« Berlinski's Wisdom
The Proteasome »

De Facto Intelligent Design in Biology

by Bradford

Intelligent Design is ___________. A Trojan horse, a wedge strategy, stealth creationism… Place your favorite cliche into the blank. In doing so ignore the real world. In that world Venter recognizes what was already plain to see. Instructions within cellular genomes reveal what life is. Venter:

This is as much a philosophical as a technological advance. The notion that this is possible means bacterial cells are software-driven biological machines. If you change the software, you build a new machine. I'm still amazed by it.

Cellular constructs which function like control structures, "performing a function similar to steering logic." Codified genetic information and instructions. Error detection and correction mechanisms. Unmistakable parallels to computer programs generated by advanced intelligence and utilized with modern technology. Perhaps investigators will even use approaches from computer science to generate breakthroughs in molecular biology. Utilize codified symbolic systems invented by intelligent agents to reveal new things about biology which can be tested and verified. Already done.

Computer screens looking like computer codes resulting from "software originally developed for finding flaws in microchip circuitry." Basing predictions about growth disruptive mutations, which can be experimentally verified, on programmed warning designs. At this point it is obligatory to emphasize that biological designs are apparent and not real. Mere mirages resulting from mindless forces of nature. The same forces which generated human consciousness. Ya know science, science, science…

Likewise, the diagram as a whole — illustrating, say, a regulatory pathway — corresponds to a sequence of statements that collectively function as a computer simulation. Ultimately, she says, this kind of software should develop to a point at which researchers can draw a hypothetical pathway or interaction on the screen in exactly the way they're already used to doing, and have the computer automatically convert their drawing into a working simulation.

Call this executable biology or whatever you like. But memorize one more thing. Intelligent design is an empirical non-starter. Now, let's all leave reality and go back to ID is a Trojan horse, blah, blah, blah.

This entry was posted on Saturday, June 26th, 2010 at 11:13 am and is filed under Biology, Intelligent Design. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site. The trackback link is: http://telicthoughts.com/de-facto-intelligent-design-in-biology/trackback/

114 Responses to “De Facto Intelligent Design in Biology”

  1. olegt Says:
    June 26th, 2010 at 11:33 am

    Bradford,

    Hasn't Bilbo used the same quote from Ventner to declare victory for ID already?

    Now, suppose—for the sake of the argument—the Darwinists pack up and leave molecular biology. What is the ID program of research on that front? I suspect it has none. As far as I know, ID's ultimate goal is to declare that living things have been designed and to leave it at that. Agree? Disagree?

  2. Comment by olegt — June 26, 2010 @ 11:33 am

  3. Bradford Says:
    June 26th, 2010 at 11:52 am

    Olegt: What is the ID program of research on that front? I suspect it has none. As far as I know, ID's ultimate goal is to declare that living things have been designed and to leave it at that.

    You missed the point completely. The objective is to learn more about biology and a productive means of doing so is to use programming concepts developed by intelligent agents to make predictions about biological organisms.

  4. Comment by Bradford — June 26, 2010 @ 11:52 am

  5. olegt Says:
    June 26th, 2010 at 11:55 am

    So, what's next, Bradford? What are IDers going to do with this precious insight? I think I know: wait for the next experimental work to come out and declare it their own.

  6. Comment by olegt — June 26, 2010 @ 11:55 am

  7. Bradford Says:
    June 26th, 2010 at 12:00 pm

    More likely IDists and non-IDists alike will get accustomed to progress being linked to the utilization of abstract conceptual tools, developed by programmers, to reveal biological function.

  8. Comment by Bradford — June 26, 2010 @ 12:00 pm

  9. olegt Says:
    June 26th, 2010 at 12:05 pm

    Bradford,

    You're mistaking a metaphor for a conceptual tool. Ventner waxes poetic about his achievements, but he does not use any programming concepts in his actual work. Analogy only takes you so far.

  10. Comment by olegt — June 26, 2010 @ 12:05 pm

  11. Bradford Says:
    June 26th, 2010 at 12:14 pm

    It was not metaphorical for Fisher to use a warning concept, found in software developed for the purpose of finding flaws in microchip circuitry, to gain biological insights.

  12. Comment by Bradford — June 26, 2010 @ 12:14 pm

  13. olegt Says:
    June 26th, 2010 at 12:19 pm

    Could you be a little more specific, Bradford?

  14. Comment by olegt — June 26, 2010 @ 12:19 pm

  15. Daniel Smith Says:
    June 26th, 2010 at 12:33 pm

    olegt: Now, suppose—for the sake of the argument—the Darwinists pack up and leave molecular biology. What is the ID program of research on that front? I suspect it has none. As far as I know, ID's ultimate goal is to declare that living things have been designed and to leave it at that. Agree? Disagree?

    I can tell you what I would advocate for (though I am mostly alone in this) and that is that ID seek to integrate what it is able to learn about the Designer through His designs into science.

    I've often used the example of finding artifacts on Mars. If we did find such things, we'd seek to discover as much (or more) about the creatures that built them as we would about the objects themselves. Such knowledge would serve to put the designs in context and aid in our understanding of their intended use. ID, by integrating theology, philosophy and metaphysics into biology, chemistry and physics would seek to form a 'universal whole' of knowledge rather than the fractured and separate types we have now.

    Put simply: If biology is designed, it is designed for a reason, and suddenly that reason becomes relevant. The artificial wall has to come down at that point.

  16. Comment by Daniel Smith — June 26, 2010 @ 12:33 pm

  17. Guts Says:
    June 26th, 2010 at 1:36 pm

    Synthetic Biology in general is a discipline that draws heavily from engineering and computer science, partly because that's where we are constructing machines that are finally approaching the sophistication of the cell

  18. Comment by Guts — June 26, 2010 @ 1:36 pm

  19. Bradford Says:
    June 26th, 2010 at 1:36 pm

    Daniel: I've often used the example of finding artifacts on Mars.

    If we found artifacts or novel natural phenomenon on another planet we would seek to understand how they work and, in the case of an artifact, its intended purpose. If we started the analysis with human artifacts (programs) and used designs within them to predict biological function our analysis of intelligently designed artifacts would be the basis for predicting natural functions which may not be obvious simply by observing cells. The perspective begins with design and then focuses on the natural rather than beginning with observing the natural and deriving function from an understanding of how things work.

  20. Comment by Bradford — June 26, 2010 @ 1:36 pm

  21. olegt Says:
    June 26th, 2010 at 4:50 pm

    Guts wrote:

    Synthetic Biology in general is a discipline that draws heavily from engineering and computer science

    I don't know much about the field, but a quick look at the Wikipedia article seems to suggest the opposite relation between synthetic biology and engineering. People working in that field apply existing basic biological knowledge to create new biological systems. That's more or less like electronics is application of basic physics to electrical engineering.

    Again, I am not a biologist, so I may be wrong. If you have specific examples in mind, I'd be interested in seeing them.

  22. Comment by olegt — June 26, 2010 @ 4:50 pm

  23. olegt Says:
    June 26th, 2010 at 4:52 pm

    The formatting in the above comment has been screwed up. Here is a second attempt. (Guts, where is that preview/edit function you promised?)

    Guts wrote:

    Synthetic Biology in general is a discipline that draws heavily from engineering and computer science

    I don't know much about the field, but a quick look at the Wikipedia article seems to suggest the opposite relation between synthetic biology and engineering. People working in that field apply existing basic biological knowledge to create new biological systems. That's more or less like electronics is application of basic physics to electrical engineering.

    Again, I am not a biologist, so I may be wrong. If you have specific examples in mind, I'd be interested in seeing them.

  24. Comment by olegt — June 26, 2010 @ 4:52 pm

  25. olegt Says:
    June 26th, 2010 at 4:59 pm

    Bradford wrote:

    It was not metaphorical for Fisher to use a warning concept, found in software developed for the purpose of finding flaws in microchip circuitry, to gain biological insights.

    If you meant this Fisher then I strongly doubt that he had any biological insights from microchip circuitry. He died in 1962, well before microchips took off.

  26. Comment by olegt — June 26, 2010 @ 4:59 pm

  27. Bradford Says:
    June 26th, 2010 at 5:34 pm

    Jasmin Fisher, Olegt. She's better looking than Abby.

