Intelligent Design

An Apology to Dr. Moran

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In a recent post I described a scenario and asked a question to Dr. Moran as follows:

In a comment to a prior post Larry Moran writes:

Craig Venter and his colleagues constructed a synthetic genome and inserted it into a cell. The DNA determined the structure and properties of the organism that grew and after many subsequent generations we have a new species that behaves exactly like it was supposed to based on the genes that the scientists built.

Now Dr. Moran, suppose that new species escaped the lab and was captured by a researcher who had no idea about Venter’s work.  Suppose further that researcher concluded that the genome of the creature had been intelligently designed.  Would that researcher’s design inference be the true and best explanation of the creature’s genome’s provenance?

Dr. Moran answered the question:

The answer is “yes,” the researcher correctly observed that the genome of the synthetic organism is nothing like the genomes of real species. It lacks pseudogenes, transposons, and any trace of junk DNA and the sequence of its genes and regulatory regions is far too perfect to have evolved naturally.

And I responded to his answer:

Dr, Moran, you astonish me. In a good way.  Thank you for admitting that design leaves indicia that are empirically detectable in biological organisms, and that a design inference is perfectly valid if those indicia are present.

I congratulate Dr. Moran for following the data where it leads and making the most reasonable inferences from that data.

Furthermore, after reviewing my response, I realized I owe Dr. Moran an apology.   I extend my apologies to him for assuming he would he would not follow the data and make a reasonable inference.  My assumption was, I realize, based on prejudice (in the sense of “pre” and “judging”) and that was especially inexcusable coming, as it did, just days after I accused Dr. Moran of being prejudiced against me.

51 Replies to “An Apology to Dr. Moran

  1. 1
    brian douglas says:

    But wasn’t your question itself a loaded question? What if the same question were asked before we had the capability to modify the genome? Under that scenario, would we infer that it was designed? Or would we simply identify it as a new species?

    Under your scenario, the reason that we might infer that it was designed is that we understand the tools and procedures and the capabilities of humans to do it.

  2. 2
    Fair Witness says:

    So, Barry, are you agreeing with Professor Moran that we would have to see absolutely no trace of junk in the genome before we are justified in inferring design?

  3. 3
    Barry Arrington says:

    Brian Douglas

    But wasn’t your question itself a loaded question?

    No. I assume that Dr. Moran did not think so either, else he would have said so.

  4. 4
    Barry Arrington says:

    Fair Witness

    So, Barry, are you agreeing with Professor Moran that we would have to see absolutely no trace of junk in the genome before we are justified in inferring design?

    I never said that. I can’t imagine why you should infer it from anything I did say. The important thing is that Dr. Moran identified what he believes to be indicia of design, and based on the presence of those indicia made a design inference.

  5. 5
    brian douglas says:

    “No. I assume that Dr. Moran did not think so either, else would have said so.”

    Fair enough. But what about my second comment? If your same question was asked before anyone knew about the tools and procedures that molecular biologists use to modify the genome, would a design inference still be the best explanation?

    Btw, how did you like Spectre?

  6. 6
    Barry Arrington says:

    Brian Douglas,

    Fair enough. But what about my second comment? If your same question was asked before anyone knew about the tools and procedures that molecular biologists use to modify the genome, would a design inference still be the best explanation?

    Look at the question again:

    Would that researcher’s design inference be the true and best explanation of the creature’s genome’s provenance?

    In the particular context of question, the “provenance” under consideration is based on the tools and procedures that molecular biologists use.

    It makes no sense to ask, essentially, “but what if that provenance were impossible, would he still come to the same conclusion?” Perhaps I don’t understand what you are driving at.

  7. 7
    Barry Arrington says:

    BD

    Btw, how did you like Spectre?

    Bond movies are, too me, much of a muchness. If you liked the first 22 installments (and I did for the most part), you will like this one.

    It has everything we have come to expect from the formula, exotic locations, fun gadgets, beautiful Bond girls, lots of shooting and explosions; comic villains; evil henchman (this time played to great effect by the green guy from Guardians of the Galaxy); martinis; Q; M; Mollypenny; witty repartee; and minions (lots and lots of minions) with guns, though they could not hit the side of a barn if they were in it.

