesn’t require a “necessary discontinuity”.

    There is a huge discontinuity between molecular replicators and biological reproduction.

    Perhaps, but evolution can result in irreducibly complex structures.

    Only directed evolution can do such a thing. Herman Joseph Muller didn’t provide any empirical support for his claim. nor did his claim support unguided evolution.

  111. 111
    Mung says:

    Mung: Neither are living organisms the simplest possible self-replicator

    Zachriel: That’s right. So reproduction doesn’t require a “necessary discontinuity”.

    I'm sorry, but your conclusion doesn't follow from anything you've written. It's a non-sequitur.

    Biological (Darwinian) evolution [i.e. the evolution of life as we know it – not life as imagined by Zachriel] requires heredity, which requires fidelity. So bringing up simpler replicators is simply a red herring.

  112. 112
    Carpathian says:

    Barry Arrington:

    Which is not to say that exchanges with Carp do not serve a purpose. He is a valuable resource for us here at UD.

    I agree with you that exchanges with me serve a purpose.

    They show that your side’s responses tend to get personal while “Darwinists” tend to stick to science.

    He supplies us with an apparently inexhaustible fount of Darwinist talking points that we take apart at our leisure.

    Really? Then answer this at your leisure.

    Mapou: While it is obvious that a code is an intelligent artifact, it is possible to use strict rules in order to automate code creation in an AI program during learning. For example, I have implemented a spiking neural network that can automatically discover and create internal patterns from signals (spikes) arriving at a set of input sensors. The discovered patterns can still be called representations (or codes) even though they were not directly made by an intelligent coder.

    Is Mapou right about that bolded sentence?

  113. 113
    Carpathian says:

    Virgil Cain:

    2- No one even knows how to model physicochemical processes producing a code. Such a thing flies in the face of our experiences and observations

    Then why would you think an alien life-form could do it if all our experiences show that we can’t.

  114. 114
    Zachriel says:

    Mung: your conclusion doesn’t follow from anything you’ve written. It’s a non-sequitur.

    It’s not a conclusion, but a statement of fact. Reproduction doesn’t require a “necessary discontinuity”.

    However, we will draw the obvious conclusion. “Necessary discontinuity” is just another name for irreducible complexity, and as irreducible complexity can plausibly evolve, there is no intrinsic barrier to the evolution of “necessary discontinuities”.

  115. 115

    From the diagram at the top of the post, with the indication of a “necessary discontinuity” … reproduction doesn’t require a “necessary discontinuity”.

    The diagram at the top of this post refers to translation — the translation of an informational medium into physical effects. It is a distinct process that is both well-documented and well understood. It is the very process that establishes the specificity and temporal control required to organize the first heterogeneous living cell on Earth. The conception of “replication” you are referring to does not achieve translation. They are two entirely different physical processes, and one does not establish the physical organization required by the other.

  116. 116
    Barry Arrington says:

    Carpathian @ 112:

    Seriously? You are going to pretend that UB has not already answered that question @ comment 49?

  117. 117
    Zachriel says:

    Upright BiPed: The conception of “replication” you are referring to does not achieve translation.

    It’s posited that translation evolved from simpler associations.

  118. 118
    Andre says:

    Translation evolved from simpler associations?

    God help us!!!!!! There are lunatics in your universe!

  119. 119
    Andre says:

    Carpathian understands the issue he does not like it one bit.

  120. 120
    Andre says:

    Zachriel what is translation? How is it achieved? What is the absolute minimum requirement for any translation?

  121. 121

    It’s posited that translation evolved from simpler associations.

    It certainly is. And it remains a physical fact that one process does not result in the other.

    (EDIT: btw Zach, not achieving translation is only the start of it.)

  122. 122
    Virgil Cain says:

    Carpathian:

    Then why would you think an alien life-form could do it if all our experiences show that we can’t.

    Wow, way to ignore the argument and prattle on like an ignoramus.

  123. 123
    Virgil Cain says:

    Zachriel:

    and as irreducible complexity can plausibly evolve

    Only if evolution is directed.

  124. 124
    Carpathian says:

    Barry Arrington,

    No, he didn’t answer the question that I asked you .

    Let’s look at comment 49 and see if I’m wrong.

    Carp,

    Mapou gave a simple example were he, as an intelligent agent, arranged a system that can create representations to be interpreted as patterns within the system.

    I agree that Mapou did this.

    In order to function, the system requires both the arrangement of the representations as well as the means to interpret them.

    I agree and have not said otherwise.

    You lifted his example out of its context, and are now daring him to prove to you that his statement was wrong — as if he is to demonstrate that the system that he arranged could have appeared on his test bench without his input.

    Not only did I not claim that his system “could not have appeared on his test bench without his input”, I believe that Mapou’s system required Mapou to design it.

    You didn’t think things through. And you most assuredly have not conceptualized the issues yet. Just once, take your blinders off and deal with the observations as they are presented, without carelessly jumping at the chance to deny them.

    Can you do that Carp? Actually do it? Can you?

    And finally, a summation that sums up nothing.

    So, did UB answer this question that I asked you?

    Mapou: The discovered patterns can still be called representations (or codes) even though they were not directly made by an intelligent coder.

    Carpathian: Is Mapou right about that bolded sentence?

  125. 125
    Carpathian says:

    Virgil Cain:

    Carpathian: Then why would you think an alien life-form could do it if all our experiences show that we can’t.

    Virgil Cain: Wow, way to ignore the argument and prattle on like an ignoramus .

    Our side provides the questions and your side provides the insults.

  126. 126
    Virgil Cain says:

    LoL! @ Carpathian- Your side provides the belligerence and strawmen and our side provides the observations.

    Why would anyone claim the ETs can’t do something just because we can’t?

  127. 127
    Box says:

    UB: Semiosis ultimately refers to the physical process by which meaningful information is exchanged within the living world. In general terms, semiosis exist anytime one thing represents or signifies another thing.

    [my emphasis]

    Exit naturalism, since it cannot ground a relationship where one clump of matter is about another clump of matter.

    There is nothing in the whole universe—including, of course, all the neurons in your brain—that just by its nature or composition can do this job of being about some other clump of matter.
    [Rosenberg, ch.8, The Atheist’s Guide to Reality]

    [my emphasis]

    UB: (…) research has demonstrated that semiosis exist throughout the living kingdom. And with the discovery of the genetic code in the 1960’s, science has now demonstrated that semiosis was the fundamental material requirement at the origin of life itself.

    So much the worse for naturalism, because it cannot be part of any investigation of semiosis, since it is compelled to deny the existence of any semiotic relationship.

  128. 128
    Barry Arrington says:

    Carpathian,

    I see. If you are going to stipulate that the genetic codes requires ID at the very least of the front-loading variety, I am happy to let you.

  129. 129
    Carpathian says:

    Barry Arrington:

    I see. If you are going to stipulate that the genetic codes requires ID at the very least of the front-loading variety, I am happy to let you.

    That works for me.

    The ID designer created a system like Mapou’s that doesn’t require further guidance from the designer.

    Since Mapou could do it, then so could the designer.

    Life evolved on its own over billions of years without further input from the designer and ID’s improbability argument doesn’t hold.

    Therefore what we observe is “Darwinism”, exactly as defined by evolutionary scientists.

  130. 130
    Carpathian says:

    Virgil Cain:

    LoL! @ Carpathian- Your side provides the belligerence and strawmen and our side provides the observations.

    Why would anyone claim the ETs can’t do something just because we can’t?

    Why would you claim “nature” can’t do something just because we can’t?

    Why does ID claim the ID designer cannot create an unguided system that generates new “codes and information”?

    Mapou has created such a system.

    Does the ID designer have limits that Mapou doesn’t?

  131. 131
    Virgil Cain says:

    Carpathian:

    Why would you claim “nature” can’t do something just because we can’t?

    2- No one even knows how to model physicochemical processes producing a code. Such a thing flies in the face of our experiences and observations

    Try to follow along…

  132. 132
    gpuccio says:

    Carpathian:

    Just to be clear:

    1) The genetic code and the pertinent information (transcription, translation, and so on) were obviously designed. But when? Of course, at OOL. Not certainly at the creation of the universe. The physical universe contains no system which can explain the genetic code, so an explicit design intervention was necessary, on our planet, and more or less at the beginning of life.

    That’s not what darwinism says. Darwinism says that the laws of nature, as they are implemented in the physical universe, can generate life, and therefore also the genetic code, without any design intervention. That is simply false.

    2) Anyway, after OOL, and therefore with the genetic code already working, a lot of new information has been designed in the course of natural history. That cannot be explained without explicit design interventions.

    Therefore, there are two different problems:

    a) The origin of the information which is implicit in the genetic code and in the translation system. That was obviously designed, and cannot be explained with the laws of nature, even if those laws of nature are themselves designed at the beginning of the universe (which I do believe). The beginning of the universe and the beginning of life are two different events, separated in time and space, and it can be inferred that each of them required a design intervention (for different reasons).

    b) The evolution of genomes and proteomes in the course of natural history presupposes the genetic code and translation apparatus, but requires lots of new complex functional information, which cannot be explained by non design explanations, even if the genetic code and all the basic information in OOL were already present.

    Therefore, we can infer specific acts of design for:

    a) The universe (cosmological argument, in all its forms)

    b) The genetic code and related apparatus (UB’s specific ID argument, based on semiosis)

    c) OOL and the whole evolution of life on our planet after that (classic ID argument, based on functional complexity)

  133. 133
    Carpathian says:

    Virgil Cain:

    Carpathian: Why would you claim “nature” can’t do something just because we can’t?

    Virgil Cain: 2- No one even knows how to model physicochemical processes producing a code. Such a thing flies in the face of our experiences and observations

    Try to follow along…

    Follow your own argument to where it leads.

    Your claim is that we, living creatures, can’t create the first living creatures, but other living creatures (aliens), can create living creatures.

    This flies in the face of our observations, since we, living creatures, can’t do it.

    Since we have observed our failure to create life, why would you claim that an unobserved alien life could?

    Why would you claim that our observed limitations of living creatures applies to physics, which is not alive and has therefore not been observed to fail at creating life?

  134. 134
    Zachriel says:

    Upright BiPed: And it remains a physical fact that one process does not result in the other.

    That is not known, but there is some evidence indicating that DNA World was preceded by RNA World.

  135. 135
    Carpathian says:

    gpuccio:

    That’s not what darwinism says. Darwinism says that the laws of nature, as they are implemented in the physical universe, can generate life, and therefore also the genetic code, without any design intervention. That is simply false.

    “Darwinism” doesn’t say that at all.

    “Darwinism” addresses the changes over time” in lifeforms.

    No one has any idea how life started.

    a) The origin of the information which is implicit in the genetic code and in the translation system. That was obviously designed, and cannot be explained with the laws of nature, even if those laws of nature are themselves designed at the beginning of the universe (which I do believe).

    There is no evidence to suggest that life was “obviously designed” by any hands-on method.

    Mapou has created a system that generates codes without further intervention from the designer.

    Why couldn’t the “designer” of the universe do the same?

    UB’s “semiotic codes” could be the result of just such a system designed by the ID designer.

    The observations of such a system in action would result in something that looks exactly like “Darwinism”.

    Whether there is an ID designer or not, there would be no evidence of such an entity if he created a system that worked like Mapou’s.

  136. 136
    Andre says:

    Zachriel

    And how does RNA solve your problem?

  137. 137
    Andre says:

    Carpathian

    Except there is evidence for a designer.

  138. 138
    Zachriel says:

    Andre: And how does RNA solve your problem?

    It provides a precursor replicator that can evolve complex protein synthesis at a later time.

  139. 139

    #134

    What is absolutely known is that the physical processes at work in the experimental effort to improve template “replication” (R18, tC19Z, B6.61, etc) do not result in translation.

    But like I said, no one can take away your faith, nor can anyone falsify any event you wish to propose from it.

  140. 140

    >>> What is the absolute minimum requirements for any translation?

    In the spirit of that question….

    from Biosemiosis.org

    A living cell is a heterogeneous system. It requires discrete parts in order to function, and reproduces itself by means of prescriptive synthesis. This process requires the translation of an informational medium. The minimum requirements for the origin of the system are therefore established by what is physically necessary to record and translate the amount of information that the system needs to successfully describe itself into memory.

    Also…

    No Organizing Principles

    In order to organize the first heterogeneous living cell, it is necessary to create utility through the mechanism of representation. It is necessary that those representations be spatially-oriented patterns; independent of the dynamic properties of their medium. It is necessary that many such patterns come together at the same time and place to collectively record prescriptive memory. It is necessary that the rules of a reading-frame code make that memory possible. And it is necessary that this memory successfully contain the construction details of the entire system itself. Yet, none of these things is brought into being by the forces of physical law.

    What then remains of the reductionist assumption is the real need for sheer chance to accomplish what physical forces and principles do not do. This situation is then superimposed against the backdrop of brilliant research scientists using intelligent design in the laboratory in an attempt to demonstrate that chance is indeed up to the task. At the same time, other prominent researchers write peer-reviewed papers and books describing the intellectual need for an infinite number of universes – specifically in order to give chance an endless number of opportunities to do what must be done. In short, origins research reflects the simple fact that no organizing forces or principles have ever been found for the material conditions required at the origin of life.

    Yet (through observation, theory, and experiment) we have come to know what those conditions are; they are described in an enormous body of knowledge. We also know that those specific conditions are exclusively associated with only one phenomenon – intelligence – which happens to be the only theory on the origin of life that is summarily rejected upfront by the institutions of science. Thus, the landscape surrounding the semiotic origin of life is not being defined by the ideals of scientific investigation — but by personal and institutional bias. And in every venue of discourse between the institutions of science and the general public, the greatest mystery of all time is presented with an absolute certainty that intelligence had no role in it. This conclusion comes from anything other than the evidence.

    There is a formidable line at the origin of life, where a representational organization necessarily comes into being. This line has been repeatedly described in the scientific literature. Pattee refers to it in terms of an “epistemic cut” between rate-independent genetic symbols and the rate-dependent dynamics they control. Johnson refers to it in terms of the necessary contingency instantiated in a physical medium. Barbieri states that any description of the living world requires objective observables that are otherwise not measurable. Yockey speaks of the symbolic nature and immateriality of the biological message recorded in monomers. Abel refers to it in terms of the primacy of formalism over function. Crick required it in the adapter hypothesis. Nirenberg demonstrated it in the ribosome. And the late British-Hungarian polymath John von Neumann wrote of it in terms of non-dynamic “quiescent descriptions” required in the logic of self-replication.

    Yet, despite the depth of observations, the general public’s awareness of genuine representations and rules at the origin of life is virtually zero. To a modern person in a modern society, who everyday uses any number of devices that require information processing (representations and rules) in order to function, the term “genetic code” seems to be understood only for its obvious necessity (in making things happen a certain way), but the term itself has been emptied of its nature. Its unique physical workings, to any large number of people, are simply unknown. That part of the science has been left out of the public discourse about origins.

    This is the challenge that Biosemiosis.org has set for itself.

  141. 141
    Andre says:

    Because it has a simpler structure and is only a single strand it must be a precursor? Is that your assumption?

    Simple to complex is true cause Darwin said so?

    Funny guy……

    That RNA serves a different purpose never crossed your mind? Simple to complex is just true..

  142. 142
    Mapou says:

    Carpathian,

    You are comparing apples and oranges. My neural network never creates new information. It simply creates representations for sensory data. The data is dictated by environmental events.

    To do what you are suggesting, a designer would have to have all possible body plans (from single cell organisms to dung beetles, caribous and whales) incorporated in the first self-replicating cell a billion years ago. This is nonsense, of course. Darwinists take the cake by claiming that RM+NS creates new information (new body plans and functionality) out of thin air.

    The voodoo science is strong with the dark side of the force.

  143. 143
    gpuccio says:

    Carpathian:

    I am afraid there is no hope.

    If I understand well (you seem very reticent to say things clearly) you believe:

    That darwinian principles can explain all evolution of life after OOL.

    That “No one has any idea how life started.”

    Except you, apparently. Because you say that:

    “There is no evidence to suggest that life was “obviously designed” by any hands-on method.”

    So, it seems that you don’t think it was designed. But then, how did it come into existence? You clarify:

    “UB’s “semiotic codes” could be the result of just such a system designed by the ID designer.”

    OK, what system? Where is it? Mapou’s system can be observed, tested. What is the system you speak of?

    You say nature. But nature works according to the laws of physics, as far as we can understand. If the designer designed something at the beginning of the universe, that something is the laws of the universe itself.

    So, if you propose that the universe includes a “system” which can generate codes, please show where that system is and how it works.

    That’s all, and for me we can stop here.

  144. 144
    Virgil Cain says:

    Carpathian:

    Your claim is that we, living creatures, can’t create the first living creatures, but other living creatures (aliens), can create living creatures.

    Wake up- this is my claim:

    1- Experiences and observations say that all codes come from intelligent agencies

    2- No one even knows how to model physicochemical processes producing a code. Such a thing flies in the face of our experiences and observations

    3- And because of that it is safe to infer that an intelligent agency designed the code even though we did not observe it happening, as is the case with the genetic code.

    Science 101. And yes that inference, as with all scientific inferences, can be refuted by demonstrating that physicochemical processes can produce the genetic code. Again, science 101

    Our opponents whine about that because they know they could never demonstrate such a thing.

    The only thing assumed is that our knowledge, based on our experiences and observations, is correct.

  145. 145
    Virgil Cain says:

    Zachriel:

    It provides a precursor replicator

    Wrong- designed RNAs can replicate but only with the assistance of other RNAs

    that can evolve complex protein synthesis at a later time.

    Spiegelman’s monster demonstrates otherwise.

  146. 146
    Virgil Cain says:

    Zachriel:

    but there is some evidence indicating that DNA World was preceded by RNA World.

    Wrong again. There is a need for a RNA world but there isn’t any evidence for one.

  147. 147
    Virgil Cain says:

    Carpathian:

    There is no evidence to suggest that life was “obviously designed” by any hands-on method.

    It’s called science and knowledge of cause and effect relationships.

  148. 148
    Zachriel says:

    Upright BiPed: What is absolutely known is that the physical processes at work in the experimental effort to improve template “replication” (R18, tC19Z, B6.61, etc) do not result in translation.

    That’s right. So no one knows if simple RNA replicators could evolve more complex relationships with peptides or not. It’s an open question. However, the claim in the original post is that such an evolutionary sequence could not plausibly occur, but simply showing that the result is irreducible doesn’t mean it couldn’t have evolved.

    Upright BiPed: In order to organize the first heterogeneous living cell, it is necessary to create utility through the mechanism of representation.

    Again, that is not necessarily the case. A replicator in a lipid membrane could be a plausible ancestral heterogeneous cell.

    Andre: Because it has a simpler structure and is only a single strand it must be a precursor?

    No one knows at this point. What we can say is that it can’t be ruled out as yet, certainly not by arguing irreducible complexity, in so many words.

  149. 149
    Virgil Cain says:

    Irreducible complexity is not an argument against evolution, per se. Directed evolution has creative powers as exemplified by genetic and evolutionary algorithms.

    How do we model drift and natural selection producing the genetic code? What predictions are borne from that?

  150. 150
    Mung says:

    Zachriel:

    So no one knows if simple RNA replicators could evolve more complex relationships with peptides or not. It’s an open question.

    Even Zachriel can’t avoid the requirement for a relational model, even simple relationships.

  151. 151
    kairosfocus says:

    Z, appealing to evolution on something that must be in place antecedent to the existence of von Neumann kinematic self replication (thus reproduction) is a reductio. Recall, coded storage for self assembly — cf here DNA — is part and parcel of the required entity. Blind faith in the magical powers of evolution . . . I am tempted to say, reification . . . is undermining our generation’s ability to think straight. KF

  152. 152
    Zachriel says:

    kairosfocus: appealing to evolution on something that must be in place antecedent to the existence of von Neumann kinematic self replication (thus reproduction) is a reductio.

    Self-replication does not require von Neumann architecture.

  153. 153

    UB: The conception of “replication” you are referring to does not achieve translation.

    Zach: It’s posited that translation evolved from simpler associations.

    UB: It certainly is. And it remains a physical fact that one process does not result in the other.

    Zach: That is not known

    UB: What is absolutely known is that the physical processes at work in the experimental effort to improve template “replication” (R18, tC19Z, B6.61, etc) do not result in translation.

    Zach: That’s right.

    You are correct, it does not result in translation.
    As already stated, they are two entirely different processes.

    Zach: So no one knows if simple RNA replicators could evolve more complex relationships with peptides or not.

    “More complex relationships” isn’t the physical requirement, translation is.

    And as we have come to agree, no one has demonstrated an engineered RNA “template-replicator” resulting in translation. Even then, translation itself is only the beginning of what is necessary.

    Zach: the claim in the original post is that such an evolutionary sequence could not plausibly occur, but simply showing that the result is irreducible doesn’t mean it couldn’t have evolved.

    The diagram at the top of this page (which you have referred to) does not make any claims about “what could not plausible occur”. Instead, it shows what *does occur* during the translation of functional effects from an informational medium.

    UB: In order to organize the first heterogeneous living cell, it is necessary to create utility through the mechanism of representation.

    Zach: Again, that is not necessarily the case. A replicator in a lipid membrane could be a plausible ancestral heterogeneous cell.

    An RNA “template-replicator” encapsulated inside a dissociated lipid membrane still does not achieve translation, and thus, is not capable of organizing the heterogeneous living cell. Your desire to make something be something other than what it is has now reached the level of incoherence. Again, no one can take away your faith Zach. And no one can falsify any conception you wish to propose from that faith.

  154. 154
    Mung says:

    Pop a strand of RNA inside a soap bubble and voila, a self-reproducing cell.

  155. 155
    Andre says:

    Zachriel

    Andre: Because it has a simpler structure and is only a single strand it must be a precursor?

    No one knows at this point. What we can say is that it can’t be ruled out as yet, certainly not by arguing irreducible complexity, in so many words.

    Who is saying irreducible complexity? Not me? I’m just stating the obvious here, you are assuming without any evidence that simple things can become more complex given enough time, and chance.

    I’d love to see actual proof for such an assumption. Which really is a contradiction in terms because an assumption is a belief without any proof. So lets rather ask for testable and verifiable evidence.

  156. 156
    Andre says:

    UB @140

    Thank you for that but I was hoping Zachriel would do some research, on it himself.

  157. 157
    Andre says:

    Zachriel

    Some homework for you….

    http://staff.jccc.net/pdecell/.....steps.html

  158. 158
    kairosfocus says:

    Z,

    the evidence of the coded tape in the living cell points to vNkSR (something that is acknowledged) . . . and here I obviously point to the DNA, mRNA, Ribosome and tRNA system with the tRNA acting as a part transfer “taxi” and position-arm device with tool tip, incorporating a CCA universal coupler . . . which assembles the vital protein component . . . which inter alia is a bridge to the cellular metabolic network.

    In this context of course the unzipping of DNA to template it into mRNA, then the whole synthesis process is strongly dependent on the products of the protein synthesis process. Chicken-egg loop involved in all the processes. Likewise, DNA duplication for replication is in the same chicken-egg, FSCO/I dense loop.

    Also, the ATP assembly process is a key energy supply support process that is integral to the system, another bridge to metabolism and an illustration of the complex integration of the cell involving vNkSR replication, metabolic process and encapsulation with smart gating.

    If you have another “easier” architecture you need to show empirical observational evidence of its presence in the cell, its effectiveness in the wild, and of how it bridges to the cells as we know.

    Where, RNA world needs adequate empirical grounding, as one case in point.

    Otherwise it is empty, comforting ideological speculation dressed up in a seemingly authoritative lab coat.

    Observations of RNA world: ______________

    Unambiguous, non question-begging observed traces today of same: _____________

    Observed adequate cause that origin of a viable DNA based cellular architecture involving RNA world roots is possible: __________

    Observations that required FSCO/I can come about by blind watchmaker chance and mechanical necessity: _______________

    This includes traces from the past of OOL that show the relevance and factual, empirical groundedness. As well as meeting the vera causa, observed adequate cause criterion for scientific inference to best explanation of what we cannot observe directly but must deal with traces and/or signs of.

    Viruses don’t work, they basically hijack the cellular mechanisms.

    The dismissal so far sounds like a squid-ink cloud not a substantial response.

    And remember, OOL is the root of the tree of life.

    The FSCO/I in it has to be accounted for prior to reproduction, taking “evolution” off the table. The only thing there in that warm pond or volcano vent or comet core etc etc, is physics, chemistry and thermodynamics informed by the underlying statistical issues.

    Your attempt to put “Evolution” back on the table when it is the reproduction subsystem relevant to differential reproductive success that here needs to be accounted for is a cart before horse fallacy. It is also a fallacy of appeal to the prejudice that “Evolution” provides a magic answer to the needle in haystack, FSCO/I blind search challenge.

    The objection you made, fails.

    But it does show the evolutionary materialist a prioris at work.

    So, it is proper to highlight also that the very fact that you imply responsible, rational freedom to argue, know and discuss fatally undermines such evo mat, as it is fatally and inescapably self-referentially incoherent. Let me cite Haldane as a simple summary on the point:

    “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter.” [[“When I am dead,” in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.]

    KF

  159. 159
    EugeneS says:

    Zachriel in 152 conveniently ignores the colossal distinction between self-replication of homogeneous (like crystals) and heterogeneous structures (like the cell).

    As if he has not been told.

  160. 160
    gpuccio says:

    Zachriel:

    I would like to ask you something.

    Let’s accept for a moment that life originated as RNA world. (I don’t believe it, but it’s for the sake of discussion).

    So, at some point we have living beings who use RNA both as an effector molecule (instead of proteins) and as an information recording molecule (instead of DNA).

    At this point, we are supposed to have already a lot of functional information (OOL has already taken place). Let’s accept it, without asking how that functional information was generated.

    The point is:

    a) Where is that information stored? Answer: in RNA sequences.

    b) What does that information code? Answer: functional RNA sequences.

    OK. Let’s call this state A.

    Now, at some point, we pass to a system where the effector molecules are proteins. And the information for those effector molecules is stored in DNA, through a symbolic code, and is then transcribed through RNA and translated through RNA and proteins.

    a) Where is that information stored? Answer: in symbolic DNA sequences.

    b) What does that information code? Answer: functional protein sequences.

    OK. Let’s call this state B.

    Now comes my point.

    The functional information in A, precious and, as far as we know, unexplained, is a treasure trove of functional sequences which implement a lot of functions. Many of them still necessary in B.

    So, is that functional information “carried on” from A to B?

    And the answer is: no.

    Why? Because the nucleotide sequence information for an effector RNA molecule which acts, say, as a polymerase in A has really nothing to do with the symbolic nucleotide sequence information which codes, according to the genetic code, for a protein which acts, similarly, as a polymerase in B. The two nucleotide sequences are completely different, and there is no relationship at all between them.