    Executable Biology

    Our research focuses on the design and analysis of executable computer algorithms that mimic biological phenomena. We call this approach Executable Biology. These kinds of models hold great promise for new discoveries in a wide variety of biological systems. Once an executable model has been built of a particular system, it can be used to get a global dynamic picture of how the system responds to various perturbations. In addition, preliminary studies can be quickly performed using executable models, saving valuable laboratory time and resources for only the most promising avenues.

    Modeling biological phenomenon can lead to new predictions, new understandings. Models of biological software are intrinsically telic.

  28. Comment by Bradford — June 26, 2010 @ 5:34 pm

  29. Guts Says:
    June 26th, 2010 at 6:19 pm

    Olegt:

    People working in that field apply existing basic biological knowledge to create new biological systems.

    The very existence of the Registry of Standard Biological Parts (mentioned in the article) shows that they are drawing heavily from the Computer Science concept of abstraction. In addition to abstraction, they re-use design concepts like modularity, standards, and protocols, in order to understand the biological systems and how to build them.

  30. Comment by Guts — June 26, 2010 @ 6:19 pm

  31. Paul Nelson Says:
    June 26th, 2010 at 6:20 pm

    Venter, guys. Venter.

    (I said "Ventner" several times in a public lecture until someone corrected me. Face is still red.)

  32. Comment by Paul Nelson — June 26, 2010 @ 6:20 pm

  33. hblavatsky Says:
    June 26th, 2010 at 6:43 pm

    I'm perplexed that a number of writers here have cited Venter's work as evidence that confirms the validity of certain (unspecified) theories in ID, however Venter has never made such claims. That seems to be an ultra-fringe interpretation of Venter's research.

    From what I can tell, Venter seems to be what the Discovery Institute call a "materialist" – his work has demonstrated that no spiritual spark of life is required to create life. The most complex component in a bacterial genome has been made using entirely non-spiritual techniques. If that's true then mundane, materialist processes could account for just about any aspect of biology.

  34. Comment by hblavatsky — June 26, 2010 @ 6:43 pm

  35. Guts Says:
    June 26th, 2010 at 6:49 pm

    I'm not aware of any ID proponent who has made the suggestion that life requires a "spiritual spark". Only the input of intelligence and foresight.

  36. Comment by Guts — June 26, 2010 @ 6:49 pm

  37. ID guy Says:
    June 26th, 2010 at 7:45 pm

    olegt:
    Now, suppose—for the sake of the argument—the Darwinists pack up and leave molecular biology. What is the ID program of research on that front? I suspect it has none. As far as I know, ID's ultimate goal is to declare that living things have been designed and to leave it at that. Agree? Disagree?

    You don't appear to know very much about ID oleg.

    ID is about the detection and study of the design.

    And if Darwinists leave molecular biology and allow IDists to have all their funding and resources, then I would say IDists would try to unlock the software.

    IOW it would be a given that living organisms are not reducible to matter and energy so there must be something else.

    IDists would seek that something else.

  38. Comment by ID guy — June 26, 2010 @ 7:45 pm

  39. hblavatsky Says:
    June 26th, 2010 at 7:50 pm

    I'm not aware of any ID proponent who has made the suggestion that life requires a "spiritual spark". Only the input of intelligence and foresight.

    Really, I'm surprised to hear that. While I admit there are (some) ID proponents who hold no spiritual beliefs concerning the origin of life most of the people I know who would describe themselves as supporters of ID are motivated by their spiritual convictions.

    Which part of Venter's work or statements suggests that the "creation" required foresight? Surely Venter's work would be just as suggestive of an intelligence that was incapable of planning or foresight?

  40. Comment by hblavatsky — June 26, 2010 @ 7:50 pm

  41. ID guy Says:
    June 26th, 2010 at 7:50 pm

    olegt:
    I don't know much about the field, but a quick look at the Wikipedia article seems to suggest the opposite relation between synthetic biology and engineering. People working in that field apply existing basic biological knowledge to create new biological systems. That's more or less like electronics is application of basic physics to electrical engineering.

    Approaching Biology from a Different Angle:

    It was a major coup in 1991 when the University of Washington, with a $12 million grant from Microsoft's chairman, William H. Gates, lured Dr. Leroy Hood to create and head a molecular biotechnology department.

    Dr. Hood, after all, was, and still is, a biotechnology superstar. In the 1980's, while at the California Institute of Technology, he led the team that invented the DNA sequencer, the machine that made the Human Genome Project possible.

    At the news conference in February announcing the publication of the genome papers, Dr. Francis S. Collins, director of the National Human Genome Research Institute, singled out Dr. Hood, saying, "We would not be here today if not for the innovation in technology."

    Dr. Hood has also helped show how the immune system creates its arsenal of antibodies. And he has helped start more than half a dozen companies, including Amgen, the largest biotech company, and Applied Biosystems, the leading maker of genetic analysis equipment.

    A little more than a year ago, Dr. Hood quit the university and delivered a stinging message. The university, he said, and universities in general, are unfit for the new age of biology.

    So now, at 62, Dr. Hood is starting over. He has formed a nonprofit research center, the Institute for Systems Biology, which he hopes will transform the study of biology.

    Systems biology is a loosely defined term, but the main idea is that biology is an information science, with genes a sort of digital code. Moreover, while much of molecular biology has involved studying a single gene or protein in depth, systems biology looks at the bigger picture, how all the genes and proteins interact. Ultimately the goal is to develop computer models that can predict the behavior of cells or organisms, much as Boeing can simulate how a plane will fly before it is built.

    But such a task requires biologists to team up with computer scientists, engineers, physicists and mathematicians.

  42. Comment by ID guy — June 26, 2010 @ 7:50 pm

  43. ID guy Says:
    June 26th, 2010 at 7:52 pm

    hblavatsky,

    Venter's work demonstrates that intelligent agencies can design a genome from scratch.

    We have never observed blind, undirected chemical processes doing so…

  44. Comment by ID guy — June 26, 2010 @ 7:52 pm

  45. Guts Says:
    June 26th, 2010 at 8:17 pm

    hb:

    Really, I'm surprised to hear that. While I admit there are (some) ID proponents who hold no spiritual beliefs concerning the origin of life most of the people I know who would describe themselves as supporters of ID are motivated by their spiritual convictions.

    Just because an IDer believes in God doesn't mean that he believes it took a "spirtual spark" to get life going. Or that there's some mystical force required for life to get going (isn't that a form of vitalism?). Cars don't require any spiritual spark but they were nevertheless intelligently designed. To put it as simply as I can, picture a supernatural being , like God, creating a rolls royce ex nihilo. Of course, a spiritual being created the car supernaturally but the car can nevertheless be replicated by humans without any spiritual spark.

    Surely Venter's work would be just as suggestive of an intelligence that was incapable of planning or foresight?

    lol, I'm sure Venter would take offense to that. On the contrary, I'm sure what Venter did took very careful planning and implementation.

  46. Comment by Guts — June 26, 2010 @ 8:17 pm

  47. Bradford Says:
    June 26th, 2010 at 8:22 pm

    hb: Surely Venter's work would be just as suggestive of an intelligence that was incapable of planning or foresight?

    Intelligence that cannot plan and has no foresight. Why then call it intelligent?

  48. Comment by Bradford — June 26, 2010 @ 8:22 pm

  49. nullasalus Says:
    June 26th, 2010 at 8:42 pm

    Bradford,

    Intelligence that cannot plan and has no foresight. Why then call it intelligent?

    I would add, as technology continues to advance, and more and more things continue to be made by humans that we once ascribed to this "nature" thing (Modified life forms? Whole new life forms? Terraforming?), supposing blindness and non-intelligence being behind what we do see is going to be a harder and harder sell. We may end up wondering, why divide the world into nature and artifact? Artifact can cover damn near everything from some ID views.

  50. Comment by nullasalus — June 26, 2010 @ 8:42 pm

  51. eric Says:
    June 26th, 2010 at 11:09 pm

    nullasalus: "We may end up wondering, why divide the world into nature and artifact? Artifact can cover damn near everything from some ID views."

    It is true that intelligence might do what matter+energy could also do. We might artificially make diamonds or rocks.

    But the distinction would still be valuable. There are some things that happen due to the built in operation of forces, etc. according to the nature of chemicals and energy. That can accomplish some kinds of effects. We can infer intervening design only for those cases of effects that we have good reason to fall outside that set of effects that innate chemical behaviors produce.

    (If you have a better way to say this, feel free. But it is the distinction I mean by the undirected/directed terminology.)

