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Nobelist Jack Szostak on origin of life research: “We’re halfway there”

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Jack W. Szostak

In “From Telomeres to the Origins of Life” (New York Times, October 19, 2011) Claudia Dreifus interviews origin of life researcher (and Nobelist, for telomeres)

Jack Szostak: What do you study now?

The origins of life. In my lab, we’re interested in the transition from chemistry to early biology on the early earth. Let’s go back to the early earth — let’s say probably some time within the first 500 million years. And let’s say the right chemistry that would make the building blocks of life has happened and you have the right molecules with which you can spark life. How did those chemicals get together and act something like a cell? You want something that can grow and divide and, most importantly, exhibit Darwinian evolution. The way that we study that is by trying to make it happen in the lab. We take simple chemicals and put them together in the right way. And we’re trying to build a very, very simple cell that might look like something that might have developed spontaneously on the early earth.

How far have you gotten?

Maybe I can say we’re halfway there.

We think that a primitive cell has to have two parts. First, it has to have a cell membrane that can be a boundary between itself and the rest of the earth. And then there has to be some genetic material, which has to perform some function that’s useful for the cell and get replicated to be inherited. The part we’ve come to understand reasonably well is the membrane part. The genetic material is the harder problem; the chemistry is just more complicated. The puzzle has been understanding how a molecule like RNA can get replicated before there were enzymes and all this fancy biological stuff, protein machinery, that we have now in our cells.

It sounds as though they have solved the easy part of the problem, but that, unfortunately, doesn’t really mean “halfway there.”

79 Replies to “Nobelist Jack Szostak on origin of life research: “We’re halfway there”

  1. 1
    Joseph says:

    Yup, perhaps 1/2 way there pertaining to the hardware (big maybe) but pertaining to the software scientists haven’t even started.

  2. 2

    The hardware is the software, Joseph.

  3. 3
    Joseph says:

    Yeah right and the computer’s hardware is also its software…

    Well Elizabeth you are wrong- there is software running the hardware (living organisms are both hardware and software, the software tells the hardware what to do, or do you really think that once all the components are there then things will just run?)

  4. 4

    No, in computers, the hardware is not the software.

    There is a meaningful distinction in computers. There is no meaningful distinction in living things.

  5. 5

    Yes, once all the components are there, the thing will just run.

  6. 6
    Joseph says:

    Unfortunately you don’t have any evidence for that claim

  7. 7
    Joseph says:

    Of course there is a meaningful distinction in living things. How do you think transcription, translation, proof-reading, error-correction, editing and splicing take place?

    That is all software driven.

  8. 8
    ScottAndrews says:

    Amazing. Two parts.
    First, a membrane.
    And then that other part, “some genetic material, which has to perform some function that’s useful for the cell.”

    I take back everything I ever facetiously said about taking this seriously. (Although everything I’ve ever said to the effect that the research favors design over abiogenesis still stands.)

    Parts come together and start “acting like a cell?” If there is no cell yet, how can any genetic material be useful to it? Things just begin performing functions for other things?

    How can Szostak possibly know that he’s ‘halfway’ to anywhere? There is not a shred, not particle of evidence that there is a ‘there’ to get halfway to!

    The least offensive way I can describe this is that it is irrational. Szostak is drawing conclusions based on nothing, and people are believing him. Don’t say it’s a hypothesis supported by data. Szostak clearly thinks he’s halfway to somewhere.

  9. 9
    bornagain77 says:

    When Szostak readily admits he really doesn’t even have a clue where “THERE” is:

    And we’re trying to build a very, very simple cell that might look like something that might have developed spontaneously on the early earth.

    How in blue blazes does he even know he is halfway to anything other than what he has imagined. Given that he is not even considering how ‘quantum entanglement/computation’ developed within molecular biology, I can assure him that he is only halfway into a pipe dream!!!

  10. 10
    Blas says:

    I bet that the part they say to know, the membrane, it is also a so story.

  11. 11

    I think I’ve heard about this kind of “half way there” before: Viz: “We want to get to 10^40 Mev. We can currently do 10^20 Mev so we must be half way there”. Exponentials; who’d have them?

  12. 12
    kairosfocus says:

    Left off: you have to have genes and metabolism inside with a self-replicating von Neumann self replicator, to be relevant to observed cell based life . . . Toughie.

  13. 13
    kairosfocus says:

    Software is an intangible that is always seen by being manifested through hardware.

  14. 14
    kairosfocus says:

    Cf embedded systems, in which the software lives inside the system and in effect is only seen as executable machine code, in the context of mRNA and protein assembly.

  15. 15
    Petrushka says:

    But Szostak is looking at pre-biotic chemistry. If anyone could say with assurance how this will turn out, there would be no need for research.

  16. 16
    ScottAndrews says:

    I don’t mean to throw a wrench in, but the distinction between hardware and software in computers isn’t quite so clear.
    When we say “hardware” and “software” we know exactly what we mean. It’s not the terms are ambiguous.

    But software and the processor are both doing the same thing. You execute a program. The program calls a function within itself or in some other library. It calls another. At the bottom it’s calling a function that resides within the processor. In a sense they are the same. The only difference is that some functions are stored in memory or elsewhere while others are etched in silicon.