    Why? For two very good reasons:

    1) The functional working of a protein and its 3D structure are completely different form the functional working and 3d structure of an RNA molecule.

    2) Even more relevant, the nucleotide sequence in a DNA coding gene is symbolic (UB’s point), and has nothing to do with biochemical laws, either of RNA or of protein molecules. It just obeys the rules of the code. It is a pure vector of aminoacid sequence information through a symbolic code.

    So, it is obvious that, if in some way a treasure trove of information about functional RNA molecules has been in some way generated during OOL in the form of an RNA world, when we pass to the re-origin of life in the form of a DNA-RNA-protein world, a completely different treasure trove of functional sequence information, for the same functions, has to be found again.

    Double luck.

    And, obviously, the whole new information about the genetic code itself and the whole apparatus implied in transcription and translation has to come into existence from scratch.

    What a theory. OK, I am really happy that I have no reason to believe it! 🙂

  161. 161
    Zachriel says:

    Upright BiPed: More complex relationships” isn’t the physical requirement, translation is.

    Translation is posited to have evolved from simpler associations.

    Upright BiPed: And as we have come to agree, no one has demonstrated an engineered RNA “template-replicator” resulting in translation.

    That is correct.

    Upright BiPed: The diagram at the top of this page (which you have referred to) does not make any claims about “what could not plausible occur”. Instead, it shows what *does occur* during the translation of functional effects from an informational medium.

    That’s fine. Translation, including the “necessary discontinuity”, is posited to have evolved from simpler associations.

    Upright BiPed: An RNA “template-replicator” encapsulated inside a dissociated lipid membrane still does not achieve translation, and thus, is not capable of organizing the heterogeneous living cell.

    Not sure what you are claiming. Posited RNA replicators within a lipid membrane are an organized heterogeneous cell capable of making other organized heterogeneous cells.

    Andre: I’m just stating the obvious here, you are assuming without any evidence that simple things can become more complex given enough time, and chance.

    It’s not an assumption, but a scientific finding. Indeed, nature is full of complexity resulting from simple interactions.

    EugeneS: Zachriel in 152 conveniently ignores the colossal distinction between self-replication of homogeneous (like crystals) and heterogeneous structures (like the cell).

    DNA is a template replicator.

  162. 162
    Zachriel says:

    gpuccio: Let’s accept for a moment that life originated as RNA world. (I don’t believe it, but it’s for the sake of discussion).

    RNA World is posited to have preceded DNA World, but may not have been the first replicator.

    gpuccio: OK. Let’s call this state B.

    State B would be RNA production of peptides (or may have even been part of state A).

    gpuccio: So, is that functional information “carried on” from A to B?

    In the 1960s, Crick and Orgel hypothesized RNA World, a time in the history of life wherein RNA would act both to store genetic information and to catalyze chemical reactions. Crick made the prediction that “the primitive ribosome could have been made entirely of RNA”. A generation later Cech and Altman showed that “the ribosome is a ribozyme” — RNA makes proteins. As such, the ribosome is a primordial structure predicted by RNA World.
    http://www.nobelprize.org/nobe.....ticle.html

  163. 163
    kairosfocus says:

    Z, you need to be building us cells capable of metabolism joined to self replication and with encapsulation with smart gating. Then showing us evidence of this at OOL and of the transition to the observed cell based life. Absent this you are building a pyramid of evo mat ideological speculation on a pinhead of fact that does not really support what is needed. KF

  164. 164
    gpuccio says:

    Zachriel:

    OK, if state B is production of proteins by RNA, and not DNA, the same argument remains true. For RNA to produce proteins you need the genetic code and the translation apparatus. Including the 20 proteins which implement the genetic code.

    And the information which produced rybozymes has to be found again, if the functions has to be assumed by proteins, for the reasons I have already stated.

    The point remains, the information (in nucleotide sequence) to effect a function by RNA has nothing to do with the information (in nucleotide sequence) to effect the same function by a protein, coded by the genetic code.

    The simple truth is that cell functions, for all we know, are effected by proteins, from LUCA on.

    The ribosome is an exception. It was an exception in the beginning, and it is an exception today.

    You say:

    ” Crick made the prediction that “the primitive ribosome could have been made entirely of RNA.””

    And then you add:

    “A generation later Cech and Altman showed that “the ribosome is a ribozyme” — RNA makes proteins. As such, the ribosome is a primordial structure predicted by RNA World.”

    You seem to suggest that the second statement is the confirmation of the “prediction” made by Crick.

    But that is not the case. I am not aware of any evidence that “the primitive ribosome was made entirely of RNA”. If you have any, please let me know.

    The fact that the main active sites in the ribosome are implemented by the RNA molecule is no such evidence. It has always been known that the ribosome is mainly an RNA structure, with many proteins playing some role. That is true now, and can very well have been true in the beginning.

    And, in the end, I am not denying that RNA can effect some functions. It does now, It did in the beginning. That is no evidence for the RNA world.

  165. 165
    Virgil Cain says:

    Zachriel:

    Translation is posited to have evolved from simpler associations.

    Of course it is. However that alone doesn’t solve the problem.

    DNA is a template replicator.

    DNA gets replicated with the help of many proteins.

    RNA World is posited to have preceded DNA World,

    The alleged RNA world lacks evidentiary support.

    As such, the ribosome is a primordial structure predicted by RNA World.

    Except the primordial world is not capable of producing a ribosome. Natural selection and drift are incapable of producing a ribosome.

    So you lose, again.

  166. 166

    Upright BiPed: “More complex relationships” isn’t the physical requirement, translation is.

    Zachriel: Translation is posited to have evolved from simpler associations.

    Yes, we’ve already been here. A process has been posited as the precursor of another process that it bears no physical relationship to, containing singular features that are entirely absent in the proposed precursor. It is also understood that this proposed precursor is widely used as an intellectual placemat to avoid the universal observation that those singular features result from a singular source. Are you able to acknowledge that source as unambiguously as our universal experience suggests? [Edit: This isn’t to suggest that you have changed your position, but are you even able to acknowledge the universal observation?]

    Upright BiPed: And as we have come to agree, no one has demonstrated an engineered RNA “template-replicator” resulting in translation.

    Zachriel: That is correct.

    Then, knowing that the physical processes involved in RNA templating do nothing whatsoever to resolve the singular issues associated with the translation of a dimensional semiotic code, what is the real impetus to keep repeating it? Why make a veritable career of going out on the web to repeat the claim at every opportunity, as if you didn’t already know the claim is seriously flawed (if not downright deceptive) from an empirical point of view? Of course, there is no need to answer that question here, after all you are not alone. There are knowledgeable people on the web that (with a completely straight face) will tell you that a “one amino acid system” can result into a “two amino acid system”. And if you bring it to their attention that a “one amino system” (what system!?) doesn’t have the informational capacity to encode itself into a translation system at all (and doesn’t resolved any of the unique physical conditions required of a semiotic code), you only incite them to increase their mockery. Do you think that is a rational scientific response to empirical facts?

    Upright BiPed: The diagram at the top of this page (which you have referred to) does not make any claims about “what could not plausible occur”. Instead, it shows what *does occur* during the translation of functional effects from an informational medium.

    Zachriel: That’s fine. Translation, including the “necessary discontinuity”, is posited to have evolved from simpler associations.

    Yes Zach, we’ve already covered this. Are you yet able to unambiguously acknowledge that to translate D/RNA into proteins requires the discontinuity?

    Upright BiPed: An RNA “template-replicator” encapsulated inside a dissociated lipid membrane still does not achieve translation, and thus, is not capable of organizing the heterogeneous living cell.

    Zachriel: Not sure what you are claiming. Posited RNA replicators within a lipid membrane are an organized heterogeneous cell capable of making other organized heterogeneous cells.

    An RNA “template replicator” that does not translate information cannot organize the heterogeneous cell. Two RNA “template replicators” that do not translate information cannot organize the heterogeneous cell any more than one can. Give it a rest already.

  167. 167
    EugeneS says:

    Zachriel #161,

    You appear to believe that repeating some sciency word combinations will help you resolve the gigantic challenge naturalism is facing at the origin of life.

    Before typing responses, you need to understand the challenge.

  168. 168

    Before typing responses, you need to understand the challenge.

    #53

  169. 169
    Carpathian says:

    Mapou:

    To do what you are suggesting, a designer would have to have all possible body plans (from single cell organisms to dung beetles, caribous and whales) incorporated in the first self-replicating cell a billion years ago. This is nonsense, of course .

    Of course it is nonsense.

    Neither the “designer” nor “Darwinism” suggests such a thing.

    If I’m dealt five cards in poker, I don’t have every possible hand that could be made.

    What I do is discard some cards and get new ones.

    That’s evolution at its simplest.

  170. 170
    Carpathian says:

    gpuccio:

    If I understand well (you seem very reticent to say things clearly) you believe:

    That darwinian principles can explain all evolution of life after OOL.

    That “No one has any idea how life started.”

    Except you, apparently. Because you say that:

    “There is no evidence to suggest that life was “obviously designed” by any hands-on method.”

    I don’t think I can be clearer.

    I said that no one has any idea how life started.

    I didn’t say, “Except me”.

    I don’t know how life started and neither do you.

    Here’s something to think about concerning how it evolved.

    Life evolved in the same way man-made products evolve and that is due to “market” pressures, not primarily “design” issues.

    If the “market” (i.e the environment), accepted a biological organism, (i.e. a product), that product would continue to be “developed” until the “market” no longer accepted it.

  171. 171
    Zachriel says:

    gpuccio: For RNA to produce proteins you need the genetic code and the translation apparatus.

    The extant genetic code is posited to have evolved from a simpler relationships, in particular, sequences of RNA that directly catalyzed the formation of peptides.

    gpuccio: And the information which produced rybozymes has to be found again, if the functions has to be assumed by proteins, for the reasons I have already stated.

    Not sure what this means. RNA produced proteins. They still do.

    gpuccio: The point remains, the information (in nucleotide sequence) to effect a function by RNA has nothing to do with the information (in nucleotide sequence) to effect the same function by a protein, coded by the genetic code.

    No one knows exactly how it happened, but the hypothesis is that RNA used DNA to store information in a more stable form. Eventually, DNA became the main storage of information.

    gpuccio: The simple truth is that cell functions, for all we know, are effected by proteins, from LUCA on.

    Right. And it’s RNA that produces proteins, not DNA.

    gpuccio: I am not aware of any evidence that “the primitive ribosome was made entirely of RNA”.

    The active site of the ribosome is a ribozyme. It’s also highly conserved. This is exactly what is expected from the hypothesis of RNA World.

    gpuccio: It has always been known that the ribosome is mainly an RNA structure, with many proteins playing some role.

    Ut Philosophus dixit, but it was Cech and Altman who won the Nobel Prize in 1989 for its discovery.

    Upright BiPed: A process has been posited as the precursor of another process that it bears no physical relationship to, containing singular features that are entirely absent in the proposed precursor.

    The posited precursor acts to store genetic information and also to catalyze chemical reactions, including the formation of peptides.

    Upright BiPed: Then, knowing that the physical processes involved in RNA templating do nothing whatsoever to resolve the singular issues associated with the translation of a dimensional semiotic code, what is the real impetus to keep repeating it?

    It’s a valid hypothesis consistent with the evidence.

    Upright BiPed: Are you yet able to unambiguously acknowledge that to translate D/RNA into proteins requires the discontinuity?

    Yes, we have already granted there is a “necessary discontinuity”, which is just a specific instance of irreducible complexity. There is no intrinsic barrier to the evolution of irreducible systems, so pointing out that the system is irreducible doesn’t mean it didn’t evolve. To determine that we have to look at the specifics. The fact that ribosomes are ribozymes is empirical support for RNA World.

    EugeneS: You appear to believe that repeating some sciency word combinations will help you resolve the gigantic challenge naturalism is facing at the origin of life.

    Not at all. The origin of life is still a great mystery. Our objection is to the argument that genetic translation is an intrinsic barrier to evolution.

  172. 172
    Mung says:

    Carpathian:

    Our side provides the questions and your side provides the insults.

    I agree with you that we could all do without the insults. You could do your part by not insulting our intelligence.

    Deal?

  173. 173
    Mung says:

    Zachriel: Self-replication does not require von Neumann architecture.

    Yes it does. Else there’s no self to replicate.

  174. 174
    Box says:

    Zachs: There is no intrinsic barrier to the evolution of irreducible systems, so pointing out that the system is irreducible doesn’t mean it didn’t evolve. To determine that we have to look at the specifics.

    Let’s do that. Can you describe a step-by-step evolution of genetic translation?

    Allow me to set up the first line for you:

    1. RNA in a membrane.
    2. …

  175. 175
    Mung says:

    We should at least give Zachriel credit for showing up for the party. 🙂

    A toast to Zachriel.

  176. 176
    gpuccio says:

    Zachriel:

    Great master of elusion!

    “The extant genetic code is posited to have evolved from a simpler relationships, in particular, sequences of RNA that directly catalyzed the formation of peptides.”

    Posited. I like your verbal creativity. 🙂

    “Not sure what this means. RNA produced proteins. They still do.”

    Not sure what I mean? I will explain it again:

    I wrote:

    And the information which produced rybozymes has to be found again, if the function has to be assumed by proteins, for the reasons I have already stated.

    That means:

    If you have a rybozime A which catalyzes reaction a, and then in some future you have protein B which catalyzes reaction a (which is more or less what must have happened according to your view, because in the RNA world RNA was the effector molecule, but in today’s world, with very rare exceptions, like the ribosome, almost all reactions are catalyzed by proteins),

    then:

    The information for the sequence of nucleotides for rybozime A

    and

    The symbolic information in the sequence of nucleotides which guides the synthesis of protein B (either in DNA or RNA)

    have no relationship one with the other.

    Therefore, from an informational point of view, they must be “discovered” independently.

    IOWs, all the information in your RNA being, which codes for rybozimes, is completely useless to define the proteins that, in the new protein based being, will take the place of the “old” rybozimes.

    Is it clear now?

    And please, don’t go on repeating this new trivial gospel: “RNA produced proteins.” It’s simply not true. Proteins, as far as we know, are “produced”, and always were, using symbolic stored information in the protein coding genes in DNA, transcribed by messenger RNA, and translated by a very complex apparatus which includes, at least, the ribosome (with its RNA and proteins), the tRNAs, and above all the 20 aa-tRNA synthetases, which are the real part of the system were the genetic code is written.

    You say:

    “No one knows exactly how it happened, but the hypothesis is that RNA used DNA to store information in a more stable form. Eventually, DNA became the main storage of information.”

    But that is not any answer to what I wrote, which was:

    The point remains, the information (in nucleotide sequence) to effect a function by RNA has nothing to do with the information (in nucleotide sequence) to effect the same function by a protein, coded by the genetic code.

    IOWs, the same point I have re-explained here. IOWs, I have never discussed the problem of how the genetic information was transferred from RNA to DNA (that is a problem too, but certainly not the biggest one). My point, instead, is that the genetic information in RNA for rybozimes is completely different, and unrelated, to the symbolic genetic information in RNA or DNA to produce a protein, even if the function of the rybozime and of the protein be the same.

    That’s why your theory “posits” an OOL where the information for rybozimes is magically found, and a re-OOL where the information for proteins is, again, magically found.

    Is that clear now? I confide in your intelligence, which has always been as great as your ability at elegant elusion.

  177. 177
    Mung says:

    Let’s start out with some basic biological facts, since Zachriel likes facts. Darwinian evolution requires two separate and distinct entities, the genotype and the phenotype.

    Reproduction involves not just the copying of the genotype, but also the construction of the phenotype.

    Enter von Neumann.

  178. 178
    Mung says:

    Carpathian:

    What I do is discard some cards and get new ones.

    That’s evolution at its simplest.

    LoL!

    Evolution is playing the hand you’re dealt.

    Why on earth would you want to discard cards and get new ones? Whatever reason you can come up with, it’s not evolution.

    Please stop insulting our intelligence. It just incites people to insult you back. But if that’s what you’re looking for …

  179. 179

    Upright BiPed: Then, knowing that the physical processes involved in RNA templating do nothing whatsoever to resolve the singular issues associated with the translation of a dimensional semiotic code, what is the real impetus to keep repeating it?

    Zach: It’s a valid hypothesis consistent with the evidence.

    Even though you agree that one process provides no evidence of the other, it’s consistent.

    Good to know.

  180. 180
    Mung says:

    Zachriel: The extant genetic code is posited to have evolved from a simpler relationships code

    Fixed it for you. How does that help your position? It certainly doesn’t rebut gpuccio’s argument in the slightest.

  181. 181
    Barry Arrington says:

    Notice to all UD contributors:

    As long as Caprathian can come up with inane metaphors for evolution, he will be impervious to evidence and logic. And his supply of inane metaphors is apparently inexhaustible.

  182. 182
    Mung says:

    Zachriel: Our objection is to the argument that genetic translation is an intrinsic barrier to evolution.

    Well, that’s not the argument. So you can stop objecting. 🙂

    Genetic translation is not a barrier to biological (Darwinian) evolution, but a prerequisite for it.

  183. 183

    Upright BiPed: Are you yet able to unambiguously acknowledge that to translate D/RNA into proteins requires the discontinuity?

    Zach: Yes, we have already granted there is a “necessary discontinuity”

    .

    Then the diagram at the top of this page, illustrating that a physicochemical discontinuity is required for translation; required for the genome to exist; required to organize the heterogeneous cell, is accurate.

  184. 184

    There is no intrinsic barrier to the evolution of irreducible systems, so pointing out that the system is irreducible doesn’t mean it didn’t evolve.

    The irreducible structure in question is the singular physical condition that allows nucleotides to be translated into amino acids. It is the physical prerequisite of Darwinian evolution. It is indeed intrinsic.

  185. 185
    Zachriel says:

    Mung: Yes it does. Else there’s no self to replicate.

    Template reproduction is a counterexample to your claim.

    gpuccio: Posited. I like your verbal creativity.

    posit, transitive verb, assume as a fact; put forward as a basis of argument.

    gpuccio: If you have a rybozime A which catalyzes reaction a, and then in some future you have protein B which catalyzes reaction a

    Rather you have ribozyme A which catalyzes the production of a peptide, then in some future you have a ribozyme which still catalyzes the production of the peptide. The balance of your comment reflects this misunderstanding.

    Mung: Darwinian evolution requires two separate and distinct entities, the genotype and the phenotype.

    No. Darwinian evolution only requires reproduction. If a single molecule can replicate, then it is subject to darwinian evolution.

    Upright BiPed: Even though you agree that one process provides no evidence of the other, it’s consistent.

    No. Not having an “engineered RNA ‘template-replicator’ resulting in translation” doesn’t mean there isn’t any evidence. One line of evidence is that RNA can act to both store genetic information and to catalyze chemical reactions. Another line of evidence is that ribosomes are ribozymes.

    Upright BiPed: Then the diagram at the top of this page, illustrating that a physicochemical discontinuity is required for translation; required for the genome to exist; required to organize the heterogeneous cell, is accurate.

    Glad we agree. However, there is nothing that prevents a priori such a system from evolving from a simpler system.

    Upright BiPed: The irreducible structure in question is the singular physical condition that allows nucleotides to be translated into amino acids. It is the physical prerequisite of Darwinian evolution. It is indeed intrinsic.

    No. Darwinian evolution only requires reproduction. If a single molecule can replicate, then it is subject to darwinian evolution.

    RNA World could have evolved the use of peptides to extend their capabilities, while later on DNA may have coopted the replication mechanism, perhaps virally.

    For an overview, see Takeuchi et al., On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems, PLOS 2011.

  186. 186
    Virgil Cain says:

    Zachriel:

    Darwinian evolution only requires reproduction.

    And Spiegelman’s monster says tat Darwinian evolution would produce more simple replicators starting with complex replicators.

    If a single molecule can replicate, then it is subject to darwinian evolution.

    Nothing new ever evolves, though.

  187. 187
    Steve says:

    Zachriel,

    Your comment below reflects your misunderstanding of evolution.

    It is not reproduction per se that evolution only requires.

    Random variation and selection require excess reproduction. It is excess reproduction which drives variation and selection.

    So by your very admission, variation and selection are sub-components in a system which is driven by excess reproduction, said excess reproduction not definable by neo-darwinian evolutionary concepts.

    Excess reproduction is costlier that one to one replication. Further, excess reproduction infers foresight- that to survive in the long term, one-off reproduction won’t cut it.

    By neo-darwinian accounts, the first multi-cellular organisms most certainly started off with one-to-one reproduction. But one-to-one reproduction would never give these multi-cellular organisms the opportunity to transform from one-off reproduction to excess reproduction.

    This is a clear barrier to neo-darwinian evolutionary concepts.

    No. Darwinian evolution only requires reproduction. If a single molecule can replicate, then it is subject to darwinian evolution.

    RNA World could have evolved the use of peptides to extend their capabilities, while later on DNA may have coopted the replication mechanism, perhaps virally.

    For an overview, see Takeuchi et al., On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems, PLOS 2011.

  188. 188
    Zachriel says:

    Steve: This is a clear barrier to neo-darwinian evolutionary concepts.

    Steve: design deniers never talk about excess reproduction

    Darwin, Origin of Species 1859: Every being, which during its natural lifetime produces several eggs or seeds, must suffer destruction during some period of its life, and during some season or occasional year, otherwise, on the principle of geometrical increase, its numbers would quickly become so inordinately great that no country could support the product. Hence, as more individuals are produced than can possibly survive, there must in every case be a struggle for existence, either one individual with another of the same species, or with the individuals of distinct species, or with the physical conditions of life.

  189. 189
    gpuccio says:

    Zachriel:

    “Rather you have ribozyme A which catalyzes the production of a peptide, then in some future you have a ribozyme which still catalyzes the production of the peptide. The balance of your comment reflects this misunderstanding.”

    Do you mean that your RNA world is an RNA-protein world? Where everything is done by proteins, except protein synthesis? IOWs, the only functions of rybozimes would be protein synthesis?

    So, in your first beings, there is only the ribosome, and maybe an RNA substitute of the 20 aa-tRNA synthetases (let’s say 20 aa-tRNA rybozimes), and all the rest of your RNA is just a symbolic template for proteins, and proteins do everything?

    IOWs, your FUCA is just the same as our prokaryotes, only with RNA instead of DNA? And the genetic code and the translation apparatus already there, well functioning? Do you realize what you are suggesting?

    You are suggesting an RNA world which is completely useless to explain anything, because its functional complexity is exactly the same as the functional complexity in a DNA-RNA-protein world (is it really a problem to add DNA, at this point?).

    So, maybe that sooner or later you will agree with me: that LUCA was FUCA, and was essentially a DNA-RNA-protein being (IOWs, the only type of autonomous living being ever observed)?

    Maybe be that sooner or later science can go back to being empirical, and based on observed facts?

  190. 190
    Mung says:

    gpuccio: is it really a problem to add DNA, at this point?

    It is. Don’t let him skate on that point either.

    Where is the evidence for double-stranded helices of RNA? Does any exist?

    And yet that is vital for copying DNA.

  191. 191

    I’m just now returning. Give me a chance to read and catch up.

  192. 192
    Mung says:

    You have a life apart from Biosemiosis dot org? That’s not a good sign.

  193. 193
    Andre says:

    Zachriel

    No. Darwinian evolution only requires reproduction. If a single molecule can replicate, then it is subject to darwinian evolution.

    So tell us sugar plum, where information comes from? The input machinery comes from? The encoding machinery comes from? The networking systems? Protocols? The decoding machinery. The output machinery? The error correction machinery? The integrity check systems?

    You can’t have one or the other, you can’t have incremental steps you can’t have step by step…. you have to have everything in place at absolutely the same time! Without it there is no replication!

  194. 194

    Zachriel,

    Upright BiPed: Even though you agree that one process provides no evidence of the other, it’s consistent.

    Zach: No. Not having an “engineered RNA ‘template-replicator’ resulting in translation” doesn’t mean there isn’t any evidence.

    No one has demonstrated any evidence that an RNA “template-replicator” results in translation. Like i said, “one process provides no evidence of the other”, and you agreed.

    Upright BiPed: Then the diagram at the top of this page, illustrating that a physicochemical discontinuity is required for translation; required for the genome to exist; required to organize the heterogeneous cell, is accurate.

    Zach: Glad we agree. However, there is nothing that prevents a priori such a system from evolving from a simpler system.

    Good to know. We agree that a physicochemical discontinuity is required for translation, for the genome to exist, and for the organization of the heterogeneous cell.

    Upright BiPed: The irreducible structure in question is the singular physical condition that allows nucleotides to be translated into amino acids. It is the physical prerequisite of Darwinian evolution. It is indeed intrinsic.

    No. Darwinian evolution only requires reproduction. If a single molecule can replicate, then it is subject to darwinian evolution.

    It’s silly to suggest that all Darwinian evolution requires is reproduction. OoL researchers have already engineered “template replicators” that weren’t capable of Darwinian evolution – and they’ve clearly said so.

    I have a question for you:

    You’ve moved RNA-specified production of protein into your RNA world, yet when asked where the information resides to specify the ordering of those amino acids, you gave an unclear answer, suggesting in “sequences of RNA that directly catalyzed the formation of peptides”.

    Are you actually suggesting that to form a peptide of say 200 monomers (which is less half the length of any extant aaRS the system would need to produce in order to make the transition to a DNA-Protein world) the structure of the RNA catalyst itself establishes the order of those amino acids?

    And if you are not saying that (as outlandish as it is) then you’ve gained absolutely nothing in regards to perceived “simplicity”, and everything in the observations made here remains in full effect.

  195. 195
    gpuccio says:

    Zachriel:

    From Wikipedia (emphasis mine):

    “RNA can also act as a hereditary molecule, which encouraged Walter Gilbert to propose that in the distant past, the cell used RNA as both the genetic material and the structural and catalytic molecule rather than dividing these functions between DNA and protein as they are today; this hypothesis is known as the “RNA world hypothesis” of the origin of life.”

    Structural and catalytic molecule. Therefore, the point seems to be that, in the RNA world hypothesis, RNA molecules did the things that after became the task of proteins.

    That was exactly my point.

  196. 196
    gpuccio says:

    Zachriel:

    And let’s not forget the energy requirements, which are the reason why “metabolism first” theories, bizarre as they are, have gained importance over “RNA first” theories.

    Again from Wikipedia:

    “Energy Used for Protein Synthesis:

    One GTP is hydrolysed to GDP as each successive amino acid-tRNA complex attaches to the A site of the ribosome. A second GTP is broken down to GDP as the ribosome moves to each new codon in the mRNA. One ATP is hydrolysed to AMP during amino acid activation. Thus, the formation of each peptide bond uses 3 high-energy molecules, one ATP and two GTP.”

    So, what took care of metabolism, ATP and GTP generation for example, in your RNA world? RNA? Proteins?