  52. Comment by eric — June 26, 2010 @ 11:09 pm

  53. eric Says:
    June 26th, 2010 at 11:26 pm

    hblavatsky: "I'm perplexed that a number of writers here have cited Venter's work as evidence that confirms the validity of certain (unspecified) theories in ID, however Venter has never made such claims. … From what I can tell, Venter seems to be what the Discovery Institute call a "materialist" "

    No one is claiming Venter is not a materialist. The significance of establishing that cells are software driven machines was explained back in Game Over, e.g. here, when you asked a similar question.

    hblavatsky: "his work has demonstrated that no spiritual spark of life is required to create life. The most complex component in a bacterial genome has been made using entirely non-spiritual techniques. If that's true then mundane, materialist processes could account for just about any aspect of biology."

    You are being misled by working from the wrong dichotomy.

    The central pivotal issue of ID inferences is not natural vs. supernatural. It is natural vs. artificial. Two different meanings of "natural" with two different complementary categories.

    Notice that design inferences have always included cases of human design. It's not about whether we detect a supernatural origin but rather about whether it is an effect that can or cannot be reached without the additional direction of an intervening intelligence.

    This is why your conclusion is not correct:

    hblavatsky: "If that's true then mundane, materialist processes could account for just about any aspect of biology."

    Not so. A cell phone is material. However, it is also artificial. Innate processes of nature would never produce it. Likewise, innate processes of matter and energy would never produce a software driven machine (e.g. a computer).

    That is why Venter's work becomes significant. Cells are seen ever more clearly to be the sort of artificial object that the innate processes of matter and energy would not create.

  54. Comment by eric — June 26, 2010 @ 11:26 pm

  55. eric Says:
    June 26th, 2010 at 11:38 pm

    Daniel Smith: "I can tell you what I would advocate for (though I am mostly alone in this) and that is that ID seek to integrate what it is able to learn about the Designer through His designs into science."

    You are certainly not at all alone with regard to a desire to learn as much as we can.

    I simply think that you may be assuming that the main obstacle is wanting to do so. In reality, the ability to infer much about the originator of technology from the technology can be quite limited, and when the originator is not human, all the more so.

    The problem is not so much that you ask for something that is wrong, but simply that it is not so easy or accessible as you seem to assume.

    What can be done — and is being done — is to better understand how the technology of the cell works. We are reverse engineering the cell, just as we would do with any other technological find (including any from Mars).

    But unlike studying ancient human civilization, we have the decided disadvantage in this case of studying something that is more advanced than what we have ever accomplished, rather than artifacts that are more primitive. We are on a learning curve, so some gracious understanding of the difficulties involved would be fitting.

  56. Comment by eric — June 26, 2010 @ 11:38 pm

  57. nullasalus Says:
    June 27th, 2010 at 12:15 am

    eric,

    But the distinction would still be valuable. There are some things that happen due to the built in operation of forces, etc. according to the nature of chemicals and energy. That can accomplish some kinds of effects. We can infer intervening design only for those cases of effects that we have good reason to fall outside that set of effects that innate chemical behaviors produce.

    (If you have a better way to say this, feel free. But it is the distinction I mean by the undirected/directed terminology.)

    I agree that a distinction would be valuable, for the same reason it's important to make distinctions between various different types of design (sculpting versus programming versus painting versus, etc.) But that wouldn't be a distinction between natural versus artifactual.

    If I code a program and run it, the program has 'innate behaviors'. It has things it will do all on its own. I can, of course, directly intervene in the program while it is running. But does that mean the program's operations, sans my direct intervention, is not artifactual? I'd say that's flat out incorrect. I'd also say it's incorrect to consider those operations "undirected".

    So again, we may eventually end up wondering: Why divide the world into these two distinct spheres of artifact and nature, when artifact could conceivably cover everything we see and undeniably covers many things (and more and more encroaches on what we used to credit "nature" without argument)? Let's just call it all artifactual, all design.

  58. Comment by nullasalus — June 27, 2010 @ 12:15 am

  59. AnaxagorasRules Says:
    June 27th, 2010 at 2:06 am

    Hi, Bradford,

    Perhaps investigators will even use approaches from computer science to generate breakthroughs in molecular biology.

    One possible paradigm is of the Microsoft Windows system (I'm serious! lol) A cell would be analogous to a computer system, the hardware being all the organelles and proteins and ribosomes and amino acids and sugars, etc. There are many application programs going on at the same time inside the cell, all of them event driven, with the operating system determining the resource allocation and priorities. The DNA houses both the operating system and the cell's application programs. There's a lot of parallel processing going on. I don't think the operating system is well understood yet, though the individual apps that create proteins are becoming more and more understood. There are probably thousands upon thousands of algorithms continuously running. Every repetitive process in the cell can be written into an algorithm.

  60. Comment by AnaxagorasRules — June 27, 2010 @ 2:06 am

  61. olegt Says:
    June 27th, 2010 at 3:07 am

    OK, Bradford, it's Jasmin Fisher. Now I know what you meant when you wrote

    It was not metaphorical for Fisher to use a warning concept, found in software developed for the purpose of finding flaws in microchip circuitry, to gain biological insights.

    Here is an excerpt from a Nature news article Computational biology: Biological logic.

    After a few moments, patience is rewarded: Fisher pulls up a screen of what looks like programming code. Pointing to a sequence of lines highlighted in red, she explains that it is a warning generated by software originally developed for finding flaws in microchip circuitry. In 2007, she, Piterman and their colleagues found a similar alert in a simulation they had devised for signalling pathways in the nematode worm Caenorhabditis elegans. Using that as a clue, they predicted and then experimentally verified the existence of a mutation that disrupts normal cell growth [1].

    [1] Fisher, J., Piterman, N., Hajnal, A. & Henzinger, T. A. PLoS Comput. Biol. 3, e92 (2007). doi:10.1371/journal.pcbi.0030092.

    I think you missed a subtle point. Fisher and company apply computer-science formalism not to biological systems directly, but rather to computer models developed to simulate biological systems. Here is a couple of paragraphs from their PLoS paper:

    Dynamic models can represent phenomena of importance to biological behaviors that static diagrammatic models cannot represent, such as time and concurrency. In addition, formal verification methods can be used to ensure the consistency of such computational models with the biological data on which they are based [2,3]. It was previously suggested that by formalizing both the experimental observations obtained from a biological system and the mechanisms underlying the system's behaviors, one can formally verify that the mechanistic model reproduces the system's known behavior [3].

    Formal models are used in a variety of situations to predict the behavior of real systems and have the advantage that they can be executed by computers; often at a fraction of the cost, time, or resource consumption that the observation of the real system would require. In addition, formal models have the advantage that they can be analyzed by computers. For example, it may be possible to predict, by analyzing a model, that all possible executions will reach a stable state, independent of environment behavior. The result of such an analysis would not be obtainable by executing the real system, no matter for how long or how many times, as there are often infinitely many possible environment behaviors. This process of computational model analysis, in the case of state-based models, is called model checking [4].

    Fisher et al. rely on existing biological models to simulate development. Computer science helps them find the right formal language to perform simulations within those models. This is not exclusive to biology. Physicists have come to rely on object-oriented programming code (exemplified by the Object Oriented MicroMagnetic Framework at NIST). It does not mean, however, that inheritance, abstraction, and encapsulation are taking over physics. They are merely the latest tools to help in the analysis of physical models.

  62. Comment by olegt — June 27, 2010 @ 3:07 am

  63. olegt Says:
    June 27th, 2010 at 3:23 am

    Guts wrote:

    The very existence of the Registry of Standard Biological Parts (mentioned in the article) shows that they are drawing heavily from the Computer Science concept of abstraction. In addition to abstraction, they re-use design concepts like modularity, standards, and protocols, in order to understand the biological systems and how to build them.

    That still looks like applied biology to me. Knowledge gained in biology is being transferred to engineering. In the process, scientists certainly gain better understanding of biological systems. Not because they apply concepts from computer science in biology but simply because they do empirical work with biological systems.

  64. Comment by olegt — June 27, 2010 @ 3:23 am

  65. ID guy Says:
    June 27th, 2010 at 8:57 am

    olegt:
    That still looks like applied biology to me.

    Applied biology:

    But such a task requires biologists to team up with computer scientists, engineers, physicists and mathematicians.

    olegt:
    Knowledge gained in biology is being transferred to engineering.

    And vice versa.

    olegt:
    Not because they apply concepts from computer science in biology but simply because they do empirical work with biological systems.