  17. 17
    Upright BiPed says:

    You want something that can grow and divide and, most importantly, exhibit Darwinian evolution.

    “Darwinian evolution” is the transfer of actual, not analogous, information. As such it places observable physical requirements on the materials within the system. Nowhere is Stzostak’s brilliant research does he pay one iota of attention to this observed reality in the systems as they are actually found. His model is therefore flawed from the outset. Just take a look at the silly videos on YouTube promoting his model. There is absolutely nothing there about these observable qualities coming about.

    When all this fails (which it will most cartainly do) please let us all remember the drumbeat of questions coming from the orthodoxy; “What practical use is there to design thinking?” Well, here are three irreversible entries onto that hypermutable list.

    Wasted money. Wasted time. Wasted science.

  18. 18
    Eocene says:

    Szostak:

    “And we’re trying to build a very, very simple cell that might look like something that might have developed spontaneously on the early earth.”

    BA77:

    How in blue blazes does he even know he is halfway to anything other than what he has imagined. Given that he is not even considering how ‘quantum entanglement/computation’ developed within molecular biology, I can assure him that he is only halfway into a pipe dream!!!
    ===

    You’ve missed an even more important point here. Look again at the man’s own words and what they are really saying.

    “And we’re trying to build a very, very simple cell . . ”

    Jack Szostak along with Gerald Joyce(RNA-World Myth Fame) both are perfect examples of how you prove Intelligent Design, but no one ever holds them accountable for their cheating and lying. We never once get a clean honest observable experiment that is likewise replicatable to help us all understand just how blind undirected forces without goals or purpose accomplish anything. So the next time an Atheist backslides on a question and does a desparate default “Burden Shift” on you and demands an explanation on just how ID explains it, point to their own work done by their religious Cult leaders.

    Ultimately it doesn’t matter what their own intended Atheistic/Agnostic goal or purpose was in the experiment. Only that it indeed was! And it needed an inteligence to manipulate and rig the thing for a forced outcome.

  19. 19

    Point taken, Scott, but that’s why there is no point in making the distinction when it comes to cells. Unlike a computer, where you have a box, with various components in it, and then you install some operating system, then some software, that sequence is meaningless when talking about cells (or brains, for that matter). You don’t have “hardware” molecules then “install software” on them. What you have is are molecules that obey the laws of physics and chemistry. You couldn’t take a cell and “wipe the operating system” or “install a new operating system” without changing the actual molecules.

    The distinction is completely meaningless in the context of a cell.

  20. 20
    material.infantacy says:

    That about sums it up.

    Building A Computer

    First half: the case.

    Second half: CPU, memory, motherboard, video card, sound card, Ethernet, hard drive, et cetera.

    Third half: BIOS and operating system.

  21. 21

    Do you have that phrase set up as a keyboard shortcut, Joseph?

    Yes, there is evidence for that claim.

    Genetic engineering for a start – you change part of a DNA molecule, and “the thing just runs”.

    Or take the paper we were discussing the other day – Joyce’s work. “We just let them cook, let them amplify themselves silly” said Joyce.

    To use your favorite phrase: you don’t have any evidence for vitalism.

  22. 22
    material.infantacy says:

    In cells, the hardware is an expression of the software, which is assembled by the hardware. Indeed, the computer analogy is not perfect, but there’s nothing more appropriate — until we invent software which instructs the construction of its own assembly and replication hardware, via an already bootstrapped system, otherwise dependent on the software and hardware that it replicates.

  23. 23

    I thought I’d responded to this:

    Scott, do read Szostak’s actual papers, not a brief transcript of an interview.

    It is you who are “drawing conclusions based on nothing”. Szostak’s hypotheses are indeed supported by data, but you need to read the actual papers to find out what.

  24. 24
    Upright BiPed says:

    What you have is are molecules that obey the laws of physics and chemistry.

    …and which exhibit properties beyond physics and chemistry.

  25. 25

    Do read his papers before you “sum…it up”.

  26. 26

    Nowhere is Stzostak’s brilliant research does he pay one iota of attention to this observed reality in the systems as they are actually found.

    Yes, he does. You seem to have forgotten about the polymer part of the story.

  27. 27
    material.infantacy says:

    You don’t have “hardware” molecules then “install software” on them. What you have is are molecules that obey the laws of physics and chemistry. You couldn’t take a cell and “wipe the operating system” or “install a new operating system” without changing the actual molecules.

    You don’t have “hardware” magnetic particles and then “install software” on them. What you have are magnetic particles that obey the laws of physics and chemistry. You couldn’t take a hard drive and “wipe the operating system” or “install a new operating system” without changing the actual magnetic particles.

  28. 28

    Yes indeed. The properties of a system can be, and usually are, different from the properties of its parts.

    And if you have a self-replicating entity where the those that replicate best have physical/chemical attributes that differ from those that replicate less well, the physical/chemical attributes of those that replicate best will embody information about how to create a system that replicates well in that environment.

    There is nothing spooky about it at all. In fact it’s self-evidently true.

