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“First cell controlled completely by a synthetic genome”

Craig VenterBig news at Craig Venter’s Synthetic Genomics:

Summary: Link 1

Press Release: Link 2

The rhetoric is interesting. What they’ve done is stuck a synthetic genome inside a nonsynthetic cell. Nonetheless, they’ve slipped into talking of a “synthetic bacterial cell.” Indeed, one headline reads “The First Self-Replicating Synthetic Bacterial Cell.” This is hype.

If something is going to be called “synthetic,” shouldn’t the whole of it be synthesized and not merely a minuscule portion of it? Also, does such a cell knowably signal design and, if so, why wouldn’t cells untouched by Synthetic Genomics do the same, i.e., implicate design?

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44 Responses to “First cell controlled completely by a synthetic genome”

  1. Bill,

    Glad to see you are making the point.

    It seems to me that it is like saying because I have added a new software program I have built a new computer.

    The genome may be a library of instructions, but a living cell is still necessary to read and act on those instructions, just as I need a pre-existing intelligently designed computer to read the new program I uploaded.

    Without the computer (cell), the software (genome) is lifeless.

    I fail to see what the big deal is. Humans have been manipulating the genome through mate selection, selective breeding, etc. etc. for as long as we have been alive.

    So now we can change the program library more directly, but we are still dependent on the existing living cellular machinery to read and implement the program.

  2. Venter said:

    it’s the first species on our planet to have it’s parent being a computer

    He implies that it’s the 1st intelligently designed species. It’s more like the 1.5 millionth.

    Quote is from video in the BBC’s report:

    http://news.bbc.co.uk/1/hi/sci.....132762.stm

  3. I found this quote from Craig Venter interesting:

    “When we look at life forms, we see fixed entities, … But this shows in fact how dynamic they are. They change from second to second. And that life is basically the result of an information process. Our genetic code is our software.”

    I write software for a living. I wonder how much the original genetic “coder” got for making life?

  4. What a sham. The grand claim that they started with 4 bottles of chemicals and WAA LAA a synthetic genome popped out leaves out quite a few important steps:

    Just the first step of assembly is as such:

    The capacity to affect the chemical synthesis of DNA has been a long time in the making. This process refer to the nonbiological, chemical production of small segments of DNA, called oligonucleotides.,,,,,,,,,,,,,,

    The specific steps for the chemical synthesis of oligonucleotides include:

    1. Attaching the first nucleotide to a solid support after deblocking the appropriate group.
    2. Removing the appropriate protecting group from the attached nucleotide in the first position to allow it to react with the next nucleotide in the oligonucleotide sequence that has had the appropriate blocking group removed from it.
    3. Allowing the nucleotides to react under carefully controlled conditions.
    4. Adding a chemical cap to any unreacted oligonucleotides. (This step is necessary because a small percentage of the nucleotides don’t react with the attached oligonucleotide chains.)
    5. Stabilizing the linkage between the two nucleotides with an oxidizing agent
    6. Washing away unreacted nucleotides.
    7. Repeating steps 2 through 6 until the entire oligonucleotide has been made.
    8. Cleaving the oligonucleotide from the solid support.
    9. Removing all the blocking groups.
    10. Purifying the oligonucleotide. This step is absolutely critical to ensure the accuracy of the biochemical recombination steps during the whole genome assembly process.

    Because the technology to chemically synthesize oligonucleotides has been in place for several decades, it’s easy for scientists to take it for granted. Today, the chemical production of oligonucleotides is virtually an automated turnkey process. Yet, it’s important not to overlook the remarkable technical accomplishment this capability represents. If it wasn’t for the dedicated efforts over the course of the last half century of some of the best scientists in the world (including Nobel Laureates), to develop and improve methods to chemically make DNA, Venter’s team would have no hope of affecting the complete synthesis of the M. genitalium genome.
    http://www.reasons.org/tnrtb/2009/01/29/

    http://www.reasons.org/tnrtb/2.....rt-3-of-4/

  5. Interesting too that even the synthetic genome is mostly copied from a natural one, so most of the design in it is not Venter’s.

    Nevertheless, this does sound like a significant step to me: If they can consistently get cells to reproduce “normally” after a synthetic genome is inserted, they have a lot more power to then tweak the genome according to design goals.

  6. lars,
    I agree it is a breathtaking step forward, I just have a huge problem with Venter’s “sin of omission” in clarifying just how constrained he was in following strict protocol, nor in his lack of admission that he did not actually create any new genes (or proteins). Shoot even for the larger pieces of DNA they had to use yeast for the final steps of assembly. As Dr. Dembski asked:

    “If something is going to be called “synthetic,” shouldn’t the whole of it be synthesized and not merely a minuscule portion of it?”

  7. If something is going to be called “synthetic,” shouldn’t the whole of it be synthesized and not merely a minuscule portion of it?

    You could say that the cell into which the DNA was inserted wasn’t a fully synthetic cell, but that its descendants – especially its indirect descendants in the second and later generations – have been “bootstrapped” away from the hybrid organism and so are fully synthetic. And indeed Synthetic Genomics talks about “boot[ing] up” in the linked announcements. But see “Reflections on Trusting Trust” for a famous illustration of the limits of bootstrapping. And Synthetic Genomics’ knowledge and understanding of the phenotype produced by the reproduction of a bacterium containing its artificial genome is much less detailed and complete than the insight a programmer has (or thinks she has) into the workings of the C compiler produced when she compiles her C source code for a C compiler using an existing C compiler whose object code she hasn’t studied exhaustively. So the claim that Mycoplasma mycoides is a fully synthetic organism is much further from the mark than the corresponding claim about a C compiler produced by the mechanism described above, even though there are surely no Trojans in M. capricolum specifically intended to hoodwink Synthetic Genomics. (In any case it’s not clear that ‘synthetic’ is the mot juste here.) “WHAT I CANNOT UNDERSTAND” …

  8. The level of sensationalism and overstating of the claims of any piece of work is directly proportional to the arrogance and egos involved. Venter is notorious for his lack of humility, and the press is willingly complicit in over-hyping the “synthetic” aspect of this work.

  9. Bill asks, “If something is going to be called “synthetic,” shouldn’t the whole of it be synthesized and not merely a minuscule portion of it?”

    Great achievement, sure, but diminished if overhyped.

    Visiting a relative in rehab recently, I observed several people with prosthetic legs, rehabbing on the double bar or the training steps. Also, there were old gentlemen and ladies learning to cope with hip replacements (by artificial stuff), and young people, mad as stink at fate, because they needed knee replacements (more artificial stuff).

    Are they all synthetic now?

  10. What about cotton/polyester blends?

  11. Is this kind of like gene patenting where they claim intellectual property rights on already existing information?

  12. “To make the synthetic cell, a team of 25 researchers at labs in Rockville, Md., and San Diego, Calif., led by bioengineer Daniel Gibson and Dr. Venter essentially turned computer code into a new life form. They started with a species of bacteria called Mycoplasma capricolum and, by replacing its genome with one they wrote themselves, turned it into a customized variant of a second species called Mycoplasma mycoides, they reported.”

    So they didn’t create life. When a group of scientists manages to make a complete membrane, cytoskeleton, nucleus, ribosome, golgi apparatus, nucleus, and the hundreds of other cell components from basic non-living chemicals and slap it all together and make it start up from total inactivity, *THEN* they can say they created life. In the meantime, this is just a step towards that goal.

  13. barb, you state:

    “by replacing its genome with one they wrote themselves,”

    if you can call plagiarizing a already existing genome and very selectively editing the preexisting information of that genome within very tight constraints, then I guess it may fairly be said that yes they “wrote” the genome themselves.

    The search space for them to find even a single novel gene, or protein, that would do anything at all, much less one that would accomplish a specific task they wanted, is beyond the 1 in 10^150 universal probability bound of Dr. Dembski. Thus they will never ever write a synthetic genome that they have truly created themselves from scratch, they will forever be “borrowing” already written material.

    Plagiarism: Don’t Do It
    http://www.youtube.com/watch?v=gC2ew6qLa8U

  14. Looks to me like Venter’s achievement merely understates the obvious; that creation of life requires intelligence. The Bible described this long before Venter’s tinkering.