  197. 197
    EugeneS says:

    Carpathian #169,

    “What I do is discard some cards and get new ones. That’s evolution at its simplest.”

    Emphasis mine. Note again, it is you who chooses new cards. Evolution has no means to choose for a future function. You have a strategy in mind. Evolution does not. You have a heuristic for winning based on your experience, if you’re a good player. Evolution does not.

    Evolution chooses only from among existing functions, it never chooses for a future function. This is where the great divide is between you, an intelligent player, and evolution, a dumb ‘player’.

    A blind unintelligent watchmaker is no watchmaker. This is where all evolutionists make a leap of faith without any empirical warrant. Evolution is no substitute for intelligence, planning or forethought. Evolution accounts for noise around existing functions and can at best drive a system back to an existing attractor. It has no means for creating genuine novelty.

  198. 198
    gpuccio says:

    Zachriel:

    Just a personal note. When I credited you with “verbal creativity” about “posit”, I did not mean to imply that you had made it up. I was simply praising your ability in choosing rare words in a specific context, for a purpose.

    Indeed, “posits” sounds a lot better than “assumes”, or “imagines”, or “fantasizes”. I appreciate your choice.

  199. 199
    Andre says:

    What does posit mean?

    posit
    ?p?z?t/
    verb
    verb: posit; 3rd person present: posits; past tense: posited; past participle: posited; gerund or present participle: positing

    1.
    put forward as fact or as a basis for argument.
    “the Confucian view posits a perfectible human nature”
    synonyms: postulate, put forward, advance, propound, submit, predicate, hypothesize, take as a hypothesis, set forth, propose, pose, assert; More
    presuppose, assume, presume
    “there are those who posit a purely biological basis for this phenomenon”
    base something on the truth of (a particular assumption).
    “these plots are posited on a false premise about women’s nature as inferior”
    2.
    put in position; place.
    “the Professor posits Cohen in his second category of poets”

    nounPhilosophy
    noun: posit; plural noun: posits

    1.
    a statement which is made on the assumption that it will prove to be true.

    Ahhhh so Zachriel has absolutely nothing. No evidence, just hoping his assumptions will be proven one day.

  200. 200
    Virgil Cain says:

    Yes, whenever an evo says “posit” they are actually dePOSITing another promissory note. 😉

  201. 201
    kairosfocus says:

    Z, that knocking at your door is a delegation of ghosts inquiring about the status of the vera causa principle. Newton and Lyell were looking particularly sad and Darwin, a bit sheepish. KF

  202. 202
    Box says:

    Upright Biped: I hope you will find the meeting of our two views in the writing I have presented.

    In my philosophy the material world symbolizes the mental world. In other words, when we look at the material world we see mental phenomena symbolized by matter.

    Well that’s very interesting Box, so do tell us, which mental phenomena are symbolized by semiotics and specifically protein production?

    I will attempt to answer that question in a moment. First some preliminary thoughts:

    (1) Translation is information transfer through contexts.

    The essence of translation is the transfer of information (meaning) from one context to another context. We can see the two separate contexts in UB’s example of a music box. Here the information resides in the spatial context of the cylinder and is transferred to another context of sounds.
    If I understand things correctly we can also see two separate contexts, neatly separated by (double) membranes, in the case of protein production. Here information is transferred from the context of the cell nucleus to the context of cytoplasm — DNA resides in the nucleus and ribosomes reside in the cytoplasm.
    – Note, with respect to symbolism, that the nucleus resides inside the cytoplasm; therefore we can envision the nucleus symbolizing the “inner world” and the cytoplasm the “outer world”.

    (2) Information relevant to one context only.

    There are two separate contexts, however the information that is being transferred is only functional in one context. In other words, the information is about one context only. In the case of the music box, the information that resides in the rotating cylinder has no function in the separate context of the rotating cylinder. Obviously it is only functional in the context of sound.

    Upright Biped: This third material condition is the preservation of the natural discontinuity that exists between the arrangement of a representation and its post-translation effect. Representations and their effects are physicochemically discontinuous; meaning that the effects of translation are not determined by the dynamic properties of the representation being translated. This is to say, the representation evokes the effect to happen, but does not determine what the effect will be.

    The discontinuity UB mentions is guaranteed by the discontinuity between the two contexts.

    Okay, how about answering our question?

    I’ll give you the short version:
    The nucleus symbolizes the “inner world” and DNA symbolizes thoughts about the “outer world” (cytoplasm) — non-functional thoughts in the context of the inner world by definition. Nucleotides are “letters”, codons are “words” and combinations of codons are “sentences/ideas about the outer world”. These “ideas” are then transferred to the outer world (cytoplasm) and transformed (translated) into functional objects/ideas.

  203. 203
    Virgil Cain says:

    Prokaryotes do not have a nucleus and still engage in transcription and translation.

    The symbols are the mRNA codons which represent amino acids, they do not become them via some physicochemical process.

    Source code in (mRNA codons) and object code out (polypeptide that folds/ gets folded into a functioning protein). It’s almost as if we got our idea for a computer program compiler from ribosomes.

  204. 204
    Zachriel says:

    gpuccio: Do you mean that your RNA world is an RNA-protein world?

    RNA World would obviously have evolved over time. RNAs catalyze. RNAs synthesize proteins. Proteins catalyze.

    gpuccio: Where everything is done by proteins, except protein synthesis?

    No. RNAs catalyze, including their own replication. But this process would be aided by increasingly complex protein networks.

    gpuccio: your FUCA is just the same as our prokaryotes, only with RNA instead of DNA?

    No. RNA within a protein complex is derived. Prokaryotes are highly derived. The first universal common ancestor may have been a simple replicator in a primitive membrane of some sort.

    gpuccio: And the genetic code and the translation apparatus already there, well functioning?

    The genetic code would have evolved from simpler associations.

    Mung: Where is the evidence for double-stranded helices of RNA?

    https://en.wikipedia.org/wiki/Double-stranded_RNA_viruses

    Zachriel: If a single molecule can replicate, then it is subject to darwinian evolution.

    Andre: where information comes from?

    It comes from mutation and selection.

    Upright BiPed: No one has demonstrated any evidence that an RNA “template-replicator” results in translation.

    While no one knows how translation evolved, there is evidence of a historical process, including the evidence from the ribosome, as already noted.

    Upright BiPed: We agree that a physicochemical discontinuity is required for translation,

    Yes.

    Upright BiPed: for the genome to exist,

    No.

    Upright BiPed: and for the organization of the heterogeneous cell.

    A replicator within a lipid membrane is heterogeneous, but the formation doesn’t entail any discontinuity.

    Upright BiPed: OoL researchers have already engineered “template replicators” that weren’t capable of Darwinian evolution – and they’ve clearly said so.

    Darwinian evolution requires a replicator subject to variation and competing for limited resources, such as in Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014: “The enzyme also can cross-replicate with a partner enzyme, resulting in their mutual exponential growth and enabling self-sustained Darwinian evolution.”

    Upright BiPed: You’ve moved RNA-specified production of protein into your RNA world, yet when asked where the information resides to specify the ordering of those amino acids, you gave an unclear answer, suggesting in “sequences of RNA that directly catalyzed the formation of peptides”.

    RNAs are catalysts. When RNA catalyzes peptides and those peptides aid the primordial cell, then those cells are subject to selection and tend to predominate the population.

    Upright BiPed: Are you actually suggesting that to form a peptide of say 200 monomers (which is less half the length of any extant aaRS the system would need to produce in order to make the transition to a DNA-Protein world) the structure of the RNA catalyst itself establishes the order of those amino acids?

    Presumably, short peptides were formed first.

    gpuccio: Structural and catalytic molecule. Therefore, the point seems to be that, in the RNA world hypothesis, RNA molecules did the things that after became the task of proteins.

    Sure, but in their own way, originally as aids, then eventually replacing many of the old structures.

    gpuccio: So, what took care of metabolism, ATP and GTP generation for example, in your RNA world?

    Early metabolism may have been fueled by natural proton gradients. No one knows at this point, of course. But there doesn’t seem to be any intrinsic barrier.

  205. 205
    Virgil Cain says:

    Darwinian evolution requires a replicator subject to variation and competing for limited resources, such as in Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014: “The enzyme also can cross-replicate with a partner enzyme, resulting in their mutual exponential growth and enabling self-sustained Darwinian evolution.”

    But no new functions evolved and Spiegelman’s monster applies.

  206. 206
    gpuccio says:

    Zachriel:

    OK, you have recited your catechism.

    The credibility of it, and how much it is supported by facts, are under the eyes of everyone, and everyone will judge for himself.

    However, thank you for your compliance. 🙂

  207. 207
    Zachriel says:

    gpuccio: The credibility of it, and how much it is supported by facts, are under the eyes of everyone, and everyone will judge for himself.

    The claim is that translation could not evolve because of a “necessary discontinuity”. Starting with a simple RNA replicator, and the synthesis of simple peptides, a translation system could plausibly evolve. Whether this happened or not, no one knows at this point, but it is sufficient to show how such a system could evolve.

  208. 208
    Virgil Cain says:

    Zachriel gets it wrong again:

    The claim is that translation could not evolve because of a “necessary discontinuity”

    The claim is that translation could not evolve via physicochemical processes because of a “necessary discontinuity”. And because no one knows how to model such a thing nor what it predicts.

    Starting with a simple RNA replicator

    You need to produce one via physicochemical processes. One that is capable of function adding and changing evolution.

    and the synthesis of simple peptides, a translation system could plausibly evolve.

    That isn’t evidence and it isn’t an argument.

  209. 209
    EugeneS says:

    Zachriel,

    “a translation system could plausibly evolve.”

    How can rate-dependent processes (i.e. physics/chemistry of the particles of matter) result in the formation of rate-independent representations/symbols/encodings?

    The hypothetical chemical evolution could not have caused the rise of representations because the discontinuity is degeneracy with respect to the chemical laws of nature. The chemistry is therefore completely irrelevant to the formation of this discontinuity. So chemistry cannot be the driver behind the formation of symbolic representations. It is the other way around. The discontinuity is the necessary condition of information processing that utilizes chemistry.

  210. 210
    Zachriel says:

    EugeneS: How can rate-dependent processes (i.e. physics/chemistry of the particles of matter) result in the formation of rate-independent representations/symbols/encodings?

    Hermann Joseph Muller (1918): “… thus a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former.”

  211. 211
    Virgil Cain says:

    Why does Zachriel continue to site someone that does not support the claim that drift and natural selection can produce IC as if it does?

    Hermann Joseph Muller was ignorant of the IC molecular machinery. He was ignorant of the structure of DNA and he was ignorant of the genetic code.

    Only Zachriel would think that ignorance is an argument.

  212. 212
    Zachriel says:

    EugeneS: How can rate-dependent processes (i.e. physics/chemistry of the particles of matter) result in the formation of rate-independent representations/symbols/encodings?

    Evolution can only precede by selectable steps, so intermediates couldn’t have evolved with the goal of creating a translation system, but only for current function. Here is one plausible model of how it might have happened:

    Wolf & Koonin, On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization, Biology Direct 2007:

    The proposed scenario for the evolution of translation consists of the following steps:

    binding of amino acids to a ribozyme resulting in an enhancement of its catalytic activity;

    evolution of the amino-acid-stimulated ribozyme into a peptide ligase (predecessor of the large ribosomal subunit) yielding, initially, a unique peptide activating the original ribozyme and, possibly, other ribozymes in the ensemble;

    evolution of self-charging proto-tRNAs that were selected, initially, for accumulation of amino acids, and subsequently, for delivery of amino acids to the peptide ligase;

    joining of the peptide ligase with a distinct RNA molecule (predecessor of the small ribosomal subunit) carrying a built-in template for more efficient, complementary binding of charged proto-tRNAs;

    evolution of the ability of the peptide ligase to assemble peptides using exogenous RNAs as template for complementary binding of charged proteo-tRNAs, yielding peptides with the potential to activate different ribozymes;

    evolution of the translocation function of the protoribosome leading to the production of increasingly longer peptides (the first proteins), i.e., the origin of translation.

  213. 213

    The ribozyme is now the genome.

    Like I said, Zach, no one can take away your faith. And no one can falsify any conception you wish to propose from that faith.

  214. 214
    Andre says:

    Let me try

    Zachriel what is an encoder without a decoder?

  215. 215
    Zachriel says:

    Upright BiPed: The ribozyme is now the genome.

    In RNA World, RNA acted both to store genetic information and to catalyze chemical reactions. An entailment of this theory is that RNA could catalyze its own replication, which has now been demonstrated.

  216. 216
    Zachriel says:

    Andre: what is an encoder without a decoder?

    We’ve already agreed that the current translation system is irreducible.

  217. 217
    Andre says:

    And do you know what that means Zachriel?

  218. 218
    Zachriel says:

    Andre: And do you know what that means Zachriel?

    Sure. Irreducible means that you can’t remove a part without the system failing, like an arch.

  219. 219
    Andre says:

    And if you can’t remove parts Zachriel what does that mean?

  220. 220
    gpuccio says:

    Zachriel:

    “The claim is that translation could not evolve because of a “necessary discontinuity”.”

    No. The claim is that semiotic systems include a necessary discontinuity, and that they are always the result of conscious design. Which is empirically verified.

    “Starting with a simple RNA replicator, and the synthesis of simple peptides, a translation system could plausibly evolve.”

    Plausibly for you and for your vivid imagination. Completely implausible at all empirical levels and with all that we know and observe.

    “Whether this happened or not, no one knows at this point,”

    In empirical science , we infer from observed facts and good methodology. We don’t simply say: “no one knows at this point”.

    “but it is sufficient to show how such a system could evolve.”

    Maybe a simple generic statement about logical (not empirical) possibility is sufficient for you (and your vivid imagination). It is certainly not sufficient for people who want to make good scientific inferences, and to understand reality from observed facts and correct methodology.

  221. 221
    gpuccio says:

    UB:

    “Like I said, Zach, no one can take away your faith. And no one can falsify any conception you wish to propose from that faith”

    Sad but true.

  222. 222
    Phinehas says:

    The hypercredulity is absolutely staggering.

  223. 223
    Vy says:

    200+ comments thanks to the delusional ramblings of a mentally unstable individual? Wow!

    Zach, let go of those RNA strands you’re clutching at.

    Even your Darwine buddies know the RNA World is fiction:

    (i) RNA is too complex a molecule to have arisen prebiotically;
    (ii) RNA is inherently unstable;
    (iii) catalysis is a relatively rare property of long RNA sequences only; and
    (iv) the catalytic repertoire of RNA is too limited.

    The RNA world hypothesis has been criticized because of the belief that long RNA sequences are needed for catalytic activity, and for the enormous numbers of andomized sequences required to isolate catalytic and binding functions using in vitro selection. For example, the best ribozyme replicase created so far — able to replicate an impressive 95-nucleotide stretch of RNA — is ~190 nucleotides in length, far too long a sequence to have arisen through any conceivable process of random assembly. And typically 10,000,000,000,000-1,000,000,000,000,000 randomized RNA molecules are required as a starting point for the isolation of ribozymic and/or binding activity in in vitro selection experiments, completely divorced from the probable prebiotic situation. As Charles Carter, in a published review of our recent paper in Biology Direct, puts it:

    “I, for one, have never subscribed to this view of the origin of life, and I am by no means alone. The RNA world hypothesis is driven almost entirely by the flow of data from very high technology combinatorial libraries, whose relationship to the prebiotic world is anything but worthy of “unanimous support”. There are several serious problems associated with it, and I view it as little more than a popular fantasy

    10^14 – 10^16 is an awful lot of RNA molecules.

    I basically agree with Bernhardt. The RNA World scenario is bad as a scientific hypothesis: it is hardly falsifiable and is extremely difficult to verify due to a great number of holes in the most important parts. To wit, no one has achieved bona fide self-replication of RNA which is the cornerstone of the RNA World.

    As if that wasn’t bad enough for you Darwinists, the OOL wizards have got four insanity-stopping paradoxes (amongst others) to deal with when making their potions:

    We have failed in any continuous way to provide a recipe that gets from the simple molecules that we know were present on early Earth to RNA. There is a discontinuous model which has many pieces, many of which have experimental support, but we’re up against these three or four paradoxes, which you and I have talked about in the past. The first paradox is the tendency of organic matter to devolve and to give tar. If you can avoid that, you can start to try to assemble things that are not tarry, but then you encounter the water problem, which is related to the fact that every interesting bond that you want to make is unstable, thermodynamically, with respect to water. If you can solve that problem, you have the problem of entropy, that any of the building blocks are going to be present in a low concentration; therefore, to assemble a large number of those building blocks, you get a gene-like RNA — 100 nucleotides long — that fights entropy. And the fourth problem is that even if you can solve the entropy problem, you have a paradox that RNA enzymes, which are maybe catalytically active, are more likely to be active in the sense that destroys RNA rather than creates RNA.

    Like I’ve said before, abiogenesis (spontaneous generation aka chemical evolution) NEVER happened, it can NOT be demonstrated and will never be demonstrated. The only evidence for it exists in the min … er … 3 pound meats of the indoctrinated.

    Abiogenesis is worse than fiction, it’s a refuted hunch that has been resurrected by reality denialists. It, like evolution and secular science in general, is nothing but Norse mythology in a cheap tux.

  224. 224
    Zachriel says:

    gpuccio: The claim is that semiotic systems include a necessary discontinuity, and that they are always the result of conscious design.

    Do you mean semiotic systems are always the result of conscious design? Or you mean ‘systems include a necessary discontinuity’ are always the result of conscious design? If the former, there’s no reason to mention necessary discontinuity. If the latter, there’s no reason to mention semiotic system.

    Or do you mean only those semiotic systems that include a necessary discontinuity, excluding semiotic systems that do not include a necessary discontinuity?

    gpuccio: Completely implausible at all empirical levels and with all that we know and observe.

    What is implausible about Wolf & Koonin?

    gpuccio: In empirical science , we infer from observed facts and good methodology. We don’t simply say: “no one knows at this point”.

    When the observed facts don’t lead to supportable conclusions, then, of course, we say we don’t know.

    Vy: (i) RNA is too complex a molecule to have arisen prebiotically;

    A number of pathways in plausible abiotic conditions have been found.

    Vy: (iii) catalysis is a relatively rare property of long RNA sequences only; and

    RNA catalysis can be initiated with sequences as short as eighteen in length.

    Vy: (iv) the catalytic repertoire of RNA is too limited.

    RNA is at least capable of self-replication.

  225. 225
    Vy says:

    A number of pathways in plausible abiotic conditions have been found.

    Your Yoda Complex self-affirming authority may work with your imaginary multiple selves but I’m gonna require more than a harebrained assertion to believe anything from you.

    RNA catalysis can be initiated with sequences as short as eighteen in length.

    More Yoda Complex blabber.

    RNA is at least capable of self-replication.

    And a squashed piece of paper is “at least” capable of rolling. It doesn’t make it a ferrari.

    I see your selective blindness kept you from seeing the rest of the post. Bravo.

  226. 226
    Carpathian says:

    EugeneS:

    Carpathian: “What I do is discard some cards and get new ones. That’s evolution at its simplest.”
    EugeneS: Emphasis mine. Note again, it is you who chooses new cards. Evolution has no means to choose for a future function. You have a strategy in mind. Evolution does not. You have a heuristic for winning based on your experience, if you’re a good player. Evolution does not.

    This is a simple analogy, which leaves out many details.

    The card game is a metaphor for the environment.

    The discarded cards are a metaphor for genetic information that did not result in a positive impact on reproduction.

    The whole point of the simple analogy was to show that genetic change is incremental, not immediate.

    A better analogy is a free-market economy.

    A product that doesn’t sell stops being produced in large quantities or stops being produced at all.

    While company A produces sophisticated toys, company B markets a pet rock that no one, even its producers, could predict could be so successful.

    The product gets produced first and then either gets accepted or rejected by the market.

    As a metaphor, the market is the ecosystem a biological organism inhabits.

    No foresight is required for success in a marketplace as history can show, whether it’s pet rocks, Barbie or the Beatles.

    Now a question for you.

    A designer would have to see the future in order to know what kind of organism to configure.

    How does the designer foresee the future?

  227. 227
    Vy says:

    Carp, your analogies are horrible.

    First, choosing cards? Then free-market economy? Really?

  228. 228
    Andre says:

    Zachriel

    Are you OK buddy?

  229. 229
    Carpathian says:

    Mung:

    Please stop insulting our intelligence. It just incites people to insult you back. But if that’s what you’re looking for …

    What are you looking for, permission to insult me?

    What I’m looking for is a response that in some way addresses the comments I make.

    Do you have a response that would suggest evolution is all-at-once instead of incremental like an accumulating poker hand?

    Do you have a response that would suggest “Darwinism” is not like a free-market economy?

    Do you have some sort of reason for thinking that when I use analogies I really am giving a one-to-one description of reality?

  230. 230
    Vy says:

    Do you have a response that would suggest evolution is all-at-once instead of incremental like an accumulating poker hand?

    Zach also made this strange claim in another thread that made it sound like evolution knew what it was doing or that it had purpose. It does NOT.

    Do you have some sort of reason for thinking that when I use analogies I really am giving a one-to-one description of reality?

    It’s one thing to give an analogy. It’s another thing for that analogy to make sense anywhere outside your imagination, and considering the immaterial (e.g. thoughts, imagination, etc.) can NOT exist under a materialistic Darwinian worldview, you’ve got nothing.

  231. 231
    Carpathian says:

    Vy:

    Carp, your analogies are horrible.

    First, choosing cards? Then free-market economy? Really?

    A fifth-grader could understand my analogies.

    A fifth-grader would understand it was an analogy and not a description of reality.

    A fifth grade class could model “Darwinism” as a free-market economy and not believe that the experiment would involve live animals being born, reproducing and dying.

    Your frustration comes from not having a response to a very simple model of what is happening in the biological world.

    Do you believe that only products that don’t sell well get produced in large quantities?

    Do you believe that organisms that can’t reproduce should have the largest populations?

  232. 232
    Carpathian says:

    Vy:

    Carpathian: Do you have a response that would suggest evolution is all-at-once instead of incremental like an accumulating poker hand?

    Vy: Zach also made this strange claim in another thread that made it sound like evolution knew what it was doing or that it had purpose. It does NOT.

    Evolution does not have a purpose.

    That’s why it only can work in increments.

    The ID designer however, works all-at-once.

    How does he foresee the future to know what configuration to build?

  233. 233
    Vy says:

    A fifth-grader could understand my analogies.

    A fifth-grader would understand it was an analogy and not a description of reality.

    A fifth grade class could model “Darwinism” as a free-market economy and not believe that the experiment would involve live animals being born, reproducing and dying.

    Only someone with less mental capabilities than a 3rd-grader would make such baseless claims.

    Your frustration comes from not having a response to a very simple model of what is happening in the biological world.

    Keep your projected frustrations to yourself.

    Do you believe that only products that don’t sell well get produced in large quantities?

    Do you believe that organisms that can’t reproduce should have the largest populations?

    Case in point.

  234. 234
    Mung says:

    Carpathian:

    What I’m looking for is a response that in some way addresses the comments I make.

    We tried that, but you refused to share your source code. Not very scientific of you, imo.

  235. 235
    Carpathian says:

    Vy:

    Carpathian: Do you believe that only products that don’t sell well get produced in large quantities?

    Do you believe that organisms that can’t reproduce should have the largest populations?

    Vy: Case in point.

    What does this mean?

    That you agree that “Darwinism” can be modeled as a free-market economy?

    Your frustration comes from not having a response to a very simple model of what is happening in the biological world.

    Instead of commenting on the model, you try and shout me down.

    Show me how the model is unworkable.

    Then show me how the designer gets information about a future that hasn’t happened in order to know what kind of specific organism to design.

  236. 236
    Virgil Cain says:

    Zachriel:

    In RNA World,

    The world that never existed.

  237. 237
    Virgil Cain says:

    Carpathian:

    Evolution does not have a purpose.

    Directed evolution does have a purpose. And it works incrementally.

    The ID designer however, works all-at-once.

    No designer I know of does that. Rome wasn’t built in a day.

  238. 238
    Mung says:

    Zachriel: A replicator within a lipid membrane is heterogeneous, but the formation doesn’t entail any discontinuity.

    Like a ship in a bottle is heterogenous?

  239. 239

    UB: Are you actually suggesting that to form a peptide of say 200 monomers (which is less half the length of any extant aaRS that the system would need to produce in order to make the transition to a DNA-Protein world) the structure of the RNA catalyst itself establishes the order of those amino acids?

    Zach: Presumably, short peptides were formed first.

    Well, I already cut the number of monomers in known aaRS by half. Perhaps GP can jump in here and tell us what the shortest extant aaRS is on the planet, then you can tell us how much of that length is unnecessary. In any case, I looked some time ago and the shortest I saw was over 400 monomers. But the question remains, does the catalyst specify the order of the amino acids?

    UB: The ribozyme is now the genome.

    Zach: RNA acted both to store genetic information and to catalyze chemical reactions.

    So the ribozyme is now the genome?

  240. 240
    Carpathian says:

    Mung:

    We tried that, but you refused to share your source code. Not very scientific of you, imo.

    Both kairosfocus and I recognize your inexperience when it comes to software.

    In KF’s case, he explained to you that you didn’t understand how a layered communications protocol works.

    He didn’t need to see any source code from you.

    He correctly understood just from your comments that you didn’t understand the concept.

    I explained to you a simple algorithm and you insisted on source code, something an experienced programmer would never have asked for.

    When I was working on a software team, we would be assigned modules to write, with only the headers and return values defined for us.

    The team leader or project manager’s only requirements were that it was small, fast and stable.

    He assumed we would provide him with something that worked and satisfied the architecture he had mapped out.

    The last thing he wanted to do was look at code.

    That was our responsibility.

    Your problem was that you couldn’t think in terms of architecture instead of lines of code.

    That shows inexperience.

  241. 241
    Mung says:

    Zachriel: The genetic code would have evolved from [a] simpler associations [genetic code].

    Fixed it for you, again.

  242. 242
    Mung says:

    Zachriel: RNAs are catalysts. When RNA catalyzes peptides and those peptides aid the primordial cell, then those cells are subject to selection and tend to predominate the population.

    And now Zachriel has posited a cell out of thin air.

  243. 243
    Carpathian says:

    Virgil Cain:

    Directed evolution does have a purpose. And it works incrementally.

    That contradicts every ID argument concerning IC.

    It also weakens KF’s 500 bit limit argument.

    If instead of 500 bits we worked with 5 bits at a time, his 500 bit FSCI limit is irrelevant.

  244. 244
    Mung says:

    Zachriel: Early metabolism may have been fueled by natural proton gradients.

    Proton gradients across the imaginary cell membrane?

  245. 245
    Mung says:

    Wow, now there’s an add on this page for harnessing the power of protein, lol. Too funny.

  246. 246
    Vy says:

    Your frustration comes from not having a response to a very simple model of what is happening in the biological world.