    I doubt you know what they are doing and it appears biologists have been applying concepts from computer science and systems engineering when studying biological organisms.

  66. Comment by ID guy — June 27, 2010 @ 8:57 am

  67. Jean Says:
    June 27th, 2010 at 9:40 am

    hblavatsky:

    his work has demonstrated that no spiritual spark of life is required to create life

    This is such a flawed conclusion I do not know where to begin. Materialists are apparently not rationalists, that's for sure. :mrgreen:

  68. Comment by Jean — June 27, 2010 @ 9:40 am

  69. eric Says:
    June 27th, 2010 at 1:50 pm

    nullasalus: "So again, we may eventually end up wondering: Why divide the world into these two distinct spheres of artifact and nature, when artifact could conceivably cover everything we see and undeniably covers many things…?"

    The reason why the distinction is important and meaningful is quite simple. Some kinds of effects can come from the built-in properties. Others cannot. So we need to be able to use words to talk about this difference. Calling everything the same thing completely fails in being able to talk about this distinction.

    When science studies the consequences of those built-in properties, they find regularity (even mathematically describable regularity). Yet, those effects have limitations, and those regularities do not of themselves imagine and seek the fulfillment of distant unrealized goals.

    This is not in any way an objection to saying that those very regularities are also designed. Yet we need to have a way to distinguish what comes as a result of those regularities and what requires additionally some direction, some guidance imposed from without (typically according to seeking goals not intrinsic to the object itself).

    If you can suggest the most helpful ways to make such distinctions, it may be possible to encourage suitable language. If, on the other hand, you were to suggest giving it all the same name (making it impossible to clearly and easily distinguish), your suggestions would likely be disregarded.

  70. Comment by eric — June 27, 2010 @ 1:50 pm

  71. nullasalus Says:
    June 27th, 2010 at 2:09 pm

    eric,

    The reason why the distinction is important and meaningful is quite simple. Some kinds of effects can come from the built-in properties. Others cannot. So we need to be able to use words to talk about this difference. Calling everything the same thing completely fails in being able to talk about this distinction.

    Right, just as it's a problem in the case of the computer program. I agreed and agree, distinctions are important. I'm questioning the utility of one particular type of distinction (nature versus artifact), at least if certain technological trends continue. I don't need to call program operations in the absence of a programmer 'undirected' or, worse yet, 'nature' to make the distinction between that and a direct intervention.

    When science studies the consequences of those built-in properties, they find regularity (even mathematically describable regularity). Yet, those effects have limitations, and those regularities do not of themselves imagine and seek the fulfillment of distant unrealized goals.

    I'm not so sure of the latter, or of science's ability to weigh in on that sort of question, depending on what you mean by 'of themselves' or goal-seeking. But again, I have nothing against distinguishing between regularity and irregularity. I just think the distinction we've used in the past (nature v artifact) may well be past its prime, and rely on some untenable unspoken ideas.

  72. Comment by nullasalus — June 27, 2010 @ 2:09 pm

  73. Guts Says:
    June 27th, 2010 at 2:38 pm

    olegt:

    Not because they apply concepts from computer science in biology but simply because they do empirical work with biological systems.

    The concepts I mentioned are concepts from engineering and computer science being applied to biology. Actual workers in the field even say this explicitly.

  74. Comment by Guts — June 27, 2010 @ 2:38 pm

  75. Daniel Smith Says:
    June 27th, 2010 at 2:50 pm

    Bradford: If we found artifacts or novel natural phenomenon on another planet we would seek to understand how they work and, in the case of an artifact, its intended purpose. If we started the analysis with human artifacts (programs) and used designs within them to predict biological function our analysis of intelligently designed artifacts would be the basis for predicting natural functions which may not be obvious simply by observing cells. The perspective begins with design and then focuses on the natural rather than beginning with observing the natural and deriving function from an understanding of how things work.

    I agree wholeheartedly Bradford.

    I would add that any artifacts found on Mars would also be studied to learn as much as we could about the civilization from which they came. Such information would also be useful in determining the meaning and purpose of the objects themselves.

    If we were to study biological life that way (as an artifact of God's civilization), we would not exclude metaphysical theories and such from biology but would rather seek to interpret biological life within various metaphysical frameworks to see how well these things fit together.

    IOW, since we are agreed that life is designed, the studies of the designer (theology, philosophy, metaphysics) become increasingly relevant.

    Science,as it now exists in many universities, has excluded all but the naturalist/materialist interpretation of empirical data. If design is agreed to, the artificial wall around empiricism can come down.

  76. Comment by Daniel Smith — June 27, 2010 @ 2:50 pm

  77. olegt Says:
    June 27th, 2010 at 4:15 pm

    Guts wrote:

    The concepts I mentioned are concepts from engineering and computer science being applied to biology. Actual workers in the field even say this explicitly.

    Let's have a look at what they say. Could you quote them?

  78. Comment by olegt — June 27, 2010 @ 4:15 pm

  79. Guts Says:
    June 27th, 2010 at 4:52 pm

    There are many examples

    Engineers in all disciplines take advantage of abstraction hierarchies to design and build complicated systems…To enable the engineering of very complex biological systems, it will be necessary to develop abstraction hierarchies for biological engineering

    here

    The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules.

    here

    Highly organized, universal structures underlying biological and technological networks mediate effective trade-offs among efficiency, robustness and evolvability, with predictable fragilities that can be used to understand disease pathogenesis. The aims of this article are to describe the features of one common organizational architecture in biology, the bow tie. Large-scale organizational frameworks such as the bow tie are necessary starting points for higher-resolution modeling of complex biologic processes

    here

    To maintain a constant internal environment requires control mechanisms: sensors, effectors, information processing and feedback systems. These terms were imported into the langauge of twentieth century physiology from control engineering in the 1940s – but they do not belong to the language of physics (or, indeed , of nineteenth century physiology)
    here

    We commonly describe membrane function using concepts (conductivity, insulation, capacitance, and so on) established previously in electrical engineering.
    here

    Almost without exception, there exist biomolecular analogues of conventional functional devices, including structural components, wires, motors drive shafts, pipes, pumps, production lines, and programmable control systems. Consequently, there is a growing realization that the new discipline of nanotechnology will provide the means to construct novel molecular architectures with greater precision and flexibility, and at a lower cost, than traditional manufacturing processes.

    here

    Viewed as information processing systems, biological organisms possess amazing capabilities to perform information-handling tasks such as: control, pattern recognition, adaptability, information-storage, etc. Thus, the functioning of biological organisms as information-processing systems is of great interest to computer scientists, and we are witnessing now a fast growing research in this field. This research is genuinely interdisciplinary in nature, involving both computer scientists and molecular scientists (biologists biochemists, biophysicists, crystallographers..). One of the leading paradigms of this research is "cell as a computer". A beautiful example of this paradigm is a single cell organism called ciliate– the gene assembly process in ciliates has turned out to be a very elegant computational process which even uses one of the basic data structures of computer science: the linked lists! This process of gene assembly (assembling genes of macronucleus from their micronuclear form) is the most involved DNA processing known in living organisms.
    here

    I can go on all day but I'm way too psyched about Argentina

  80. Comment by Guts — June 27, 2010 @ 4:52 pm

  81. Darwiniana » ID, and…’software driven’?? Says:
    June 27th, 2010 at 4:59 pm

    [...] From Venter This is as much a philosophical as a technological advance. The notion that this is possible means bacterial cells are software-driven biological machines. If you change the software, you build a new machine. I'm still amazed by it. [...]

  82. Pingback by Darwiniana » ID, and…’software driven’?? — June 27, 2010 @ 4:59 pm

  83. olegt Says:
    June 27th, 2010 at 5:01 pm

    Guts,

    I have not gone to all of the links, just the first two. They describe applications of biology to engineering, not the other way around. Here is an excerpt from the first link:

    Abstraction hierarchies are a human invention designed to assist people in engineering very complex systems by ignoring unnecessary details. If the process to design a biological system was to write down the string of nucleotides, it would immediately become untenable even for experts to design anything but very simple systems. Most people just aren't capable of processing that kind of detail all at once. If instead, an abstraction hierarchy is specified, it allows the designer of a biological system to ignore some of the implementation details and focus only on the high-level design issues.

    It's an engineering approach to engineering, not biological problems.