  15. Now that Craig Venter and company have created an entire genome (admittedly mostly conceptually copied from previous organisms, but still), will we see an end to the argument that we have never seen intelligence produce the code for life, and that therefore life, or at least its code, could be natural (meaning a combination of law and chance) just as easily as it could be a product of intelligence, since we have not seen either produce this code? More important, will we see a formal retraction of this argument? Or will opponents of ID who have used this argument simply shift the discussion somewhere else, ignoring the egg on their faces, or hoping nobody will notice?

  16. 16

    Paul Giem,

    …will we see an end to the argument that we have never seen intelligence produce the code for life, and that therefore life, or at least its code, could be natural…

    Biochemists have been synthesizing DNA and RNA molecules to order for decades. Now Venter’s team, composed of similar intelligent humans, has assembled a whole cellular genome and got it to function. It’s a nice technical feat, and it should lead to further advances. But what does this have to do with special creation of life by an unknown and uncharacterized disembodied entity?

  17. Can someone break down what was actually accomplished in laymen’s terms? If I’m understanding it correctly, Venter used the DNA sequence of a certain organism for a pattern, and simply duplicated the DNA piece by piece, and then stuck that synthesized DNA in a cell and it divided. Is that accurate? Was the entire DNA synthesized, or just a part?

  18. Jasondulle-

    That’s how I’m understanding this as well, and if it is the case then this much more than slightly misleading people. As I said above it seems comparable to genetic patenting where people simply discover genetic sequences and claim them as intellectual property.

  19. One quick question. Why is the guy wearing Two-Face’s coat from Batman?
    :)

  20. Above-

    it matches his personality exactly.

  21. I found this interesting:

    The researchers picked two species of Mycoplasma, simple germs that contain a single chromosome and lack the cell walls that form barriers in other bacteria. First, they chemically synthesized the genome of M. mycoides, that goat germ, twice as large as the germ genome they’d previously built.

    Then they transplanted it into a living cell from a different Mycoplasma species, albeit a fairly close cousin.

    At first, nothing happened. The team scrambled to find out why, creating a genetic version of a computer proofreading program to spell-check the DNA fragments they’d pieced together. The result: They found that a typo in the genetic code, in one of the synthetic genome’s million chemical base pairs, was rendering the manmade DNA inactive, delaying the project three months to find and restore that bit.

    It shows you how accurate it has to be, one letter out of a million,” Venter said.

    That fixed, the transplant worked. The recipient cell started out with synthetic DNA and its original cytoplasm, but the new genome “booted up” that cell to start producing only proteins that normally would be found in the copied goat germ. It reproduced into a small colony of germs in a lab dish. The researchers had tagged the synthetic DNA to be able to tell it apart, and confirmed that those new ones really looked and behaved like M. mycoides, not the recipient cell.

    A new source of random mutation?

  22. Adel DiBagno (#16)

    I agree with you that Venter has simply extended the amount and percentage of DNA that can be successfully inserted into a cell and can prove functional. I thought the argument that “we haven’t seen intelligent agents produce a whole genome, and therefore the coming into existence of a whole genome is no evidence of intelligent design” was always bogus. But now even the starting premise is wrong.

    It appears to me that you are afraid that admitting that intelligence is a more reasonable hypothesis than processes not including intelligence might lead to “an unknown and uncharacterized disembodied entity”. Then your real problem is not scientific. It is philosophical or theological. This is science against religion, or at least philosophy. That’s okay, as long as we are clear.

  23. 23

    Paul Giem:

    Thank you for your response.

    I agree about the bogosity of the argument you describe, although I’ve not seen it expressed by anyone.

    Regarding fear of hypotheses, whether a hypothesis is reasonable depends upon antecedent evidence that the hypothesizer perceives. Perceptions may differ. But an hypothesis is not an end in itself. It is the beginning of the journey for the scientist.

  24. Adel DiBagno (#23),

    Thank you for your response, and especially your agreement on the bogosity of the argument. Unfortunately, I have seen this argument used. I can find a very similar argument on short notice (see
    http://www.uncommondescent.com.....ent-294475
    ). It is not exactly the same, but awfully close, and invalidated by the same data.

    You are right that hyotheses are a starting point. But the two points that I were making are data now. Craig Venter, arguably an intelligent agent, created DNA code. We have not yet seen nature without intelligence do it, nor do we have a coherent well-supported theory of how unaided nature did it. Those are data, not hypotheses. They support a hypothesis that intelligence was involved in the creation of life. This hypothesis has more evidence supporting it than the hypothesis that intelligence was not involved in the creation of life. I tend to go with the supported hypothesis.

  25. 25

    Dr Giem,

    The link you provided doesn’t look to me like an argument that is relevant to the Venter accomplishment. The poster presented six points of difference between computer machine code and DNA. This seems far afield from the argument that “we haven’t seen intelligent agents produce a whole genome, and therefore the coming into existence of a whole genome is no evidence of intelligent design.” Perhaps you can elaborate to clarify your point of comparison.

    As I said before, you can pick and choose whatever evidence you like to propose an hypothesis, but an hypothesis is useless scientifically, unless it has testable entailments. Don’t you agree?

    I would enjoy seeing proposals for testable entailments of your favored hypothesis.

  26. Adel Dibagno,

    Let me quote the relevant part of the link. Daniel King was replying to the argument that only intelligent beings were known to produce code (language was another word that was used) and therefore the code in the cell was also produced by intelligent beings. He expended some effort arguing that DNA code was analogous to computer code, and not the same fundamental kind of thing. Bfast argued that there were no significant differences (significant meaning more than differences between various kinds of computer code. The post I referred you to was his differentiation between computer code and DNA code:

    Here are what I reckon to be some differences between computer machine language and DNA:

    1. Provenance – computer machine language was designed by human beings :: DNA was not designed by human beings.

    But now we know that DNA can be designed by human beings. That is no longer a differentiation between the two kinds of code.

    In fact, Venter’s accomplishment has leapfrogged over all the objections that Daniel King made. It is no longer that relevant whether DNA code is analogous to computer code, or a member of the same kind of entity. The fact is, DNA has been made by humans, who are intelligent, whether or not DNA is a member of the code family. We know of only one source for a complete DNA genome. It is intelligence. The parallel is now direct. If one wishes to maintain that the most probable source of DNA code is not intelligence, then one must show that an alternative pathway is feasible, either by demonstration or by demonstrating a reasonable step-by-step process.

    I am temporarily out of time, but I will try to give you some proposals for testing my favored hypothesis soon. I’m enjoying testing it.

  27. 27

    @ Bornagain77

    Venter has repeatedly indicated this particular accomplishment represents a “baby step” which was built on both past successes and failures. I’d recommend Venter’s video on TED, where he explains what previous work it took to reach this particular goal, including why this particular variant of M. mycoides was chosen, what work was performed by his team, etc.

    @ O’Leary

    Your analogy fails on multiple levels.

    First, it commits the equivocation fallacy. A plastic or metal prosthetic is not synthetic in the way that artificially created insulin is synthetic. Venter’s cell is a synthetic of the latter, not the former. This is why we use the term “artificial limb” rather than “synthetic limb.” A more approprate analogy would be creating synthetic bone structures, muscle tissue, nerves or skin that closely resemble those naturally developed in living organisms.

    Second, I’m guessing the “artificial stuff” in these residents did not completely take over activity at a cellular level, going forward. Nor would this “artificial stuff” eventually control the entire cellular structure of their future offspring.

    Third, you seem to have mistaken the process for the result. Synthetic insulin is a product that E. coli does not produce naturally; just as the original recipient M. capricolum cell did not naturally reproduce the specific variant of M. mycoides as defined by Venter’s synthetic DNA. The fact that we enlist nature in the form of E. coli to create insulin does not make the result non-synthetic.

    @Phinehas

    While there were areas of that need to be accurate to one letter from a million, the synthetic DNA was tagged by varying approximately one thousand base pairs. This would not be possible unless there were areas that allowed variation.

  28. 28

    Dr Giem,
    Thank you for the clarification. You quoted Daniel King: “DNA was not designed by human beings.” And then you said “But now we know that DNA can be designed by human beings.” I think you are equivocating on the word “design” here. As I understand Daniel, he meant that the origin of DNA as a chemical entity in the Universe cannot be attributed to human agency. What Venter’s team did was fashion a particular sequence of DNA from chemical resources available in recent history.

    Perhaps Daniel’s meaning is clearer in what he said in post #212:

    To the best of my knowledge, computer code was invented by human beings, whereas, to the best of my knowledge, DNA was not invented by human beings.
    But if you want to argue that human beings invented DNA 3.5 billion years ago, that is your privilege.