    Carry on with the nonsensical projections.

    Instead of commenting on the model, you try and shout me down.

    Better check with your resident random brain reactions doctor, you’re going overboard.

    Show me how the model is unworkable

    Sorry but I don’t deal in nonexistent Darwinian imaginary models.

    Then show me how the designer gets information about a future that hasn’t happened in order to know what kind of specific organism to design.

    You’re kidding, right?

    How does a programmer see into a future that hasn’t happened to know what specific software to design?

    If you can’t see the problem with that question then good luck.

  247. 247
    Mung says:

    Upright BiPed.

    I love how you are sticking with the issue of specification. Amino acid sequences are specified.

  248. 248
    Virgil Cain says:

    Carpathian:

    That contradicts every ID argument concerning IC.

    Only in your little-bitty mind.

  249. 249
    Carpathian says:

    Vy:

    Carpathian: How does a programmer see into a future that hasn’t happened to know what specific software to design?

    Vy: If you can’t see the problem with that question then good luck.

    Are you trying to equate a programmer with the ID designer?

    Do you honestly believe that those two scenarios are comparable?

    Your ID designer has to build multiple organisms for a future that is a century away and unknown, while a programmer writes code for a market driven product that needs to work better than their competitor’s toy for the coming Christmas season.

  250. 250
    Phinehas says:

    Carp:

    The problem with your analogies isn’t that they are not understandable. It is that all the work of the analogy is being done by the way it is different to reality.

    It’s a bit like natural selection. To the extent that it is natural, it isn’t selecting. And to the extent that selection is happening, it can’t be natural.

    Endlessly anthropomorphizing natural processes to sneak in the desperately needed intelligence won’t work for any but the least sophisticated or educated reader.

  251. 251
    Carpathian says:

    Virgil Cain:

    Only in your little-bitty mind.

    Very scientific.

  252. 252
    Vy says:

    Evolution is blindly selective randomness, no purpose, no capabilities, no path. It is in essence, useless.

    Even Atheist horseman-wannabe and pals know this:

    [Darwin’s] alternative to intelligent design was design by the completely mindless process of natural selection, according to which organisms possessing variations that enhance survival or reproduction replace those less suitably endowed, which therefore survive or reproduce in lesser degree. This process cannot have a goal, any more than erosion has the goal of forming canyons, for the future cannot cause material events in the present. Thus the concepts of goals or purposes have no place in biology (or any other of the natural sciences), except in studies of human behavior. (p. 282)

    . . . natural selection: it is a completely mindless process without forethought or goal. (p. 285)

    And, indeed, this is what I teach—that natural selection, and evolution in general, are material processes, blind, mindless, and purposeless.

    In case you missed it above, evolution is useless.

    If you still can’t see why you’re analogies only make sense in your 3 pound meat then you need help.

  253. 253
    Carpathian says:

    Phinehas:

    It’s a bit like natural selection. To the extent that it is natural, it isn’t selecting. And to the extent that selection is happening, it can’t be natural.

    But “natural selection” isn’t actually “selection” at all.

    It is a metaphor.

    What actually happens is that failures are eliminated .

    It is a metaphor, a metaphor, a metaphor…., a metaphor.

    No one selects .

    Just like a product that is not bought by customers in a market, organisms that can’t propagate their species, disappear.

  254. 254
    Mung says:

    : The Eighth Day of Creation: Makers of the Revolution in Biology
    : Horace Freeland Judson
    : p. 585

    The man who released the present-day understanding of molecular specificity in living processes was Frederick Sanger. His determination, beginning in the mid-forties, of the amino acid sequences of bovine insulin proved that they have no general periodicities. His methods and this surprising result had many consequences, of course: the most general and profound was that proteins are entirely and uniquely specified.

    Sydney Brenner remembered going to a talk Sanger gave at that time [1951] – the excitement, especially among the younger scientists, as they emerged. “At last, we knew what proteins were.” With that vanished any possibility of a general law, a physical or chemical rule, for their assembly. “With that, you absolutely needed a code,” Monod said.

    A similar transformation, at just the same time, was overtaking nucleic acids…The role that Sanger played for proteins was played for nucleic acids, but in a minor key, by Chargaff…[his] demolition of the tetranucleotide hypothesis by 1949 and 1950 released the possibility, and made it highly likely, that nucleic acids were specific in sequence too.

    The structure of DNA then made specificity comprehensible. “Nobody, absolutely nobody, until the day of the Watson-Crick structure, had thought that the specificity might be carried in this exceedingly simple way, by a sequence, by a code,” Delbruck said. “This was the greatest surprise for everyone.”

  255. 255
    Carpathian says:

    Vy:

    In case you missed it above, evolution is useless.

    Evolution is not “purpose-driven”.

    It is not “useless” since thanks to evolution, we are here debating it.

  256. 256
    Vy says:

    Are you trying to equate a programmer with the ID designer?

    And when someone gives you a somewhat analogical scenario, you start to blab about equation. Hmm.

    Do you honestly believe that those two scenarios are comparable?

    To you and your ilk? Hardly.
    To those who’ve cleared their brains of the fogma? Absolutely.

    Your ID designer . . .

    ID Designer? Talk about redundant.

    . . . has to build multiple organisms for a future that is a century away and unknown

    And this is impossible because . . . ?

    while a programmer writes code for a market driven product that needs to work better than their competitor’s toy for the coming Christmas season

    You haven’t met a lot of programmers, have you?

  257. 257
    Virgil Cain says:

    Carpathian- I have already explained it to you, several times. Designing agencies and telic processes can produce irreducible complexity in incremental steps if that is part of the plan. And usually plans require complex systems to be built from the bottom- up, incrementally.

    It case you missed it- directed evolution, ie Intelligently Designed evolution, is purposeful.

    Unguided evolution is useless and can’t explain anything beyond disease and deformities.

  258. 258
    Vy says:

    It is not “useless” since thanks to evolution, we are here debating it.

    Norse-mythologists tell the cow “thank you” too and just like the claims of Darwinists, it’s a harebrained assertion valid only in their respective bubble universes.

  259. 259
    Virgil Cain says:

    Carpathian:

    What actually happens is that failures are eliminated .

    And that is exactly why it is impotent with respect to IC. Thank you.

  260. 260
    Phinehas says:

    Carp:

    It is a metaphor.

    No one selects.

    You don’t have to tell me that. But “natural selection” without selection is just “natural.” And “natural” doesn’t explain anything. But we need to pretend we are explaining something, since there is the pesky appearance of design. So, we smuggle intelligence into our metaphors to make it seem reality is capable of what it isn’t. You’ve merely repeated this pattern with your poker analogy.

  261. 261
    kairosfocus says:

    Carpathian, you are fixated on troubles with brittle designs. Here, a sound design will be adaptable — exactly what is being irresponsibly extrapolated into body plan level macro evo, and increasingly evo before there was a reproducing life form. Reductio. KF

  262. 262
    Zachriel says:

    Vy: I’m gonna require more than … assertion

    Sure.

    Z: A number of pathways in plausible abiotic conditions have been found.

    See Powner et al., Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions, Nature 2009. Also, see Ferris, Montmorillonite-catalysed formation of RNA oligomers: the possible role of catalysis in the origins of life, Philosophical Transactions B 2006.

    Z: RNA catalysis can be initiated with sequences as short as eighteen in length.

    This study indicates that catalytic activity can occur in very short RNA polymers. Stadlbauer et al., Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides, Chemistry – A European Journal 2015.

    Vy: And a squashed piece of paper is “at least” capable of rolling. It doesn’t make it a ferrari.

    You said the repertoire of RNA was too limited, and while ribozymes are far more limited than protein enzymes, they are capable of several important functions, including replication.

    Vy: Zach also made this strange claim in another thread that made it sound like evolution knew what it was doing or that it had purpose.

    Quite the contrary. In fact, we just stated on this very thread @212 that evolution can only precede by selectable steps, so intermediates couldn’t have evolved with the goal of creating a translation system, but only for current function.

    Upright BiPed: So the ribozyme is now the genome?

    In RNA World, RNA acted both to store genetic information and to catalyze chemical reactions. An entailment of this theory is that RNA could catalyze its own replication, which has now been demonstrated.

    Mung: And now Zachriel has posited a cell out of thin air.

    Actually, cells are observable, and we have evidence that extant cells are descendants of a long line of cells through common descent.

  263. 263
    bFast says:

    Virgil Cain (257), “Designing agencies and telic processes can produce irreducible complexity in incremental steps if that is part of the plan.”

    I think that the whole premise behind IC is that IC cannot be developed in incremental steps. I guess it is possible to develop IC in incremental steps, as I develop computer software one keystroke at a time, but IC by its definition doesn’t begin to function until all of the steps are complete.

    If that is not the case, the IC can be developed via Darwinan means as well as via intelligent means.

  264. 264
    Virgil Cain says:

    Still no evidence for any RNA world. And still nothing that can get around Spiegelman’s monster.

    But Zachriel will never let the facts get in its way.

  265. 265
    Virgil Cain says:

    bFast:

    I think that the whole premise behind IC is that IC cannot be developed in incremental steps.

    And yet we do it all of the time.

    I guess it is possible to develop IC in incremental steps, as I develop computer software one keystroke at a time, but IC by its definition doesn’t begin to function until all of the steps are complete.

    Which is why physicochemical processes can’t produce it, unless you want to rely of sheer dumb luck. And the more complex the system the more luck you require. Ergo not science.

    If that is not the case, the IC can be developed via Darwinan means as well as via intelligent means.

    And Darwinian processes can produce computer codes? They can produce cars? Really?

  266. 266
    Zachriel says:

    bFast: If that is not the case, the IC can be developed via Darwinan means as well as via intelligent means.

    Irreducible structures can evolve, as has been explained @109.

  267. 267
    Virgil Cain says:

    Zachriel:

    Irreducible structures can evolve,

    By directed evolution, yes.

    as has been explained @109.

    Baldly asserted, not explained. And nothing to do with Darwinian evolution.

  268. 268
    Box says:

    Box: The essence of translation is the transfer of information (meaning) from one context to another context. (…) we can also see two separate contexts, neatly separated by (double) membranes, in the case of protein production. Here information is transferred from the context of the cell nucleus to the context of cytoplasm — DNA resides in the nucleus and ribosomes reside in the cytoplasm.

    Virgil Cain: Prokaryotes do not have a nucleus and still engage in transcription and translation.

    Prokaryotes represent a different way of being. Here contexts are vague, boundaries are blurred and, admittedly, aren’t helpful for my ‘two-contexts-concept’.

    Prokaryotes easily exchange genetic material with one another (calling into question the species concept for this group of organisms). In feeding, they are “dependent on the uptake of dissolved substance across their membrane,” secrete enzymes into the surrounding medium, and have, therefore, “external digestion.”

    [Craig Holdrege]

    Among archaea, Halobacterium volcanii forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another.[16] Another archaeon, Sulfolobus solfataricus, transfers DNA between cells by direct contact. Wiki

    However, I believe that what we see is a trend towards two contexts, that is, a first attempt of a division between “inner world” and “outer world”. For those interested I can recommend this short article by Craig Holdrege (PDF).

  269. 269
    EugeneS says:

    Carpathian,

    “No foresight is required for success in a marketplace”

    What?! Where did you read this?! Enterprise level businesses hire whole sales teams in order to study markets and predict the need for certain product features. A minimum of intelligence is required to produce at least something that is of competitive quality. Production, and competitive production especially, nowadays requires thorough planning and optimization of the production process. So competitive quality of products or services does require brains.

    I am amazed by your analogies. You, as well as other overly optimistic evolutionists, jump to conclusions from analogies that invariably involve intelligent actors. The critical bit that you oversee is decision making and planning. If you believe that markets somehow self-regulate, I can refer you to the “terrible 1990’s” in Russia (informal widely accepted term) when people in power were obsessed with applying crazy Darwinist ideas to economy. Russia nearly collapsed as a result.

    A designer must first conceive a design and then choose appropriate means to implement it. When I mean the design of the biosphere, I certainly mean God. I say that to avoid any ambiguity. What God and His distinguished creature, human, have in common, among other things, is intelligence.

    Intelligence is the capability of achieving set goals by planning, making appropriate decisions and using appropriate implementation means. Designs of quality are optimized, sometimes against more than one criteria (pareto-optimality). Intelligence have many extra niceties such as being able to tell designs from non-designs.

    Now, about foreseeing the future. If I design a certain thing, I need not be omniscient to achieve my goal. In this context, all I need to foresee is the possible outcomes at various stages. In other words, I need to have an understanding of logistics. E.g. Robinson Crusoe’s design of a boat failed because he had not foreseen the infeasibility of the logistical problem of transportation.

  270. 270
    Mung says:

    EugeneS: I am amazed by your analogies.

    They are like an apple falling off a tree and discovering Isaac Newton.

  271. 271

    Box, thank you for your 202

  272. 272

    UB: Are you actually suggesting that to form a peptide of say 200 monomers (which is less half the length of any extant aaRS that the system would need to produce in order to make the transition to a DNA-Protein world) the structure of the RNA catalyst itself establishes the order of those amino acids?

    Zach: Presumably, short peptides were formed first.

    UB: Well, I already cut the number of monomers in known aaRS by half. Perhaps GP can jump in here and tell us what the shortest extant aaRS is on the planet, then you can tell us how much of that length is unnecessary. In any case, I looked some time ago and the shortest I saw was over 400 monomers. But the question remains, does the catalyst specify the order of the amino acids?

    Zach: — s i l e n c e —

    UB: The ribozyme is now the genome.

    Zach: RNA acted both to store genetic information and to catalyze chemical reactions.

    UB: So the ribozyme is now the genome?

    Zach: RNA acted both to store genetic information and to catalyze chemical reactions.

    The information has to be somewhere Zach. But you are not going to answer. So be it.

  273. 273
    Alicia Cartelli says:

    While we’re speaking hypothetically, what about a ribozyme capable of using itself as a template for both replication and peptide bond formation?

  274. 274
    Virgil Cain says:

    Box, There very well could be a boundary in prokaryotes. For example, are the ribosomes outside of the ringed DNA? But OK, the “inner world” consists of transcription, one type of nucleotide sequence to another type and the “outer world” consists of translating that nucleotide sequence into a polypeptide. The DNA symbolizes the mRNA and the processed mRNA symbolize the amino acids.

    I just figured I would say something about prokaryotes before an opponent zeroed in on it.

  275. 275
    Virgil Cain says:

    Alicia Cartelli:

    While we’re speaking hypothetically, what about a ribozyme capable of using itself as a template for both replication and peptide bond formation?

    Does it sell popcorn at halftime? Do you think physicochemical processes can A) produce your ribozyme B) provide the raw materials to carry on and C) be capable of evolving new functions?

  276. 276
    gpuccio says:

    Zachriel:

    “Do you mean semiotic systems are always the result of conscious design? Or you mean ‘systems include a necessary discontinuity’ are always the result of conscious design? If the former, there’s no reason to mention necessary discontinuity. If the latter, there’s no reason to mention semiotic system.”

    In this discussion, in this context, and given the subject of this thread, I mean “semiotic systems” as defined by UB. That’s what we are discussing here. IOWs, semiotic systems which include a necessary discontinuity, and all the other features which UB describes.

    Like the genetic code with its translation apparatus.

    And they are always found to be the result of conscious design.

  277. 277
    gpuccio says:

    Alicia Cartelli:

    “While we’re speaking hypothetically, what about a ribozyme capable of using itself as a template for both replication and peptide bond formation?”

    Your question shows well what the problem is.

    Let’s say that we have rybozime A.

    Let’s say that its function is to replicate itself. IOWs, it is an RNA polymerase.

    Therefore, its nucleotide sequence will be dictated and constrained by the biochemical laws which govern the 3d folding of RNA and its biochemical activities.

    Now, let’s say that the same molecule also serves as a template for peptide bond formation, as you say.

    I suppose that what you mean is that the sequence of A can be used by some translation system, like a ribosome, to produce a peptide which is functional.

    OK, but then the sequence of nucleotides in A must be dictated and constrained by a completely different set of rules: the symbolic code which maps 3-nucleotide words to aminoacids, IOWs the genetic code, and the biochemical rules that govern the 3d folding and biochemical activities of an aminoacid sequence.

    Can you see the problem? I hope you can, because Zachriel apparently can’t.

    That’s what I mean when I say that the functional information in RNA effector molecules cannot be in any way related to the functional information in RNA or DNA which codes for protein effector molecules.

    That’s what I mean when I say that any functional information in the imaginary RNA world in no way could have been “passed” to the present DNA-RNA-protein world.

    That’s what I mean when I say that, if OOL generated an RNA world, then we need a new OOL (re-OOL) for the DNA-RNA-protein world.

    It’s already impossible, from all empirical points of view, to find the functional information for thousands of effector sequences once. It’s obviously “even more impossible” (if we can say so) to find that information twice.

  278. 278
    Mung says:

    Zachriel: What is implausible about Wolf & Koonin?

    Although the individual ribozyme-catalyzed reactions involved in the postulated scheme are feasible, the succession of multiple evolutionary steps that appear to be required for the emergence of translation might be legitimately viewed as far fetched, particularly, considering the inevitably inefficient ribozyme-mediated replication that must have been prevalent in the RNA World.

  279. 279
  280. 280
  281. 281
    Dionisio says:

    mike1962

    Interesting paper. Thank you for posting it.

    Here’s the same paper:

    http://www.biologydirect.com//content/2/1/14

  282. 282
    Alicia Cartelli says:

    Gpuccio, first, I would caution you against using terms such as “RNA polymerase” when talking about a hypothesized first living molecule. The RNA polymerases we see today are far more complex, specific, and precise than what is being proposed. The hypothesized ribozyme we are talking about simply has an active site that is capable of creating a phosphodiester bond between some type of NTP, at some level of efficiency and with some level of repeatability. While the 3D shape of the ribozyme will be dictated by folding of the RNA molecule, this is not to say that every nucleotide must be perfectly maintained; some will be much more important than others in preserving the shape of the active site, just as we see in protein. The main idea is that the molecule can copy itself with some degree of repeatability. What I proposed was that this active site is also capable of forming a peptide bond under certain conditions. These conditions change the active site in some way, or ion cofactors are made available, or a combination, who knows. Anyways, the active site is now capable of joining amino acids to some degree and the template that had been previously been used to make a new RNA strand is now used as a template for making a peptide strand. The 3-nucleotide code that we see today doesn’t even exist yet, so that goes out the window. The template-amino acid interaction is purely based on chemistry; certain amino acids will temporarily associate more tightly with certain nucleotide bases, which will result in the addition of amino acids based on their type. It may not always be the same amino acid that is added when one base is present in the catalytic site, but it will always be a relatively hydrophobic amino acid. And with a different base present in the catalytic site, it will always be a relatively hydrophilic amino acid that is added due to nucleotide-amino acid interactions again.

    Is there any research backing up this just so story of mine?
    Well, I mentioned some of it to Upright a while ago and he brushed it off, no surprise there. But yes, recent research has demonstrated that there is a chemical link between the amino acids added and the nucleotide sequences that code for them. In fact, 19 of the 20 common amino acids used by living organisms today demonstrate a polar/nonpolar (R-group), purine/pyrimidine (2nd nucleotide base) dichotomy. My understanding is that this is a chemical leftover of the system I have proposed or a relative of it. Also, research already mentioned above has shown that specific amino acids in a protein are not nearly as critical as their general properties; the vast majority of amino acids in the vast majority of proteins can be swapped with amino acids of similar chemical properties and there is little to no effect on protein function.

    So, as for “that’s what I mean when I say…” you simply don’t know what you are talking about and shouldn’t be saying anything. Especially when it comes to a topic as complex as this. You are just not equipped to do so.

  283. 283
    Mapou says:

    gpuccio,

    Thank you for carefully explaining the intractable (if you assume naturalism) discontinuity problem in going from a highly hypothetical (i.e., untestable) RNA world to a RNA/DNA protein synthesis world. It’ll be interesting to see how they squirm their way out of this one. They’re good at it.

    Edit: Oops! Too late. AC just replied before I did.

  284. 284
    Alicia Cartelli says:

    Yup, I’m squirming away!
    If the peanut gallery has anything intelligent to say though, I’m all ears.

    I won’t hold my breath.

  285. 285
    Andre says:

    Alicia

    The main idea is that the molecule can copy itself with some degree of repeatability. What I proposed was that this active site is also capable of forming a peptide bond under certain conditions.

    Do you have anything that verifies your idea? Anything to show with your proposal?

    I tried to find something to support what you said but Eugene Koonin kills your ideas and proposals dead in his paper…..

    http://www.ncbi.nlm.nih.gov/pm.....MC3293468/

  286. 286
    Andre says:

    Alicia

    If the peanut gallery has anything intelligent to say though, I’m all ears.

    Maybe you can help since you’re so smart……..

    If I have an encoder but no decoder what do I have?

  287. 287
    Andre says:

    Alicia, Zachriel Carpathian know the answer of course, I wonder if any of them will write to Eugene Koonin to correct him when he says;

    “Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.”

    Probably not……

  288. 288
    Alicia Cartelli says:

    I mentioned some research that supports what I have said, Andre.
    When you have something intelligent to say, I’ll respond.

    Go ahead, try to rebut my scenario, shouldn’t be too hard to do.

  289. 289
    Andre says:

    Alicia

    A link, as, Ive requested to the research that supports what you say would be invaluable, I’m not sure if you’ll take my word on something just like I’m unlikely to take your word for it, I prefer you to show me the supported paper.

    As for intelligence, did you know that; of The 10 smartest people on the planet 8 are theists and 6 are Christians, will you take my word for it or should I show you?

    Intelligent enough?

  290. 290
    gpuccio says:

    Alicia Cartelli:

    What can I say?

    As you say, I “don’t know what I am talking about and shouldn’t be saying anything”.

    You say all.

    “the vast majority of amino acids in the vast majority of proteins can be swapped with amino acids of similar chemical properties and there is little to no effect on protein function”

    That’s probably why a lot of aminoacid sequences are so conserved, even from prokaryotes to humans (see ATP synthase, and a lot of others. Histones, for example).

    Oh, I am sorry, I have said something. What a bad guy I am.

    I know the research you mention. It proves absolutely nothing. Except for the vivid imaginations of those who need to believe something according to their heart’s desire.

    In my unforgivable arrogance, I would even try to rebut your scenario. If it were a scenario, and not, as you say, a just so story, and not even a good one: RNA polymerases (yes, I am a repeat offender!) which spend their time (and the cell’s resources) generating random peptides, which certainly confer huge reproductive advantages and support the glorious march of neo darwinian natural selection to the glorious achievements of the genetic code and of LUCA complexities. A great scenario indeed.

    You see, “the peanut gallery”, of which I am a proud member, “has nothing intelligent to say”. Not to you, not according to your idea of intelligence. Your idea of intelligence and mine are probably very different.

    So, I leave you to your intelligent squirming. Thank you for the (not so kind) attention.

  291. 291
    gpuccio says:

    Mapou:

    Thank you for your comment at #283.

    And yes, you were too late! 🙂

  292. 292
    Andre says:

    Alicia

    Tell me

    peptide bond under certain conditions.

    Are you referring to prebiotic conditions here?

    Except you have some serious problems…..

    Molecular biologist’s dream” is a phrase coined by Gerald Joyce and Leslie Orgel to refer to the problem of emergence of self-replicating RNA molecules, as any movement towards an RNA world on a properly modelled prebiotic early Earth would have been continuously suppressed by destructive reactions. It was noted that many of the steps needed for the nucleotides formation do not proceed efficiently in prebiotic conditions. Joyce and Orgel specifically referred the molecular biologist’s dream to “a magic catalyst” that could “convert the activated nucleotides to a random ensemble of polynucleotide sequences, a subset of which had the ability to replicate”

    Aaahh so the average Darwinist, materialist, RNA-world punter, science denier, has to rely on magic to get this done……

    You have nothing……..

  293. 293
    gpuccio says:

    Mapou:

    At least, Wolf and Koonin are sincere:

    “The scenarios for the origin of the translation system and the genetic code outlined here are both sketchy and highly speculative. Why, then, bother building such conceptual,qualitative models at all? The justification for this kind of theorizing can be succinctly put in the short phrase: we have to get from there to here. There being the early, cooling earth with no complex organic molecules, and here being a minimally complex genetic system with modern type translation, transcription, and replication machineries, a system that would be subject to biological evolution much like modern organisms”

    Sketchy and highly speculative. That’s sincerity. Euphemistic sincerity, but sincerity just the same.

    Why, then, bother building such conceptual,qualitative models at all?

    They say it themselves:

    “We have to get from there to here”.

    And, I add:

    “We cannot even consider design explanations”.

    So, sketchy and highly speculative scenarios are all that is left.

  294. 294
    Dionisio says:

    gpuccio

    I think it’s time for you to tell your interlocutors exactly what Mina said: “parole, parole” 🙂

    BTW, your interlocutors have done something positive in this discussion: they have motivated you, UB, KF and others to write very insightful comments on the discussed subject, which has turned very hot, as it was expected.

    If your interlocutors have troubles understanding Mina’s Italian words, then tell them -as Paul McCartney told Michelle- the only words we know they’ll understand: where’s the beef?

    And you keep writing. Many are enjoying it!

    🙂

  295. 295
    kairosfocus says:

    Alicia:

    Wiktionary on peanut gallery:

    The phrase comes from nineteenth-century vaudeville theatres and refers to the cheap seats at the back of the theatre or in the upper balcony. It came to be applied to other venues as well, referring to the section where less-educated or less-seriously-interested patrons sat. The “peanut” comes from the popularity of that cheap snack in those sections, and the possibility that patrons might throw peanuts at the stage if displeased.

    In the mid-twentieth century, the “Howdy Doody Show” associated “peanut gallery” specifically with children.

    Noun

    peanut gallery ?(plural peanut galleries)

    (historical) In the nineteenth century, the cheap seats at the back of a theatre or in the upper balcony.[1]
    (historical) The upper balcony in racially segregated venues such as a theatre to which black patrons were restricted.[2] ?[quotations ?]
    (idiomatic) Any source of heckling, unwelcome commentary or criticism, especially from a know-it-all or of an inexpert nature. May also now refer to general audience response: “Let’s hear it from the peanut gallery.”

    Enough already from the peanut gallery; if you think you can do a better job, go right ahead.

    In short, arrogantly dismissive contempt and presumed base that we the Magisterium know, you are just ignorantly throwing peanuts from the cheap seats frequented by the ignorant and ill-bred.

    With all due respect, that about sums up the underlying presumptuous attitude of those who have taken science ideological captive to imposed a priori evolutionary materialism, and who usually refuse to soberly address its inescapable self-referential incoherence, amorality and undermining of the base of responsible rational freedom necessary for fact based reasoned discussion and prudent analysis.