  84. Comment by olegt — June 27, 2010 @ 5:01 pm

  85. Guts Says:
    June 27th, 2010 at 5:05 pm

    No Olegt, they say quite explicitely that it's an engineering concept applied to biology:

    Engineers in all disciplines take advantage of abstraction hierarchies to design and build complicated systems.
    …
    To enable the engineering of very complex biological systems, it will be necessary to develop abstraction hierarchies for biological engineering

  86. Comment by Guts — June 27, 2010 @ 5:05 pm

  87. olegt Says:
    June 27th, 2010 at 5:26 pm

    Guts,

    The passage you quoted last mentions biological engineering, not basic biology. In case you really don't understand the difference, here is a brief explanation:

    Biological Engineers or bioengineers are engineers who use the principles of biology and the tools of engineering to create usable, tangible products(e.g. the vulva of a rabbit is bioengineered to have the same 'specs' of a human vulva; therefore allowing transplant.)In general, biological engineers attempt to either mimic biological systems in order to create products or modify and control biological systems so that they can replace, augment, or sustain chemical and mechanical processes. Bioengineers can apply their expertise to other applications of engineering and biotechnology, including genetic modification of plants and microorganisms, bioprocess engineering, and biocatalysis.

    Once again, engineering principles are used to solve engineering problems, not problems in basic science.

  88. Comment by olegt — June 27, 2010 @ 5:26 pm

  89. Guts Says:
    June 27th, 2010 at 5:28 pm

    lol, we were talking about how engineering is informing Synthetic Biology, remember? Besides, in order to construct biological systems you need to understand how biological systems work. That is why they are putting actual biological "parts" into abstraction hierarchies, this is inspired by computer protocols and they say so explicitely, take a look at the tables.

    Besides that, I showed many examples of engineering and computer science concepts used to understand basic biology alone.

  90. Comment by Guts — June 27, 2010 @ 5:28 pm

  91. olegt Says:
    June 27th, 2010 at 5:31 pm

    Guts wrote:

    Besides that, I showed many examples of engineering and computer science concepts used to understand basic biology alone.

    I don't think so. Biological engineering, yes; basic biology, no.

  92. Comment by olegt — June 27, 2010 @ 5:31 pm

  93. Guts Says:
    June 27th, 2010 at 5:36 pm

    What's wrong with the examples I gave?

  94. Comment by Guts — June 27, 2010 @ 5:36 pm

  95. olegt Says:
    June 27th, 2010 at 5:44 pm

    Guts wrote:

    What's wrong with the examples I gave?

    See here.

  96. Comment by olegt — June 27, 2010 @ 5:44 pm

  97. Guts Says:
    June 27th, 2010 at 5:48 pm

    Many of the examples I gave had nothing to do with biological engineering. So what's wrong with those?

  98. Comment by Guts — June 27, 2010 @ 5:48 pm

  99. ID guy Says:
    June 27th, 2010 at 6:49 pm

    I think olegt may have found the problem with materialistic biology- they don't employ the correct tools and that is why the answers to the questions still elude them. :mrgreen:

    "Wow this code is very computer-like- but let's not use any computer science concepts to help us."

    "Wow this system is very much like data communications, but let's not use any IT concepts to helps us."

    But perhaps oleg can tell us how does Venter's work support blind, undirected processes?

    You seem to have issues with IDers saying this helps the case for ID.

    Are there are experiments that show the "power" of blind, undirected processes?

    Please give us your best shot…

  100. Comment by ID guy — June 27, 2010 @ 6:49 pm

  101. Salvador T. Cordova Says:
    June 27th, 2010 at 7:13 pm

    Olegt:

    Now, suppose—for the sake of the argument—the Darwinists pack up and leave molecular biology.

    It's already happened implicitly, it's Darwinian in name only. Consider this by Andreas Wagner:

    However, fitness is hard to define rigorously and even more difficult to measure….An examination of fitness and its robustness alone would thus not yield much insight into the opening questions. Instead, it is necessary to analyze, on all levels of organization, the systems that constitute an organism, and that sustain its life. I define such systems loosely as assemblies of parts that carry out well-defined biological functions.

    Andreas Wagner
    Robustness of Evolving Systems

    Characterizing function in terms of reproductive success is next to futile, it is better to define function in terms of: "assemblies of parts that carry out well-defined biological functions."

    This means matching behaviors to known engineering templates.

    Compare Wagner's phrase: "assemblies of parts that carry out well-defined biological functions" to Behe:

    several well-matched, interacting parts that contribute to the basic function

    What would the research program be? Deciding if an entire object is design is only one step, identifying all the designs is another. This is a rich area of research to find "several well-matched, interacting parts that contribute to the basic function". When reverse engineering an artifact that we already accept as designed, we are still looking to identify all the designs in the artifact. We don't have to stop when we conclude and intelligence made the artifact, rather, that is only the beginning. When we stumble across hieroglyphics, concluding that the hieroglyphics are designed is only the first step of the real exploration!

    We didn't use "fitness" criteria to elucidate possible function in introns and pseudogenes, we used the hypothesis of "interacting parts that contribute to the basic function".

    That is a superior method for deducing biological function vs. fabricating stories of why such and such evovled.

    Lewontin points out, fitness is very difficult to define. If one can't measure a fundamental quantity (in principle), one has to wonder how useful a theory is that relies on that quantity.

    One can measure how well something accords with a template or pattern. Identifying function is identifying patterns, and the study of patterns that consistent with engineering designs is consistent with inteligent design:

    ID is the study of patterns that signify intelligence

    Bill Dembski

    Characterizing functioning in terms of fitness is of limited utility. Consider certain people's ability to do certain things (such as having photographic memory or infrared vision) which other people can't. We can recognize functions which they posses far in advance of having to put together some story of natural selection. In fact fabricating selectionist stories are totally useless in such cases to elucidating such functions. It actually obfuscates, misleads, and confuses!

    Instead, we identify function by pattern recognition and this is "de facto" ID in biology. Natural selection as a theory is:

    1. next to useless for identifying function

    2. is probably not the explanation of function anyway at the molecular level (Nei, Kimura, Juke, King)

    3. doesn't explain speciation (Pagels)

    4. is suspect as a mechanism for fundamental forms ( Davidson, Newman, Muller, so many others)

    5. must have been disengaged in several instances for the genome to form (Lynch, Ho, others)

    6. Does not explain the origin of life

    7. Does not account for much early evolution of prokaryotes and eukayotes (Woese)

    One has to then ask in light of this, what good is it as a scientific hypothesis.

    It's major empirical claim of "fitness" can't be measured since it's values are context specific, and thus, pretty much subjective! For example, on what grounds is sickle cell anemia "fit"? It depends on the way you look at it. Fitness is nebulous.

    Lewontin writes:

    FINALLY, WE MUST CONSIDER the way in which differential
    fitness constrains the occupancy of the taxonomic
    space. Unfortunately the determination of fitness
    is a great deal more complicated than is usually
    supposed. It is easy to say that fitness of a type is its
    “relative probability of survival and reproduction” but
    turning that phrase into a coherent measure that can
    do work in evolutionary explanation is not so easy.
    First, it is obvious that the fitness of a type
    depends on the environment in which the organism
    lives. But the environment is not independent of the
    organism. Organisms, by their biology, determine what
    aspects of the external world are relevant to them and
    constantly change their environment by their life
    activities. That means that as a collection of organisms
    evolves, their environment evolves with them.

    …

    The difficulties of the concept of fitness are,
    unfortunately, much deeper than the problem of frequency
    and density dependence. The problem is that
    it is not entirely clear what fitness is. Darwin took the
    metaphorical sense of fitness literally. The natural
    properties of different types resulted in their differential
    “fit” into the environment in which they lived.
    The better the fit to the environment the more likely
    they were to survive and the greater their rate of
    reproduction. This differential rate of reproduction
    would then result in a change of abundance of the different
    types.
    …
    In modern evolutionary theory, however, “fitness”
    is no longer a characterization of the relation of the
    organism to the environment that leads to reproductive
    consequences, but is meant to be a quantitative expression
    of the differential reproductive schedules themselves.
    Darwin’s sense of fit has been completely
    bypassed.