    You are still left with the hypothesis that a non-human intelligence created DNA and life 3.5 billion years ago. This hypothesis presupposes the existence of some sort of creative intelligence acting at that point in time, which is yet another untested hypothesis.

  29. 29

    @ Dr. Glem (#26)

    The statement “But now we know that DNA can be designed by human beings.” seems unnecessarily ambiguous.

    Human beings design organisms using DNA. They did not actually design the repertoire valid of chemicals that can be used to form valid DNA sequences. Nor did they design the process by which DNA ultimately results in organisms. While we may extend DNA or create an entirely new system at some point in the future, we are currently limited in the kinds of DNA strands we can create.

    However, in the very near future, it’s more likely we will first create our own abstractions of existing DNA which will allow us to design organisms at a higher level. However, this abstraction will eventually need to be translated back to DNA, which again is something human beings did not design.

    On the other hand, human beings did design both computer languages and the hardware that executes them.

    CPUs have their own instruction sets, byte orders, architectures and unique processing sections which can be geared towards various tasks, such as playing back video, processing audio, etc. These features are designed by human beings to meet our specific needs. The same can be said with computer programming languages, which are designed to strike a balance between execution speed and developer productivity. While these languages are abstractions of a lower level instruction set, it is an instruction set of our own design.

    As such, a more accurate analogy would be Quantum computing, which is based on quantum mechanics. Again, we did not design the core instruction set nor did we design the process by which instructions are processed. Instead, we enlist quantum mechanics to solve computational problems. It’s likely that we will build abstractions on quantum mechanics to make solving computations problems easier, but they will ultimately need to be translated to the laws of quantum mechanics itself, which human beings did not design.

    On a related note: If DNA is a language in the way that programming code is a language, would this not imply that the process of life itself (replication) is based a form of computation?

  30. Synthetic Biology?
    Proof Of Something Else, No Synthetic Cell.
    So What Else is New?
    Genomes Are RNA’a Functional Organs

    I admit having read only the first four paras. Made me feel so empathically embarrassed. Could’nt read further…

    A. From “Genome from a bottle”
    Synthetic DNA makes cells switch species
    http://www.sciencenews.org/ind....._a_bottle_

    - An unprecedented wholesale genome swap. Stitched and transferred the entire M. mycoides
    acteria genome into emptied-from-genome M. capricolum cell. This genome switch caused the M. capricolum cell to switch species. The newly converted cell was nearly identical to the natural M. mycoides.

    - “Proof of concept experiment, take the sequence out of a computer, build it and boot it up to make a synthetic cell”.

    B. From “03.2010 Updated Life Manifest”

    The RNA genes are life’s prime strata organisms. They evolved their DNA-images as their organ, their continuously updated operational worklogs primal Earth’s organisms libraries, and genomed them, i.e. nucleusized them, and celled them with their other organ, the outer cell membrane.

    It is the RNA genes and their DNA replicas, life’s prime strata organisms, that evolve, and the evolution of genomes, the 2nd stratum of life, and of the 3rd life stratum cellular organisms, is an interenhancing consequence of their genes’ evolution.

    Dov Henis
    (Comments From The 22nd Century)
    03.2010 Updated Life Manifest
    http://www.the-scientist.com/c......page#5065
    Cosmic Evolution Simplified
    http://www.the-scientist.com/c......page#4427
    EOTOE.Embarrassingly obvious expanding horizons beyond Darwin And Einstein.
    http://www.molecularfossils.co.....ersal.html

  31. Jonathan Wells has a article up at ENV discussing Venter’s work:

    Has Craig Venter Produced Artificial Life?
    Excerpt: In contrast to Caplan’s exaggerated claims, CalTech biologist and Nobel laureate David Baltimore said that Venter has “overplayed the importance” of his results, which represent “a technical tour de force” rather than a scientific breakthrough. Venter “has not created life, only mimicked it,” Baltimore said.
    http://www.evolutionnews.org/2....._arti.html

    A someone else stated, Venter is being more than a just little slightly misleading in all this.

    and This article from wikipedia showing the tight grouping of the bacteria shows Venter’s group is even stretching terms to say a certain species of bacteria was changed into another species:

    The Mycoplasma mycoides cluster

    Mycoplasma mycoides is part of the Mycoplasma mycoides cluster, a group of closely related infectious mycoplasmas, first named by Weisburg et al.[4]

    The cluster sensu stricto contains the genera Mycoplasma mycoides and Mycoplasma capricolum and comprises six species and subspecies:

    * M. mycoides subsp. mycoides biotype Small Colony (MmmSC)
    * M. mycoides subsp. mycoides biotype Large Colony (MmmLC)
    * M. mycoides subsp. capri (Mmc)
    * M. capricolum subsp. capricolum (Mcc)
    * M. capricolum subsp. capripneumoniae(Mccp)
    * Mycoplasma sp. ‘bovine group 7′ (MBG7)

    The last one is disputed with respect to the question of being a separate species.[5][6]

    In 2009 L. Manso-Silván et al. proposed to consider M. mycoides subsp. mycoides biotype Large Colony as equal with M. mycoides subsp. capri. Furthermore they proposed the name Mycoplasma leachii sp. nov. for Mycoplasma sp. ‘bovine group 7′ as a separate species.[5]
    [edit] Minimal genome project

    As part of the Minimal Genome Project, a team of the J. Craig Venter Institute synthesized in 2010 a modified version of the 1,000,000 base pair M. mycoides genome and implanted it into a DNA-free bacterial shell of Mycoplasma capricolum; the resulting organism was shown to be self-replicating.[7][8]

  32. Adel DiBagno (28),

    The problem is fundamentally quite simple. There is a rational-scientific argument, and there is a theologically driven response to it. The theologically driven response is often wrapped in the mantle of science, but in fact depends on a theological premise: God either doesn’t exist (the atheist version), or won’t change nature (the “theistic evolution” version).

    The rational-scientific argument goes something like this:

    1. Intelligence exists. We know of at least one set of examples (and the denial of that fact has certain unavoidable negative self-referential consequences). The nature of intelligence is not known, but of its existence there can be no rational question. It is not known that intelligence is limited to modern humans, so at least initially that must be left as an open question (as it is when discussing SETI).

    2. Human intelligence can design and create certain objects that exist in nature. Other objects in nature resemble these humanly designed and created objects, and it seems reasonable to postulate a human or humanlike intelligence as a cause for these objects. DNA code is now known to be created by humans, and therefore DNA code could reasonably be postulated to have been originally (on our earth) created by humanlike intelligence.

    (In a nutshell, this is “some objects look designed.” This part is independent of the following part)

    3. For some objects, there is not a known reasonably plausible pathway to their formation that does not involve intelligence. This includes, at the present, DNA code adequate in amount and specificity to run a cell. That is, we see neither DNA code spontaneously assembling in said amounts and specificities to do the job, nor do we have adequate theoretical constructs as to how it would have happened. And in fact there are reasons to believe that the formation of DNA of adequate length and specificity is highly unlikely without intelligent intervention.

    4. Therefore, one can draw a tentative conclusion that these objects, including DNA code in particular, were originally created by intelligence that at least in some respects is humanlike. This conclusion is subject to revision, for example, if we discover that Venter made his central claims fraudulently, or if we discover a good detailed theoretical path from no code to DNA code without involving intelligence, or if we find that a certain mixture of montmorillonite clay, phosphoric acid, carbon dioxide, zinc sulfate, ammonia, water, etc., when acted on by, say, ultraviolet light, would consistently turn out the DNA code for the required genes in some Mycoplasma. But the evidence we have right now is most consistent with the idea that some intelligence was involved at the origination of the DNA code for life on earth.

    The theologically driven response immediately recognizes that if we accept that tentative conclusion and attempt to build on it, we have great difficulty avoiding the conclusion that there is a supernatural intelligence that can, and did, interact with (the rest of?) the universe. This it is not willing to grant. Therefore, the response is to raise challenges to the logic at every possible point, challenges that basically boil down to “any reasonable God wouldn’t do that” or “God doesn’t exist.”

    So for example, I have heard arguments that “God doesn’t design like human designers”, as if we could know this before we started investigating.