  29. 29
    Collin says:

    Fine. The hardware that is also the software is not there. Is that a more accurate statement?

  30. 30
    material.infantacy says:

    We think that a primitive cell has to have two parts. First, it has to have a cell membrane that can be a boundary between itself and the rest of the earth. And then there has to be some genetic material, which has to perform some function that’s useful for the cell and get replicated to be inherited. The part we’ve come to understand reasonably well is the membrane part. The genetic material is the harder problem; the chemistry is just more complicated. The puzzle has been understanding how a molecule like RNA can get replicated before there were enzymes and all this fancy biological stuff, protein machinery, that we have now in our cells.

    The point is made by Szostak’s own words from the interview, innit?

    Maybe I can say we’re halfway there.

    You sound defensive.

  31. 31

    Well, I’m defending research that is much more substantial than you are inferring.

    Szostak’s work is not just about the lipid vesicles, but about how their probability of reproducing may be influenced by included polymers, and how the actual sequences of those polymers might further affect reproductive success.

  32. 32
    Collin says:

    Liddle, you have a good point, but material.infantacy also has a good point. Obviously Szostak himself thinks that the genetic material is the harder half of the problem.

    But I actually admire his optimism. It is a good quality in a scientist and I don’t think he is trying to be dishonest or anything. I just think he has overstated his case a little. After all, he seems to not even think it’s a problem that the cell membrane part was created in a lab under controlled conditions.

  33. 33
    Upright BiPed says:

    In what part of the model do those polymers take on the essential charateristics of representations and protocols?

  34. 34

    When the sequence itself affects the probability of reproduction.

  35. 35

    Yes, he does think so. But his lipid vesicle idea was pretty good, as one of the problems that has to be solved with the polymer part is how to make it part of a whole system that reproduces, and in which the polymer components are kept together and passed on to the clone.

    So the membrane work has huge implications for the polymer part, and isn’t really separate.

  36. 36
    material.infantacy says:

    Do the sequences that favor molecular replication also represent functions required for a proto self replicator? The sequence specificity required for assembling proteins is what’s at issue — and how that comes about in genesis with the stored sequences in DNA.

  37. 37
    material.infantacy says:

    “Wasted money. Wasted time. Wasted science.”

    I’ll politely disagree with the wasted science part.

    Eventually the research might indeed be valuable for instructing the next generation of scientists how brilliant nanotechnology is intelligently designed.

  38. 38
    Upright BiPed says:

    The transfer of information during protein synthesis is semiotic. It requires an arrangement of material that to act as a representation which is immaterial to its resulting effect within the system. It requires a second coodinated arrangement of material that establishes the immaterial mapping from the representation to the material effect. It requires the material effect to be altered by the input of the representation, and it requires each of these physical things to operate discretely from one another.

  39. 39
    Upright BiPed says:

    check

  40. 40
    Upright BiPed says:

    That wasn’t an answer. It was specifically a non answer.

  41. 41
    material.infantacy says:

    And I was responding to the man’s own words.

    I don’t believe the research is insubstantial — I believe that it doesn’t support what it promotes, and there’s a big difference.

    While at most the research moves along how abiogeneses might have produced the first life, at the least it demonstrates how intelligent design definitely gets it done.

    Quite obviously, I took issue with the “halfway there” comment, in the context of Szostak’s other remarks. It’s a valid criticism, and a good opportunity for a bit of fun.

  42. 42

    Which post are you replying to?

  43. 43
    material.infantacy says:

    Collin, there’s also a connotation of promoting the efficacy of self organization. It’s hard to escape the tacit suggestion that self organization solves the problem — that once you can isolate a host of good molecules via a membrane to keep the devil substances out, the rest eventually takes care of itself.

    This is the assumption that ID thought challenges, and hence the catalyst for the various “halfway there” jabs. I think this point was lost on EL, who seemed to take some offense at my comments as criticisms of the research itself.

    m.i.

  44. 44
    mike1962 says:

    EL: The distinction (software vs hardware) is completely meaningless in the context of a cell.

    Hardware refers to physical entities. Software refers to temporal relationships of those physical entities, and the order in which events occur. A change in the DNA nucleotides amounts to a software change which can result in a hardware change. Similar to how a change in a CNC “tape” can change the shape and function of the object that the CNC produces.

    There is clearly a distinction between software and hardware operating within a cell.

  45. 45
    Upright BiPed says:

    BIPED: In what part of the model do those polymers take on the essential charateristics of representations and protocols?

    LIDDLE: When the sequence itself affects the probability of reproduction.

    Setting completely aside the unresolved issue of how these polymers are being reproduced (at all) with mutable inheretance (in order to have one version be more successful than another). There is absolutely no substance in your answer whatsoever as to the issue of how two arranegments of matter became coordinated to result in a specified effect while all three remain physically isolated from one another. Zero.

  46. 46
    lastyearon says:

    Mike,
    So what the cell is, is hardware, and what the cell does is software ?

  47. 47
    lastyearon says:

    the issue of how two arranegments of matter became coordinated to result in a specified effect

    Arrangements of matter become coordinated to produce specific effects all the time. Are they all miracles?