    Tip to anyone who aspires to be an arch-villain: If you are going to supply guns to your minions, for goodness sake have them spend some time at the range. If you don’t, we can expect more scenes like the one in Spectre where Bond is being chased by dozens of minions all shooting automatic weapons at him and missing, while he picks them off one by one with his one gun, while repeatedly exposing himself to automatic weapons fire.

  8. 8
    Jack Jones says:

    And The Aston Martin did not come about by a tornado in a junkyard.

  9. 9
    brian douglas says:

    ” Perhaps I don’t understand what you are driving at.”

    I just assumed, possibly erroneously, that you were attempting to draw an analogy between your scenario and the appropriateness of inferring design as the best explanation for biological structures found in nature. My point is simply that inferring design as the best explanation in your question to Dr. Morin is predicated on knowing and understanding the tools and procedures used by humans to modify genomes. We cannot necessarily extrapolate the strength of this inference to other biological structures because we have no understanding of the tools and procedures that were used.

    But if you were not attempting to draw this analogy, I apologize.

  10. 10
    Barry Arrington says:

    BD,

    Dr. Moran made a design inference in this particular case based on indicia of design that were bracketed by him.

    His brackets are his own.

    If other people want to make other design inferences based on other indicia of design present in organisms “found in nature,” who am I to say they shouldn’t.

  11. 11
    Jack Jones says:

    [Insult to Dr. Moran deleted]

    Mr. Jones, desist.

  12. 12
    Jack Jones says:

    @brian douglas

    Do you believe your brain was intelligently designed or do you believe it came about by dumb chance?

  13. 13
    brian douglas says:

    JJ: “Do you believe your brain was intelligently designed or do you believe it came about by dumb chance?”

    Why does it have to be one or the other? The opposite of design is not dumb chance.

  14. 14
    REC says:

    @10

    I can’t recall anyone in the history of this debate declaring that ALL design inferences are invalid.

    Regarding the bacterium with a synthetic genome:

    1) It has watermarks (Creator’s names, excerpts of literature, an html link) that match specific external sources.

    2) It has assembly artifacts-repeated sequences at regular patterns.

    3) It descends, in some ways, from no natural bacteria. Despite sequences being borrowed from nature, no progenitor could produce it in ordinary descent with modification.

    ID has failed to find pre-specifications, design artifacts, etc. I could be wrong, but I’d like to see a quote that design can NEVER be inferred.

    Barry also posits that inferring design in lab-created artificial life is tantamount to inferring design in nature, and oddly insinuates granting the above points admits any design inference. That is false.

  15. 15
    Barry Arrington says:

    REC @ 14:

    Suppose someone pushed back at you and said, “REC, your design inference is a scientific show stopper. You have committed the designer-of-the-gaps fallacy. All scientific claims must employ methodological naturalism, and you violate the principle of methodological naturalism when you make a design inference in biology. Besides all that, it all just a cop out unless you can tell me who designed the designer.”

    What would you say?

  16. 16
    REC says:

    Barry @ 15,

    I’d say again that you are confusing A design inference with ALL design inferences. All three statements could be valid against A certain design inference (which you haven’t stated). They are obviously invalid against my inferences in 14.

    Again, I should emphasize I haven’t made a design inference regarding nature. I’ve made 3 above regarding a piece of human made technology.

  17. 17
    Andre says:

    REC

    The very fact that we can reverse engineer a genome should give you a clue that the original was engineered.

  18. 18
    Jack Jones says:

    @13 “The opposite of design is not dumb chance.”

    The antonym of design is chance.

    If you believe no intelligence involved, that is dumb chance.

  19. 19
    REC says:

    @17

    Actually “we” didn’t reverse-engineer a genome. A modified genome of an existing bacteria was synthesized and inserted into another bacteria.

    So modifying something requires it to be engineered? Were all the rivers and lakes the Army Corp of Engineers modified designed?

    I’d say a major impediment to synthetic biology is that it isn’t easily engineered. Shotgun approached and directed evolution are the norm.

  20. 20
    brian douglas says:

    JJ: “The antonym of design is chance. If you believe no intelligence involved, that is dumb chance.”

    A diamond is not a chance arrangement of carbon. Does that mean that it is designed.

    My knowledge of evolutio, as limited as it is, is that there are certainly chance elements to it, but that it is not all chance. You could fall back on your tornado in a junkyard analogy, but that only demonstrates that you know even less about evolution than I do.