    …

    But if we cannot do that, what does it
    mean to say that a type with one set of natural properties
    is more reproductively fit than another? This problem
    has led some theorists to equate fitness with outcome.
    If a type increases in a population then it is, by
    definition, more fit. But this suffers from two difficulties.
    First, it does not distinguish random changes in
    frequencies in finite populations from changes that are
    a consequence of different biological properties.
    Finally, it destroys any use of differential fitness as an
    explanation of change. It simply affirms that types
    change in frequency. But we already knew that.
    Santa Fe Bulletin 2003

    Thus natural selection, which cannot be reliably measured except in a few contexts, is unfit to be a pervasive scientific theory. It is appropriate for a few instances, but certainly not in the characterization of function as Wagner and Lewontin and Allen Orr have unwittingly conceded.

    Pattern recognition is a better approach, and pattern recognition is defacto ID.

    But one does not have to accept that inteligence design is real:

    a scientist may view design and its appeal to a designer as simply a fruitful device for understanding the world, not attaching any significance to questions such as whether a theory of design is in some ultimate sense true or whether the designer actually exists. Philosophers of science would call this a constructive empiricist approach to design. Scientists in the business of manufacturing theoretical entities like quarks, strings, and cold dark matter could therefore view the designer as just one more theoretical entity to be added to the list.

  102. Comment by Salvador T. Cordova — June 27, 2010 @ 7:13 pm

  103. olegt Says:
    June 27th, 2010 at 8:08 pm

    Guts wrote:

    Many of the examples I gave had nothing to do with biological engineering. So what's wrong with those?

    Having read the third article, I have to concede the point: biologists do see useful parallels between biological and engineering networks (e.g. their robustness and optimality). Here is a nice nontechnical review by the same authors: M. E. Csete and J. C. Doyle, Reverse engineering of biological complexity, Science 295, 1664 (2002). doi:10.1126/science.1069981.

    The $64,000 question is what do these parallels mean? Do they mean that living organisms were made by a designer who thought like human designers or that both human designers and evolutionary processes reach similar fixed points? There is some interesting work on computer networks with heuristically optimal topology (HOT), which may shed light on the latter, evolutionary scenario.

  104. Comment by olegt — June 27, 2010 @ 8:08 pm

  105. ID guy Says:
    June 27th, 2010 at 8:19 pm

    olegt:
    Do they mean that living organisms were made by a designer who thought like human designers or that both human designers and evolutionary processes reach similar fixed points?

    No, it means that we are starting to think like the designer(s) of life.

    And why the equivocation with "evolutionary processes"?

    What does that even mean?

  106. Comment by ID guy — June 27, 2010 @ 8:19 pm

  107. Guts Says:
    June 27th, 2010 at 8:40 pm

    Olegt, would be interested in a link/reference / whatever when you get the chance. The only thing I will add for now is the importance of not to get too caught up in the false dichotomy of evolution vs. design. That is what fle is all about after all, is that it may not be either/or but both/and.

    By the way I should be done with the major upgrade of this site by this week which means you'll be getting edit/preview back.

  108. Comment by Guts — June 27, 2010 @ 8:40 pm

  109. ID guy Says:
    June 27th, 2010 at 8:58 pm

    Guts,

    It is also about how one defines "evolution".

    The main issue is these clowns use it to try to convince people that ID is anti-evolution, meaning it argues for stasis, the fixation of species.

    Perhaps someone from TT can author an essay about that.

    It could be something like this.

    Just sayin'- it would be useful to have something like that to reference- like a PRATT list…

  110. Comment by ID guy — June 27, 2010 @ 8:58 pm

  111. Guts Says:
    June 27th, 2010 at 9:07 pm

    How about a #7, the blind watchmaker is a wild horse broken by the rational designer of life.

  112. Comment by Guts — June 27, 2010 @ 9:07 pm

  113. ID guy Says:
    June 27th, 2010 at 9:51 pm

    Even a wild horse is evidence for a designer… :o

    So a designer designs a wild horse so that it can be broken by the designer.

    Perhaps someone else should write the essay… ;-)

  114. Comment by ID guy — June 27, 2010 @ 9:51 pm

  115. Bradford Says:
    June 28th, 2010 at 8:40 am

    AnaxagorasRules:

    One possible paradigm is of the Microsoft Windows system (I'm serious! lol) A cell would be analogous to a computer system, the hardware being all the organelles and proteins and ribosomes and amino acids and sugars, etc. There are many application programs going on at the same time inside the cell, all of them event driven, with the operating system determining the resource allocation and priorities. The DNA houses both the operating system and the cell's application programs. There's a lot of parallel processing going on. I don't think the operating system is well understood yet, though the individual apps that create proteins are becoming more and more understood. There are probably thousands upon thousands of algorithms continuously running. Every repetitive process in the cell can be written into an algorithm.

    I see the analogies too. Parallels between technology and biology can lead to new insight for either one. The former is unquestionably intelligently designed of course. But whether the symbolism, inherent to programs, is a product of ID can be definitively determined by the physical necessity involved in assignment. Hence the emphasis on codon bias in translation scenarios by anti-IDists. It is conceivable though that an advanced intelligence could align physical necessity with assignment. In theory that type of thing cuts both ways where evidence is concerned.

  116. Comment by Bradford — June 28, 2010 @ 8:40 am

  117. kornbelt888 Says:
    June 28th, 2010 at 3:16 pm

    "One possible paradigm is of the Microsoft Windows system (I'm serious! lol) "

    Cells are a lot more reliable than Windows, thank the Designer.

  118. Comment by kornbelt888 — June 28, 2010 @ 3:16 pm

  119. AnaxagorasRules Says:
    June 28th, 2010 at 5:20 pm

    Hi, Bradford,

    But whether the symbolism, inherent to programs, is a product of ID can be definitively determined by the physical necessity involved in assignment. Hence the emphasis on codon bias in translation scenarios by anti-IDists.

    Aside from physical necessity (perhaps even at the molecular level there is an element of choice), it isn't chemically apparent why an organism prefers one synonymous codon over another, though it makes a lot of sense if the goal was to implement redundancy (i.e. backups). That an organism prefers one synonymous codon over the others actually indicates order, consistency, and planning for contingencies. Additionally, that a Type A organism prefers a different synonymous codon than a Type B organism actually indicates a discontinuity (in that one regard) between the types. Discontinuity is not a Darwinian-friendly concept.

  120. Comment by AnaxagorasRules — June 28, 2010 @ 5:20 pm

  121. Daniel Smith Says:
    June 28th, 2010 at 6:54 pm

    Bradford: Parallels between technology and biology can lead to new insight for either one. The former is unquestionably intelligently designed of course.

    As is the latter…

  122. Comment by Daniel Smith — June 28, 2010 @ 6:54 pm

  123. Salvador T. Cordova Says:
    June 28th, 2010 at 6:57 pm

    olegt wrote:

    Having read the third article, I have to concede the point: biologists do see useful parallels between biological and engineering networks (e.g. their robustness and optimality). Here is a nice nontechnical review by the same authors: M. E. Csete and J. C. Doyle, Reverse engineering of biological complexity, Science 295, 1664 (2002). doi:10.1126/science.1069981.

    The $64,000 question is what do these parallels mean? Do they mean that living organisms were made by a designer who thought like human designers or that both human designers and evolutionary processes reach similar fixed points? There is some interesting work on computer networks with heuristically optimal topology (HOT), which may shed light on the latter, evolutionary scenario.

    I respect what you just said.

    What I think can be established by empirical science is that there are analogies. In physics we establish analogies between pendulums, simple harmonic motion, sinusoids, etc.. It is not that much more of a stretch to identify other analogies in the natural world than have analogs in the engineering world.

    Whether the Intelligent Designer really exists is perhaps outside of empirical science, unless of course He appears to us one day. But I think the observation of analogies is appropriate and useful to make and will fit comfortably in mainstream science.

    I am aware of activity in the IEEE and ACM (association computing machines) which seeks to find these analogies.

    The $64,000 question is what do these parallels mean? Do they mean that living organisms were made by a designer who thought like human designers or that both human designers and evolutionary processes reach similar fixed points?

    I cannot say formally whether an Intelligent Designer (God, ET's, whatever) was invovled. My philosophical belief is that God was the Designer, but that is not a scientific inference, only a circumstantial an personal view. My belief might be true, but there is an insufficient amount of evidence to make a direct inference, only a circumstantial one….

    The question of whether evolutionary processes can make such structures is in principle a testable and falsifiable hypothesis. I'm not so sure the best in the mainstream really think Natural Selection is the primary answer. I expect there will be continued debate over which mechanisms can effect certain structures.

    Right now, there is not even agreement over what parts of biology function, much less how they evolved. 20 years from now, our knowledge could be substantially greater than what we're working with today. I don't think there is any need to try to settle the issue today as I trust that the scientific method of observation, hypothesis forming, and experiment will bring us closer to the truth.