    However, FYI, the relevant expertise here to address the credible origin of functionally specific, complex organisation and/or associated information [for short, FSCO/I] is not primarily biology or biochemistry etc, it is logic (and particularly on abductive inference to the best explanation) and it is information systems. Some knowledge of thermodynamics and its statistical underpinnings will be helpful.

    The essential point is that OOL is the root of the darwinist tree of life and/or its modern variations.

    And in that warm little pond or volcano vent or comet core or whatever environment du jour, the only relevant blind forces are physics, chemistry and particularly thermodynamice, in a context where the space of contingencies is beyond astronomical. That is a blind search soon runs into combinational explosion problems, readily seen from the number of possibilities for strings of at least 500 – 1,000 bits; i.e. 3.27*10^150 – 1.07*10^301, and doubling for each extra bit. Where, the principle highlighted by Orgel in 1973 that one may reduce any nodes-arcs configuration to a string in a description language and derive complexity thereby, is relevant. The relevant functions are known to be highly configuration dependent per observed life forms and particularly protiens, D/RNA and the interlocking organisation of the cell. Where, what is to be accounted for is an encapsulated, smart gated, metabolising entity with integral code using self replication. That is, before reproduction is on the table, codes, communication and storage systems and the von Neumann kinematic Self-Replicator architecture [vNkSR] have to be accounted for.

    Hence, BTW, the focus of UB’s biosemiosis site.

    The basic challenge is quite simple in concept: FSCO/I, due to the requisite of having the right parts in the right arrangement and correctness of coupling, naturally leads to deep local isolation of islands of function in the relevant config spaces, posing a beyond astronomical needle in haystack search challenge.

    Indeed, for just 1,000 bits,and converting the scope of search of 10^80 atoms at 10^13 – 4 operations/s, for 10^17 s into one straw, the haystack for 10^301 possibilities is so large it dwarfs the observable cosmos. In short an observed cosmos scale blind search rounds down to a skinny zero search, a maximally sparse search.

    Worse, searches are in effect elements taken from the power set, i.e. the search for a golden shot search is from a higher order space of scope 2^(10^301), calculator smoking territory.

    This is the sort of analysis that grounds the trillion case observational base that FSCO/I is only seen to come about by intelligently directed configuration; as your own comments in this thread exemplify. (Yes, text is a case in point.)

    Indeed, inductively, we are well warranted to conclude that FSCO/I is a strong, empirically reliable, analytically grounded sign of design as cause.

    Going over to the vera causa principle championed by Newton and acknowledged by Lyell and Darwin, to control ideologically motivated speculation, when we seek to explain temporally and/or spatially remote phenomena that we do not directly observe, we should confine causal explanations to factors observed to be adequate to cause the like effects as we see from the traces of what we seek to account for.

    On the strength of this, now that we know the informationally dense, intricately organised functionally specific complexity involved in the cell, the relevant conclusion is that per vera causa the only relevant explanation of the FSCO/I involved is design.

    At the very minimum, a reasonable person would acknowledge that such is a possible and serious candidate explanation. The resistance we see and the convoluted, fallacious logic behind it, are symptoms of ideological domination, not a true reflection of the balance on the merits.

    Going further, OOL is the root of the tree of life.

    Once design sits at the table at OOL as of right, it is present all the way along the tree leading up to ourselves.

    Johnson’s reply to Lewontin, Nov 97 is apt:

    For scientific materialists the materialism comes first; the science comes thereafter. [Emphasis original] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence.

    [–> notice, the power of an undisclosed, question-begging, controlling assumption . . . often put up as if it were a mere reasonable methodological constraint; emphasis added. Let us note how Rational Wiki, so-called, presents it:

    “Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific “dead ends” and God of the gaps-type hypotheses.”

    Of course, this ideological imposition on science that subverts it from freely seeking the empirically, observationally anchored truth about our world pivots on the deception of side-stepping the obvious fact since Plato in The Laws Bk X, that there is a second, readily empirically testable and observable alternative to “natural vs [the suspect] supernatural.” Namely, blind chance and/or mechanical necessity [= the natural] vs the ART-ificial, the latter acting by evident intelligently directed configuration. [Cf Plantinga’s reply here and here.]

    And as for the god of the gaps canard, the issue is, inference to best explanation across competing live option candidates. If chance and necessity is a candidate, so is intelligence acting by art through design. And if the latter is twisted into a caricature god of the gaps strawman, then locked out, huge questions are being oh so conveniently begged.]

    That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

    . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [Emphasis added.] [The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

    KF

  296. 296
    kairosfocus says:

    F/N: Lewontin’s inadvertent admission:

    . . . to put a correct view of the universe into people’s heads [==> as in, “we” have cornered the market on truth, warrant and knowledge] we must first get an incorrect view out [–> as in, if you disagree with “us” of the secularist elite you are wrong, irrational and so dangerous you must be stopped, even at the price of manipulative indoctrination of hoi polloi] . . . the problem is to get them [= hoi polloi] to reject irrational and supernatural explanations of the world, the demons that exist only in their imaginations,

    [ –> as in, to think in terms of ethical theism is to be delusional, justifying “our” elitist and establishment-controlling interventions of power to “fix” the widespread mental disease]

    and to accept a social and intellectual apparatus, Science, as the only begetter of truth

    [–> NB: this is a knowledge claim about knowledge and its possible sources, i.e. it is a claim in philosophy not science; it is thus self-refuting]

    . . . . To Sagan, as to all but a few other scientists [–> “we” are the dominant elites], it is self-evident

    [–> actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question , confused for real self-evidence; whereby a claim shows itself not just true but true on pain of patent absurdity if one tries to deny it . . . and in fact it is evolutionary materialism that is readily shown to be self-refuting]

    that the practices of science provide the surest method of putting us in contact with physical reality [–> = all of reality to the evolutionary materialist], and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [–> i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim] . . . .

    It is not that the methods and institutions of science somehow compel us [= the evo-mat establishment] to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes [–> another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [–> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door . . . [–> irreconcilable hostility to ethical theism, already caricatured as believing delusionally in imaginary demons]. [Lewontin, Billions and billions of Demons, NYRB Jan 1997,cf. here. And, if you imagine this is “quote-mined” I invite you to read the fuller annotated citation here.]

  297. 297
    kairosfocus says:

    F/N 2: Newton’s counsel in Opticks Query 31, by utter contrast:

    As in Mathematicks, so in Natural Philosophy, the Investigation of difficult Things by the Method of Analysis, ought ever to precede the Method of Composition. This Analysis consists in making Experiments and Observations, and in drawing general Conclusions from them by Induction, and admitting of no Objections against the Conclusions, but such as are taken from Experiments, or other certain Truths. For [speculative, empirically ungrounded] Hypotheses are not to be regarded in experimental Philosophy. And although the arguing from Experiments and Observations by Induction be no Demonstration of general Conclusions; yet it is the best way of arguing which the Nature of Things admits of, and may be looked upon as so much the stronger, by how much the Induction is more general. And if no Exception occur from Phaenomena, the Conclusion may be pronounced generally. But if at any time afterwards any Exception shall occur from Experiments, it may then begin to be pronounced with such Exceptions as occur. [–> this for instance speaks to how Newtonian Dynamics works well for the large, slow moving bodies case, but is now limited by relativity and quantum findings] By this way of Analysis we may proceed from Compounds to Ingredients, and from Motions to the Forces producing them; and in general, from Effects to their Causes, and from particular Causes to more general ones, till the Argument end in the most general. This is the Method of Analysis: And the Synthesis consists in assuming the Causes discover’d, and establish’d as Principles, and by them explaining the Phaenomena proceeding from them, and proving [= testing, the older sense of “prove” . . . i.e. he anticipates Lakatos on progressive vs degenerative research programmes and the pivotal importance of predictive success of the dynamic models in our theories in establishing empirical reliability, thus trustworthiness and utility] the Explanations. [Newton in Opticks, 1704, Query 31, emphases and notes added]

  298. 298
    kairosfocus says:

    F/N 3: Plato’s warning about evolutionary materialism and its impacts on civilisation and thought in The Laws Bk X, c 360 BC:

    Ath. . . .[The avant garde philosophers and poets, c. 360 BC] say that fire and water, and earth and air [i.e the classical “material” elements of the cosmos], all exist by nature and chance, and none of them by art . . . [such that] all that is in the heaven, as well as animals and all plants, and all the seasons come from these elements, not by the action of mind, as they say, or of any God, or from art, but as I was saying, by nature and chance only [ –> that is, evolutionary materialism is ancient and would trace all things to blind chance and mechanical necessity] . . . .

    [Thus, they hold] that the principles of justice have no existence at all in nature, but that mankind are always disputing about them and altering them; and that the alterations which are made by art and by law have no basis in nature, but are of authority for the moment and at the time at which they are made.-

    [ –> Relativism, too, is not new; complete with its radical amorality rooted in a worldview that has no foundational IS that can ground OUGHT, leading to an effectively arbitrary foundation only for morality, ethics and law: accident of personal preference, the ebbs and flows of power politics, accidents of history and and the shifting sands of manipulated community opinion driven by “winds and waves of doctrine and the cunning craftiness of men in their deceitful scheming . . . ” cf a video on Plato’s parable of the cave; from the perspective of pondering who set up the manipulative shadow-shows, why.]

    These, my friends, are the sayings of wise men, poets and prose writers, which find a way into the minds of youth. They are told by them that the highest right is might,

    [ –> Evolutionary materialism — having no IS that can properly ground OUGHT — leads to the promotion of amorality on which the only basis for “OUGHT” is seen to be might (and manipulation: might in “spin”) . . . ]

    and in this way the young fall into impieties, under the idea that the Gods are not such as the law bids them imagine; and hence arise factions [ –> Evolutionary materialism-motivated amorality “naturally” leads to continual contentions and power struggles influenced by that amorality at the hands of ruthless power hungry nihilistic agendas], these philosophers inviting them to lead a true life according to nature, that is,to live in real dominion over others [ –> such amoral and/or nihilistic factions, if they gain power, “naturally” tend towards ruthless abuse and arbitrariness . . . they have not learned the habits nor accepted the principles of mutual respect, justice, fairness and keeping the civil peace of justice, so they will want to deceive, manipulate and crush — as the consistent history of radical revolutions over the past 250 years so plainly shows again and again], and not in legal subjection to them.

  299. 299
    EugeneS says:

    Alicia,

    “While we’re speaking hypothetically”

    No, we’re not.

  300. 300
    Virgil Cain says:

    Alicia Cartelli:

    But yes, recent research has demonstrated that there is a chemical link between the amino acids added and the nucleotide sequences that code for them.

    There is a CORRELATION, Alicia. There isn’t any chemical link.

    What Alicia is saying is akin to saying that there is a electrical connection between the ASCII code and the letters it represents.

    And it’s strange that Alicia would say something about intelligent responses when she posts diatribe like this.

  301. 301
    Andre says:

    There is only two reasons our interlocutors behave the way they do…

    Ignorance or deceit.

  302. 302
    EugeneS says:

    Andre #301,

    “Ignorance or deceit.”

    I.e. non-design or design 😉

  303. 303

    AC, I didn’t “brush off” your comments, its just that your proposition isn’t new and doesn’t clarify any of the important issues.

  304. 304
    Zachriel says:

    Upright BiPed: does the catalyst specify the order of the amino acids?

    Already answered. It’s hypothesized that the process began with free amino acids binding to ribozymes enhancing their catalytic activity, which then evolved into a functional peptide ligase, then evolution of self-charging proto-tRNAs used initially to accumulate amino acids.

    gpuccio: IOWs, semiotic systems which include a necessary discontinuity, and all the other features which UB describes.

    That doesn’t really answer the question, which concerns the content of the argument. Does the conclusion follow from semiotic system, or from necessary discontinuity?

    gpuccio: I suppose that what you mean is that the sequence of A can be used by some translation system, like a ribosome, to produce a peptide which is functional.

    Yes, RNA can code for proteins, and can also act as a peptide ligate.

    gpuccio: The scenarios for the origin of the translation system and the genetic code outlined here are both sketchy and highly speculative.

    Sure they are. The events happened billions of years ago and left no physical fossils. Nonetheless, such hypotheses can and do guide research.

    In any case, the hypothesis shows that the argument that such a process could not have happened is fallacious. It is quite possible for a “semiotic system” with “necessary discontinuities” to have evolved.

  305. 305

    I would caution you against using terms such as “RNA polymerase” when talking about a hypothesized first living molecule.

    lol

  306. 306

    Upright BiPed: does the catalyst specify the order of the amino acids?

    Zach: Already answered. It’s hypothesized that the process began with free amino acids binding to ribozymes enhancing their catalytic activity, which then evolved into a functional peptide ligase, then evolution of self-charging proto-tRNAs used initially to accumulate amino acids.

    You still haven’t answered.

  307. 307
    Zachriel says:

    Upright BiPed: does the catalyst specify the order of the amino acids?

    RNA can specify the order for amino acids, and can also act as a peptide ligate.

  308. 308
    Alicia Cartelli says:

    Gpuccio, you should take a look at Hong & Pedersen (2003) J Bioenergetics and Biomembranes. They align peptide sequences from many of the subunits of ATP synthase in many different organisms. You’ll quickly see just how wrong you are.
    You really should not have said anything.
    For someone who consistently demonstrates a lack of understanding of complex biological processes, saying “I know the research and it proves nothing,” is quite funny.
    Please return to your seat in the peanut gallery, thanks.

    Eugene, the RNA world is a hypothesis last I checked.

    And Upright brushes me off again…
    No surprise there, we know ignorance is bliss.
    Do you not like the term “living molecule?”
    It’s pretty commonplace, even making its way into general biology textbooks today.
    You should get with the times Upright.

  309. 309
    EugeneS says:

    Zachriel,

    “Already answered. It’s hypothesized that the process began with free amino acids binding to ribozymes enhancing their catalytic activity, which then evolved into a functional peptide ligase, then evolution of self-charging proto-tRNAs used initially to accumulate amino acids.”

    Slowly, slowly by tiny selectable steps off we march to the Moon…

  310. 310
    Andre says:

    Alicia

    Are you talking about this paper?

    http://link.springer.com/artic.....3786618422

    What about it supports your claim?

    I’m all ears…..

    They used BLAST, so we have a guy here called ThickPhyton that will dispute any alignments done with BLAST. Didn’t you know that BLAST had a bug in it?

  311. 311
    Mung says:

    Alicia Cartelli:

    Anyways, the active site is now capable of joining amino acids to some degree and the template that had been previously been used to make a new RNA strand is now used as a template for making a peptide strand. The 3-nucleotide code that we see today doesn’t even exist yet, so that goes out the window. The template-amino acid interaction is purely based on chemistry; certain amino acids will temporarily associate more tightly with certain nucleotide bases, which will result in the addition of amino acids based on their type.

    Yes. How does we go from this to a system of Translation. That is the question.

  312. 312
    Mung says:

    Alicia Cartelli:

    Well, I mentioned some of it to Upright a while ago and he brushed it off, no surprise there. But yes, recent research has demonstrated that there is a chemical link between the amino acids added and the nucleotide sequences that code for them. In fact, 19 of the 20 common amino acids used by living organisms today demonstrate a polar/nonpolar (R-group), purine/pyrimidine (2nd nucleotide base) dichotomy.

    And now you have just gone from a system without translation to a system of translation, with a wave of your magic wand. You’ve just completely ignored the problem that needs to be explained.

    Also, if my memory is correct, I have read this paper you are referring to and this research you are talking about is actually a mathematical analysis. Your conclusions then are not warranted.

    If the peanut gallery has anything intelligent to say though, I’m all ears.

    Always glad to be of service.

  313. 313
    Mung says:

    Andre: If I have an encoder but no decoder what do I have?

    Some people think the decoder came first. So if you have a decoder but no encoder what do you have?

  314. 314
    Mung says:

    gpuccio,

    Thank you for posting that specific quote. It’s a keeper.

    There being the early, cooling earth with no complex organic molecules, and here being a minimally complex genetic system with modern type translation, transcription, and replication machineries, a system that would be subject to biological evolution much like modern organisms”

    Contra Zachriel.

  315. 315
    Mung says:

    Upright BiPed:

    AC, I didn’t “brush off” your comments, its just that your proposition isn’t new and doesn’t clarify any of the important issues.

    That is correct. As I say, I read that paper, carefully. And it doesn’t say what Alicia needs it to say and it’s not even attempting to explain translation.

  316. 316
    Carpathian says:

    Vy:

    Carpathian: . . . has to build multiple organisms for a future that is a century away and unknown

    Vy: And this is impossible because . . . ?

    It is not impossible for an entity that can see or control the future like the God of Genesis.

    For any other designer trying to engage in biological ID, it is impossible.

    That leaves the only designer capable of biological design, the Christian God.

    This makes the ID movement religious.

  317. 317
    Mung says:

    Zachriel: Yes, RNA can code for proteins, and can also act as a peptide ligate.

    RNA carries the message, which has already been encoded.

  318. 318
    Mung says:

    John Maynard Smith and Eors Szathmary know what needs to be explained:

    “We discuss how the translating machinery may have originated in Chapter 4.”

  319. 319
    Carpathian says:

    Mung:

    Alicia Cartelli: But yes, recent research has demonstrated that there is a chemical link between the amino acids added and the nucleotide sequences that code for them.

    Mung: And now you have just gone from a system without translation to a system of translation, with a wave of your magic wand. You’ve just completely ignored the problem that needs to be explained.

    This research indicates it is not a coded translation but rather a chemical reaction .

    This is not then a system that translates codes.

    It is instead one of chemical reactions.

  320. 320
    Virgil Cain says:

    Carpathian:

    This research indicates it is not a coded translation but rather a chemical reaction

    No, it doesn’t. It says there is a correlation.

  321. 321
    Virgil Cain says:

    I love how Alicia comes here, spews a few bluffs, ignores the refutations and then acts as if she refuted what IDists have said. And of course she always spews the condescending diatribe when she can’t bluff her way through.

  322. 322
    Virgil Cain says:

    Carpathian:

    For any other designer trying to engage in biological ID, it is impossible.

    Just repeating your tripe doesn’t make it so.

  323. 323

    Zachriel,

    In order to propose that life began in an RNA world that transitioned into a DNA-Protein system, you have to build a DNA-Protein system in an RNA world.

    In comment #50 above you can see a portion of what’s at stake. I am asking what object in the RNA world held the information so that we can talk about how it held that information.

  324. 324
    Mapou says:

    Cartelli:

    Yup, I’m squirming away!
    If the peanut gallery has anything intelligent to say though, I’m all ears.

    I won’t hold my breath.

    Funny, but we have not been holding our breath waiting for the dirt worshippers to say anything intelligent either. Worshipping the power of dead dirt to create life is not very intelligent, to say the least.

  325. 325
    Carpathian says:

    Virgil Cain:

    Carpathian: For any other designer trying to engage in biological ID, it is impossible.

    Virgil Cain: Just repeating your tripe doesn’t make it so.

    Then show everyone how it is possible for a biological designer to even gather the information required to know what to evolve.

    How far ahead would he have to look?

    Does he control the weather?

    Can he fine-tune the universe?

    All of these require a Genesis type of god.

  326. 326
    kairosfocus says:

    Carpathian, start with, run a computer/mathematical simulation based on knowledge of the capabilities of chemistry and the self replicating system; say in a terraforming environment. Then inject plants, animals etc in ecosystem webs, and tune relevant parameters, making sure to design robust not brittle things. Indeed, as was already pointed out, you seem to be fixated on brittle systems not robust, adaptable ones. We already do a lot of things like that, including Monte Carlo type simulations in decision support systems. KF

  327. 327
    Carpathian says:

    Virgil Cain:

    Carpathian: This research indicates it is not a coded translation but rather a chemical reaction

    No, it doesn’t. It says there is a correlation.

    Here’s something for you to mull over.

    This is a variable

    char DNA_1;

    This is a pointer to a variable.

    char *pDNA;

    To put it extremely simply , DNA_1 can be used as is, but pDNA is not the final data as the code it contains has to be translated by the processor in order for the actual data to be accessed.

    That is a level of indirection that does not exist in DNA, according to the research cited by Alicia Cartelli.

  328. 328
    kairosfocus says:

    Carpathian,

    all of this is in reality a red herring.

    We do know inductively on trillions of cases in point backed by relevant analysis of needle in haystack searches, that functionally specific complex organisation and associated information, FSCO/I, is a strong, empirically robust, index of design as cause. The world of life is chock full of such, from OOL up. The cosmos that is fine tuned for life is, too.

    The first does not call for anything more than a molecular nanotech lab some generations beyond Venter et al. (Where the integration of intelligently gated encapsulation, metabolic automata and code based self replication to get the cell going, points to how reproduction itself is a further instance of the FSCO/I to be explained, not an easy rhetorical out to dodge the need to properly explain FSCO/I. As in, reproduction based on codes has to be accounted for first, before “evolution” can be appealed to, which then runs into the issue of islands of function and needing to account for highly complex new body plans, all the way from goo to Godel.)

    The second does point to a very powerful designing entity beyond the physical cosmos and able to instantiate it.

    In short, FSCO/I is evidence.

    Evidence that on inference to best current, empirically grounded explanation (on trillions of cases) points to design. And we also have the point that purposeful intelligently directed configuration is the credible cause of design pointing to designers.

    So FSCO/I is by implication evidence pointing to designer.

    The proper way to address it is not to in effect find excuses to foot-drag and resist.

    If you have good evidence that FSCO/I can and reliably does come about by blind watchmaker chance and necessity, we are open to it.

    But, we are also very aware that a major reason for this sort of rhetoric as you are indulging, is that the party of magical dirt cannot come up with credible counter examples.

    So, the very style of objections you are making is back-handed, grudging testimony to the strength of the design inference.

    Thank you for your inadvertent support.

    KF

  329. 329
    kairosfocus says:

    Carpathian, I think you need to actually take a good look at protein synthesis, from unzipping, creating mRNA, transfer to ribosome, start, extension, halting, folding, and the use of codes that manifest themselves in loading the universal CCA joint of the tRNA with specific AAs. This points to mRNA as machine level code, with a NC nanotech assembler that uses it to create the workhorse molecule of the cell. Again, you are off on a red herring, strawman chase. KF

  330. 330
    Carpathian says:

    kairosfocus,

    A computer simulation of the pre-Cambrian world would be logistically impossible.

    An ID type of designer, who is not God, would not have the resources to run trillions of simulations of the entire global ecosystem of Earth.

    We could not if we harnessed all the world’s computing power be able to even simulate the global weather for a year and come up with an accurate forecast for Portland any particular day of 2016.

    We would not be able to even input the data from every point on Earth at a pre-determined date and time.

    This would be crucial before being able to run an accurate simulation.

    Now include the genomes of every single organism and their interactions with the climate and each other and try to predict what the predator to prey relationship would be everywhere on Earth.

    It’s logistically impossible to predict what the future will be like.

    You have to know beforehand just like the God of Genesis.

    As far as tuning parameters, just how would a non-god do this?

    A non-god has no control over the laws of physics.

    Today’s weather depends on yesterday’s and we can’t do anything about that.

    Only a god could.

    If I’m wrong, show me how to accomplish that.

  331. 331
    Alicia Cartelli says:

    Andre, the Hong paper visually shows you how the majority of proteins in ATP synthase are made up of peptide sequences that are not highly conserved. There are some select regions in these proteins that are, but the vast majority of the amino acids vary among different species. This was the opposite of what gpuccio was trying to claim. I was just showing him the error in his ways.

    No magic wand needed Mungy, simply chemical interactions. The series of papers I am referring to are Wolfenden et al. 2015. Do you guys really think it’s just coincidence that 19 of the 20 amino acids follow this dichotomy? The paper shows it exists, I am applying the information to this hypothetical first living molecule.

    Mapou, I love when you use the term “dirt worshippers.” It just goes to show everyone the typical level of intelligence they can find here at UD.

  332. 332
    Carpathian says:

    kairosfocus:

    The first does not call for anything more than a molecular nanotech lab some generations beyond Venter et al.

    Just who would run this lab if life doesn’t exist yet?

  333. 333
    Mung says:

    kf, over at TSZ I’ve introduced the term Theopodophobia. What do you think?

  334. 334
    Carpathian says:

    kairosfocus:

    In short, FSCO/I is evidence.

    FSCO/I is a label you use to describe configurations of matter.

    How these configurations of matter came to be is what the debate is about.

    Simply adding attributes to your label does not win the day for ID.

    Your side brings up the improbability of “nature” to produce these configurations and I am bringing up the improbability of a designer other than the Genesis God to build these configurations.

    Show me how a non-living, non-god entity, that cannot control the physics of the universe, is able to design and then distribute life.

    Since the ID designer pre-dates life, he cannot be alive and also cannot be God if ID is to be taken as science.

    Walk me through that process.

  335. 335
    Andre says:

    Alicia

    Please post some links to your papers….. You know as well as I do you’re bluffing.

  336. 336
    Zachriel says:

    Upright BiPed: In order to propose that life began in an RNA world that transitioned into a DNA-Protein system, you have to build a DNA-Protein system in an RNA world.

    DNA polymers, which are closely related to RNA chemically, could coopt the RNA replication mechanism, coding for its own purposes, perhaps virally.

  337. 337
    Virgil Cain says:

    Carpathian- There isn’t any evidence for a world without the current transcription and translation system

    How these configurations of matter came to be is what the debate is about.

    And all you have to explain it is “it just happened” and “a long series of luck accidents”.

  338. 338
    Alicia Cartelli says:

    Initial work was done in the late 70s, early 80s:
    Wolfenden et al. (1979) Science
    Wolfenden et al. (1981) Biochemistry

    Recent work has applied this to an early-earth environment and the evolution of early translational systems:
    Wolfenden et al. (2015) PNAS
    Carter & Wolfenden (2015) PNAS

    They point to chemical interactions that were likely important in the evolution of the earliest translational machinery.

  339. 339

    UB: In order to propose that life began in an RNA world that transitioned into a DNA-Protein system, you have to build a DNA-Protein system in an RNA world.

    In comment #50 above you can see a portion of what’s at stake. I am asking what object in the RNA world held the information so that we can talk about how it held that information.

    Zach: DNA polymers, which are closely related to RNA chemically, could coopt the RNA replication mechanism, coding for its own purposes, perhaps virally.

    So, an RNA template replicator exists. Then a DNA molecule – with a purpose – takes over. Perhaps virally.

    Like I said Zach, no one can take away your faith, nor can anyone falsify anything you wish to propose from that faith.

  340. 340
    Andre says:

    Alicia

    Please stop your bluffing. It’s OK to try and deceive me but to deceive yourself is whacky. You’ve used words like plausible, likely, assumed, coulda, woulda bit absolutely nothing concrete.

  341. 341
    Andre says:

    Alicia

    Let me be clear nobody is asking for possible or plausible scenarios we want actual proof. Can you do that?