  21. 21
    Jack Jones says:

    “A diamond is not a chance arrangement of carbon. Does that mean that it is designed.”

    A diamond is necessary, When it comes to how life originated then there is nothing in chemistry that makes life necessary, that leaves chance or design.

    If you believe life originated spontaneously in nature and then evolved by an accumulation of errors eventually leading to human brains, then you have faith in dumb chance.

    “My knowledge of evolutio, as limited as it is, is that there are certainly chance elements to it, but that it is not all chance”

    Your knowledge clearly is limited, when you do not understand your faith, then you shouldn’t be here arguing for it.

  22. 22
    REC says:

    @21

    Why is a diamond necessary? It is one of many, many arrangements of carbon. It isn’t the lowest energy configuration of carbon. Diamonds are metastable, and far from equilibrium.

    So is life.

  23. 23
    brian douglas says:

    JJ: “Your knowledge clearly is limited, when you do not understand your faith, then you shouldn’t be here arguing for it.”

    I wasn’t arguing for or against evolution. I was just pointing out your false claim that the opposite of design is dumb chance. I don’t have to be an expert on evolution or ID to prove that.

  24. 24
    Jack Jones says:

    “Why is a diamond necessary?”

    It must be as they are arising plentiful in nature.

    If life was originating in nature all the time according to known chemistry then we would say it was necessary.

    What we know about the law of Biogenesis shows that the best explanation is that life originated by that which is not governed by natural law.

    Why do people reject the known law of Biogenesis for how nature operates and then appeal to nature for how life originated.

  25. 25
    Jack Jones says:

    ” I was just pointing out your false claim that the opposite of design is dumb chance”

    It can only be design or chance as life originating in nature is not necessary based on known chemistry.

    Your claim is thus rejected.

    “I wasn’t arguing for or against evolution.”

    You really do not know what you are arguing for, do you?

  26. 26
    brian douglas says:

    JJ: “Why do people reject the known law of Biogenesis for how nature operates and then appeal to nature for how life originated.”

    You should do a little reading before you comment. The law of biogenesis was demonstrated by Pasteur to prove that things like maggots did not spontaneously generate on rotting meat. It states that life comes from other life by reproduction. By that account, ID also violates this law.

    OOL is the big unknown. Anyone who claims to know for a certainty how it occurred is either lying. Plain and simple.

  27. 27
    Jack Jones says:

    “You should do a little reading before you comment. The law of biogenesis was demonstrated by Pasteur to prove that things like maggots did not spontaneously generate on rotting meat.”

    The fact that you are ignorant does not say anything about what I have read.

    The law of Biogenesis says that in nature, life comes from previous life.

    Saying it only applies to things like maggots on rotting meat when it comes to how nature operates is special pleading.

    “It states that life comes from other life by reproduction.”

    As far as nature operates.

    “By that account, ID also violates this law.”

    No, I believe that the creation of life was a supernatural cause, The supernatural is not governed by natural law.

    Your belief that life arose naturally is not consistent with how nature is known to function. You are rejecting empirical knowledge of how nature operates with your faith that life arose naturally. Your faith that life arose naturally is not consistent with how nature is known to function.

    As you can only get life from previous life in nature then that shows the better inference is that initially it was created supernaturally.

  28. 28
    brian douglas says:

    “No, I believe that the creation of life was a supernatural cause, The supernatural is not governed by natural law.”

    How convenient.

    “Your belief that life arose naturally is not consistent with how nature is known to function.”

    You don’t know what I believe about the origin of life. In fact, I have no idea how it came about. It sounds like you are the one letting their faith bias their ability to examine the evidence to draw the most likely explanation.

    “As you can only get life from previous life in nature then that shows the better inference is that initially it was created supernaturally.”

    No, the law of biogenesis refers to the fact that existing life forms could not arise spontaneously. I don’t know anyone who is proposing that any of the existing life forms is the same as the first life form. Nobody knows what the first life form looked like.

  29. 29
    J-Mac says:

    My question to Dr. Moran was on the previous thread “Venter’s synthetic genome” was related to his knowledge of how synthetic Venter’s genome was. There was no answer. I guess Larry still thinks that all nucleotides are synthesized chemically.

    Also, here is the Venter’s team about the “perfect” synthetic genome that is not that synthetic after all and how natural process have been doing the work for him “perfectly”.