    I have heard the argument that humans are evolved intelligence, which is allowed, but not unevolved intelligence. That is basically begging the question. If DNA code was originally designed, then we didn’t entirely evolve without intelligence. Note that the denial of unevolved intelligence entails the denial of God, at least with the meaning they give to unevolved. So this is, in effect, an antitheological assumption.

    You said,

    As I understand Daniel, he meant that the origin of DNA as a chemical entity in the Universe cannot be attributed to human agency. What Venter’s team did was fashion a particular sequence of DNA from chemical resources available in recent history.

    Daniel was arguing that a fundamental difference between DNA and computer code was that one was designed by humans and the other was not. That might be partially true in a hairsplitting way before Venter, but it is not true any longer. Even before Venter, we had some computer code being produced by computers, and of course now DNA code has been produced by humans. There may be (still is) a tendency there, but it is not a fundamental difference any more.

    You said,

    You are still left with the hypothesis that a non-human intelligence created DNA and life 3.5 billion years ago. This hypothesis presupposes the existence of some sort of creative intelligence acting at that point in time, which is yet another untested hypothesis.

    That “untested hypothesis” bit might be true initially, but it is not true eventually. Initially, let us say that we follow the logic and evidence I outlined above. We might postulate a hypothesis that intelligence was required for DNA code during the origin of life, and then further postulate that intelligence was required to organize the rest of the cell during the origin of life, and then that intelligence was further required to produce significant improvements in the code. As long as there is no step-by-step process (Darwinian or otherwise) for obtaining these by processes not involving intelligence, while the original hypothesis may be designed to accommodate the evidence regarding DNA code, and therefore not testable in that regard, each further instance where intelligence seems to be required is another fulfillment of predictions made by this hypothesis, which then becomes a theory, and thus the theory is testable, and has been tested. Thus your comment about ID being an “untested hypothesis” can be misleading.

    In fact, to be technical, even the original hypothesis has been tested once. Remember that it appeared before Venter’s work, and predicted that intelligent agents might someday be able to reproduce DNA code, whereas nature without the intervention of intelligent agents would not be able to do so. Thus, the hypothesis is being tested as we speak write, by the folks at Harvard, and so far has passed the test. If some OoL researcher ever manages to find a reasonable pathway from non-living materials to a string of functional genetic code without the intervention of intelligence, the hypothesis will fail. But it is holding up to the test very well right now, thank you.

    I’ll still get back to you regarding the testable entailments of my favorite hypothesis.

  33. veilsofmaya (#29)

    I read your post as defending the position then taken by Daniel King. If I am wrong, feel free to correct me.

    I may not have always expressed myself clearly, so it is possible that there is some ambiguity in my remarks. In that case, it would be helpful if you would agree where you can, disagree with me where you can’t agree, and explore the ambiguity where it is not clear. I will try to do the same to you.

    You said,

    The statement “But now we know that DNA can be designed by human beings.” seems unnecessarily ambiguous.

    Human beings design organisms using DNA. They did not actually design the repertoire valid of chemicals that can be used to form valid DNA sequences. Nor did they design the process by which DNA ultimately results in organisms. While we may extend DNA or create an entirely new system at some point in the future, we are currently limited in the kinds of DNA strands we can create.

    I have been more clear lately in referring to DNA code. That is, Venter did not invent the concept of DNA code, nor did he personally figure out that it could be used as an essential part of life. Those points you are making are valid and granted. However, Venter did create long stretches of DNA, with code carefully enough put in place so that it was functional. Apparently this can be a tricky task, as one point mutation created a non-functional DNA strand. So what I was referring to was not the concept of DNA, but rather the physical making of a particular long functional strand of DNA.

    Your comments about computers are mostly correct, but they leave out computer programs writing other programs, sometimes not under the complete control of the original programmers. Thus the difference between DNA code and computer code, at least in this instance, is a difference in degree, not in kind.

    But as I noted in #26, Venter’s accomplishment has leapfrogged over the whole question. It is no longer a matter of claiming that DNA code is code just like computer code, and that computer code is only known to be ultimately traceable to (human) intelligence. We now know that DNA code itself can be produced by (human) intelligence. Thus a form of intelligence is sufficient to produce not just code, but the DNA code necessary for life. The argument that this is only an analogy and therefore invalid, has been shown not to have much predictive power. I’m therefore not that interested in rehashing the details. Angels, heads of pins, and all that.

    What I would be interested in would be a critique of #32.

  34. Adel DiBagno,

    I promised to get back to you regarding the testable entailments of my favorite hypothesis. I will at least partially fulfill that promise here. I will first outline my favorite hypothesis, then the testable entailments, then some tests I have done. I should point out that this hypothesis is not the official or majority view of ID adherents here or elsewhere.

    I also should note that I am not offering a formal defense of my position. The closest you can get to that can be found by clicking on my name and reading the first 5 chapters of Scientific Theology. A briefer defense can be found here, and an even briefer one here:
    http://www.uncommondescent.com.....ent-293535
    Rather, I am offering a brief outline without supporting evidence, except at the end of the logical chain.

    First, I find the ID argument, especially on the origin of life, persuasive. I see a short logical chain leading to a supernatural, super-intelligent Being as the ultimate Source of life. I see this Being as interested in life, and it being reasonable that He/She/It (I’m opting for He for traditional reasons) would try to communicate with His creatures. I believe that He has likely done it in the history of Judaism, Christianity, Zoroastrianism, and Confucianism, with greater or lesser clarity, and probably early Islam before Mohammed, IMO, became too vindictive. I don’t know enough about other religions to have a firm opinion. I do think that, in all cases, one should get as close as possible to the original material before making a judgment.

    That being the case, the scriptures of Judaism, Christianity, and Islam all seem to indicate that the creation story in Genesis is authoritative. Therefore I should at least consider that possibility. It seems reasonable to conclude from the story that life started at creation, and that a worldwide Flood destroyed that creation, a few thousand years ago. If there has been no acceleration of radioactive decay, and the fossil record isn’t that old, and there was carbon-14 before the Flood, (all reasonable first assumptions IMO), then we might expect to find significant levels of carbon-14 in fossil material such as coal that is up to 350 million years old. On the other hand, if it is really that old, there should be essentially no carbon-14 in it. This makes a testable difference, that I actually made efforts to get tested. For links to the prediction, literature research, and testing results, go to my website and read three articles linked there.
    Carbon-14 dating models and experimental implications
    Carbon-14 in fossil carbon
    Other Resources: John Baumgardner: Carbon-14 Evidence for a Recent Global Flood and a Young Earth

    There is also another project alluded to in “Carbon-14 dating models and experimental implications”, that of bones from Nineveh. My prediction has so far been confirmed, and the results will be in the peer-reviewed literature soon.

    So I am having fun making predictions and testing them. It may not be traditional ID, but hey, it’s working.

    I hope that answers your question.

  35. 35

    @ Dr. Glem. (#33)

    You said:

    I read your post as defending the position then taken by Daniel King. If I am wrong, feel free to correct me

    This is not a defense of Daniel’s position, but a response to what appears to be unnecessarily ambiguous and equivocal wording in your comment.

    In an attempt to clarify, I’ll point out areas in your comment which seem to muddy the way you’re using the phrase “DNA can be designed by human beings.”

    However, Venter did create long stretches of DNA, with code carefully enough put in place so that it was functional. Apparently this can be a tricky task, as one point mutation created a non-functional DNA strand.

    Venter’s accomplishment was designing a process which can produce strands that meet the existing standard of DNA as found in bacteria and other living organisms. Venter did not design this standard or even extend it.

    For Venter to have “designed” DNA, he would have needed to define which particular chemicals could be found in a valid DNA strand, rather than humans having discovered them via observation. This would make much of our research work unnecessary since, as the designer, they could have simply asked Venter since he would be the authoritative source on DNA.

    More problematic to your claim, DNA was in “use” far before Venter had been born. This clearly makes it impossible for him to have designed it.

    Your comments about computers are mostly correct, but they leave out computer programs writing other programs, sometimes not under the complete control of the original programmers.

    That my comment is mostly incorrect is rather ambiguous as well. Can you please point to which parts were inaccurate?

    Furthermore, what you’ve described is a computer writing other programs in an existing language, not designing a new programming language. While this would be possible, languages created by a computer would always be translated into CPU instructions, which were designed by a human being.

    For a computer to “design” something significantly unique, it would need to design the entire CPU, including it’s instruction set, architecture, etc. along with a corresponding language. However, early computers utilized binary because it was the easiest for human beings to implement in and understand.