  48. 48
    lastyearon says:

    It’s only when you assume that the specified effect is special, or purposeful that you find it hard to believe it occurred without intervention by an intelligent designer.

    This is another example of assuming your conclusion that life was designed.

  49. 49
    material.infantacy says:

    Agreed.

    Now turn this 90 degrees and have the CNC mill produce itself as the object, as directed by a new set of instructions. The instructions are what determine the object that’s created. The ability to self-replicate would be a function of the software. The ability to replicate other objects would also. In either case the hardware is constant, and needs to be in place ahead of any instructions it receives.

    Hardware and software are indeed separate. There’s nothing conceptually inhibiting about using the sophisticated production facility of a living cell to produce other nano machines, given different software — that is, a different, but still very specific, permutation of the nucleotides in the same DNA molecule.

  50. 50
    Upright BiPed says:

    I will grant you this lyo, your answer has as much substance as Dr Liddle’s

  51. 51
    material.infantacy says:

    My 9.2 was at mike1962.

  52. 52
    lastyearon says:

    Thank you. : )

  53. 53
    Upright BiPed says:

    LYO, I don’t “assume” anything. Please don’t project strawman onto what I say.

    I am talking about the observed physical entailments of recorded information transfer, nothing else.

  54. 54

    But the point is that you don’t need to first install hardware then install software!

    So it would be nonsense to say: first Szostak has to make the molecules then he has to program them.

    They aren’t different things.

  55. 55
    ScottAndrews says:

    Elizabeth,

    How could you possibly know what I have or haven’t read? Do you conclude that I didn’t read anything because I don’t agree with it?

    You can’t say you’re halfway to a conclusion when you’ve produced a single result that may or may not be relevant the conclusion you think you’re halfway to.

    And he can’t claim to be halfway to an explanation without assuming the explanation he’s looking for exists.

    And he’s admittedly trying to build a cell (his word) which couldn’t have less to do with seeing if a cell could build itself.

    The point is that it doesn’t matter if his hypotheses are supported by data. It’s has nothing to do with whether his experiments are repeatable or his findings accurate. He’s not hypothesizing anything that relates back to abiogenesis.

    Answer this, if you wish: Without knowing (A) whether abiogenesis is possible, which is what he is supposedly attempting to demonstrate, or (B) if A is true, whether the formation of fatty vesicles he tested played a role in that process, how can he reason that he is on his way to anything? That’s assuming two conclusions.

    Yes, his hypothesis is supported by data. But the only conclusions that can be drawn, even provisionally, are that his experiments are repeatable. And, if he achieves his stated goals, we may conclude that he can, in fact, synthesize living cells in a laboratory.

    The trouble is that you use such obvious statements as ‘all conclusions are provisional and ‘his hypotheses are supported by data’ to blur the reality that he can’t possibly know whether he’s even pointed in the right direction or whether the event he’s seeking to replicate ever occurred, let alone claim to be halfway or even one step toward it.

  56. 56
    Upright BiPed says:

    The input is not the output, Dr Liddle.

    Not only are the conceptually distinct in common parlance, but they are indeed physically isolated from one another inside of every living cell on Earth.

  57. 57
    Joseph says:

    Elizabeth:

    Genetic engineering for a start – you change part of a DNA molecule, and “the thing just runs”.

    Actually you change part of teh DNA and the software tells it what to do- the software that was already in the cell.

    What Joyce observed doesn’t require software. It is just simple template replication- ONE bond was created, nothing more.

    Craig Vetner- plugged in synthesized DNA and the cell’s software took over. Without the cell’s already existing software he wouldn’t be able to do that.

  58. 58
    material.infantacy says:

    EL, you’re assuming your conclusion, unless you’re position is that Szostak’s research does nothing to bring us to a proto self replicator.

    If the research is supposed to explain the origin of self-replicating organisms, then you need to explain the hardware and the software (the sequence specificity of proteins stored in DNA).

    Interviewer: What do you study now?
    Szostak: The origins of life. In my lab, we’re interested in the transition from chemistry to early biology on the early earth.

    To claim that a cell is just the result of molecular self-replication is begging the question, ignoring the enormous problem of the sequence specificity required to assemble proteins.

  59. 59

    Setting completely aside the unresolved issue of how these polymers are being reproduced (at all) with mutable inheretance (in order to have one version be more successful than another).

    Well, it’s on the way to being resolved. We were talking about this the other day, with reference to the Joyce work. In Joyce’s work, molecules replicated, with variance, and the best replicators eventually outnumbered the originals. As Joyce says, it’s not “artificial life” yet, because the molecules were carefully designed, and had to be “fed” with other carefully designed molecules. Nonetheless, they cross-replicated on their own, with mutatiblity, and the best mutants won.

    But I guess we can set that aside eh 🙂

    There is absolutely no substance in your answer whatsoever as to the issue of how two arranegments of matter became coordinated to result in a specified effect while all three remain physically isolated from one another. Zero.

    Which “two arrangements of matter” are you talking about? If vesicles with one sequence of polymer reproduce better than vesicles with a different sequence, then the ones with the first sequence are transferring information as to how to reproduce better to their offspring. The “specified effect” is “reproducing better”. Could be simply because one sequence is richer in materials that are more readily available. A number of possibilities are mentioned in that video you don’t like.