    “Abstract
    We report the design, synthesis, and assembly of the 1.08–mega–base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including “watermark” sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.”

  30. 30
    Mung says:

    Larry has been a pretty good sport. He even got me to take a second look at Lynch through a different lens.

    Thanks Larry.

  31. 31
    Barry Arrington says:

    REC @ 16:

    They are obviously invalid against my inferences in 14.

    Translation: I accept the indicia of design that I accept and I reject those I reject, for my own idiosyncratic reasons. Therefore, the objections are invalid with respect to my design inference, because my design inference is a good one, and yours is not.

    Does that pretty much capture it REC?

  32. 32
    Jack Jones says:

    “How convenient.”

    Supernatural definition, of, relating to, or being above or beyond what is natural.

    Thus by Definition, The SUPER-natural is ABOVE nature and not governed by it.

    “You don’t know what I believe about the origin of life. In fact, I have no idea how it came about. It sounds like you are the one letting their faith bias their ability to examine the evidence to draw the most likely explanation.”

    I am letting the evidence guide me, Now if you reject the SUPER-natural and are unsure of its existence like Professor Moran, You either believe the logical contradiction of the origin of nature being nature. Or you believe that you can count back an infinite amount of past natural events.

    Now….It is not logically possible to count back an infinite amount of natural events, therefore we know nature began to exist at one point and that there could not have been an infinite amount of natural events before this time

    Furthermore, to believe in an infinite amount of finite natural events would mean that you believe in the oxymoron of “infinite finiteness”

    Now you are welcome to believe that you can count back an infinite amount of past events but it is not based on reason.

    ” I don’t know anyone who is proposing that any of the existing life forms is the same as the first life form. Nobody knows what the first life form looked like.”

    Well you are welcome to believe that a living organism arose in nature spontaneously, It goes against the law of biogenesis for how nature is known to operate.

    The better inference which is consistent with the scientific evidence is to that which is above nature and not governed by it, The SUPER-natural by definition is above nature and not governed by natural law.

  33. 33
    REC says:

    “Therefore, the objections are invalid with respect to my design inference, because my design inference is a good one, and yours is not”

    Correct, except that you haven’t even stated your design inference in this thread. I do feel my statements regarding the human-designed synthetic genome are valid and well evidenced. I don’t think any ID inference comes even close.

    Shouldn’t we evaluate design inferences based on their validity and the evidence supporting them? Isn’t it illogical and absurd to say ALL design inferences are valid because ONE design inference is?

    Rainbows are designed because Rainbow Brite* says so.
    *A fictional US cartoon.

  34. 34
    bornagain says:

    A few notes on Mycoplasma that just might suggest design instead of unguided material processes:

    Verse and Music:

    Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information – David L. Abel and Jack T. Trevors – Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8
    “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?”
    http://www.biomedcentral.com/c.....2-2-29.pdf

    First-Ever Blueprint of ‘Minimal Cell’ Is More Complex Than Expected – Nov. 2009
    Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae’s transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation.
    “At all three levels, we found M. pneumoniae was more complex than we expected,”
    http://www.sciencedaily.com/re.....173027.htm

    There’s No Such Thing as a ‘Simple’ Organism – November 2009
    Excerpt: In short, there was a lot going on in lowly, supposedly simple M. pneumoniae, and much of it is beyond the grasp of what’s now known about cell function.
    http://www.wired.com/wiredscie.....s-of-life/

    Simplest Microbes More Complex than Thought – Dec. 2009
    Excerpt: PhysOrg reported that a species of Mycoplasma,, “The bacteria appeared to be assembled in a far more complex way than had been thought.” Many molecules were found to have multiple functions: for instance, some enzymes could catalyze unrelated reactions, and some proteins were involved in multiple protein complexes.”
    http://www.creationsafaris.com.....#20091229a

    To Model the Simplest Microbe in the World, You Need 128 Computers – July 2012
    Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That’s a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,,
    The bioengineers, led by Stanford’s Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What’s fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell’s lifecycle processes.,,,
    ,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore’s Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that’s only a fraction of what will eventually be required to consider the simulation realistic.,,,
    http://www.theatlantic.com/tec.....rs/260198/

    twitter discussion criticizing the cell model.. – 2012
    Umm – claims of first full computer simulation of an organism seem, well, way way overhyped… one of the worst NY Times science articles I have seen in a while… I do not think they made a complete model …
    Another commenter, Steffen Christensen, voiced his agreement:
    Aye: a model is NOT a complete simulation…There are what, 1000s of molecule types in a typical cell, and their model tracks less than 30?!? They might’ve done a better job of it. You know, modeled spatial interactions, 1000s of moieties, etc… As it is, I just feel… disappointed.
    http://phylogenomics.blogspot......on-of.html

    OK Atheists, time to remind yourself that what you are seeing was not designed, but rather evolved.