    In fact, I think we will eventually migrate away from binary systems as quantum computing becomes mainstream. In doing so, we will be literally be enlisting the basic building blocks of the universe and with the laws of quantum mechanics to solve computational problems.

    Only when a binary computer created some form of non-binary system could it really be considered completely unique from human design.

    Thus the difference between DNA code and computer code, at least in this instance, is a difference in degree, not in kind.

    It’s unclear how a computer designing another program, programming language or even an entire fundamentally new computing system either supports or undermines this claim. Can you elaborate?

    But as I noted in #26, Venter’s accomplishment has leapfrogged over the whole question

    Again, Venter designed an organism using a synthetic DNA strand. He did not design DNA. This is the difference between authoring a book and creating the alphabet and language that the book was written in.

    As such, it’s unclear how Venter’s discovery has “leapfrogged” anything.

  36. 36

    @ Dr. Glem

    While I appreciate your response, my question regarding the consequences of your comparison between DNA and programming languages remains.

    If, as you suggest, there “..,is no longer a differentiation between the two kinds of code. [DNA and computer code] ” this seems to imply there would be no differentiation between cellular reproduction and computation.

    Would this be an accurate statement?

    If not, how do they differ?

  37. 37

    I wrote:

    That my comment is mostly incorrect is rather ambiguous as well. Can you please point to which parts were inaccurate?

    But should have wrote:

    That my comment is only mostly correct is rather ambiguous as well. Can you please point to which parts were inaccurate?

  38. veilsofmaya (#35-37)

    Perhaps you did not intend it, but your style strongly reminds me of someone who is more interested in making debate points than exploring ideas with someone else. I will illustrate what I mean.

    I wrote,

    I may not have always expressed myself clearly, so it is possible that there is some ambiguity in my remarks. In that case, it would be helpful if you would agree where you can, disagree with me where you can’t agree, and explore the ambiguity where it is not clear.

    I think that was a fair request, and you seemed to agree:

    This is not a defense of Daniel’s position, but a response to what appears to be unnecessarily ambiguous and equivocal wording in your comment.

    In an attempt to clarify, I’ll point out areas in your comment which seem to muddy the way you’re using the phrase “DNA can be designed by human beings.”

    The above statement implies that I wrote something that coudl be taken two (or more) ways. Bur rather than explore the ambiguity, you launched into an attack on a strawman:

    Venter’s accomplishment was designing a process which can produce strands that meet the existing standard of DNA as found in bacteria and other living organisms. Venter did not design this standard or even extend it.

    For Venter to have “designed” DNA, he would have needed to define which particular chemicals could be found in a valid DNA strand, rather than humans having discovered them via observation. [Omit snark]

    More problematic to your claim, DNA was in “use” far before Venter had been born. This clearly makes it impossible for him to have designed it.

    The first sentence quoted actually concedes that Venter designed, just not DNA in your view. You then try to persuade me that Venter did not design DNA.

    The problem is that designing DNA is ambiguous. It could mean designing the concept of DNA, the concept of DNA and all its relationships with RNA, translation machinery, and proteins, or simply a certain piece of DNA. You take me to task for supposedly being in error here. But you ignore where I specifically said,

    I have been more clear lately in referring to DNA code. That is, Venter did not invent the concept of DNA code, nor did he personally figure out that it could be used as an essential part of life. Those points you are making are valid and granted. However, Venter did create long stretches of DNA, with code carefully enough put in place so that it was functional. Apparently this can be a tricky task, as one point mutation created a non-functional DNA strand. So what I was referring to was not the concept of DNA, but rather the physical making of a particular long functional strand of DNA.

    Why, in that case, are you attacking a strawman? It is tiresome discussing concepts with someone who will mischaracterize what one says right after one has attempted to prevent the mischaracterization.

    You quote me,

    Your comments about computers are mostly correct, but they leave out computer programs writing other programs, sometimes not under the complete control of the original programmers.

    You then ask,

    That my comment is mostly incorrect [later revised to "only mostly correct"] is rather ambiguous as well. Can you please point to which parts were inaccurate?

    If you had read the passage you quoted carefully, you would have known. “[your comments] leave out computer programs writing other programs, sometimes not under the complete control of the original programmers.”

    You seem to be objecting to what I said, using the same definition of “design” that misunderstood my point regarding human design of functional stretches of DNA code. I was here talking about functional stretches of computer code, not a completely new design for code. Why you would think the contrary is beyond me.

    Given this point, your paragraph starting with “It’s unclear how a computer . . . ” is completely misguided, and I feel no need to elaborate on a concept that I already told you I do not hold.

    I will grant you that what Venter did was more like authoring a book (actually more like printing a book) than creating an alphabet and language. However, my point is that Venter was able to print the book, so to speak, and we haven’t seen books printed without an intention to print a book and very careful execution of the plan, arguing that the original printing was also deliberate.

    Of course, you can’t see how Venter’s discovery has “leapfrogged” anything when you think this way. If you understand what I actually wrote, you might find it easier to comprehend what I was writing about.

    In #36, you say,

    If, as you suggest, there “..,is no longer a differentiation between the two kinds of code. [DNA and computer code] ” this seems to imply there would be no differentiation between cellular reproduction and computation.

    That is one of the worst pieces of quote mining I have seen. I will give the quote in context:

    But now we know that DNA can be designed by human beings. That is no longer a differentiation between the two kinds of code.

    I did not say, nor did I mean, that there was no longer a differentiation between the two kinds of code. I meant that being designed by human beings (in the sense I have gone over above, the deliberate creation of long stretches of very carefully planned DNA that turn out to be functional), does not differentiate between DNA code and computer code. Again, why you cannot see what I meant is beyond me. You may disagree with what I wrote, but it appears that when you were writing you failed to even be accurate about what you were discussing.

    Of course there is a differentiation between cellular reproduction and computation. But that is like saying there is a differentiation between running a spaceship and copying the ASCII code for a book Both require at least minimal computation, but the kind of data manipulation is different, and the results are vastly different, while both are done with computer code.

    In fact, IIUC, Venter and company used DNA for two different functions. One was to actually run a cell, including reproduction. The other was to store data containing his name, the names of some associates, and the name of his company, encoded as if they were English letters standing for amino acids. The latter stretch of DNA was short compared to the former, but long enough so that the likelihood of this stretch arising by chance was vanishingly low. So just like computer code, DNA code has now been intelligently designed and created to store data without any other significant function for the cell itself.

    I explained at the end of the post that the whole subject seemed a moot point to me, then noted that

    What I would be interested in would be a critique of #32.

    I am still waiting for you to address the points made there. Then it will be easier to believe that you are more interested in exploring ideas than in making debate points.

  39. 39

    @ Dr. Glem (#38)

    You wrote:

    The problem is that designing DNA is ambiguous. It could mean designing the concept of DNA, the concept of DNA and all its relationships with RNA, translation machinery, and proteins, or simply a certain piece of DNA. You take me to task for supposedly being in error here. But you ignore where I specifically said…

    Dr. Glem,

    In the fallacy of equivocation, one references or presents a particular definition of term which is supported by a specific event or data, but then changes it’s definition or uses it in an ambiguous way at a different point in their argument to suggest the data or event supports their conclusion. As such, the statement you quoted would represent the former part, in which you present one definition of design as it applies to Venter’s accomplishment. This is how equivocation works.

    Why, in that case, are you attacking a strawman? It is tiresome discussing concepts with someone who will mischaracterize what one says right after one has attempted to prevent the mischaracterization.

    Because you continue to use the naked phrase “design DNA”, which I specifically referenced in my response and directly contrasted with what Venter actually accomplished. We do not say that an architect can “design CAD programs” or can “design iron, concrete and glass.” Architects can “design buildings.” Unless English is not your native language, this appears to be an intentionally ambiguous phrase.

    If you had read the passage you quoted carefully, you would have known. “[your comments] leave out computer programs writing other programs, sometimes not under the complete control of the original programmers.”

    To be specific, It’s unclear how the omission of computer programs writing other programs made anything in my comment “incorrect.” Incomplete, perhaps, but this would only be the case If completeness was the goal. Furthermore, if this were the case, computer programs writing other programs is also incomplete, as I illustrated. Would this make this aspect of your comment incorrect as well?