  60. 60
  61. 61

    No, I am not “assuming my conclusion”.

    Szostak, and others, are working on possible scenarios by which very simple self-replicating entities, possibly no more than lipid vesicles enclosing simple polymers that self-replicate when subjected to some cyclical effect such as regular temperature oscillations in a convection current.

    One of the hard parts is figuring out how self-replicating molecules might form spontaneously, but there are already some clues, and some self-replicating RNA molecules and peptides have been produced in labs.

    Once you have a self-replicating molecule – one that catalyses the formation of a copy of itself from new materials – then you have information transfer. The sequence in the “parent” molecule is transferred to the “daughter” molecule.

    So the vesicle fills with copies of the enclosed molecule (this is why the vesicle is important – if this was just happening in an open environment, you wouldn’t get a concentration of copies of the same molecule) and eventually divides in two, resulting in two vesicles with molecules with that same sequence in both. Rinse and repeat.

    You’ve got the very beginning of a cell. Now let’s say that some of those self-replicating molecules tend to enhance the chance of successful “cell” division. Possibly by catalysing some useful molecule, possibly there might be an optimal length of polymer, whatever. Now those proto-cells that have “better” sequenced polymers will start to outnumber those that have less good sequences. So the population is now dominated by proto-cells whose polymer sequences are “selected” for successful replication, and this “information” – about how to replicate successfully – continues to be passed on, with any variant that improves things still further tending to dominate the population, and any variant that doesn’t being “eaten” by the competition.

    No question is being “begged” here. If Szostak can show how the right ingredients tend to result in an evolving protocell, then he’s pretty well shown a mechanism by which life could have begun, even if we never know for sure how it did begin.

    The specificity, of course, evolves. In the early days, all that may be specified is polymer length, or polymer constituents (optimal length; optimal balance of constituents); later, polymers that catalyse reproduction-enhancing molecules will tend to be selected; later still, polymers that tend to catalyse the formation of other catalysts well tend to be selected.

    But before we know how (or whether) this happens, we need to know something about how those first self-replicating molecules were generated, and what they were – did RNA come first, or peptides? Or did they co-evolve?

  62. 62
    Upright BiPed says:

    Question #1: I fear you becoming a living characature of yourself.

    Question #2: You know exactly what I am talking about.

    – – – – – –

    Dr Liddle you said that you were going to attack my argument. Why not stop with this, and simply do it.

  63. 63

    UBP, as happens so often, I have no idea what you are talking about, I’m afraid.

    The thing seems absolutely straightforward to me. If something replicates itself then information is transferred from parent to offspring.

    And if that information includes accrued information about how best to survive in that environment, as natural selection ensures, then the information has considerable effect.

    What more do you want?

  64. 64
    ScottAndrews says:

    This theme seems to repeat that all you need is replication with variance and you get evolution.

    Especially in the initial phases, why would any selective or environmental pressure be so considerate and thoughtful as to precisely distinguish between one variation and the other? Isn’t it more probable by far that it would be an all-or-nothing affair? Everything gets wiped out?

    I can’t imagine a more likely time for an extinction event than ten seconds after these hypothetical molecules start self-replicating. It’s a bit like lighting a match in a blizzard.

    One of the hard parts is figuring out how self-replicating molecules might form spontaneously

    Especially since as soon as you figure it out and repeat the test it’s not quite so spontaneous.

    Otherwise, why not add the word “spontaneously” to every experiment ever performed and every result ever achieved? If you can do it and you can repeat it then it can happen spontaneously.

    An electric current can pass through a tiny filament made of the correct material and generate bright light without burning up, spontaneously.

    A projectile can be launched at the correct velocity and enter orbit, spontaneously.

    A compound to regrow hair in your bald spot can be formed from substances X, Y, and Z in the proper proportions and at the correct temperature, spontaneously.

    As I’ve pointed out more than once, and you have not refuted, and now Szostak has stated clearly, abiogenesis research is design research, and the possibility of the steps of each experiment repeating spontaneously with a similar result is a tacked-on question mark.

    But now I realize it’s even more fun if you go the other way. Every repeatable experiment is a now a demonstration of what might happen spontaneously. This really makes my day.

  65. 65
    kellyhomes says:

    Upright,
    I often hear that ID is about studying the designs to come to conclusions about the designer, as the designer cannot be studied directly.

    As you have obviously taken a great deal of time studying information transfer, could you tell me where and how “Intelligent Design” actually relates to all these observed physical entailments of recorded information transfer you keep talking about?

    Or in other words, great, symbols and all that. Fantastic. But what does it all amount to? What new can you tell me about the design, the designer or anything about how anything came to be the way it is?

    It requires a second coodinated arrangement of material that establishes the immaterial mapping from the representation to the material effect.

    And who or what is coordinating that arrangement of material? When? How? How many times?

    Can you actually tell me something about it other then it happens? If not, what use is your argument, if say for example Elizabeth accepts it? Will it have no entailment in the real world, will you instead go on to find another person who disagrees and you’ll wear them down over time until everybody in the world agrees with you? Once that happens will we be able to move on to studying the design for information bout the designer?