  342. 342
    kairosfocus says:

    Carpathian, the red herring-strawman chase continues. FSCO/I — a summary term for something identified by Orgel and Wicken in the 70’s . . . I notice the implied who are you dismissal hint — is a strong sign of design as cause. So, if such a designer is empirically indicated per inference to best explanation and we are able to see that a designer of life needs very good computation simulation or the equivalent powers indeed and one for the cosmos needs in addition sheer raw power in scads to implement a cosmos, then it seems that we have in hand a pivotal observational base indeed. Just the FSCO/I in those contexts allows us to reasonably infer to design and requisites of design point to significant powers. BTW, on life, I’d suggest that several generations of Moore’s law scaling point to pretty awesome computing power so I remain at the point, molecular nanotech lab is all that is required. KF

    PS: All of us are using computers that 40 – 50 years ago would have been supercomputer territory, or at least big iron mainframe territory. Well do I recall in the 80’s hearing of a VAX based national computer centre with several gigs in RAM and how awesome and even vaguely menacing that sounded. Now, that’s in our tablets and notebooks.

  343. 343
    Alicia Cartelli says:

    You asked for the papers that I based my hypothetical system on, I provided them.
    And all you can respond with is to point out that the conversation is a hypothetical thought experiment?
    You don’t say.
    If you come up with something intelligent, then I’ll respond to you. Until then, have a nice day.

  344. 344
    kairosfocus says:

    F/N: Here is Orgel, 1973:

    . . . In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . . .

    [HT, Mung, fr. p. 190 & 196:] These vague idea can be made more precise by introducing the idea of information. Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure. [–> this is of course equivalent to the string of yes/no questions required to specify the relevant “wiring diagram” for the set of functional states, T, in the much larger space of possible clumped or scattered configurations, W, as Dembski would go on to define in NFL in 2002.] One can see intuitively that many instructions are needed to specify a complex structure. [–> so if the q’s to be answered are Y/N, the chain length is an information measure that indicates complexity in bits . . . ] On the other hand a simple repeating structure can be specified in rather few instructions. [–> do once and repeat over and over in a loop . . . ] Complex but random structures, by definition, need hardly be specified at all . . . . Paley was right to emphasize the need for special explanations of the existence of objects with high information content, for they cannot be formed in nonevolutionary, inorganic processes. [The Origins of Life (John Wiley, 1973), p. 189, p. 190, p. 196. Of course, that immediately highlights OOL, where the required self-replicating entity is part of what has to be explained (cf. Paley), a notorious conundrum for advocates of evolutionary materialism; one, that has led to mutual ruin documented by Shapiro and Orgel between metabolism first and genes first schools of thought. Behe would go on to point out that irreducibly complex structures are not credibly formed by incremental evolutionary processes and Menuge et al would bring up serious issues for the suggested exaptation alternative. Finally, Dembski highlights that CSI comes in deeply isolated islands T in much larger configuration spaces W, for biological systems functional islands. That puts up serious questions for origin of dozens of body plans reasonably requiring some 10 – 100+ mn bases of fresh genetic information to account for cell types, tissues, organs and multiple coherently integrated systems. Wicken’s remarks a few years later on wiring diagram organisation etc now take on fuller force in light of the further points from Orgel at pp. 190 and 196 . . . ]

  345. 345
    kairosfocus says:

    F/N2: Wicken, 1979:

    ‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [[originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [[“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65.]

    FSCO/I is real, it is commonplace, it is informational, that information requires adequate causal explanation and the empirical evidence strongly points to design.

    That is what is on the table, and that is what is being ducked.

    KF

  346. 346
    Andre says:

    Alicia

    A good day to you too and when you actually have anything be so kind to inform us.

    Regards

  347. 347
    kairosfocus says:

    Alicia, hints and suggestions that on reasonable grounds, exaggerate the significance. How do I know that? Had there been a genuine breakthrough, it would have been trumpeted from the roofs and we would hear that announced with fanfares and drum rolls year by year, day by day over these past 30 years since. We are not seeing that, so immediately you are going beyond what is reasonably warranted, making unwarranted extrapolations that do not squarely answer to the origin of relevant information and organisation. The want of substantial details sends much the same message. KF

  348. 348
    kairosfocus says:

    Mung, please explain. KF

  349. 349
    Box says:

    Alicia Cartelli:
    Carter & Wolfenden (2015) PNAS

    For those interested, that paper has been debunked at good ol’ evolutionnews.org.

  350. 350
    Mung says:

    kf,

    Fear of the divine foot.

  351. 351
    Mung says:

    Alicia Cartelli:

    You asked for the papers that I based my hypothetical system on, I provided them.

    Your hypothetical system went from no translation to translation as if by magic. Any plans to fill in the missing pieces in your hypothetical system?

  352. 352
    Mung says:

    According to John Maynard Smith and Eors Szathmary, “RNA is therefore suitable as the genetic material only in organisms with very small genomes.”

    Now in addition to that problem, RNA, not being double-stranded like DNA, can fold on itself to take on a 3D shape. Of course, that would also hinder the utility of RNA as genetic material.

  353. 353
    Mung says:

    The key to the translation system would appear to be the transfer RNA (tRNA). Have either Zachriel or Alicia addressed that?

    Or it could be the assignment enzyme, which attaches the appropriate amino acid to the tRNA.

    Perhaps both are needed.

    There’s also an enzyme that detaches the amino acid from the tRNA so that it can be added to the peptide chain.

    And, of course, there is the ribosome.

    I love having gpuccio around as well to help keep them honest about the biochemical details.

    Even a dumbed down system is still quite complex.

    Again from John Maynard Smith and Eors Szathmary:

    We have, therefore, no intermediate between a complete system [of translation] and no system at all to guide us in guessing at it’s evolution.

    It’s like the missing link from hell.

  354. 354
    Alicia Cartelli says:

    Kairos, I never said this work was a breakthrough, only that my hypothetical “first translational system” was based on some of the findings in these papers. Don’t get your panties in a bunch.

    Box, evolutionnews “debunked” that paper? Get real. The majority of what evolutionnews talks about in that link is the UNC press release. And pretty much everything they say is either wrong or demonstrates a fundamental misunderstanding.

    Mungy, for the third time now, my system translates using the same template that would be used for replication, but amino acids are also present in the active site now. Amino acid sequence is controlled by chemical interactions with the nucleotides of the template and the code would be something like this: purine base – polar amino acid, pyrimidine base – hydrophobic amino acid. Joining these amino acids together by the active site creates an amino acid sequence based on the nucleic acid template sequence: translation.
    My system does not use tRNA, it is a much simpler system, but also a much less efficient system than that which we see today. There are always trade-offs in biology, but the ability to create the first proteins would be well worth it for life.
    “There’s also an enzyme that detaches the amino acid from the tRNA so that it can be added to the peptide chain.”
    What enzyme is that?
    You think Gpuccio is keeping anyone “honest about the biochemical details?” That’s a good one. He doesn’t even understand basic biology. He’s still trying to figure out how little of the peptide sequences in ATP synthase subunits are actually conserved across species. This is after I gave him a paper that shows him how wrong he is in picture form. Do I need to find a pop-up book?

  355. 355
    Andre says:

    Alicia

    A Trade off is of course and engineering term. Don’t let it go lost on you. Seriously though if you have a hypothetical then please can you share your findings so you can shut us up once and for all. Have you ever considered that all we want is to be proven wrong?

  356. 356
    Andre says:

    Alicia

    And the fact that you are doing some reverse engineering work also seem to have escaped you.

    What is a trade off and how does it apply to engineering?

    http://link.springer.com/artic.....BF01581342

    And what on earth is reverse engineering?

    http://searchsoftwarequality.t.....ngineering

  357. 357
    Alicia Cartelli says:

    Andre, you’re grasping at straws and barely making sense.
    I’ve explained my system multiple times now and you seem to lack any coherent response.
    You’ve reached the end of your usefulness.
    Take care now!

  358. 358
    Andre says:

    Then show us your reverse engineered system!

  359. 359
    gpuccio says:

    Mung:

    “I love having gpuccio around as well to help keep them honest about the biochemical details.”

    Thank you.

    I am in a delicate position. I don’t want to discuss with Alicia Cartelli, because I don’t like her attitude, absolutely offensive and unrespectful of others, and her inability to understand what a discussion is.

    However, I have a few things to say, so I will say them to you and to all who are interested.

    ATP synthase is a complex molecule, and a very conserved one. It is essentially formed by 2 parts, FO and F1.

    The most conserved sequences are those in subunits alpha and beta of the F1 structure. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex. Gamma, delta and epsilon sequences also contribute to F1.

    Subunits A, B and C are the main components of FO.

    The sequences which I have always debated here at UD as an example of extremely conserved functional sequences are the alpha and beta subunits of F1. That can easily be verified, in all my posts on the subject, for example here:

    http://www.uncommondescent.com.....on-part-1/

    The paper linked by Alicia Cartelli is a very good paper about the structural and functional properties of ATP synthase, in particular the interactions between its different parts. It does show that many residues are critically conserved and have important functions in those interactions, while other parts are less conserved, or not conserved. And so?

    What it does not show is the desgree of conservation of the alpha and beta subunits of F1. I quote:

    The sequence alignment of the gamma subunit shows that the overall sequence is not that conserved in comparison to the alpha and beta subunits, although subunit gamma is one of the essential subunits for the function of the F1 motor

    The paper then analyzes subunit gamma, and the subunits of FO.

    Just as a reminder, I have blasted again the human beta subunit of F1 against bacteria.

    The first hit (Azospirillum halopraeferens) shows an alignment of 479 AAs (out of 529):

    Identities:392/479(82%)
    Positives: 425/479(88%)
    Expect (obviously!): 0.0

    The 106th hit (the last in my first page of results, Kiloniella sp.) shows an alignment of 457 AAs (out of 529):

    Identities:366/457(80%)
    Positives: 403/457(88%)
    Expect (obviously!): 0.0

    Does anyone want to argue that these are not extremely conserved sequences?

    Just for the record.

  360. 360
    Box says:

    Alicia Cartelli,

    Earlier work also uncovered the existence of a pronounced bias in the relationship between amino acid hydrophobicity and the genetic code. Thus, a pyrimidine at the second codon position signals amino acids whose average hydrophobicity is much greater than those coded by a purine at the same position (2, 3). The values reported here allow a more detailed analysis, described in a companion paper (16), which reveals that two separate codes for amino acid size and hydrophobicity appear to be embedded in different parts of their tRNA sequences, with size (represented by vapor-to-cyclohexane equilibria) encoded in the acceptor stem, and hydrophobicity (represented by water-to-cyclohexane equilibria) embedded in the anticodon.

    Here (and elsewhere in their paper) Carter and Wolfenden seem to suggest that the genetic code and the protein code may be linked to “hydrophobicity” and “size” respectively. Clearly, this is an absurd attempt to explain the codes and the bridge between them. The commentary at evolutionnews.org eloquently explains why:

    At best, he gets piles of amino acids with similar properties and folds. That’s not selection; that’s just sorting. You can find that in riverbeds where rocks of various sizes sort themselves out in layers. Those “patterns” are even “preserved”, but that constitutes neither a code nor a specification.

  361. 361
    Zachriel says:

    Upright BiPed: So, an RNA template replicator exists.

    A complex network of RNA and peptides.

    Upright BiPed: Then a DNA molecule – with a purpose – takes over. Perhaps virally.

    There’s no “purpose” in the sense of having a conscious choice, but something that provides a stepwise selective advantage.

    Upright BiPed: nor can anyone falsify anything you wish to propose from that faith.

    The argument in the original post is that semiotic systems include a necessary discontinuity, and that they are always the result of conscious design. To contradict this assertion, it is only necessary to provide a plausible pathway, not necessarily the historical transition. However, we would point out there is evidence that DNA synthesis appears to be a relic of RNA metabolism, and some families of DNA polymerases are likely homologous with RNA polymerases.

  362. 362
    Zachriel says:

    Box: The commentary at evolutionnews.org eloquently explains why

    Sorting implies an historical sifting process.

  363. 363
    Mung says:

    Alicia Cartelli:

    Do I need to find a pop-up book?

    Probably not for gpuccio, but I’d sure love to have one!

    My cartoon guide to genetics has nice pictures but they don’t pop up and my complete idiot’s guide, well, that’s for idiots.

  364. 364
    Zachriel says:

    gpuccio: The claim is that semiotic systems include a necessary discontinuity, and that they are always the result of conscious design.

    Which is the claim?

    1. Semiotic systems are always the result of conscious design because they include a necessary discontinuity.

    2. The subset of semiotic systems which include a necessary discontinuity are always the result of conscious design.

    If #1, then it’s an argument from irreducibility applied to a specific case. If so, we can rewrite the claim as ‘systems with a necessary discontinuity, e.g. semiotic systems, are always the result of conscious design.’

    We presume #2 is not the case, as the post seems to suggest that a necessary discontinuity is inherent in semiotic systems.

  365. 365
    Mung says:

    Mung: There’s also an enzyme that detaches the amino acid from the tRNA so that it can be added to the peptide chain.

    Alicia Cartelli: What enzyme is that?

    Peptidyl transferases are also a type of aminoacyltransferase that catalyze the formation of peptide bonds, as well as the hydrolytic step that leads to the release of newly synthesized proteins off the tRNA.

    wikipedia

    The tRNA needs to be detached. It doesn’t just detach by magic. (Well, perhaps we are seeing real magic in action.)

  366. 366
    Mung says:

    Thanks gpuccio,

    I understand what you are saying and respect it. You’ve provided a good example. But you can always keep me honest if I say anything dumb. 🙂

  367. 367
    Carpathian says:

    kairosfocus:

    BTW, on life, I’d suggest that several generations of Moore’s law scaling point to pretty awesome computing power so I remain at the point, molecular nanotech lab is all that is required.

    Since this lab had to exist before life did, who would be running it?

    It couldn’t have been God since God doesn’t need computers.

    Since it wasn’t God and it was not a living being, I’m going to say with some confidence that the lab never existed.

    Other than the God of Genesis then, there is no plausible designer.

  368. 368
    Carpathian says:

    kairosfocus,

    Show me how a non-living, non-god entity, that cannot control the physics of the universe, is able to design and then distribute life.

    Since the ID designer pre-dates life, he cannot be alive and also cannot be God if ID is to be taken as science.

  369. 369
    Barry Arrington says:

    Carpathian,

    You’ve been participating on this blog for years. Yet, your comment at 368 illustrates that you do not have the first clue about what ID posits. Since you’ve been exposed to the truth countless times, I can only surmise that you are either blindingly stupid or willfully ignorant, or perhaps both. Please try to do better. I won’t be holding my breath.

  370. 370
    Alicia Cartelli says:

    Thank you for the basic biology lesson gpuccio. And now let me get this straight, to support the claim that “a lot of amino acid sequences are so conserved,” you specifically take the subunits with the most highly conserved sequences in one of the most important biomolecules across all domains of life. In the same breath you admit that the other subunits are not nearly as well conserved, but hey, let’s just ignore those! Have you ever heard the phrase “confirmation bias?”
    Also, your conservation percentages ignore the amino acids that are present in one species and not the other, while this is necessary to align the sequences, those can all be considered differences in amino acid sequence, which is the topic at hand. So from the comparison between subunits in human and A. halopraeferens, the resulting ~80% range will be significantly reduced when you take into account the 50 amino acids that are not present in this bacterial species.

    “The commentary at evolutionnews eloquently explains.”
    Please, Box. That’s a good one. The points evolutionnews tries to make amount to stabs in the dark.
    First they play word games with “selection” vs. “sorting” and “piles of amino acids” The question is how is a genetic code produced? And the researchers propose that an early code emerged which recognized amino acids based on hydrophobicity and size via early tRNA molecules. Again this system is not as precise as the one we see today, but the ability to consistently add hydrophobic or hydrophilic amino acids or large or small amino acids or some combination of these properties would be plenty to produce proteins. This certainly is a “code” or “specification” although it is not as simple as the codon-amino acid code that we see today. Instead it is some 3D shape and the underlying sequence of the early tRNA which binds a type of amino acid.
    Pretty much everything on evolutionnews either begins with something taken out of context or is flat-out wrong.

    Mung, the only thing that “detaches the amino acid from the tRNA so that it can be added to the peptide chain” is the ribosome.

  371. 371
    Carpathian says:

    Barry Arrington:

    You’ve been participating on this blog for years. Yet, your comment at 368 illustrates that you do not have the first clue about what ID posits. Since you’ve been exposed to the truth countless times, I can only surmise that you are either blindingly stupid or willfully ignorant, or perhaps both. Please try to do better. I won’t be holding my breath.

    Did Mapou get it wrong too?

    Mapou, an IDist, says ID is Creationism and I agree with him as do many others here.

    He has provided a very open and realistic comment on ID.

    Instead of making personal statements about me, why don’t you just answer a few simple questions and follow the evidence.

    ID states there was a designer of life.

    Did I get that wrong?

    kairosfocus claims that there was a lab of some sort which created life.

    Did I get that wrong?

    If this lab is where life was created, it must have been run by entities which themselves were not alive.

    Am I wrong to think that?

  372. 372

    The argument in the original post is that semiotic systems include a necessary discontinuity, and that they are always the result of conscious design. To contradict this assertion…

    The OP provides a short description of the material conditions required to translate a spatially-oriented representation, such as a nucleic codon. This is the physical basis of the open-ended (evolvable) information system required to organize the heterogeneous living cell. As the author of the OP, I am not aware that the words “conscious design” appear anywhere in that description. In any case, these are observations gleaned from scientific investigation; proposed in theory, confirmed by experiment, and documented in peer-review. You’ve contradicted nothing because you haven’t provided any details that would provide the basis of a contradiction. And your notion that in order to contradict these observations you only need to contrive a physics-free idea that seems plausible to the person making the proposal is patently ridiculous. To contradict the observations you’ll need to address the issue of energy degeneracy – how a rate-dependent process formalizes a necessary set of rate-independent representations in linear sequence memory. Additionally, to contradict the issue of spatial-orientation, you’ll need to address the issue of how the necessary systematic rules of interpretation become simultaneously formalized in that memory. You’ve done neither.

    Alternatively, having provided no details, there is nothing anyone can say to falsify your beliefs. All that can be done is to continue to point out the flaws. And with each round, you can fall back on the lack of detail. This is exceptionally true of subject matter that has interdependent objects, like translation. It does grow tiresome though. It is also notable that you refuse to acknowledge our universal experience regarding the systems being discussed. In the end, you will walk away from this conversation with the firm commitment that you’ve contradicted the observations, and this will be the outcome regardless of anything that is said here. For that, nothing can be done, so it is of little consequence.

    – – – – – – – – – – – –

    Biosemiosis.org — Bibliography

  373. 373
    Zachriel says:

    Upright BiPed: As the author of the OP, I am not aware that the words “conscious design” appear anywhere in that description.

    That was gpuccio’s description. You probably haven’t made your point clear. Can you state provide a brief statement of your claim?

    We’ve asked a few times? What is a heterogeneous cell? Does a posited RNA World cell qualify?

    Upright BiPed: To organize the first living cell, a set of physical representations and a set of physical protocols must arise together. One set must encode the information and the other set must establish (specify) what the result of that encoding will be.

    RNA World posits that the same molecule encoded the information and determined what the result of that encoding would be.

  374. 374
    Andre says:

    Alicia

    I’m dissapointed you huffed and you puffed but you did not blow the house down.

  375. 375
    Mung says:

    Alicia Cartelli:

    The question is how is a genetic code produced? And the researchers propose that an early code emerged which recognized amino acids based on hydrophobicity and size via early tRNA molecules.

    A feature missing from your model:

    My system does not use tRNA…

    Which, you claim, is based on these papers:

    …my hypothetical “first translational system” was based on some of the findings in these papers.

    Mung: There’s also an enzyme that detaches the amino acid from the tRNA so that it can be added to the peptide chain.

    Alicia Cartelli: What enzyme is that?

    Mung: Peptidyl transferases.

    Alicia:

    Mung, the only thing that “detaches the amino acid from the tRNA so that it can be added to the peptide chain” is the ribosome.

    Is it really that difficult for you to admit I was right? Or is the wiki page wrong?

  376. 376
    Alicia Cartelli says:

    Oh little andre, I’m not trying to blow any houses down, don’t worry. All I wanted to do was have a conversation about a hypothetical early translational system, but that is obviously asking way too much from a bunch of scientifically illiterate, biological science-challeneged UDers.
    Don’t know why I ever bothered in the first place.

  377. 377
    Andre says:

    Alicia

    Calling people little and by design spelling their name in small letters won’t really get you any conversations sorry.

  378. 378
    Andre says:

    Alicia

    And I have already said no hypotheticals, no assumptions just the facts please.

  379. 379
    Box says:

    Alicia Cartelli on the take-down of Carter and Wolfenden at evolutionnews.org :

    AC: The points evolutionnews tries to make amount to stabs in the dark. First they play word games with “selection” vs. “sorting” and “piles of amino acids”.

    Alicia, we both know that this is not playing word games. The crucial difference between “evolution” and “sorting” is befittingly pointed out. The first may be going somewhere, the second certainly not.

    AC: The question is how is a genetic code produced? And the researchers propose that an early code emerged which recognized amino acids based on hydrophobicity and size via early tRNA molecules.
    Again this system is not as precise as the one we see today, but the ability to consistently add hydrophobic or hydrophilic amino acids or large or small amino acids or some combination of these properties would be plenty to produce proteins.

    What are you going on about? You do understand that there is no code whatsoever, right?

    AC: This certainly is a “code” or “specification” although it is not as simple as the codon-amino acid code that we see today.

    I take it that you are jesting. For now I simply refuse to believe that there are people out there who hold that sorting on size and hydrophobia is a “code” and/or “specification” which is relevant to the problems at hand.

  380. 380
    Alicia Cartelli says:

    Correct Mung, my translational system is based largely on the papers that demonstrate the polar/nonpolar, purine/pyrimidine dichotomy and that this dichotomy is preserved at high temperatures. Later evolution of tRNA molecules, from portions of the original ribozyme I suggest, would make the system more efficient and increase the selectivity for amino acids.
    Yes, it is very difficult for me to admit that you are right….because you aren’t right.
    Wiki is on the verge of being wrong, that page and some related ones are very disorganized and confusing especially to the layman. Bottom line is if you go to the bottom of the page under external links, you’ll see that there are really no “peptidyl transferase” enzymes, just the ribosome. There is Gamma-glutamyl transpeptidase and transglutaminase, but both of these enzymes either connect R-groups of fully formed proteins or attach functional groups to proteins. Biologists often do a poor job in the naming convention department, sorry.

    What, Box? “Evolution” and “sorting” is not what is being compared or contrasted or anything. You are completely lost. And just because it’s not a linear sequence of letters that we have assigned to certain chemical structures, but instead is a 3-dimensional structure that specifies binding of certain amino acids, doesn’t mean it cannot be considered a “code.” I can arrange the atomic coordinates of the 3D structure into a long line of text if that would make you feel better about calling it a code.

  381. 381
    StephenB says:

    Carpathian

    Show me how a non-living, non-god entity, that cannot control the physics of the universe, is able to design and then distribute life.

    Bad logic. That is a second order philosophical question that ID’s scientific methodology cannot address.

    The primary scientific question is this: Based on empirical evidence that can be measured, was the cause of life natural or artificial.

    Using philosophical methods, one can, indeed, show that only a supernatural God could create a material universe out of nothing. That has nothing to do with ID science. Please explain why you think it does.

    Since the ID designer pre-dates life, he cannot be alive and also cannot be God if ID is to be taken as science.

    There you go again, conflating traditional philosophical methods with ID’s scientific methods, neither of which you appear to be familiar with.

    Walk me through that process?

    If you don’t know ID’s process, why would you presume to evaluate it? Isn’t that putting the cart before the horse? How can you say that ID’s methods are flawed if you don’t know what they are? Isn’t that illogical?

  382. 382
    Box says:

    Alicia:

    What, Box? “Evolution” and “sorting” is not what is being compared or contrasted or anything.

    It isn’t?

    Alicia: You are completely lost.

    Am I?

    Alicia, get a grip on yourself. Read again — this time with comprehension:

    At best, he gets piles of amino acids with similar properties and folds.

    That’s not selection; that’s just sorting.

    You can find that in riverbeds where rocks of various sizes sort themselves out in layers. Those “patterns” are even “preserved”, but that constitutes neither a code nor a specification.

    [evolutionnews.org]
    [my emphasis]

  383. 383
    Carpathian says:

    StephenB:

    Carpathian: Show me how a non-living, non-god entity, that cannot control the physics of the universe, is able to design and then distribute life.

    StephenB: Bad logic. That is a second order philosophical question that ID’s scientific methodology cannot address.

    That is not philosophical at all.

    It’s logic based on premises kairosfocus provided.

    If a lab created life, whoever ran the lab could not have been alive.

    Carpathian: Walk me through that process?

    StephenB: If you don’t know ID’s process, why would you presume to evaluate it? Isn’t that putting the cart before the horse? How can you say that ID’s methods are flawed if you don’t know what they are? Isn’t that illogical?

    It is not ID’s processes I was asking KF about, it was the idea of a lab creating life that was run by something alive.

    No IDist has ever stepped through the processes involved in ID, not even Dembski.

  384. 384
    Alicia Cartelli says:

    “At best, he gets piles of amino acids with similar properties and folds.”
    What does that even mean, box? What is a “pile of amino acids?” Because to me it sounds like they’re trying to describe a protein, without actually saying the word “protein.” (But that’s just how evolutionnews works)
    “Amino acids with similar properties and folds” sounds to me like “repeatable production of proteins,” which, last I checked, is the basis of translation. You do know what a protein is right? A polymer of amino acids with specific folds, and in nature we see proteins with similar folds and properties performing the same function?
    Again, you are lost.
    When will you guys learn?

  385. 385
    Mung says:

    Alicia Cartelli:

    Biologists often do a poor job in the naming convention department, sorry.

    You’re not a biologist?

    They don’t just have a problem with naming:

    The ribosome … has enzymes that detach the amino acid from the tRNA, attach it to the growing amino acid chain, and release the tRNA, which can now be used again.

    – John Maynard Smith and Eors Szathmary. The Origins of Life. p. 41

    https://en.wikipedia.org/wiki/John_Maynard_Smith

    https://en.wikipedia.org/wiki/E%C3%B6rs_Szathm%C3%A1ry

    Silly Biologists. Telling tales. Fooling the poor dumb IDiots.

  386. 386
    Mung says:

    By the way, Alicia, did you bother following the wikipedia links yourself?

    Enzymes that catalyze the transfer of an aminoacyl group from donor to acceptor resulting in the formation of an ester or amide linkage.

    here

    Acyltransferases that use AMINO ACYL TRNA as the amino acid donor in formation of a peptide bond. There are ribosomal and non-ribosomal peptidyltransferases

    here

    I was willing to give you the benefit of the doubt. Why?