    “Biologists must constantly keep in mind that what they see was not designed, but rather evolved.”
    Francis Crick – What Mad Pursuit

    As for the rest of us

    Verse and Music:

    Isaiah 6:3
    And they were calling to one another: “Holy, holy, holy is the LORD Almighty; the whole earth is full of his glory.”

    World’s First Wireless MIDI Controller for Acoustic Guitar – ACPAD
    https://www.youtube.com/watch?v=eJFfnTkyj-g

  35. 35
    brian douglas says:

    JJ: “Supernatural definition, of, relating to, or being above or beyond what is natural.”

    AKA, Magic.

    “I am letting the evidence guide me, Now if you reject the SUPER-natural and are unsure of its existence like Professor Moran, You either believe the logical contradiction of the origin of nature being nature. Or you believe that you can count back an infinite amount of past natural events.”

    What about “OOL is the big unknown. Anyone who claims to know for a certainty how it occurred is either lying. Plain and simple.” Didn’t you understand. I haven’t ruled out anything with regard to OOL. What I have dot done, as you have speared to do, is come to a conclusion.

    “Well you are welcome to believe that a living organism arose in nature spontaneously, It goes against the law of biogenesis for how nature is known to operate.”

    I agree. It definitely goes against how modern life operates. We have never seen a maggot develop without a fly parent, or a human, a tardigrade, or a paramecium. But nobody knows anything about the nature of the first life form (replicator, whatever). We do t know if the law of biogenesis applies to it. It very well might, but we can’t draw that conclusion with current knowledge.

  36. 36
    Jack Jones says:

    “AKA, Magic.”

    Incorrect. A supernatural creation is consistent with both logic and the evidence.

    With your dismissal of the supernatural then you either believe nature originated nature or you believe that you can count back an infinite amount of past natural events, but if there were an infinite amount of past natural events then we wouldn’t have reached this moment in time.

    Now…You are welcome to believe that you are capable of magically counting back an infinite amount of past natural events or illogical believe that nature existed before it existed.

    But you are the one with the magical thinking, Illogical thinking. You can’t grasp basic logic.

    When your reasoning is illogical then it provides you with no grounding to judge.

    You really have no ground to stand on when accusing others.

    “What about “OOL is the big unknown. Anyone who claims to know for a certainty how it occurred is either lying.”

    No. If I take the position that Life was created based on current knowledge then that doesn’t prevent others from explaining and providing good reasons why that is wrong.

    However as you are not able to reason properly and understand straight forward logic then you are not really in a position to be making any arguments here.

    “But nobody knows anything about the nature of the first life form (replicator, whatever). We do t know if the law of biogenesis applies to it. It very well might, but we can’t draw that conclusion with current knowledge.”

    You are welcome to believe that chemistry was different in the past, But if chemistry was inoperable in the past and processes in the present were not operative, then how did that rain fall for the primordial soup for which chance evolutionists have faith life arose from?

    Was gravity inoperable in the past?

    Those mutations which you have faith created your brain, how did they occur to past organisms if present processes were not operative in the far distant past?

    You are not consistent as a chance evolutionist and if you are here hiding behind the idea that you have no beliefs but just want to criticize what others believe then it shows you up to be a coward.

    Don’t be a cowardly chance evolutionist.

    People can know that you are engaging in special pleading when you say that natural processes in the present existed in the past but then say that chemistry operated differently in the past.

    To say that life came from non life violates how we know nature operates therefore we know that life cannot have arisen naturally and has to come from a source that is not governed by natural law.

    As you do not believe your brain was intelligently designed to understand the truth and as you have shown that you are not able to think logically then you really have no dog in this hunt.