    As for the suggestion that I’m unwilling to explore ideas, I’ve already suggested a more accurate analogy in quantum computing, as it mirrors areas that were not created by human beings. However, you have yet to acknowledge it in any of your responses. Nor have I suggested that your initial or continued omission of quantum computing makes your response “mostly correct.”

    That is one of the worst pieces of quote mining I have seen. I will give the quote in context:

    But now we know that DNA can be designed by human beings. That is no longer a differentiation between the two kinds of code..

    Again, you’ve used the naked phrase DNA can be designed by human beings which is clearly ambiguous in this context. Let’s remove the ambiguity by replacing it with the definition you claim to be using and see if it fits.

    But now we know that human beings can use DNA to design organisms. That is no longer a differentiation between the two kinds of code..

    But we’ve already used DNA to design organisms in the past, such as designing a variant of E. coli to synthesize insulin. As such, this definition doesn’t appear to make sense in this context.

    How about…

    But now we know that human beings can use long, synthetic DNA strands to design organisms. That is no longer a differentiation between the two kinds of code..

    But, Venter is not free to put any sequence in a strand because he must adhere to the existing standard of DNA. We’re found a new way to write new programs. Rather than modifying a few statements here and there, we can define the entire program, but we are still using an existing language.

    Neither of these clarified paragraphs appear to support the claim that Venter’s discovery has “leapfrogged” all of King’s objections.

    As for misrepresenting your position, your earlier comment seems to suggest otherwise…

    It is no longer a matter of claiming that DNA code is code just like computer code, and that computer code is only known to be ultimately traceable to (human) intelligence.

    So, given the ambiguity and previous comment, it could easily have been interpreted to mean that this was the final part piece of the puzzle that proved equivocation. This also also seems to have been your position in your discussion with King.

    Of course there is a differentiation between cellular reproduction and computation

    And there is a vast difference between the first computer and modern day digital computers. But I’m guessing you would suggest they both perform computations on information.

    The other was to store data containing his name, the names of some associates, and the name of his company, encoded as if they were English letters standing for amino acids.

    Which I already covered under creating abstractions of DNA, in that a simpler symbols can stand for a number of unique DNA molecules, and vice versa.

    However, this is not anything unique to what Venter accomplished. We could map symbols to DNA before having created synthetic DNA and we have used DNA as software which was processed using enzymes as hardware. The field of DNA computing was initially developed in 1994 by Leonard Alderman. However, like quantum computing, the researchers did not develop DNA or the corresponding enzymes, they just enlisted them to solve their own computational problems.

    It’s unclear how DNA could be used to in this way if the process of cellular reproduction was not a form of computation.

    I am still waiting for you to address the points made there. [#32]

    But that argument contains a condensed version of this comment in point 02. And it suffers from the same problem.

    DNA code is now known to be created by humans, and therefore DNA code could reasonably be postulated to have been originally (on our earth) created by humanlike intelligence.

  40. veilsofmaya (#39),

    Thank you for your clarification. You are more interested in getting the other person to accept your definition than you are in understanding the concept. For you, design must always mean from scratch, including the concept. I am fine with using the term as in “the plagiarism happened by design”, even though the person may be copying a pattern he or she has seen before.

    You claim that the clause “DNA can be designed by human beings” is ambiguous. You may be right. So you take a couple of stabs at the actual meaning. Thank you for trying. Your first try at clarification is “human beings can use DNA to design organisms.” You then note that “this definition doesn’t appear to make sense in this context.” You then try “human beings can use long, synthetic DNA strands to design organisms.” You note that Venter and company were constrained as to which DNA sequences they could use. You agree that “we’[v]e found a new way to write new programs”, but “we are still using an existing language.”

    Let me help you with a more wordy explication of the clause. Long strings of functional (as in able to replace the DNA found in a “simple” cell functionally) DNA code can be deliberately planned and created by humans. Does that help you to understand what I was getting at?

    Let me restate the point I was making in #32, and then reply to that.

    1. Intelligence exists.

    2. Intelligent beings can intend to make, and make, certain objects. One of them is DNA of sufficient length and specificity to replace the DNA in a cell functionally.

    3. For some of these objects, specifically including the DNA in cells, there is not a known reasonably plausible theoretical pathway to their formation that does not involve intelligence, nor is there experimental evidence that this has happened.

    4. Therefore, one can draw a tentative conclusion that these objects, including DNA code long enough and specific enough to run a cell, were created by intelligence that at least in some respects is humanlike. That conclusion is subject to revision, if we discover new facts, or find that the old facts were not actually facts, but incorrect. But the evidence we have right now is most consistent with the idea that some intelligence was involved at the origination of the DNA code for life on earth.

    Now I will wholeheartedly agree with you that the original plan from scratch was more difficult than the copying of DNA code (not the actual DNA) while inserting a watermark where it would not kill the organism. That would suggest that the intelligence was smarter, or better informed, or both, than Craig Venter. But that is a question to be settled after we have decided whether intelligence was involved.

    Notice that I did not use the word “design” in the argument. Hopefully, you will not be so confused as to what I mean this time.

  41. 41

    @ Dr. Glem. (#40)

    You wrote:

    you are more interested in getting the other person to accept your definition than you are in understanding the concept.

    I’m more interested in what appears to be a change in the definition you use to support your concept.

    For you, design must always mean from scratch, including the concept. I am fine with using the term as in “the plagiarism happened by design”, even though the person may be copying a pattern he or she has seen before.

    Not necessarily. I’m noting that …

    A. The naked phrase “Design DNA” could refer to multiple meanings and that one of these meanings does not seem to support your conclusion.

    B. There are clear and significant differences between these definitions, which I’ve illustrated via the analogy of Quantum computing.

    C. Only one of these definitions accurately represents the factual role that Venter and other human beings human beings have played in designing organisms.

    You then note that “this definition doesn’t appear to make sense in this context.”

    Please note that I was referring to the context of that specific paragraph, including the suggestion that the ambiguous accomplishment was something that occurred only recently.

    Let me help you with a more wordy explication of the clause. Long strings of functional (as in able to replace the DNA found in a “simple” cell functionally) DNA code can be deliberately planned and created by humans. Does that help you to understand what I was getting at?

    It’s a simple process to remove the ambiguity. We design DNA strands. These strands represent specific sequences of molecules which meet the existing standard of DNA and are usually used in the process of designing organisms.

    However, we’ve done this before with various differences of degree. In the context of design, which seems to be your focus, it’s unclear how creating significantly longer strands is that different of an accomplishment from creating shorter strands or modifying existing strands. That is, unless your referring to Venter having designed the specific processes he and his team used to make synthetic DNA strands.

    Surely, Venter could have defined a long, yet specific, DNA strand in a computer in the recent past. In fact, Venter played a key role in sequencing human DNA, so we know that human DNA has already existed as ones and zeros in a computer. Furthermore, it’s extremely likely we have designed digital human DNA strands which are used in various simulations regarding the expression and treatment of various diseases and conditions. So, its not that we have not “designed” DNA strands, but that we’ve been able to physically build strands from molecules that work in existing cells.

    Clearly, Venter’s recent and unique accomplishment was the process by which these strands were assembled and the end result which was a synthetic organism.

    2. Intelligent beings can intend to make, and make, certain objects. One of them is DNA of sufficient length and specificity to replace the DNA in a cell functionally

    This is much clearer, but it leads me to an observation. Human beings can intend to make a wide range of things. We can plan missions to other solar systems and “design” elevators that stretch into space. The things we can intend to build seem only limited by our imagination.

    For example, as a strong agnostic, I’d suggest it’s likely the various forms of gods and goddesses throughout history represent a constant process of iterative design on the part of human beings. In fact, since not all religions can be true, at least a significant number of (and possibly all) of our conceptions of god(s) represent examples of solutions we human beings have designed to a number of problems we’ve encountered.

    However, I don’t think you’d suggest this is evidence that God was intelligently designed by human beings.

    3. For some of these objects, specifically including the DNA in cells, there is not a known reasonably plausible theoretical pathway to their formation that does not involve intelligence, nor is there experimental evidence that this has happened.

    I’m a critical rationalist. That is, I’m aware of the problem of induction as posed by Hume, the crisis it caused at the time and the impact in had on the scientific method in both principle and practice. Empirical evidence is used to weed out competing theories and explanations, not to justify one theory in particular. Nor does it seek to address all logically possible explanations.

    As such, the lack of a “known reasonably plausible theoretical pathway” does not necessarily pose a problem for Evolution as a theory. Nor does a lack of “experimental evidence that this has happened.”