  124. Comment by Salvador T. Cordova — June 28, 2010 @ 6:57 pm

  125. chunkdz Says:
    June 28th, 2010 at 7:08 pm

    Olegt: There is some interesting work on computer networks with heuristically optimal topology (HOT), which may shed light on the latter, evolutionary scenario.

    I'm interested. What've you found?

  126. Comment by chunkdz — June 28, 2010 @ 7:08 pm

  127. Dennett’s Strange Idea is a Bad Idea for Recognizing Biological Function | Uncommon Descent Says:
    June 29th, 2010 at 4:50 pm

    [...] 5. HT: Bradford at TelicThoughts who inspired this thread: De Facto Intelligent Design in Biology [...]

  128. Pingback by Dennett’s Strange Idea is a Bad Idea for Recognizing Biological Function | Uncommon Descent — June 29, 2010 @ 4:50 pm

  129. Daniel Smith Says:
    June 29th, 2010 at 7:36 pm

    Sal Cordova: Whether the Intelligent Designer really exists is perhaps outside of empirical science, unless of course He appears to us one day.

    I disagree.

    Obvious design = obvious designer.

    If we found obvious designs on Mars we wouldn't think twice about whether or not a designer "exists". We'd presume a designer existed, then study the designs to find out more about him/her/it.

    I cannot say formally whether an Intelligent Designer (God, ET's, whatever) was invovled. My philosophical belief is that God was the Designer, but that is not a scientific inference, only a circumstantial an personal view. My belief might be true, but there is an insufficient amount of evidence to make a direct inference, only a circumstantial one….

    This is just a bit sad to me. There are quite literally mountains of evidence for God, yet – because "science" has been corrupted by a modern infusion of "materialist/naturalist/atheist-only" interpretations – we who know the truth are reduced to a quasi-grovelling at the materialist altar for some kind of "empirical respect".

    When one understands the metaphysical case for God vs. that for atheism, one cannot but interpret the empirical data within a "God exists and created all things" framework.

    Forgive me Sal for the tone, but statements like that just bug the begeezus out of me!

  130. Comment by Daniel Smith — June 29, 2010 @ 7:36 pm

  131. Salvador T. Cordova Says:
    June 29th, 2010 at 8:00 pm

    Forgive me Sal for the tone, but statements like that just bug the begeezus out of me!

    That's fine, but I spoke what my conscience said. What would be direct evidence for me? Seeing the Designer Himself create life. That's direct evidence. Do I demand that before I believe? No, but it would be reassuring.

    I believe in the Intelligent Designer, but I can't say I have seen Him at work with my own eyes. I've seen intelligent designers making cars…so I can believe that an intelligent designer (humans) build cars.

    But with respect to life, that is a different story, maybe mostly of degree, if not kind.

    What would constitute a direct empirical observation for me? God offers to participate in an experiment and show His power in creating life. That would be convincing. But far be it for any to put God to the test.

    There are records of Jesus creating life out of dead matter (like Lazarus). I believe the account is true, but formally speaking it is outside modern day observation. If I had seen those miracles with my own eyes, it would be easier for me (and others) to believe.

    I have some skepticism of the ID hypothesis, and that is, namely design is inferred (a design inference) but the activity of design is not directly observed.

    are quite literally mountains of evidence for God

    I don't see it that way, I think the evidence is difficult to discern. There are a lot of Christians who have been driven from the faith because their peers insists on the existence of "mountains of evidence" and yet they (the Doubting Thomases) don't see it that way.

    What "mountains of evidence" means for some is different for each person.

    Maybe my faith is smaller than yours, maybe only a mustard seed size.

    If I were to characterize myself, it would be a Doubting Thomas. Not someone who hates Christianity, but someone who has reasons to believe it with some doubts mixed in.

    Part of my involvement with ID was to help address my doubts. I have no doubt now that there is no salvation in Darwinism or Atheism, salvation must come from elsewhere. Of that I am certain.

  132. Comment by Salvador T. Cordova — June 29, 2010 @ 8:00 pm

  133. eric Says:
    June 29th, 2010 at 11:23 pm

    Salvador T. Cordova: "The question of whether evolutionary processes can make such structures is in principle a testable and falsifiable hypothesis."

    If only it were so. Sadly, in practice, abiogenesis is not yet allowed to be considered falsifiable or subject to the weight of evidence. It is required as an axiom.

    We are already in a state where we have no empirical support or describable theory for something as basic as the transition to developing multi-molecular machines using RNA World replication. It is an empty leap of blind faith without support. Yet, under current practice, this state would be considered permanently tolerable.

    The fact that our knowledge of chemistry is against believing such a thing does not matter. The fact that we already know RNA World replication absolutely cannot replicate such a structure does not matter. The fact that the RNA World cannot make use of the cell's multi-molecular machinery does not matter. Only keeping faithful to the faith without end matters.

    Outside of biology, in what other area of science would the complete absence of discernible support for an idea — an idea that cannot even be clearly described and exists as a vague unspecified hope — be considered a perpetually acceptable state of affairs? We are expected to assume it must be true regardless. Incredible.

    Salvador T. Cordova: "I'm not so sure the best in the mainstream really think Natural Selection is the primary answer."

    The best and clearest thinking evolutionists have known for decades now (emphasis added)…

    …the idea that natural selection is "capable of generating organismal complexity" has been an erroneous misinterpretation of how natural selection works…

    As John Endler has clearly pointed out in Natural Selection in the Wild (1986, Princeton University Press), natural selection is not a "mechanism" that "does" anything: "…natural selection does not explain the origin of new variants, only the process of changes in their frequency." (Endler, 1986, pg. 245).

    See Dodge #2 for more and links.

    p.s. Your own faith is on a far more solid evidential foundation than the counter factual blind leaps made for abiogenesis have ever been. You know of witness reports of events where you were not present. Abiogenesis believers do not even have reports of abiogenesis events to counter the weight of contrary chemical observations.

  134. Comment by eric — June 29, 2010 @ 11:23 pm

  135. eric Says:
    June 29th, 2010 at 11:31 pm

    A sincere OPEN QUESTION for those who think codon assignments derive from the attraction of codon patterns to amino acids:

    Within that hypothesis, what is the explanation given for the origin of the STOP codons? Attraction to the absence of an amino acid?

    There may be a sensible answer. If there is, I just don't know what it is.

    [Keep in mind that it will not work to simply point out a STOP is needed or else it would not work. That is a consideration that a designer could make -- one who is pursuing the goal of making it work. Chemicals don't care if any such goal is ever reached. They have no intrinsic interest in making a working coding system for future use.]

  136. Comment by eric — June 29, 2010 @ 11:31 pm

  137. eric Says:
    June 29th, 2010 at 11:57 pm

    nullasalus: "I just think the distinction we've used in the past (nature v artifact) may well be past its prime, and rely on some untenable unspoken ideas."

    Yet, it will certainly continue to be used, unless and until a superior way of talking about the distinction — one equally clear and concise, not requiring clumsy verbose wording to avoid some other misunderstanding — is provided and promoted. It would be an empty hope to expect otherwise.

    The simplest approach (so far) is to simply acknowledge and affirm that the existing term "nature" does not imply that the built-in regularities science studies cannot also be designed. Easy to understand. While some may choose to doubt nature is designed, I don't know that anyone finds that a hard concept to understand.

    Indeed, western natural philosophy (that motivated the development of science in the west) held that nature was designed. There is nothing in the word "nature" that is essentially hostile to or incompatible with the idea that the regularities science discovers in nature are designed.

  138. Comment by eric — June 29, 2010 @ 11:57 pm

  139. KC Says:
    July 1st, 2010 at 6:23 pm

    eric writes:

    A sincere OPEN QUESTION for those who think codon assignments derive from the attraction of codon patterns to amino acids:

    Within that hypothesis, what is the explanation given for the origin of the STOP codons? Attraction to the absence of an amino acid?

    First of all, no stereochemical hypothesis for the origin of the genetic code postulates that all of the codon assignments originated that way. I suggest reading Yarus’s paper on the Escaped Triplet hypothesis. As for stop codons, though, nobody knows for sure. One suggestion I've seen is that the stop codons may have been originally associated with uncharged tRNAs which cannot bind to an amino acid, resulting in termination of the elongation process. Today, or course, proteins bind to the stop codons rather than tRNAs. I think the idea is that proteins were more efficient at competing for binding to the stop codons than the uncharged tRNAs .