  37. 37
    brian douglas says:

    Joe, who said that chemistry worked differently in the past than it does now? Certainly not me. Please try to keep up. I just suggested that the earliest life form was probably very different than life today. Not exactly a novel idea. As such, the law of biogenesis, which applies to all life today, was never intended to apy to OOL events.

    For all I know, the first life form may have been designed. I don’t know. And neither does anyone. But, whether or not a supernatural cause is the most likely explanation is up for debate.

    Since you obviously believe that life has a supernatural origin, how do you propose we test this?

  38. 38
    Jack Jones says:

    “Joe, who said that chemistry worked differently in the past than it does now? Certainly not me. Please try to keep up. I just suggested that the earliest life form was probably very different than life today. Not exactly a novel idea.”

    Who the hell is Joe?

    “As such, the law of biogenesis, which applies to all life today, was never intended to apy to OOL events.”

    That’s known as special pleading.

    The law of biogenesis says that in nature that life only comes from previous life.

    You are welcome to believe that chemistry operated differently in the past but it is not based on how nature is known to operate.

    “For all I know, the first life form may have been designed. I don’t know. And neither does anyone. But, whether or not a supernatural cause is the most likely explanation is up for debate.”

    Of course it can be debated, And the law of biogenesis shows that as far as nature operates, life only comes from previous life.

    “Since you obviously believe that life has a supernatural origin, how do you propose we test this?”

    The way chemistry operates every day in nature tests the idea of life originating spontaneously and it just does not happen.

    Thus design is the best inference.

    If you tell me that I have to empirically demonstrate a supernatural designer doing the design then my response is this.

    When did you empirically demonstrate that everything has to be demonstrated empirically?

    I have shown with Empiricism that the cause of the first life could not have originated naturally as it violates the law of biogenesis, as far as nature operates, life only comes from previous life.

    We infer based on the law of biogenesis that the first life form was brought into being by a non natural cause.

    You infer that life originated based on what is not known to occur in nature.

    When did you empirically demonstrate life originating from non living matter in a natural environment?

    Now….You have engaged in special pleading, You are appealing to unknown chemistry and an unknown life form, as you believe in what is naturally known then you have to stick with what we do observe in nature, You are not being consistent with your strict natural position.

    If you want to demonstrate when this unknown life form was observed to arise spontaneously in nature then please do tell.

    My position is based on what we do observe and that is the law of biogenesis, your position is based on what we do not observe.

    My position is consistent with known empiricism for how nature operates, Your position is not consistent.

    We both make inferences, Your inference is based on rejecting what is empirically known about how nature operates and thus you have no grounding to appeal to nature.

    If you want to demonstrate life originating spontaneously from non living matter in a natural environment then I invite you to do so.

  39. 39
    PaV says:

    Here, again, is Larry Moran’s reply:

    The answer is “yes,” the researcher correctly observed that the genome of the synthetic organism is nothing like the genomes of real species. It lacks pseudogenes, transposons, and any trace of junk DNA and the sequence of its genes and regulatory regions is far too perfect to have evolved naturally.

    Just an observation here: Dr. Moran bases almost all of his “design inferences” on the “absence” of what is seen in the genome: no ‘transposons,’ no ‘junk-DNA’, and no pseudogenes.

    There is one bit of positive “design inference”, viz: “the sequence of its genes and regulatory regions is far too perfect.” By this I presume he means that we don’t see much evidence for recombination/crossing over. Perhaps I’m wrong in what his remark means, but that is how I take it.

    Putting all of this together in search of a common element, it appears Dr. Moran is basically saying that since we do not see RANDOMNESS, we are therefore allowed to infer a “designer.”

    If you turn this view around, Dr. Moran is basically saying is that “nature” is generally a random, wasteful process, in opposition to intelligence.

    Well, this is a basic ID position.

    ID also sees “natural processes” as involving not only ‘random’ events, but events which, per the Second Law of Thermodynamics, tend toward disorder; i.e., tend towards degradation. Your view, Dr. Moran, I believe is consistent with this, especially as you make your ‘design inference.’

    However, it is precisely ‘against’ such negative, wasteful randomness that nature brings about, that ID feels emboldened to state her ‘design inference’ as seeing ‘order’ in the midst of ‘disorder.’ That is, if ‘nature’ is chaotic—a disordered affair—then whence the ‘order’?