  66. 66
    kellyhomes says:

    Scott,

    This theme seems to repeat that all you need is replication with variance and you get evolution.

    I’m convinced. So tell me the ID version of the OOL story.

  67. 67
    Upright BiPed says:

    Kellyhomes,

    I see you question, but have not studied it. I will respond when I arrive home.

  68. 68
    ScottAndrews says:

    Kelly,

    Please see the Szostak’s research in which he is attempting to intelligently design a living cell. Some say that the research is preposterous and that he’s overly optimistic, but don’t dismiss it without reading it. The hypotheses are supported by data. All conclusions are provisional. That’s how science works.

  69. 69

    This theme seems to repeat that all you need is replication with variance and you get evolution.

    Well, you do! As long as the variance results in differential reproductive success!

    Especially in the initial phases, why would any selective or environmental pressure be so considerate and thoughtful as to precisely distinguish between one variation and the other? Isn’t it more probable by far that it would be an all-or-nothing affair? Everything gets wiped out?

    Well, that’s the point of a lot of the research. For instance, regarding the membranes, Szostak has done some very interesting work showing reproductive advantage for quite low levels of phospholipids in the membrane. And other experiments have set out to test hypotheses regarding the effects of different sequences on the ability of the vesicle to divide – I’m not sure how much of that have been tested, but there are certainly quite a few testable hypotheses.

    I can’t imagine a more likely time for an extinction event than ten seconds after these hypothetical molecules start self-replicating. It’s a bit like lighting a match in a blizzard.

    Well, that’s the beauty of the lipid vesicle hypothesis. They are in tents.

    Especially since as soon as you figure it out and repeat the test it’s not quite so spontaneous.

    Otherwise, why not add the word “spontaneously” to every experiment ever performed and every result ever achieved? If you can do it and you can repeat it then it can happen spontaneously.

    I think there is an equivocation with the word “spontaneously” here.

    Take sodium and potassium. If you drop a little piece of sodium into water, it doesn’t always ignite “spontaneously” although it will give off enough hydrogen that if you hold lighted match near it, it will. However, if you drop potassium into the water instead, it will ignite “spontaneously”.

    The fact that a human being does the dropping, and does so intentionally, or deliberately, doesn’t alter the fact that in one case you get “spontaneous” combustion and in the other you may have to help it with a match.

    So if, in a lab, scientists succeed in putting together non-replicating ingredients and they “spontaneously” combine to form self-replicating molecules, then the fact that the scientist put the things together doesn’t affect the “spontaneity” of the reaction. The scientists have merely shown that if a certain set of conditions are fulfilled, self-replicating molecules are likely to emerge.

    The next step is to use that finding to predict evidence about early earth – were those conditions, or similar conditions, likely to have been found then?

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    That’s the spirit, Scott 🙂

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    ScottAndrews says:

    I catch on, even if it’s slow!

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    material.infantacy says:

    EL wrote,

    Szostak, and others, are working on possible scenarios by which very simple self-replicating entities, possibly no more than lipid vesicles enclosing simple polymers that self-replicate when subjected to some cyclical effect such as regular temperature oscillations in a convection current.

    Great, fine. I have no problem with that in principle. Simple self-replicating molecules are apparently reasonable given very controlled conditions. If vesicles containing simple polymers can self-replicate as a single entity, explicitly without externally introduced catalysis, then I’d be duly impressed. But that by itself does not spell “proto-cell” as anything resembling a DNA based cellular organism. See below.

    One of the hard parts is figuring out how self-replicating molecules might form spontaneously, but there are already some clues, and some self-replicating RNA molecules and peptides have been produced in labs.

    Indeed, even the simplest starting point of self-replicating molecules is “one of the hard parts.” That’s classic understatement. As it stands, carefully controlled conditions denotes intelligent intervention. This isn’t just putting chemicals into a beaker, heating it up, shaking it around, and watching the magic happen. It represents intelligent (artificial) selection.

    Once you have a self-replicating molecule – one that catalyses the formation of a copy of itself from new materials – then you have information transfer. The sequence in the “parent” molecule is transferred to the “daughter” molecule.

    Agreed. The information transferred is very specifically the sequence required for that molecule to reproduce. However, that’s all — Information transfer doesn’t imply all of sequence space (only the capacity or potential to encode other sequences). The information is specific to the reproduction of that molecule and arguably nothing else.

    So the vesicle fills with copies of the enclosed molecule (this is why the vesicle is important – if this was just happening in an open environment, you wouldn’t get a concentration of copies of the same molecule) and eventually divides in two, resulting in two vesicles with molecules with that same sequence in both. Rinse and repeat.

    Got it. So a vesicle-enclosed molecule can putatively self-replicate, and pass the same information, beneficial to its own replication, to the duplicate.

    You’ve got the very beginning of a cell.

    There’s an assumption that begs the question. It’s an assumption that the research is supposed to provide evidence for, not assume from the start. Statements like this are the reason for tens of thousands of words are generated in comments on this site every day. This is the contested point — not just contested here, but by ID in general.