  387. 387
    Virgil Cain says:

    Alicia Cartelli,

    Do you think physicochemical processes can A) produce your ribozyme B) provide the raw materials to carry on and C) be capable of evolving new functions?

    I know why you would want to avoid those questions. But by not answering them you prove to be a hoax. Also the fact that you confuse correlation with a chemical connection proves tat you are incapable of learning.

  388. 388
    gpuccio says:

    Mung:

    Excuse me if again I take you as interlocutor for my personal ramblings. You are an old friend, and I confide that you will pardon me.

    Seeing that Alicia Cartelli (#370) has profited so much of my “basic biology lesson”, I am tempted to offer her some basic methodology and epistemology lesson, too. Always ready to perform some good action! 🙂

    The point is, if a sequence (in this case, the beta subunit of ATP synthase, human form, but the same would be valid for the alpha subunit) exhibits a striking homology with at least a hundred bacterial forms of the same molecule, which in the evolutionary tree are distant at least 2-3 billion years, in terms of any possible evolutionary theory, and especially of the neutral model of evolution, there can be one and only one reasonable explanation for that: a very, very strong functional constraint on the sequence.

    Let’s see. For the sake of simplicity, we can consider just two sequences: the human sequence, and the first hit in my blast: Azospirillum halopraeferens.

    Now, we can observe that the two sequences exhibit 392 identities (82% of the alignment). How is it possible?

    Can it be a casual outcome? No. Absolutely not.

    The expect value is given here as 0.0. That is, more or less, the number of similar results expected by chance in a database of sequences such as the one we are using.

    IOWs, there is really no chance at all to observe such an homology by chance.

    Maybe the sequence has just remained as it was 3 billion years ago? But, if that were the case, the whole evolutionary theory, and especially the neutral model, would be complete bullshit. I think we can exclude that. Neutral mutations do happen, and in 3 billion years a sequence has all the time in the world to change deeply, to become completely different from the original one, if no functional constraint is working.

    Therefore, we are left with one and only one explanation: the 392 AAs which are identical in the human and bacterial form (Maybe a few more, maybe a few less), have been under very strong functional constraints for about 3 billion years.

    I can really see no other possible explanation.

    Now, that is simply true, whatever the results of any other comparison with other species are. The simple fact is that the observed homology cannot be a random outcome.

    Now, I will try to explain what a confirmation bias is. Wikipedia will help, as usual:

    “Confirmation bias is the tendency to search for, interpret, favor, and recall information in a way that confirms one’s beliefs or hypotheses, while giving disproportionately less consideration to alternative possibilities. It is a type of cognitive bias and a systematic error of inductive reasoning. People display this bias when they gather or remember information selectively, or when they interpret it in a biased way.”

    So, my reasoning about the beta subunit of ATP synthase in no way represents a confirmation bias. Why? Because in no way I am “giving less consideration to alternative possibilities”. Very simply, there are no alternative possibilities at all.

    Let’s see again. I start with a question: are there biological sequences which are highly conserved for billions of years, and therefore exhibit strong functional constraints, according to all forms of evolutionary theories?

    To answer that, I take a few sequences, let’s say all the sequences of ATP synthase, and blast them. The result? Some are strongly conserved, like the alpha and beta subunits, others are less conserved. Indeed, all those sequences exhibit some conservation, but it is very different from sequence to sequence.

    So, I can answer my initial question: Yes, there are sequences which exhibit strong conservation. In this group, for example, the alpha and beta subunits do exhibit that, while other sequences are less conserved.

    Where is the confirmation bias? Nowhere to be seen. I started with a clear question, and I gave a clear, unbiased answer.

    Please note that I never assumed that any protein sequence, or any sequence in the ATP molecules, needs to be strongly conserved. If my question had been: are all the sequences in ATP synthase strongly conserved? The answer would have been: no. Some are strongly conserved, some others are not. But I have never in my life assumed or proposed that all proteins sequences need to be highly conserved. I just look for those that are, and I affirm functional constraints for those sequences.

    Now, just to close, I would like to give here the definition for “cognitive bias”, which is the larger category which includes also confirmation bias. Again, Wikipedia will help:

    “A cognitive bias refers to a systematic pattern of deviation from norm or rationality in judgment, whereby inferences about other people and situations may be drawn in an illogical fashion.”

    Now I will make a judgement, and I take full responsibility for it:

    To affirm that there is confirmation bias in the reasoning of another person, while there is none, is a good example of cognitive bias: an inference about other people drawn in an illogical fashion.

  389. 389
    Mung says:

    gpuccio,

    You are always a gentleman so it is not within my heart to offer you insults in exchange for kindness.

    I can really see no other possible explanation.

    Maybe common descent is false. Do you think perhaps Alicia doesn’t accept common descent?

    😉

  390. 390
    Alicia Cartelli says:

    Mungy, I will concede as soon as you provide me with the name of an enzyme “that detaches the amino acid from the tRNA so that it can be added to the peptide chain.” Provided that enzyme (ribozyme) name isn’t “the ribosome.”

    Gpuccio, this was your original statement:
    “That’s probably why a lot of aminoacid sequences are so conserved, even from prokaryotes to humans (see ATP synthase, and a lot of others. Histones, for example).”
    We are not arguing about the evolutionary importance of sequence similarity. Don’t try to twist what the original conversation was about. Evolution was never part of the conversation. We are arguing whether or not the majority of proteins have highly conserved sequences, of which you used the two wide-ranging examples ATP synthase and histones. Then you had to backtrack and say “oh I only meant the alpha and beta subunits of ATP synthase.” So, like I said, you specifically picked the most conserved peptide sequences to support your claim that “a lot of amino acid sequences are so conserved.” This is the definition of confirmation bias. No need to write a novel about how you moved the goalposts. What you should have done was provide some statistic that this % of proteins have at least this % of sequence conservation. But you didn’t.

    What about the 50 amino acids present in our beta-subunit and not in that of A. halopraeferens? They certainly weren’t conserved, but your 82% doesn’t reflect that.

  391. 391
    Mung says:

    Alicia, “the ribosome” is not an enzyme. So why would I say that the name of the enzyme is the ribosome?

    Here’s how a book on molecular biology puts it:

    As the peptide chain continues to grow it is constantly cut off from the tRNA holding it and joined instead to the newest amino acid to be brought by its tRNA into the A-site, hence the name “acceptor” site.

    Now I can understand why your “model” has no tRNA. It doesn’t have a ribosome either. Nor does it have proteins. Lots of imagination, it has lots of that.

    You’re still faced with the problem that’s already been pointed out. You have to re-create the entire system again.

    Oh, and in addition to the things I’ve already pointed out:

    Initiation Complex
    Elongation Factors
    Release Factors

    Get busy.

  392. 392
    Alicia Cartelli says:

    That’s why I said “ribozyme,” mungy.
    I’m still waiting for the name of an enzyme “that detaches the amino acid from the tRNA so that it can be added to the peptide chain.”

  393. 393
    StephenB says:

    Carpathian

    That is not philosophical at all.

    Anything related to the logical possibility that the God of Genesis could or could not create something from nothing is a philosophical proposition. Science has nothing to say about it.

    It’s logic based on premises kairosfocus provided.

    No, it is based on your false interpretation of kairosfocus’ comment. He said nothing about God and Genesis. It was you who introduced that element. You appear to know nothing about the scientific inference to the best explanation. Please take this opportunity to tell us how you think it works.

    If a lab created life, whoever ran the lab could not have been alive.

    This statement is illogical twice over. If someone is “running” the lab, then that same someone is doing the creating. Also, any “whoever” would be alive by definition. I don’t know of any “who’s” who are not alive. Do you?

    No IDist has ever stepped through the processes involved in ID, not even Dembski.

    Again, you are talking nonsense. How can you know if any IDist has ever stepped through the process if you don’t know what that process is? Obviously, you cannot. Describe the ID process so that we can know that you are not just writing aimlessly for effect.

  394. 394
    Box says:

    Alicia:

    “Amino acids with similar properties and folds” sounds to me like “repeatable production of proteins,” which, last I checked, is the basis of translation.

    So, a chain of amino-acids sorted on size and hydrophobia is in your opinion similar to the functional proteins we find in organisms? Tell me more about the “translation” you envision. For one thing, what is being translated?

  395. 395
    Alicia Cartelli says:

    “a chain of amino-acids sorted on size and hydrophobia is in your opinion similar to the functional proteins we find in organisms?”
    Yes. I don’t know why you guys are so obsessed with the word “sorting,” but yes. If you can repeatedly create a chain of amino acids not with an exact sequence, but at least with the same general types of amino acids (large/small, hydrophobic/philic) in the same order, then it would be very similar to the proteins we see in organisms today. Just take a look at the conversation I’m having with Mung, you’ll see that nature has already demonstrated that many of the amino acids in the majority of proteins do not need to be preserved when comparing across species (they can and often are replaced with amino acids of a similar type) and this is in organisms who must maintain a high level of fitness. For the first living organisms, things did not need to be nearly as regulated, efficient, etc.
    And to your last question; a nucleic acid sequence is being translated to an amino acid sequence.

  396. 396
    Andre says:

    Alicia

    Hold on a minute… these first organisms.did not need that much regulation? Hahahaha hahahaha you are absolutely wrong. Dead wrong.

  397. 397
    gpuccio says:

    To all (except Alicia Cartelli):

    Moving the goalposts?

    My statement:

    ““That’s probably why a lot of aminoacid sequences are so conserved, even from prokaryotes to humans (see ATP synthase, and a lot of others. Histones, for example).””

    Alicia Cartelli:

    “We are arguing whether or not the majority of proteins have highly conserved sequences, of which you used the two wide-ranging examples ATP synthase and histones.”

    Well, a lot does not mean the majority. I could list hundreds of proteins which have extremely high conservation, and therefore very high functional constraint. Which certainly qualifies as “a lot”, but certainly does not qualify as “the majority”.

    And, obviously, we have always been “arguing about the evolutionary importance of sequence similarity”, because the evolutionary importance of sequence similarity means functional constraint, and that’s what we were arguing about.

    Before Alicia Cartelli moved the goalposts and tried to squirm away.

    Not so intelligently.

    Now, I am really finished with this person.

  398. 398
    Mung says:

    Alicia Cartelli:

    I’m still waiting for the name of an enzyme “that detaches the amino acid from the tRNA so that it can be added to the peptide chain.”

    Why? You’ve already conceded that biologists suck at naming things. Whatever it’s name is, it’s not “the ribosome.”

    Suffice it to say that such an enzyme exists. Even you have not disputed that fact.

    Meanwhile, your toy model is just that, a toy. Not something for grownups. It’s not something capable of translation.

    Do get back to us when you have something of substance.

  399. 399
    Alicia Cartelli says:

    Care to explain why I’m dead wrong Andre? Or are we just supposed to believe that you know what you’re talking about. All signs point to no.

    Usually when I use the phrase “a lot” I’m talking about a significant portion of a whole, Gpucc. Feel free to list these “hundreds of proteins.” Evolution was never part of the conversation. We were simply looking at sequence conservation. You really are lost.
    Good chat.

  400. 400
    Alicia Cartelli says:

    I haven’t disputed that fact? Why do you think I’m asking for the name of the enzyme? I know you won’t come up with one because I know it doesn’t exist. The only enzyme “that detaches the amino acid from the tRNA so that it can be added to the peptide chain” is not an enzyme, it is a ribozyme and it is called the ribosome.
    And my model does translate, thank you. If it’s so childish, the. It shouldn’t be too hard for you to pick it apart.

  401. 401

    I’ll drop in here for the 400-ish comment:

    Biosemiosis.org is now one week old. Looking at the site analytics, the site has now been viewed in 167 cities in 32 countries. It is amazing how much of Europe is represented in discussions of biosemiosis. The sister site Complexity Cafe has been viewed in 129 cities in 26 countries. In both cases the volume must be improved, but I am satisfied given that it has only been announced in this one article for seven days, and has been off the front page of UD for four of those days. Bottom line: I have much work to do.

    Thank you to all who have participated.

  402. 402
    Mung says:

    Over at TSZ Reciprocating Bill admonished me for bumping a similar prior thread here at UD a couple years ago and not recalling the relevant contents of that thread.

    May this thread go as long and have the same results!

    still unrefuted

  403. 403
    Andre says:

    Alicia

    Can we use you as a guinea pig? Let’s stop the regulatory systems in your cells and see how long you last? Deal?

  404. 404
    Mung says:

    Alicia Cartelli:

    I haven’t disputed that fact?

    No, you haven’t. Do you follow your own posts/arguments? I mean, seriously. Earlier you confused me with someone else:

    Alicia Cartelli:

    Just take a look at the conversation I’m having with Mung, you’ll see that nature has already demonstrated that many of the amino acids in the majority of proteins do not need to be preserved when comparing across species (they can and often are replaced with amino acids of a similar type) and this is in organisms who must maintain a high level of fitness.

    When and where did you and I have this conversation?

    I haven’t disputed that fact?

    No, you haven’t. If you’re following our conversation, as I have been doing, you haven’t claimed that the enzyme does not exist, you’ve merely quibbled over what it’s name is.

    Alicia Cartelli:

    I haven’t disputed that fact? Why do you think I’m asking for the name of the enzyme? I know you won’t come up with one because I know it doesn’t exist. The only enzyme “that detaches the amino acid from the tRNA so that it can be added to the peptide chain” is not an enzyme, it is a ribozyme and it is called the ribosome.

    Make up your mind. It doesn’t exist. It exists but doesn’t have a name. It exists and it’s name is “the ribosome.” But really, it’s a ribozyme.

    If it’s a ribozyme, surely you can tell me it’s name.

    The ribosome itself is composed of two sub-units, and these have to be brought together during the process of translation.

    So when the authors say:

    The ribosome … has enzymes that detach the amino acid from the tRNA, attach it to the growing amino acid chain, and release the tRNA, which can now be used again.

    You could at the very least explain why they are wrong.

    You could also explain why the following is wrong:

    Acyltransferases that use AMINO ACYL TRNA as the amino acid donor in formation of a peptide bond. There are ribosomal and non-ribosomal peptidyltransferases.

    But you won’t. You didn’t even have the good sense to do your research. Apparently you thought you could rest easy assuming I would not do mine. Your bad.

    The ribosomal peptidyl transferase center (PTC) resides in the large ribosomal subunit and catalyzes the two principal chemical reactions of protein synthesis: peptide bond formation and peptide release.

    Just as I had said.

    Further, dispelling all doubt:

    The crystallographic structures compellingly confirmed that peptidyl transferase is an RNA enzyme.

    Now, please tell me again why you are right and I am wrong. Please go easy on me. I’m just an IDiot. A “scientifically illiterate, biological science-challeneged UDer.”

    Alicia Cartelli:

    …there are really no “peptidyl transferase” enzymes…

    The ribosomal peptidyl transferase center: structure, function, evolution, inhibition.

  405. 405
    kairosfocus says:

    Carpathian (et al):

    This thread has been picked up elsewhere at UD, I clip a response from there:

    ________________

    >>Per clearing up the smoke of burning strawmen, I note that the matter to be explained per observation is biological life on earth. Encapsulated, smart-gated, metabolising automaton using code-based vNkSR cell based life.

    In the exchange you did not link, 342 in context, I wrote (but having a RW life had not got back to follow up yet, this is a wee hours pause to comment):

    FSCO/I — a summary term for something identified by Orgel and Wicken in the 70’s . . . — is a strong sign of design as cause. So, if such a designer is empirically indicated per inference to best explanation and we are able to see that a designer of life needs very good computation simulation or the equivalent powers indeed and one for the cosmos needs in addition sheer raw power in scads to implement a cosmos, then it seems that we have in hand a pivotal observational base indeed. Just the FSCO/I in those contexts allows us to reasonably infer to design and requisites of design point to significant powers. BTW, on life, I’d suggest that several generations of Moore’s law scaling point to pretty awesome computing power so I remain at the point, molecular nanotech lab is all that is required.

    In short I pointed out that the actual empirical evidence in hand does not allow us to translate an inference to design of cell based life on earth does not in itself suffice to infer as to whether a designer of such life would be within or beyond the observed cosmos. Something that . . . had you been familiar with say the first actual technical work by Thaxton et al (TMLO) . . . you should know has been acknowledged by leading design thinkers for over 30 years.

    Your talking points have majored on distorting this into an argument to in effect be that inferring design on FSCO/I in cell based life is an inference to God as designer.

    Not so, kindly stop the caricaturing.

    Next, you make a typical materialist error, conflating life with biological life; and often, biological life on earth. This generates a perceived contradiction that is sometimes triumphalistically put up by the ill-informed.

    I suggest that you need to step up to the level of worldview thinking, and recognise that there are serious views out there that have a much broader understanding of life than biological life and biological life on earth. Views, that cannot be cavalierly dismissed by dressing up inherently self-refuting evolutionary materialist scientism in a lab coat.

    Going up to cosmological level, the evidence in hand points to multi-dimensional fine tuning of the observed cosmos in ways that fit it for C-chemistry, aqueous medium, cell based life. Where, we evidently sit on a locally deeply isolated operating point on physics and cosmological arrangements, making an inference to design a best explanation even in the face of multiverse speculations. Not least, as it is implausible to find ourselves in this sort of world on such, a Boltzmann Brain type world or similar would be far more reasonable to expect on such speculations.

    This level brings to the table the sort of point championed by leading astrophysicist (and lifelong agnostic), Sir Fred Hoyle, a generation ago:

    From 1953 onward, Willy Fowler and I have always been intrigued by the remarkable relation of the 7.65 MeV energy level in the nucleus of 12 C to the 7.12 MeV level in 16 O. If you wanted to produce carbon and oxygen in roughly equal quantities by stellar nucleosynthesis, these are the two levels you would have to fix, and your fixing would have to be just where these levels are actually found to be. Another put-up job? . . . I am inclined to think so. A common sense interpretation of the facts suggests that a super intellect has “monkeyed” with the physics as well as the chemistry and biology, and there are no blind forces worth speaking about in nature. [F. Hoyle, Annual Review of Astronomy and Astrophysics, 20 (1982): 16]

    That, would be a far more useful context for your reflection, especially when the two halves are tied together with wider worldview issues such as the requisites of that responsible, rational intellectual freedom that are necessary to turn discussion into anything more than blind programming issuing glyphs representing — oops, that is already loaded with issues necessitating responsible, rational freedom — ultimately meaningless mouth noises. Especially when linked, underlying ontological, cosmological and moral issues are brought to the table in that light. Because, on pain of self-referential absurdity, we must be responsibly and rationally free to seriously discuss. (No this is not strictly self-evident to most of us today, we typically lack the understanding and background for that insight that absent such freedom, rationality itself collapses.)

    Finally, I suggest this as an in a nutshell summary (with onward info) on what ID actually is: http://www.uncommondescent.com.....cientific/ — which was put up for reference only a few days past.>>
    _________________

    More can be added, but I trust the above is sufficient to outline the matter.

    KF

  406. 406
    kairosfocus says:

    AC: Pardon but empirically uncontrolled, speculative hypotheses do not count, especially in a context that is foundational to the matter and where an alternative that otherwise meets inference to best explanation is being ideologically locked out. In short, your onward response boils down to admission that you cannot pass the observed adequate cause, vera causa test. The design inference, as of right earned by inductive and analytical basis, sits at the table of discussion for the tree of life, from the roots on up to body plans including ours. KF

  407. 407
    kairosfocus says:

    GP, 397 and 381 http://www.uncommondescent.com.....ent-586823 : Need I say, constraints on functional sequences point to precisely the reality of molecular level deeply isolated islands of function . . . where IoF is of course a descriptive phrase I picked up from you many years past. That of course points onward to the beyond astronomical resources, needle in haystack blind watchmaker search challenge just to get to the component parts of the cell, much less to organise and operate the cell as a whole. Beyond lie the dozens of multicellular body plans. So, we are looking here at digitally coded, functionally specific information [dFSCI] backed up by the functional requisites of operating DNA as a physical string based storage medium . . . do I need to talk about birds nests in fishing line triggered by line twisting as just a first regulatory issue? — and the molecular nanotech info processing, communication, control/regulatory and linked numerically controlled machinery such as the ribosome. Scads of FSCO/I to be addressed where on inductive and analytical grounds it is a strong sign of intelligently directed configuration as cause. AKA, design. KF

  408. 408
    kairosfocus says:

    Mung, muy interesante. KF

    PS: The authors seem to strain to push in RNA world, not realising the IoF, needle in haystack search, chicken-egg loop significance of: “The PTC is characterized by the most pronounced accumulation of universally conserved rRNA nucleotides in the entire ribosome.”

  409. 409
    kairosfocus says:

    GP, oops, 388. KF

  410. 410
    kairosfocus says:

    SB:

    Thanks for intervention at 381:

    http://www.uncommondescent.com.....ent-586804

    and again at 393

    http://www.uncommondescent.com.....ent-586864

    I add, that having substituted a strawman caricature that the design inference is about in effect directly inferring designer per god of gaps and appeal to ignorance (instead of on tested, observed empirically reliable sign, inferring design process as best explanation causal process), C is pounding away at the strawman of his own making.

    So, he does not understand the actual design inference process, which is inference to best current causal process explanation on tested, reliable sign.He is too caught up in the caricature of his own manufacture.

    Worse, he likely then imagines we are lying as “intelligent design creationists,” by way of the design inference that has been presented ever so many times. I have even taken time to elaborate the Dembski flowchart, to a more comprehensive aspect by aspect framework.

    I doubt that he realises that such is ideologically distorted, agenda serving caricature in disregard to duties of care to truth and fairness on his part.

    Let us hope that he and others of like ilk will at length wake up from their self-bewitchment of believing their own agit-prop.

    KF

  411. 411
    Mung says:

    Q: How does one restrict the activity of an enzyme that does not even exist?

    Inhibition of ribosomal peptidyltransferase by chloramphenicol. Kinetic studies.

    A: By introducing an inhibitor that does not exist!

  412. 412
    gpuccio says:

    Mung and all:

    This is very recent, and could be of some help:

    Ribosomal Proteins: Role in Ribosomal Functions

    http://www.els.net/WileyCDA/El.....00687.html

    Published online: June 2015

    Abstract
    The assignment of specific ribosomal functions to individual ribosomal proteins is difficult due to the enormous cooperativity of the ribosome; however, important roles for distinct ribosomal proteins are becoming evident. Although ribosomal ribonucleic acid (rRNA) has the major claim to certain aspects of ribosome function, such as decoding and peptidyltransferase activity, there are also protein-dominated functional hot-spots on the ribosome such as the messenger RNA (mRNA) entry pore, the translation factor-binding site and the exit of the ribosomal tunnel. The latter is binding site for both chaperones and complexes associated with protein transport through membranes. Furthermore, the contribution of ribosomal proteins is essential for the assembly and optimal functioning of the ribosome.

    Key Concepts
    A universal nomenclature for the ribosomal proteins was introduced in 2014, which terminates the babylonic chaos of the various nomenclature systems.
    About two thirds of the bacterial ribosomal proteins have counterparts in archaeal and eukaryotic ribosomes.
    Both rRNA and ribosomal proteins are essential for assembly, structure and function of the ribosomes.
    A few ribosomal proteins are essential for the assembly, but lack a function in the mature ribosome.
    In addition to rRNA-dominated functional hot-spots such as the decoding centre and the peptidyl-transferase centre, there are also protein-dominated functional hot-spots such as the entry pore for the mRNA on the 30S subunit, the docking site for G-protein factors and the exit of the tunnel harbouring the nascent peptide chain.

  413. 413
    kairosfocus says:

    Oops, mangled a sentence — here I repost:

    In short I pointed out that the actual empirical evidence in hand does not allow us to translate an inference to design of cell based life on earth [into inferring] as to whether a designer of such life would be within or beyond the observed cosmos.

    KF

  414. 414
    Vy says:

    It is not impossible for an entity that can see or control the future like the God of Genesis.

    Glad you know.

    For any other designer trying to engage in biological ID, it is impossible.

    I agree it is impossible but for different reasons.

    That leaves the only designer capable of biological design, the Christian God.

    Yup.

    This makes the ID movement religious.

    Nope. That’s the point ID separates from biblical creation (YEC) and aliensdidit.

    I could very well say evolution is religious because it elevates time, chance and probablymaybecouldness to godhood much like the ancient Greeks did with night, chaos, love, earth etc. but I doubt you’ll agree with me.

    Do remember that Michael Ruse is on record for calling evolution a religion:

    Evolution is promoted by its practitioners as more than mere science. Evolution is promulgated as an ideology, a secular religion—a full-fledged alternative to Christianity, with meaning and morality.I am an ardent evolutionist and an ex-Christian, but I must admit that in this one complaint—and Mr [sic] Gish is but one of many to make it—the literalists are absolutely right. Evolution is a religion. This was true of evolution in the beginning, and it is true of evolution still today.

    ‘… Evolution therefore came into being as a kind of secular ideology, an explicit substitute for Christianity.

    And that’s not a quotemine despite the baseless claims of the Darwine choir.

  415. 415
    Vy says:

    While we’re speaking hypothetically, what about

    And this is where the newest meatbag on UD (to my knowledge) took off.

    If wishes were horses . . .

  416. 416
    Alicia Cartelli says:

    Are you kidding me Andre, how clueless are you? Just because we have a huge amount of regulation in our cells, that doesn’t mean the first living cells three billion years ago couldn’t get away with inefficient and unregulated processes. I’m done speaking with you, it’s pointless.

    Sorry Mung, it’s tough to keep track of all the scientifically illiterate I encounter on here. Anyways, from the start when you said “There’s also an enzyme that detaches the amino acid from the tRNA so that it can be added to the peptide chain. And, of course, there is the ribosome,” I have been ~99% sure that you were wrong. The first sentence is the ribosome. The ribosome has the only peptidyl transferase activity that “detaches the amino acid from the tRNA so that it can be added to the peptide chain.” I gave you a chance to prove me wrong, so one more time, all you have to do is come up with the name of an enzyme that “detaches the amino acid from the tRNA so that it can be added to the peptide chain,” that isn’t “the ribosome.” Goodluck!

    Kairos, I just wanted to talk about a hypothetical first translational system and how it could possibly evolve, but that’s asking too much of the biologically illiterate here.

    Mung and gpucc, papers on ribosomal proteins and how drugs inhibit the ribosome are really of little help, but I wouldn’t expect you guys to know that.

  417. 417
    Virgil Cain says:

    Alicia Cartelli, how clueless are you? There isn’t any evidence for a more primitive cell, so you lose, again.

    Do you think physicochemical processes can A) produce your ribozyme B) provide the raw materials to carry on and C) be capable of evolving new functions?

    I know why you would want to avoid those questions.

  418. 418
    Alicia Cartelli says:

    Sure there is, yes, yes, and yes, Virgy.
    I’m not avoiding any questions, I’m trying to avoiding stupidity.
    I guess I should stop visiting UD.