    IOW, if “the sequence of its genes and regulatory regions is far too perfect” for Venter’s organism to be confused with what we find in ‘nature,’ then, so, too, are any sequences that are highly conserved. Such highly-conserved sequences must also be “far too perfect” to be confused with something ‘nature’ might produce.

    So, Dr. Moran, you’re right at home with our views.

    Here’s the only difference I would assume to exist: I would presume that you think there are forces in ‘nature’ that defy the Second Law of Thermodynamics, producing “order” from “disorder,” and that the main such force is “random genetic drift.”

    ID, OTOH, thinks that the only known antidote to “disorder” is an “orderer”; hence, an intelligent being of some sort.

    Here, though is the problem: the power of intelligence over the tendency to disorder is known to exist. We have seen it at work. In fact, Dr. Venter has used his intelligence to construct a genome that is “far too perfect” to have “evolved naturally.” This is proof of the power of intelligence over the degradating forces of nature.

    Since this is evident to humans, we would have to have “proof” that “random genetic drift” can ape this ability—pardon the pun—before we could logically posit that intelligence is not at work. What “proof” do we have?

    After all, can “random” events somehow mimic the work of intelligence? Can it really overcome the dissipative forces of nature?

    And, of course, Dr. Behe’s First Law of Adaptation tells us that the power of what is called evolution lots of times is no more than the power to break down what previously was functioning—not the reverse. So, there is a hill to be climbed.

    BTW, I’m currently reading Provine’s “Random Genetic Drift.” I must say it’s an interesting read. I don’t think he puts much trust in the current models used by population geneticists since they all rely on Fisher’s Genic F. I still have a way to go.

  40. 40
    Phinehas says:

    Nice post, PaV (as usual). Should we expect someone to respond with the “crayfish” or only the lonely sound of silence?

  41. 41
    brian douglas says:

    Joe: “You are welcome to believe that chemistry operated differently in the past but it is not based on how nature is known to operate.”

    Translation: I can’t argue based on logic and evidence so I will misrepresent (aka, lie) about what was said.

    Again, who has claimed that chemistry worked differently in the past?

  42. 42
    Larry Moran says:

    PaV says,

    Just an observation here: Dr. Moran bases almost all of his “design inferences” on the “absence” of what is seen in the genome: no ‘transposons,’ no ‘junk-DNA’, and no pseudogenes.

    I know what real genomes look like. They are messy, sloppy, and inefficient just like everything else in biology.

    When I see a genome that looks perfect I have to assume that it is not the product of evolution and naturalistic processes.

    What’s wrong with that?

  43. 43
    Virgil Cain says:

    Larry Moran- Your position cannot explain any genomes, perfect or otherwise. Also ID is not anti-evolution.

  44. 44
    Virgil Cain says:

    brain dead:

    I just suggested that the earliest life form was probably very different than life today.

    When you find evidence to support that claim please be sure to present it.

    For all I know, the first life form may have been designed. I don’t know. And neither does anyone.

    The evidence says it was designed and no one can refute that inference.

    Since you obviously believe that life has a supernatural origin, how do you propose we test this?

    ID does not require the supernatural.

  45. 45
    Jack Jones says:

    Mr Cain @44

    “The evidence says it was designed and no one can refute that inference.”

    Don’t even bother wasting time on the commentator that goes by the name brian douglas. You are trying to educate somebody that is not teachable.

    There was an Act in education “No child left behind”

    Maybe he was that child that should have been left behind.

    He can’t argue with reason and logic and provide any intelligent content in his posts.

    You are wasting your time trying to educate somebody that stupid, it would be like trying to educate a brick.

    I was attempting to educate him and he provided no substance in reply. I realize he is only here to be an ankle biter.

    At least zach and others provide arguments but you are dealing with an ankle biter that has no arguments or substance.

    Look at his post @41, Where he still calls me another persons name but provides absolutely 0 content in response to what I last posted to him and is unable to refute my post.

    That shows he is trolling and not capable of rational debate.

    Spend your time on people that have something to add to the debate and not that ankle biter.

  46. 46
    PaV says:

    Dr. Moran:

    I know what real genomes look like. They are messy, sloppy, and inefficient just like everything else in biology.

    When I see a genome that looks perfect I have to assume that it is not the product of evolution and naturalistic processes.

    You asked what’s wrong with saying this. Let me take a stab at it.