    Now let’s say that some of those self-replicating molecules tend to enhance the chance of successful “cell” division. Possibly by catalysing some useful molecule, possibly there might be an optimal length of polymer, whatever.

    That’s a host of gaps and possiblys. I don’t find them offensive or disconcerting, but can we agree that large chasms are potentially being leaped over here? If not, I would invoke the question begging again as the reason for this, that you don’t find this leaping problematic in demonstrating what you already know to be true.

    Now those proto-cells that have “better” sequenced polymers will start to outnumber those that have less good sequences. So the population is now dominated by proto-cells whose polymer sequences are “selected” for successful replication, and this “information” – about how to replicate successfully – continues to be passed on, with any variant that improves things still further tending to dominate the population, and any variant that doesn’t being “eaten” by the competition.

    Fine, stipulating every bridge (most yet to be built) that must be crossed to get here, where these “proto-cells” (and I’m only for the sake of argument using that word) can reproduce with a form of heritable variation. However it should be pointed out that you have yet to introduce a variation mechanism in your explanation. In the interest of charity I’ll assume that your initial replicator reproduces with some type of variation, as is probably the case in the actual experiments.

    However there are some things that should be addressed. First, if your initial self-replicator could reproduce effectively, what constitutes “better” replication? We’ve already stipulated to a vesicle-enclosed replicator, so the function and its sequence is already present. Are we modifying conditions such that sequence variations which might have been previously dysfunctional are now at an advantage? Is there evidence to suggest that these sequences can be varied slightly to respond favorably to environmental changes? (Please don’t invoke known cellular mechanisms here, that gap hasn’t been bridged yet.) These are not nitpicks. They are fundamental issues in determining whether favorable sequences can be morphed into more favorable sequences via “slight successive modifications.”

    Second, do the sequences that favor molecular replication have collinearity with sequences that denote functional proteins — that minimal set that must be present in order to process DNA for extant self-replicating, living organisms? This is capital. If the sequences that favor the replication of your “proto-cell” don’t have any correspondence to sequences which denote necessary functional proteins, then it remains in a separate domain entirely, and we have no hope of getting from A to B via this mechanism. If this isn’t a problem, please explain.

    No question is being “begged” here. If Szostak can show how the right ingredients tend to result in an evolving protocell, then he’s pretty well shown a mechanism by which life could have begun, even if we never know for sure how it did begin.

    A scenario by which life “could have” evolved is a hypothesis. If you’re excepting any such hypotheses as evidence for abiogenesis leading to life-as-we-know-it, because it satisfies your unshakable belief that life evolved from simple molecular self-replicators, then you’re begging the question, and my charge stands.

    The specificity, of course, evolves. In the early days, all that may be specified is polymer length, or polymer constituents (optimal length; optimal balance of constituents); later, polymers that catalyse reproduction-enhancing molecules will tend to be selected; later still, polymers that tend to catalyse the formation of other catalysts well tend to be selected.

    Sequence spaces are vast, in the extreme. As an example, with 52 aminos, I can represent every atom in the universe within that sequence space. The implication is that, with a few hundred aminos, I could fashion, via protocols, many disparate realms of functional sequences with huge spaces between them, one having nothing to do with the other, with no hope of leaping the gaps without intelligent intervention (that is, by searching randomly, a few modifications at a time).

    As that suggests, there’s no reason to presume, as you apparently do, that a sequence which favors the replication of a simple molecule has any correspondence to sequences denoting proteins required for actual self-replicating organisms. This is a consequence of materialist reductionism in biology, which will continue to be refuted as science perpetually elucidates the unfathomable sophistication of the simplest cellular organisms. (That is my prediction.)

    But before we know how (or whether) this happens, we need to know something about how those first self-replicating molecules were generated, and what they were – did RNA come first, or peptides? Or did they co-evolve?

    Or were they designed? This is the possibility that you refuse to acknowledge, choosing instead to assume that which Szostak’s research is attempting to provide evidence in support of.

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    ScottAndrews says:

    Elizabeth,

    For instance, regarding the membranes, Szostak has done some very interesting work showing reproductive advantage for quite low levels of phospholipids in the membrane. And other experiments have set out to test hypotheses regarding the effects of different sequences on the ability of the vesicle to divide

    These are properties of the organism itself. What about the environment? Is a wave splashing over the top of the pumice raft or gust of air going to distinguish between levels of phospholdipids?

    So if, in a lab, scientists succeed in putting together non-replicating ingredients and they “spontaneously” combine to form self-replicating molecules, then the fact that the scientist put the things together doesn’t affect the “spontaneity” of the reaction.

    I supposed that depends on what you mean by “putting together.” Even if they can reduce it to steps simple enough that they can repackage and market it as Sea Monkeys 2.0 there’s a lot more going on than dropping potassium into water. I can just see the kids carrying around their petri dishes and challenging each others’ organisms to duel the the extinction.

    First Szostak, etc., must perform the most complex chemical reactions every observed, making painstaking preparations and adjusting everything to perfection.

    That’s only step one. Then they must edit themselves out of the process. That’s going to be tough.