    In other words, problem solving is ultimately about the power of explanation, not empirical observations alone.

    Therefore, one can draw a tentative conclusion that these objects, including DNA code long enough and specific enough to run a cell, were created by intelligence that at least in some respects is humanlike.

    First, please see above.

    Second, you wrote:

    So for example, I have heard arguments that “God doesn’t design like human designers”, as if we could know this before we started investigating.

    But there is a difference as it seems the only clear intersection between human designers and God is the assertion of design. Given what we observe, he would be unlike any designer we know of.

    To give one example, when human beings intentionally design, we do so in a way that avoids and manages risk in direct proportion with our ability and knowledge. It reflects our desire to have our cake and eat it too.

    To illustrate, we could eliminate the majority of vehicular deaths. But at our current level of knowledge and ability, this limits us to driving something similar to a tank, which is expensive, slow, guzzles fuel and could still fall off a cliff. As such, the vehicles we humans design reflect a balance between our perceived risks and our ability to avoid them.

    However, if we had the knowledge and ability to make cars that were affordable, agile and fuel efficient, yet impervious to collisions, we would. imagine some kind of system or field that absorbs both collisions and inertia, rending them harmless to occupants. Thrill seeking drivers could optionally turn of some of these features just as they can optionally turn of traction control on recent model high-end sports cars and sedans. Even then, we’d still likely mandate some automatic, low-level safety system that protected the driver from any form of serious injury, despite the vehicle otherwise being completely destroyed.

    Again, our designs reflect a desire to maximize control over risk in a way that is directly in proportional with our ability and knowledge to do so.

    While I’m not an expert, it’s unclear how the “design” of DNA reflects this observed property of human-like design.

    Sure, we have what could be thought of as a backup copy in each cell with mitochondrial DNA, but it’s located directly inside what is essentially a furnace that produces waste and toxins. This seems like an extremely poor place to intentionally store important information.

    Does this represent the remnants of symbiotic bacteria, which shed much of it’s own genome once housed in our cells or an example of a maximizing control of risk proportional with the supposed designers ability? Does the “design” of DNA reflect a risk the designer was trying to manage in some intentional way?

    But the evidence we have right now is most consistent with the idea that some intelligence was involved at the origination of the DNA code for life on earth.

    Again, as a critical rationalist, it’s clear to me that any theory can make any prediction. What we’re left with is the arguments and explanations behind each theory. I’d suggest your conclusion does not follow from the “evidence” but from your religious views.

  42. veilsofmaya (#41)

    I’m granting your points A, B, and C. In fact, I thought that was apparent earlier. If you grant, as you seem to in parts A and C, that there is one meaning that does work for what I was doing, then I think we have agreement here. I do thank you for the discussion, as it helps me to see where some with your general viewpoint are coming from, and helps me to clarify my points better and be less likely to be misunderstood.

    You seem to think that Venter didn’t do anything significant for my argument that hadn’t been done already. Perhaps you are right. I have attempted to engage Allen MacNeill a few times on this point, and he always disappeared from the thread or ignored the comment. There are three points where it appears to me that Venter extended the argument. First, there is a difference in degree. Creating the functional DNA to run a cell is a much more extensive process than creating the DNA to make TPA. The size is impressive. Second, Venter did not simply copy DNA and change a piece here and there. He created rather than copied. It is the difference between a photograph with a little retouching and a painting. Third, Venter put in the equivalent of a signature.

    But I agree that a case could be made that the argument I was making was valid even before Venter. He simply made it essentially impossible, rather than merely difficult, to argue against my point 2.

    You are right that humans can make a wide range of things. Some are imaginary, like characters in novels. Some are real, like trains. Some of those real things do not find counterparts outside of intelligent intervention in otherwise unintelligent nature.

    I am quite aware that there are problems with induction. The case of classical mechanics gives real-life importance to the theoretical problem that Hume raised. That is why I stressed that my conclusion, point 4, is tentative, and can be held only as long as the evidence supporting it is valid and not superseded.

    But here I fear that you have overreached. You say,

    As such, the lack of a “known reasonably plausible theoretical pathway” does not necessarily pose a problem for Evolution as a theory. Nor does a lack of “experimental evidence that this has happened.”

    If you had said “does not prove Evolution wrong”, you would have been correct. But what you are asking me to buy is essentially that there is no problem here. That is, don’t worry about the fact that there is currently no known reasonably plausible theoretical pathway to a string of DNA long enough to keep a cell going. Don’t worry that we haven’t seen nature without intelligent agents create such a string. Have faith that Evolution can make it happen, faith against the presently available evidence. With enough of this faith, the fact that the general theory hasn’t become specific, or that we haven’t actually seen it happen, “does not necessarily pose a problem”.

    I am assuming that you are using the word Evolution in the grand sense, which may be why you capitalized it. As I’m sure you know, the original Darwinian theory left out the origin of life, and many evolutionists try to exclude the origin of life from evolutionary theory (Nick Matzke, IMO to his credit, disagrees). But it appears that you consider the origin of DNA strings long enough to allow cells to grow and divide multiple times to impinge on Evolution. Here it appears that we have another area of agreement.

    Now, I tend to be an empiricist. I have lived long enough to see several theories in medicine fall, to empirical observations. Thus, if I see a theory that sounds good, but requires events to happen for which, after careful study, there is no evidence, I tend to go with the observation rather than the theory. That seems to the case here. Thus I do see that the observations I have noted, and you have not disputed, pose a problem for a theory that requires DNA strings long enough, and accurate enough, to run a cell, to be created without the participation of any intelligence.

    You finally get to your real objection to the (abductive) logical inference I made. You are afraid of what would happen if you admit the validity of the logic. You are afraid that it might lead to God.

    In spite of the fact that you label yourself as a “strong agnostic” (I assume that is an agnostic that leans strongly towards atheism), you try to adjudicate a theological quarrel that I have with some theistic evolutionists, taking their side on the matter. I find this amusing. How would someone leaning toward atheism be able to say that

    it seems the only clear intersection between human designers and God is the assertion of design. Given what we observe, he would be unlike any designer we know of.

    ? You don’t believe in God, but you are sure he would be unlike us? I am asking theistic evolutionists to have a little humility about their “knowledge” of the properties of God. How much more for you? Take your own comment, “I’m not an expert”, to heart.

    You comment, appropriately enough, that humans make tradeoffs when they design. You seem to be implying that the designer of life didn’t make those tradeoffs. At least that is how I read it when you say,

    it’s unclear how the “design” of DNA reflects this observed property of human-like design.

    Maybe that’s why you comment,

    However, if we had the knowledge and ability to make cars that were affordable, agile and fuel efficient, yet impervious to collisions, we would.

    You seem to be setting up a standard for God to follow. That is, this is a theological argument. Quite a feat for a strong agnostic. (You may protest that you are taking my beliefs and using them against me. But if that were really the case, I should recognize my beliefs in your critique, which I do not.)

    Perhaps the designer of life did use tradeoffs, like human designers. Perhaps human skin, and the recurrent laryngeal nerve of giraffes (and to a lesser extent humans) represent tradeoffs. Until you can design better humans from scratch, you might keep in mind that you are not an expert here. Neither am I, but then I never claimed to be one.

    It is also “clear to me that any theory can make any prediction. What we’re left with is the arguments and explanations behind each theory.” That is, unless the theory is willing to stick its neck out and make predictions, which can be rewarding or damaging, as the case may be. Would you be sanguine as to the prospects of Harvard University, which got a 5-year grant to solve the problem of the origin of life? Do you think it will be solved in our lifetime, or ever? Do you think we will solve even the problem of creating cell-managing pieces of DNA without intelligent guidance? Is there any evidence upon which to base this belief? Or are you the one whose “conclusion does not follow from the ‘evidence’ but from your religious views”?

  43. 43

    @ Dr. Glem (#42)

    You wrote:

    Have faith that Evolution can make it happen, faith against the presently available evidence.

    Dr. Glem,

    I’m not suggesting we have an absolute and complete understand of the mechanisms by which evolution occurs. And we are even farther way from an absolute and complete understanding of how biogenesis occurred. This is uncontroversial.

    However, the task that really lies before us is problem solving. While evidence is important, we criticize the explanations behind rival theories and the one left standing is tentative accepted.

    With enough of this faith, the fact that the general theory hasn’t become specific, or that we haven’t actually seen it happen, “does not necessarily pose a problem”.