    When you “see” a genome, you’re ‘seeing’ a genome. Presumably it has been taken from an organism and sequenced. So you’re looking at something functioning as a genome, taken from an organism, and now sequenced. How can you differentiate between a new form of life having a genome without what you call “junk,” and something that is “not the product of evolution and naturalistic processes”?

    There’s another way of going about this: you don’t accept ENCODE’s latest determination of function within the human genome. But, what if their figure turns out to be correct, and that things such as “transposons” (which, very recently, was shown to carry around with them a whole molecular machinery) and “pseudo-genes” (which, too, have been implicated with some kind of molecular role), and the rest of what you would term “junk-DNA,” really have functions? Then what? Then, logically, you would have to say that the “rubbish” nature produces is really “perfect,” and that Venter’s genome is “junk.”

    Meantime, you see what you think is wasteful excess, and “conclude” that it is “junk,” and use the “absence of junk” to reach what I presume you consider to be a ‘scientific’ conclusion; while ID sees nucleotide sequences which nature would say should be in random order, but which are far from a ‘random’ condition, from which ID concludes (and I presume you would agree that it, too, is a ‘scientific’ conclusion) that only an intelligent agent is capable of manipulating nature in this way.

  47. 47
    Mung says:

    Larry Moran:

    I know what real genomes look like. They are messy, sloppy, and inefficient just like everything else in biology.

    Nothing sloppier than a sloppy biologist!

    Everything in biology is sloppy, inefficient, and messy.

    I don’t believe you.

  48. 48
    Jack Jones says:

    Larry Moran says “I know what real genomes look like. They are messy, sloppy, and inefficient just like everything else in biology.”

    “Janine Benyus has a message for inventors: When solving a design problem, look to nature first. There you’ll find inspired designs for making things waterproof, aerodynamic, solar-powered and more. Here she reveals dozens of new products that take their cue from nature with spectacular results.”

    Inventors are looking to living things in nature to model for their designs because according to Larry.

    ” I know what real genomes look like. They are messy, sloppy, and inefficient just like everything else in biology.”

    That’s bad logic from Larry and could have come from Curly and Moe too.

    What is messy, sloppy and inefficient is Larry Moran’s thinking.

  49. 49
    brian douglas says:

    ““Janine Benyus has a message for inventors: When solving a design problem, look to nature first. There you’ll find inspired designs for making things waterproof, aerodynamic, solar-powered and more. Here she reveals dozens of new products that take their cue from nature with spectacular results.”

    3 billion years of experimentation will do that. What’s your point?

  50. 50
    PaV says:

    brian douglas:

    3 billion years of experimentation will do that.

    Do you mean “random” experimentation?

    You’re using a word that we associate with intelligent beings to describe something that does not, per your view presumably, involve intelligence.

    Here’s what “random” experimentation would look like: a ‘scientist’ would go into a lab, he would open a petrie dish with a culture, he would spit on it, cover it up again, and see what tomorrow brings. And then when tomorrow comes, since this is all “random,” he won’t note what day of the week it was.

    Continue this process for 3 million years and what do you think you will get?

  51. 51
    PaV says:

    Since Larry hasn’t responded, I’d like to add what is truly a sign that the genome was intelligently designed.

    The following is from the link that Dr. Moran provided:

    As in the team’s 2008 publication in which they described the successful synthesis of the M. genitalium genome, they designed and inserted into the genome what they called watermarks. These are specifically designed segments of DNA that use the “alphabet” of genes and proteins that enable the researcher to spell out words and phrases. The watermarks are an essential means to prove that the genome is synthetic and not native, and to identify the laboratory of origin. Encoded in the watermarks is a new DNA code for writing words, sentences and numbers. In addition to the new code there is a web address to send emails to if you can successfully decode the new code, the names of 46 authors and other key contributors and three quotations: “TO LIVE, TO ERR, TO FALL, TO TRIUMPH, TO RECREATE LIFE OUT OF LIFE.” – JAMES JOYCE; “SEE THINGS NOT AS THEY ARE, BUT AS THEY MIGHT BE.”-A quote from the book, “American Prometheus”; “WHAT I CANNOT BUILD, I CANNOT UNDERSTAND.” – RICHARD FEYNMAN.

    An intelligently designed “code” that conveys information, using the same techniques that provide for a full-scale working genome. How interesting?

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