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    Upright BiPed says:

    Hello Kellyhomes

    Upright,
    I often hear that ID is about studying the designs to come to conclusions about the designer, as the designer cannot be studied directly.

    Erecting a strawman as your first complete sentence typically makes for an unfortunate conversation to follow. This is usually the case because the inevitable questions that follow will rarely be based on anything above the strawman, and they often go downhill from there. All a design proponent needs to do is open his to her mouth and there will be an opponent somewhere demanding a definition of terms, yet when it comes to the definition of ID, the terms apparently can’t be repeated often enough. This is evidenced by the fact that late in 2011 someone could actually enter an ID forum and suggest that ‘ID was about studying the designs to make conclusions about the designer’. Let me not fail to do my part by repeating that ID makes the minimal proposition that there is physically observable evidence which is best explained by the act of an intelligent agent, rather than an undirected natural process. I believe the definition posted 24/7/365 on this site uses these terms: ‘ID holds that certain features of the universe and of living things are best explained by an intelligent cause rather than an undirected process’. And if should you feel there must be some ulterior motive in not making statements about the designer, you’ll be happy to know that the reason such conclusions aren’t made is because there is no evidence within the grasp of ID methodology to support them. The only general ability that ID can assign to the designer is enumerated in the title of the theory – the ability to cause an act of intelligence. Limiting one’s conclusions to the actual evidence is typically appreciated within the empirical sciences, and it would be helpful if the opponents of ID would keep that in mind as they make demands for definitions. The part about not making claims about the designer is based upon the evidence, not the investigator.

    As you have obviously taken a great deal of time studying information transfer, could you tell me where and how “Intelligent Design” actually relates to all these observed physical entailments of recorded information transfer you keep talking about?

    A system that demonstrates the physical entailments of information transfer, also positively demonstrates the existence of a semiotic state. This is a prediction of ID which is supported by the physical evidence.

    – – – – – – – –

    The remainder of your post is either an extension of your strawman, or falls into the general defensive position of “What good is it?” The utility of seeking the truth about reality is something you either value or you don’t.

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    material.infantacy says:

    BiPed, well stated. That said, careful explanations won’t dissuade trollish comments indicting ID as religion in disguise, for the purpose of spraying graffiti on the walls here. I know that you know this, so your continued efforts to set the record straight for lurkers and other onlookers is appreciated by me, and I’m sure many others here.

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    eigenstate says:

    I believe the definition posted 24/7/365 on this site uses these terms: ‘ID holds that certain features of the universe and of living things are best explained by an intelligent cause rather than an undirected process’.

    I have indeed read similar positions here. But I think I regularly skip over “best explanation” in these contexts, as in other areas where I’m used to working (software, science), “best explanation” has some settled semantics. Heliocentric astronomy being a “better explanation” than Ptolemaic epicycles. Both are natural explanations, but heliocentrism performs better — precise predictions with better economy.

    But in reading your post, after lurking here a bit, that “best explanation” seems like a foreign concept to me, and have now this notion that “best explanation” is NOT like comparing apples to apples, comparing the performance of one natural model of the solar system to another model of the solar system (for example).

    I did look at the FAQ info a bit, but didn’t find anything that address what makes a “best explanation” or a “better explanation”. What does ID propose as concrete semantics for “better explanation” and “best explanation”, since it’s apparently not what my scientist friends (and I) understand by that term? Someone have a link that UD would affirm as “correct” on this, on site or off?

    I know this must have been covered at length here somewhere. This search didn’t come up with definitions for the term (as far as I looked, which was a ways), but rather just invocations of the term. This post doesn’t quite get there and seems to be as close as I could come.

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    Joseph says:

    eigenstate,

    The design inference is based on our knowledge of cause and effect relationships in accordance with uniformitarianism. And real-life investigations tell us that it matters to any investigation whether or not that which is being investigated arose via agency involvement or nature, operating freely.

    So that would be why ID is the best explanation because it goes hand-in-hand with our knowledge of cause and effect relationships

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    eigenstate says:

    Joseph,

    I understand the point about knowledge of cause and effect, but for someone who believes in an omniscient, all powerful, invisible God, direct intervention by God would always be the best explanation for any phenomena. This is the basic problem (as I understand it) with modern Islam and science: its occasionalism makes “Allah holding every atom together” the best explanation over any scientific or natural one.

    If ID understands “best explanation” to be predicated on known powers of design (directed cause and effect), doesn’t ID fall into that that very same occasionalism, if what you are saying is true? I don’t find much overt support for occasionalism in what I’ve read on this blog, so I think the answer lies elsewhere.

    Here a simple way to frame it, I think: why is heliocentric astonomy a “better explanation” than “God makes the planets go where they go”? I’m sure ID advocates here do not commonly hold to the former explanation, but based on our knowledge of directed cause and its effects, that would seem to be a better explanation than the physics explanations we do accept?

    When does “better” affirm a naturalist explanation for ID advocates? That’s not at all clear from what UprightBiped was saying, and seems even less clear from your response. It’s not as simple as “when I just don’t think that could happen”, is it? There’s a principle being applied by ID advocates as to when “best explanation” goes to natural answers vs. supernatural answers that I can’t get a handle on, from reading this blog and its comments.

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