  419. 419
    Mung says:

    gpuccio:

    Mung and all:
    This is very recent, and could be of some help:
    Ribosomal Proteins: Role in Ribosomal Functions

    Thank you. Also just showing up over at ENV was a link to this article.

    Researchers explore how a cell’s protein-making factories are assembled

    Ribosomes, the molecular factories that produce all the proteins a cell needs to grow and function, are themselves made up of many different proteins and four RNAs. And just as an assembly line must be built before it can manufacture cars, these tiny factories must be constructed before they can put proteins together.

  420. 420
    Mung says:

    Ribosomes are composed of two subunits, one small and one large; this study focused on the assembly of the small subunit, which happens first.

    “Following ribosome assembly, all ribosomes must have the same composition with four ribosomal RNAs and all ribosomal proteins in their appropriate positions… We wanted to understand how four ribosomal RNAs and 79 different proteins are assembled to make a functional ribosome that later is able to produce all cellular proteins.”

    As has been pointed out upthread, it’s an absolute miracle that two different translation systems were discovered, the ACToy one, and then the one we actually see.

  421. 421
    Alicia Cartelli says:

    I could probably pull up 50 articles about the details of ribosomal function, all published in the last few months. I don’t know what you guys think you’re accomplishing by linking these articles, the first translational machinery was almost nothing like what we see today. I would assume the only thing they share is some type of peptidyltransferase activity. (How’s that search for an enzyme name going mungy?)

  422. 422
    Andre says:

    Alicia

    The first transitional machinery….

    Do you have any actual first transitional machinery to make your case?

    I bet you the only place we’ll find the first transitional machinery is in you imagination. Why are we entertaining trolls?

  423. 423
    Mung says:

    Alicia Cartelli:

    Mung and gpucc, papers on ribosomal proteins and how drugs inhibit the ribosome are really of little help, but I wouldn’t expect you guys to know that.

    Actually we understand perfectly. It’s the no amount of evidence can convince me syndrome and you are a classic case.

    Wrapping up, because you’ve had your chance:

    Alicia Cartelli:

    …there are really no “peptidyl transferase” enzymes…

    Alicia Cartelli:

    Why do you think I’m asking for the name of the enzyme? I know you won’t come up with one because I know it doesn’t exist.

    Yet:

    The crystallographic structures compellingly confirmed that peptidyl transferase is an RNA enzyme.

    oops. big oops. credibility gone.

  424. 424
    Alicia Cartelli says:

    Everything in biology points to chemical/biological evolution producing life and eventually the diversity of species we see today. Why not informally hypothesize about what the earliest systems could have been. I’m just here for some friendly banter, but it’s tough to do when nobody else understands molecular biology. Guess I should’ve known better.

  425. 425
    Mung says:

    Alicia Cartelli:

    Why not informally hypothesize about what the earliest systems could have been.

    Because it’s been done already. Heard of John von Neumann?

  426. 426
    Alicia Cartelli says:

    Mungy, are you kidding me? They’re talking about the ribosome. As I said from the start, your job is to find an enzyme that functions as a peptidyltransferase and “detaches the amino acid from the tRNA so that it can be added to the peptide chain,” that ISN’T the ribosome.

    And for the last time, the ribosome is technically not an “enzyme” it is a ribozyme. Which is what the authors of the paper you quoted call it in the next line that you conveniently left out. The authors were putting a bit of historical perspective in, and they also mentioned in subsequent lines about the importance of this ribozyme in the “pre-biotic RNA world and contemporary biology.”

  427. 427
    Andre says:

    Alicia

    I am certain that in your mind Darwinian evolution just has to be true. You may make accusations that we don’t understand biology all OK by me by what I do know is that you just have no clue about engineering. Perhaps you might be able to heal your brain from the Darwin virus if you actually spent some time learning about engineering and design principles and how they apply in biology? I can only hope for your cure from the lunacy that has infected you.

  428. 428
    Alicia Cartelli says:

    It’s not a matter of “it has to be right,” Andre, it’s a matter of looking at the claims made and the evidence supporting them an seeing that’s it’s the best explanation we have for the diversity of life seen today. And you don’t know how deep my understanding of engineering is, but it is quite obvious how little people here understand biology. Don’t worry about me and my “viruses,” I’d be more concerned with your need to argue about things you have no understanding of. Now that seems like borderline lunacy to me.

  429. 429
    Andre says:

    Alicia

    Wow…. “it has to be ”

    and if you are wrong? I mean afterll you’ve only produced hypotheticas… Nothing testable at all.

  430. 430
    Alicia Cartelli says:

    Andre, you’re not even making sense anymore. I said it’s not a matter of “it has to be. ” And I’m not too worried about the theory of evolution being wrong; there’s decades of work from thousands of scientists all over the globe independently piecing the process and history of evolution together. My hypothetical system is nothing but a talking point; something you are not equipped to talk about unfortunately.

  431. 431
    kairosfocus says:

    AC:

    Everything in biology points to chemical/biological evolution producing life and eventually the diversity of species we see today

    Of course the ideologised a priori materialism imposition partyline sez so, but then comes the vera causa observable adequate cause test and bye bye party line.

    So much the worse for the evidence, we go with the ideology, in effect.

    Fail.

    KF

  432. 432
    Andre says:

    A talking point you’ve tried to defend as a fact. When you find this theory of evolution please make sure to share it with everyone. And you are right for 150 or so years everyone has been trying to prove Darwin right. But how do we trust the convictions of a monkey’s mind if there are any convictions in such a mind at all?

    Darwin was wrong about natural selection acting on variation to build from molecules to man and so are you.

  433. 433
    Alicia Cartelli says:

    Kairos, you can use all the Latin phrases you want, but it still just amounts to you denying what the majority of the world has already accepted as scientific fact.

    I’ve defended a few things as fact here, but my hypothetical system is not one of them, Andre. You are just lost as usual

  434. 434
    Mung says:

    Alicia Cartelli:

    And for the last time, the ribosome is technically not an “enzyme” it is a ribozyme.

    What is wrong with you?

    Mung said:

    Alicia, “the ribosome” is not an enzyme.

    Glad to see you’re finally on board. Your credibility is still shot though.

  435. 435
    Alicia Cartelli says:

    mungy, I’ve said from the start that the ribosome is a “ribozyme.”
    Still waiting for the name of an ENZYME with peptidyltransferase activity that “detaches the amino acid from the tRNA so that it can be added to the peptide chain.”
    You are a complete waste of time, and to single you out for that says a lot here at UD.
    Until you come up with the enzyme or admit that it doesn’t exist, I will not be responding to you.
    Toodaloo!

  436. 436
    Virgil Cain says:

    Talk about dishonesty or delusion-

    Alicia Cartelli says there is evidence for a more primitive cell. She conflates a need for evidence. And to the following questions:

    Do you think physicochemical processes can A) produce your ribozyme B) provide the raw materials to carry on and C) be capable of evolving new functions?

    she answered yes, yes and yes. Great, Alicia, thank you. Do you have any evidence to support your enthusiasm? Or any way to test to see if your answered are warranted?

  437. 437
    Virgil Cain says:

    Alicia Cartelli:

    Everything in biology points to chemical/biological evolution producing life and eventually the diversity of species we see today.

    Nothing in biology points to chemical/biological evolution producing life and eventually the diversity of species we see today. We wouldn’t even know how to test such a claim. It would be like saying that physicochemical processes can produce cars and computers.

  438. 438
    kairosfocus says:

    AC, 433:

    you can use all the Latin phrases you want, but it still just amounts to you denying what the majority of the world has already accepted as scientific fact.

    First, the phrase comes from Newton. Who, wrote in Latin; then the standard language of scholarship. It stuck around and is a term for an epistemological principle of phil of sci.

    Namely, to prevent unbridled metaphysical/ideological speculation dressed up in a lab coat, in explaining traces of temporally or spatially remote (so, not directly observable) things causally, it is reasonable to insist that proposed causes be shown capable of producing the effects in the here and now observable. Then, one may reasonably argue to like causes like, especially when a unique factor is identified.

    The Alinsky-rule attempt to personalise, polarise, trivialise (oh, it’s just him putting on airs . . . ) and dismiss fails.

    Next to that, a scientific, theoretical explanation is not and cannot be a fact, indeed that is one reason such need to be testable and tested.

    The fact that you have confused a theoretical explanation that has not passed the vera causa test for a fact, in fact inadvertently shows that you have been caught up in ideological bewitchment by lab coat clad evolutionary materialism.

    Ideology is not fact.

    Confident manner assertions even when made while dressed in lab coats, are not facts.

    Question-begging ideological a pioris imposed on scientific investigations and their findings are not facts.

    In case you forgot, here is Rational Wiki’s telling, massively question-begging summary, complete with a shoal of projected strawman caricatures:

    “Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific “dead ends” and God of the gaps-type hypotheses.”

    They say bluntly what many others put in subtler form.

    Ideological captivity of science, in a nutshell.

    Undermining the credibility of science as open-mindedly seeking the truth about our world in light of empirical, observational evidence.

    And, BTW, a priori evolutionary materialism is inherently self-referentially incoherent and self-refuting; never mind the lab coat and domineering of ideologues over science, education and media institutions etc.

    Going on, science, logic and warrant are not matters of majority vote or edicts of august bodies whether dressed in lab coats, judicial robes or whatever.

    Reasoning either provides good grounds or it fails to.

    In this case FSCO/I is to be explained at OOL and origin of body plans down to our own.

    It will not escape the notice of the astute observer that if you had the goods, they would have long since been triumphantly trotted out.

    That’s the 800 lb gorilla in the middle of the room that is being studiously ignored.

    The balance on the merits is as I have described. On a trillion member observation base backed up by the needle in haystack island of function search challenge, FSCO/I has just one empirically reliable observed cause, intelligently directed configuration — aka design. Thus per inductive inference to best explanation, it is a credible signature of design.

    This holds for OOL, the root of the tree of life, and that drastically shifts understanding of balance of credibility on origin of FSCO/I rich body plans.

    Never mind what the lab coat clad magisterium wishes to impose.

    Or even pretend is “fact.”

    KF

  439. 439
    Mung says:

    Alicia Cartelli

    Still waiting for the name of an ENZYME with peptidyltransferase activity…

    The crystallographic structures compellingly confirmed that peptidyl transferase is an RNA enzyme.

    Alicia Cartelli:

    Until you come up with the enzyme or admit that it doesn’t exist, I will not be responding to you.

    The general consensus here seems to be that the less you say here the better off we all are.

  440. 440
    Alicia Cartelli says:

    That’s all fine and dandy, Kairos, but again, no need for the Latin, and no need for you to write a novel just to deny what has already been accepted as scientific fact by the majority of the people on planet earth. You’re a dying breed and if those who actually engage in science have even heard of Intelligent Design, what goes on at the DI, or is “published” in your journal, you guys are nothing but the laughing stock.
    Don’t venture too far from UD, Kairos, you won’t like what you find.

  441. 441
    Alicia Cartelli says:

    For the last time, they are talking about the ribosome when they say “RNA enzyme.” You are looking for an enzyme that isn’t the ribosome (which is technically a ribozyme). I’m done with you; you will not be able to find an enzyme that “detaches the amino acid from the tRNA so that it can be added to the peptide chain,” other then the ribosome (which as I said from the beginning is technically a ribozyme, despite incorrect usage of the term “enzyme” even by researchers).

  442. 442
    Virgil Cain says:

    Alicia Cartelli:

    That’s all fine and dandy, Kairos, but again, no need for the Latin, and no need for you to write a novel just to deny what has already been accepted as scientific fact by the majority of the people on planet earth.

    The majority accept some form of ID. Who actually thinks we owe our existence to a long series of accidents, some that worked out and some that didn’t?

    Alicia did you know that without our large moon we wouldn’t exist? Couple that fact with the other fact of total solar eclipses along with the perfect timing of intelligent observers who can use them to make scientific discoveries about the universe in which they live.

    As long as you have your imagination and your denialism you will be alright. Just don’t take a long look at the real world, Alicia.

  443. 443
    kairosfocus says:

    AC,

    dismissiveness does not answer to the substantial issue. On a trillion member observational base, the reliable and only actually observed cause of FSCO/I is intelligently directed configuration, which is backed up by the needle in haystack search challenge. From OOL forward, design sits at the explanatory, observationally anchored inductive reasoning table as the only explanation that passes the vera causa test.

    You are also still unable to acknowledge the difference between a fact and an explanation preferred by an institution-dominating ideology.

    Your dismissiveness therefore boils down to, you have no answer on the merits but have no wish to actually examine the case on the merits.

    Sad, but not particularly unexpected on such matters, on long experience.

    I think it is particularly revealing to observe your insistence on calling an explanatory model that has not met the vera causa test a “fact,” and your appeal to in effect ideological dominance, on a matter where cogent correction has been given.

    That speaks for itself on the true balance on the merits.

    I suggest to you, it is time for serious re-thinking.

    KF

  444. 444
    kairosfocus says:

    PS: You may wish to adjust your usage of the term enzyme i/l/o recent developments that are reflected in, say, Wiki:

    Enzymes /??nza?mz/ are macromolecular biological catalysts. [–> notice, focus on function not composition as AA chain based molecules. That functionality of course is typically a manifestation of FSCO/I] Enzymes accelerate, or catalyze, chemical reactions. The molecules at the beginning of the process are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life.[1]:8.1 The set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology.

    Enzymes are known to catalyze more than 5,000 biochemical reaction types.[2] Most enzymes are proteins, although a few are catalytic RNA molecules. Enzymes’ specificity comes from their unique three-dimensional structures.

  445. 445
    Box says:

    Kairosfocus:

    And, BTW, a priori evolutionary materialism is inherently self-referentially incoherent and self-refuting (…)

    KF very good to point this out time and again.
    Materialists, like Alicia Cartelli, are standing on quicksand.

  446. 446
    Daniel King says:

    Virgil Joe:

    The majority accept some form of ID.

    That settles it. It must be correct.

  447. 447
    Alicia Cartelli says:

    Yup, here we go with the FSCO/I nonsense. Thanks, but no thanks Kairos. When faced with a decision between the “science” behind ID and the field of evolutionary biology, I’m gonna go ahead and stick with the well proven scientific field (hint, it’s not ID). And oh yes, for correct usage of terms we turn to none other than Wikipedia, as if I needed more convincing of your scientific illiteracy.
    It’s been a fun weekend guys, but unless someone has something interesting to say, hopefully I won;t be back.
    Enjoy life on ID island!

  448. 448
    Mung says:

    Alicia Cartelli:

    For the last time, they are talking about the ribosome when they say “RNA enzyme.”

    You claimed it did not exist. You are wrong. You also said you weren’t arguing about the name, but about whether or not it existed. It exists. Even you admit that. So now you all of a sudden want to argue about it’s name.

    credibility. shot.

  449. 449
    kairosfocus says:

    AC, functionally specific complex organisation and associated information is not “nonsense.” The resistance to such a simple description of a reality you have to instantiate even to object speaks volumes. The associated irritation itself speaks volumes. KF

  450. 450
    Steve says:

    Glad you quoted Darwin. His comment shows he was totally oblivious to excess reproduction as a designed object.

    He believed excess reproduction was a problem for the biosphere, when actually we can observe that it is excess reproduction which supports and balances life. He saw the glass half-empty, when in fact it was half-full.

    With reference to this comment by Darwin, we can also see that Zachriel is yet again not willing to grapple with an issue head on, but simply prefers to lean on ‘their’ rope-a-dope style of argumentation.

    Yes, I understand Zachriel you will not allow yourselves to get pinned down on any issue as the cost to Neo-Darwinism’s reputation would be just too costly.

    If you had any integrity, you would reply directly to the issue and show evidence of how evolution is the cause of excess reproduciton, and how excess reproduction is a make-shift solution to a random problem faced by early life.

    You could alternately show how one-to-one reproduction was so cheap energy-wise and how in fact there was no barrier to increased reproduction etc etc.

    Yet you chose to copy/paste a quote from Darwin that exposes his ignornance of the actual positive effect of excess reproduction on the biosphere.

    So I guess the next question would be do Zachriel agree with Darwin that excess reproduction was/is a problem for life in general?

    Steve: This is a clear barrier to neo-darwinian evolutionary concepts.

    Zachriel says: Steve: design deniers never talk about excess reproduction

    Darwin, Origin of Species 1859: Every being, which during its natural lifetime produces several eggs or seeds, must suffer destruction during some period of its life, and during some season or occasional year, otherwise, on the principle of geometrical increase, its numbers would quickly become so inordinately great that no country could support the product. Hence, as more individuals are produced than can possibly survive, there must in every case be a struggle for existence, either one individual with another of the same species, or with the individuals of distinct species, or with the physical conditions of life.

  451. 451
    Alicia Cartelli says:

    Mung it would appear that your reading comprehension is what is shot. Let’s go back to what I originally said @370 when this conversation started:
    ‘Mung, the only thing that “detaches the amino acid from the tRNA so that it can be added to the peptide chain” is the ribosome.’
    Then @375 you assert that the enzyme is “peptidyl transferase”
    But the problem is that the only peptidyl transferase “enzyme” that “detaches the amino acid from the tRNA so that it can be added to the peptide chain,” is actually a ribozyme and it is called the ribosome.
    @380 I explain to you how the non-ribosomal peptidyl transferases do not “detach the amino acid from the tRNA so that it can be added to the peptide chain.” but instead link R-groups of amino acids within fully formed proteins. And it is at this point that you begin to lose it altogether with enzyme vs. ribozyme and what you were actually looking for. But that’s alright, when your background in biology amounts to next to nothing, how could anyone expect better?
    I’m done with you Mungy, say whatever you want, just know that it’s probably wrong.

    I’ve hung around here long enough to know that FIASCO is a bust, Kairos.

    Bye now!

  452. 452
    kairosfocus says:

    DK, VC is replying to an appeal to consensus and pointing out that there is significant weight of view the other way. KF

  453. 453
    Virgil Cain says:

    Daniel Koochy-koo, aka my little pufferfish @ 446- Given the evidence, out of all of the options to explain it, only ID posits testable entailments.

  454. 454
    Virgil Cain says:

    Alicia Cartelli:

    When faced with a decision between the “science” behind ID and the field of evolutionary biology, I’m gonna go ahead and stick with the well proven scientific field (hint, it’s not ID).

    Evolutionary biology is devoid of details and lacks methodology to test its grand claims. The only thing proven is that genomes change. The concepts of natural selection and drift are irrelevant for medical research. Biology is fine without the “evolutionary” label in front of it. We can study life without the imaginary narrative of universal common descent via NS and drift.

  455. 455
    kairosfocus says:

    AC, a saddening resort to schoolyard level, ill-bred name twisting, namecalling and dodging of an issue as close to hand as that to comment, you had to create text strings dependent for function on specific configuration of ASCII characters: *-*-*- . . . -*. The rhetorical violence of the reaction is a clear indication of the actual unanswered force of the point on the only observed origin — trillion cases+ in hand — of functionally specific complex organisation and associated information [FSCO/I] and of the root issue, the sadly obvious fallacy of the ideologised, closed and patently hostile mind. KF

    PS: The onlooker may wish to look here for a discussion on the significance of the functional form of complex specified information, the form relevant to the world of life as Dembski noted in NFL and as had been highlighted in the 1970’s by Orgel and Wicken.

  456. 456
    kairosfocus says:

    F/N: Just for reference, here is Orgel, 1973:

    . . . In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . . .

    [HT, Mung, fr. p. 190 & 196:] These vague idea can be made more precise by introducing the idea of information. Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure. [–> this is of course equivalent to the string of yes/no questions required to specify the relevant “wiring diagram” for the set of functional states, T, in the much larger space of possible clumped or scattered configurations, W, as Dembski would go on to define in NFL in 2002, also cf here, here and here (with here on self-moved agents as designing causes).] One can see intuitively that many instructions are needed to specify a complex structure. [–> so if the q’s to be answered are Y/N, the chain length is an information measure that indicates complexity in bits . . . ] On the other hand a simple repeating structure can be specified in rather few instructions. [–> do once and repeat over and over in a loop . . . ] Complex but random structures, by definition, need hardly be specified at all . . . . Paley was right to emphasize the need for special explanations of the existence of objects with high information content, for they cannot be formed in nonevolutionary, inorganic processes. [The Origins of Life (John Wiley, 1973), p. 189, p. 190, p. 196.]

    . . . and here is Wicken, 1979:

    ‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [[originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [[“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65.]

    The direct root of the descriptive phrase and its acronym, is obvious. So is its relevance and pivotal importance. Also, its commonplace presence in a world of technology.

    The truth is, starting with something so simple as a 6500 fishing reel, and going to cases of text, oil refineries etc, we can find direct cases all over the world of life; which, is based on functionally specific, complex organisation and associated (often, CODED) information in the cell and in organisms.

    Where, at OOL, appeal to incremental blind progressive changes through chance variations and differential reproductive success leading to incremental branching tree evolution is off the table as the vNkSR required has to be accounted for as a case of FSCO/I. The force of vera causa then comes to bear and design sits at the table as of right.

    Beyond, it then sits at the table and is confronted by a curious fact: there are in fact zero cases of actually observed macro-evolutionary origin of body plans. All is gross extrapolation from micro changes that typically have to do with breaking not creating bio-information (per Behe’s first rule).

    In short, when we observe the locking out of design as a serious contender, we see the imposition of an ideology on origins science, not an objectively grounded scientific inference much less the confident manner assertion of fact, Fact, FACT!

    So in the above, we see speaking with disregard to truth in hopes of profiting from what is said or suggested being thought to be true. We see doubling down in the face of challenge. We see projection of motivation that is irrelevant and baseless. We see the ideologised, closed mind. We see unwarranted hostility and contempt. We see something so puerile as resort to name twisting and namecaling dismissal. And, underneath is the ideological assumption of having cornered the market on the plausible — truth having long since been driven out.

    In that context, UB’s discussion, however reasonable, will meet the sort of violent reaction we just saw from an advocate of a priori evolutionary materialist scientism and/or its fellow traveller ideologies.

    But in the end, such ideologies, the closed minded mentality they inculcate and their domineering agendas will fail.

    KF

    PS: Those fixated on the “fact” claim, may find here helpful: http://iose-gen.blogspot.com/2.....l#isevofct

  457. 457
    Box says:

    Alicia Cartelli,

    AC: It’s been a fun weekend guys, but unless someone has something interesting to say, hopefully I won;t be back.

    How does it fail to qualify as “something interesting” when someone points out that your position is self-referentially incoherent? You don’t even blink. What does that tell us about you and your position?

    AC: Enjoy life on ID island!

    Enjoy “your” life in a universe with “no design, no purpose, no evil, no good, nothing but pitiless indifference.”

  458. 458
    kairosfocus says:

    Box, that is not the only sign but it is one. KF

  459. 459
    Zachriel says:

    Steve: Glad you quoted Darwin. His comment shows he was totally oblivious to excess reproduction as a designed object.

    Your claim was that “design deniers” never talk about excess reproduction. That was false. It’s been part of the theory of evolution since its inception.

    Steve: If you had any integrity, you would reply directly to the issue and show evidence of how evolution is the cause of excess reproduciton

    Evolution by natural selection is due to heredity, fecundity, and differential reproductive potential due to heritable variations.

    Steve: You could alternately show how one-to-one reproduction was so cheap energy-wise and how in fact there was no barrier to increased reproduction etc etc.

    The simplest mechanism of fecundity is binary fission.

  460. 460

    @upright biped

    What about Edwina Taborsky?

    Biological Organisms as Semiosic Systems: the importance of strong and weak anticipation

    https://tidsskrift.dk/index.php/signs/article/viewFile/71446/128775

    “The semiosic biological system is not a random or mechanical process but an informed, reasoned and self?
    controlled process.”

    Quite a dated article now. She was “accused” by a reviewer of intelligent design science, which accusation she then rejected saying intelligent design is different.

    That group of scientists around CASYS conferences, Peter Rowlands, Daniel Dubois, Peter Marcer, Vanessa Hill, Edwina Taborsky, astronaut Edgar Mitchell, Walter Schempp. They are very much more advanced than any intelligent design science in producing theory based on the fact that freedom is real.

  461. 461

    Mohammad,

    In this paper, I will focus on anticipation, … Anticipation refers to the establishment and operation of symmetry inducing normative habits of morphological formation. Anticipation is not only related to predictions but to decisions: hyperincursive systems create multiple choices and a decision process selects one choice … Strong anticipation refers to an anticipation of events generated by the system itself. Weak anticipation refers to an anticipation of events predicted or forecasted from a model of a system’. — Edwina Taborsky

    I am not sure what response you are wanting from me regarding anticipatory systems. The writing I have done on semiosis is specifically limited to the physical process of representation — i.e. what is necessary for a representation to be a representation.

    Also, I have no desire at all to pass judgment on the specialized thoughts of semiosis provided by others, but in reading Taborsky’s paper, I am quickly reminded of comments made by Pattee:

    While the language of physics is reasonably simple and unambiguous, I discovered quickly that the terminologies of semiotics are so complicated and controversial that I could not hope to find consensus on primitive symbol system terminology. As I stated earlier, linguistic terminology originated at the highest levels with human language and human behavior. Not only that, but in the recent past it was believed that symbolic language was what distinguished humans from lower animals. Consequently, the idea of a symbolic language at the origin of life was simply resisted by many linguists, anthropologists, and philosophers as unreasonable except as a vague metaphor or distant analogy.

    Evolution does not exhibit sharp and clear distinctions between functional activities like language usages even though we can see enormous differences between genetic symbol systems and the brain’s symbol systems. The important question for biosemiotics is what similarities are fundamental and what differences are irrelevant for their primary survival functions.

    I define symbol as a material constraint not determined by physical laws that controls specific physical dynamics of a self-replicating system. My usage is consistent with other definitions of a symbol, like Peirce’s triadic symbol–interpreter–referent definition. However, all the detailed refinements of Peirce’s complicated terminologies I find empirically ambiguous and unnecessary at the cellular level. I should add that symbols are arbitrary only to the extent that they are not proximally or structurally determined by laws. However they are non-arbitrary to the extent that they have been naturally or artificially selected to satisfy functional requirements.

    p.s. – If a reviewer accused Edwina Taborski of being an intelligent design advocate, they must have not read her paper. She clearly discounts “agency” within the text of the paper.

  462. 462
    Mung says:

    Upright BiPed: I am not sure what response you are wanting from me regarding anticipatory systems.

    Speaking of which.

    Anticipatory Systems: Philosophical, Mathematical, and Methodological Foundations

    But not cheap.

  463. 463
    Mung says:

    I hope I’m not the only one who will miss Alicia Cartelli.

  464. 464
    Mung says:

    peptidyltransferase – the ribosomal enzyme that catalyzes the elongation step in polypeptide synthesis

    Oxford Dictionary of Biochemistry and Molecular Biology

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