    Dr Glem, we may never know the exact details, but based on the advances we’ve made in the last 20-30 years, it seems probably that we’ll learn much more than we know now.

    Nor is this necessarily the same thing as faith. Please see The Neural Correlates of Religious and Nonreligious Belief

    But it appears that you consider the origin of DNA strings long enough to allow cells to grow and divide multiple times to impinge on Evolution

    While ID’s claim extends across both evolution and biogenesis, I conceder them separate problems to be solved.

    Now, I tend to be an empiricist. I have lived long enough to see several theories in medicine fall, to empirical observations.

    Essentially you’re referring to the explicit acknowledgment of probability, which is one way the problem of induction was resolved. We cannot be sure the sun will rise tomorrow, but it’s very probable since it’s risen so many times before. But I’d also note that we can actually understand how starlight works based on a chain of difficult to vary explanations. And it’s these explanations that result in having accepting the source of starlight as nuclear fusion, not merely empirical observations. This is despite the fact that we’ve never actually been to the center of the sun to observe the process.

    Thus I do see that the observations I have noted, and you have not disputed, pose a problem for a theory that requires DNA strings long enough, and accurate enough, to run a cell, to be created without the participation of any intelligence.

    The reason I think this rival theory is unlikely is the explanation, not necessary the evidence. Again both theories can and often do make the same empirical predictions. Please see this TED talk by David Deutsch for further reference.

    You are afraid of what would happen if you admit the validity of the logic.

    As a supposed empiricist, have you empirically observed my fear?

    Personally, If God actually does exist, I think it’s highly unlikely that most of the concepts we created are accurate. We know this because many of the concepts we observe contradict each other, including many important issues, such as salvation, etc. One example: does it make sense to say God a he? This seems clearly based on tradition, dogma, etc. God is a he because men were dominated in the past and God supposedly dominates everything. The human bias seems readily apparent. I’d suggest the same with a perfect being using the carrot and the stick, giving out an eternal punishment with no possibility to learn and improve from it, etc. I could go on, but we’re diverging from the original topic.

    So, if some infinitely perfect, powerful and knowledgeable being does exist, I would not fear it.

    You comment, appropriately enough, that humans make tradeoffs when they design. You seem to be implying that the designer of life didn’t make those tradeoffs.

    I’m not just referring to any tradeoff, as theists already suggest God traded free will for love, etc. Instead, I’m suggesting human beings maximize risk control in proportion to our ability. That is, our goals, perceived risks and ability control over those risks can be seen in our designs. It appears to be built into everything as part of our intentional design process.

    Until you can design better humans from scratch, you might keep in mind that you are not an expert here. Neither am I, but then I never claimed to be one.

    Nor am I suggesting “better” designs. Am I not a human being? As such, wouldn’t the kind of human being I would design be relevant to your claim? If not, then what does it mean to suggest the designer was human-like? Other than the assertion of the act of design, what parts actually do overlap with human beings?

    As for the rest of your comment, please see the video by David Deutsch. We may never solve these problems, but this still doesn’t mean a theory that some non-material being created everything from nothing should be accepted by default.

  44. veilsofmaya (#43),

    You don’t know the mechanisms “by which evolution occurs”, and you don’t know “how biogenesis occurred”, nor does anyone else. Good. We agree on the general concept.

    But you still state it as “how biogenesis occurred”, as if we know that it occurred, and that it occurred without any help from any intelligence. That is faith (or if you don’t like the word faith, try belief, trust or some other word that means belief in some concept without being able to prove it).

    I find it interesting that you accept the concept that “we criticize the explanations behind rival theories and the one left standing is tentative accepted.” I take it that the logical consequence of this reasoning is that if one can criticize the explanations behind non-intelligence-directed processes leading to the genetic code currently believed to be necessary for life, that intelligence-directed processes should be accepted, at least tentatively.

    (Some colleagues of yours try a little two-step here. They protest that evidence against evolution should not be interpreted as evidence for intelligent design, but that evolution can be proved, or at least supported, by evidence against intelligent design. Nice gig if you can get it.)

    You write,

    Dr Glem, we may never know the exact details, but based on the advances we’ve made in the last 20-30 years, it seems probably that we’ll learn much more than we know now..

    That’s not even a promissory note. it just says that we’ll learn much more than we now know, not that we will have either a plausible theory for the origin of DNA code not involving intelligence, or that we will have experimental evidence of DNA code arising without intelligent intervention.

    I have experimental evidence that intelligence can produce DNA code. All you have is promises that someday we’ll get there. That’s what I mean by faith against the evidence. If it makes it easier for you to see the point, you can call it belief against the evidence. If you want to differentiate it from religious faith, go ahead. I’m not sure I buy the fundamental distinction, but what I was referring to is not religious. It is scientific. We have a demonstrated explanation for a phenomenon. You have a general theory that A. hasn’t been able to get specific, and B. hasn’t been able to show experimental results supporting it. That is metaphysical belief against science.

    All you can do at this point is issue a promissory note. Now I would agree that sometimes it makes sense to issue such notes. When Uranus was noted to move in ways that defied Newtonian physics, belief in the general theory of gravitation allowed scientists to find the planet Neptune.

    But not all promissory notes are valid. When the same procedure occurred with Mercury, Vulcan was never found. Instead, General Relativity replaced Newtonian physics. Neither I, nor you, nor anyone else knows whether the origin of life without intelligence will turn out to be the next “moon shot”, attainable but with a great deal of effort, or the next perpetual motion machine, not attainable at all (as far as we know).

    Your point about the sun is interesting but beside the point. A theory that does not have empirical data opposing it can be tentatively accepted, even if the data that it explains are relatively sparse and have a considerable chain of inference leading to actual data. But when the theory has not been demonstrated in spite of multiple efforts, and an opposing theory has, it makes no sense to accept the defective theory in preference to the opposing theory.

    You ask,

    As a supposed empiricist, have you empirically observed my fear?

    Not directly, but otherwise why the sudden switch from scientific issues (the origin of long complex functionally specified strings of DNA) to “What would God do”? Your question about God being a He is somewhat sophomoric, and my answer is here (p. 66).

    Your question about eternal punishment is similarly misguided. If eternal conscious punishment is so bad, why not do like Antony Flew and believe in a God, just not the (now) traditional Christian one? I agree with you that this is a problem for traditional Christianity. But traditional Christianity could be wrong on this point and right on many others. But, as you note, we’re diverging from the initial topic. The question of intelligent design should be determinable without bringing God into the picture. Bringing God into the picture suggests that one side is afraid of where the evidence might point, rather than simply looking at the evidence itself.

    You quote me, and ask,

    Until you can design better humans from scratch, you might keep in mind that you are not an expert here. Neither am I, but then I never claimed to be one.

    Nor am I suggesting “better” designs. Am I not a human being? As such, wouldn’t the kind of human being I would design be relevant to your claim? If not, then what does it mean to suggest the designer was human-like? Other than the assertion of the act of design, what parts actually do overlap with human beings?

    I’m not sure what your reference to “your claim” is about. I would say that in this context, “human-like” is able to plan and execute like humans, and able to be at least partly understood by humans. The designer could be more like humans than that, but further similarities would have to be determined by further evidence.

    You would do well to be careful about using Deutsch’s video. (BTW, he has a delightful accent, or perhaps in deference to the Queen, lack of accent.) Deutsch makes the point that explanations that are hard to vary (I presume he means to add, but are still accurate), are the way knowledge advances. Thus evolutionary explanations and global warming are apparently anti-science on this reading. Global warming morphs into climate change when record cold spells hit. It seems to be impervious to evidence that changes in the altitudinal temperature gradient are the reverse of what is expected. And evolution is notorious for predicting drab coloration sometimes, and bright coloration sometimes, and mimicry when mimicry doesn’t offer protection. The examples could be multiplied.

    Your final sentence lays it out directly.

    We may never solve these problems [presumably how life originated without the assistance of intelligence], but this still doesn’t mean a theory that some non-material being created everything from nothing should be accepted by default.

    First of all, it is not by default. The object in question has subparts that can be exactly duplicated by intelligent agents. We are inferring from positive as well as negative evidence. Secondly, intelligent design does not exclude more than one designer, or the deliberate design of “white noise” as a background. But most importantly, the real objection is to “some non-material being”. The science indicates intelligent design. The objections are theological.

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