    Dave Wisker

  140. Comment by KC — July 1, 2010 @ 6:23 pm

  141. Daniel Smith Says:
    July 1st, 2010 at 7:59 pm

    Sal: I don't see it that way, I think the evidence is difficult to discern. There are a lot of Christians who have been driven from the faith because their peers insists on the existence of "mountains of evidence" and yet they (the Doubting Thomases) don't see it that way.

    I understand where you are coming from Sal. I am also, by nature, a skeptic. If everyone says one thing, I'll immediately look for reasons to doubt that one thing. When it comes to Christianity, I'm entirely suspicious of man-made rules and their adherents. I find it telling that church-goers will inevitably parrot the teachings of their respective denominations as if they had studied the bible and found the truth for themselves. I believe there is a true Christianity that is not going to be found in the doctrinal statements of any denomination.

    Now, when it comes to science, let me see if I can help you see a little of what I see…

    The "mountain" of evidence I spoke of is all circumstantial. None of us have direct, eyewitness evidence of God. But take Aquinas' fifth way for an example: Literally everywhere you look, things in nature act as if they have a job to do. That this is true is borne out by the fact that these 'bits of matter' will reliably and repeatedly tend towards certain ends – as if it were their intention to do so. If this were not so, science would literally be impossible – for all of natural science is based on discovering and cataloging the repeatable tendencies of nature and making predictions based on that information. Natural laws are nothing more than these tendencies revealed to the point where we can definitively say they constitute 'laws of nature'.

    Now, we know that 99.999% of nature has no mind by which it can 'intend' anything – so why does that which can't intend, tend towards predictable ends as if it could? Why do things with no mind of their own act as if they are single-mindedly carrying out instructions? The only thing we can reasonably conclude is that the intentionality we observe in mindless nature is the product of a mind that exists outside of nature. This can only be something analogous to the common human conception of God.

    Now, when one accepts that this premise could be true, one then views everything one sees as either confirming evidence of God or not. I can say unequivocally that I see God's handiwork in everything I've come to know through science: biochemistry, molecular biology, evolutionary biology… (I've only really studied the biological sciences so far) and that nothing I know of (so far) contradicts this premise.

    For this reason, I see the entire universe as 'evidence for God'.

    I hope that helps you understand where I'm coming from Sal.

  142. Comment by Daniel Smith — July 1, 2010 @ 7:59 pm

  143. Salvador T. Cordova Says:
    July 2nd, 2010 at 1:03 pm

    I see God's handiwork in everything I've come to know through science: biochemistry, molecular biology, evolutionary biology… (I've only really studied the biological sciences so far) and that nothing I know of (so far) contradicts this premise.

    Agreed that it appears a Mind beyond anything we can imagine made life. The source of doubt is this: the MIND that made life doesn't interact with us directly very much.

    Sometimes it seems God is very indifferent to our pleas for assitance and help. I've come to accept that perhaps our struggle and difficulty to find him was also part of His plan. God said if we seek him with all our might, we'll find Him. For me, it has surely taken a lot of effort to finally discern His activity in the world since He really doesn't show up in person like the people we know.

    The fact that the Darwinists have had to rely on faulty logic and equivocations to defend their theory, the fact that the OOL researchers refuse to comprehend the true issue in OOL (like the emergence of computation from pure chemistry) have re-assured me that MIND was necessary to make the computers and software that are part of life.

    I'm a libertarian. Darwinists are free to believe whatever they want, I'm not insisting they abandon their unscientific beliefs, but I will debate them in the public square.

    But as far as me personally who was once a Darwinist myself, my eyes have been opened to the truth, and truth has set me free.

  144. Comment by Salvador T. Cordova — July 2, 2010 @ 1:03 pm

  145. don provan Says:
    July 2nd, 2010 at 3:31 pm

    Daniel Smith: The only thing we can reasonably conclude is that the intentionality we observe in mindless nature is the product of a mind that exists outside of nature.

    Since we don't know where this mindfulness is coming from, there's no reason at all to conclude it is from outside nature. It could just as easily be something within nature that we simply haven't detected directly.

    Now, when one accepts that this premise could be true, one then views everything one sees as either confirming evidence of God or not.

    What you described was a logical conclusion, not a premise. But you are, in fact, simply asserting a premise: that God is the source of anything you think has intention. The actual logical conclusion is that we simply don't know where that intention comes from. Even if we're really sure it comes from outside nature, we still have no logical reason to think it comes from something with the characteristics we ascribe to God. We have to get that from our religious beliefs and our faith.

  146. Comment by don provan — July 2, 2010 @ 3:31 pm

  147. fifth monarchy man Says:
    July 2nd, 2010 at 6:05 pm

    The actual logical conclusion is that we simply don't know where that intention comes from.

    No, the logical conclusion is simply that the intention we see has a source. Full Stop

    Your contention that we don't know what the source is is an additional proposition that is not in anyway related to the facts in evidence.

    You may assert that you do not know what the source of this perceived intention is but such a claim does not follow logically from the premises Daniel laid out.

    we still have no logical reason to think it comes from something with the characteristics we ascribe to God. We have to get that from our religious beliefs and our faith.

    Or from historic evidence and personal acquaintance.

    I agree that Daniel's (Thomas's) argument only gets you so far but disagree that “faith and belief” is what is necessary to seal the deal.

    I would contend that the Sensus Divinus and historic evidence are more than enough to do that job.

    peace

  148. Comment by fifth monarchy man — July 2, 2010 @ 6:05 pm

  149. don provan Says:
    July 2nd, 2010 at 6:37 pm

    fifth monarchy man: Your contention that we don't know what the source is is an additional proposition that is not in anyway related to the facts in evidence.

    It's not a contention, it's simply the null hypothesis. My statement is precisely the same as "the logical conclusion that the intention we see has a source. Full Stop." I have no idea what logic you're applying in order to equate "Full Stop" to "and we know what that source is."

    Or from historic evidence and personal acquaintance.

    That "personal acquaintance" is a religious belief, as is the conclusions you are drawing from what historical evidence there is.

  150. Comment by don provan — July 2, 2010 @ 6:37 pm

  151. Daniel Smith Says:
    July 2nd, 2010 at 7:51 pm

    don provan: Since we don't know where this mindfulness is coming from, there's no reason at all to conclude it is from outside nature.

    Here are the facts Don:

    Fact #1: Intentionality is solely the product of intellect.

    Fact #2: The objects we are talking about exhibit intentionality but are known not to have intellect.

    Logical conclusion: The intentionality we observe in these objects points to an intellect outside the objects themselves, and–since these objects comprise all of nature–the intellect must be outside of nature.

    It could just as easily be something within nature that we simply haven't detected directly.

    Keep dreaming Don!

  152. Comment by Daniel Smith — July 2, 2010 @ 7:51 pm

  153. Daniel Smith Says:
    July 2nd, 2010 at 8:16 pm

    Sal Cordova: Agreed that it appears a Mind beyond anything we can imagine made life. The source of doubt is this: the MIND that made life doesn't interact with us directly very much.

    Sometimes it seems God is very indifferent to our pleas for assitance and help. I've come to accept that perhaps our struggle and difficulty to find him was also part of His plan. God said if we seek him with all our might, we'll find Him. For me, it has surely taken a lot of effort to finally discern His activity in the world since He really doesn't show up in person like the people we know.

    If God had to show himself to us directly–even though his majesty is clearly evident from what he has made–what cause would there be for reward in that?

    As it is, God seems to have chosen to create a universe, beautiful beyond belief; and promise a reward to those who seek him out because they have come to understand–from that–that he must exist – in spite of the fact that they have never directly witnessed him.

    There is justification for reward in that.

  154. Comment by Daniel Smith — July 2, 2010 @ 8:16 pm

  155. Daniel Smith Says:
    July 2nd, 2010 at 8:20 pm

    Don Provan: It could just as easily be something within nature that we simply haven't detected directly.

    To expand on this:

    No, it couldn't Don. If it were, it would have to be something in the objects themselves – which would necessitate that each thing in nature have a mind of its own.

    This is absurd.

  156. Comment by Daniel Smith — July 2, 2010 @ 8:20 pm

  157. fifth monarchy man Says:
    July 2nd, 2010 at 9:22 pm

    It's not a contention, it's simply the null hypothesis.

    God’s existence like the existence of other minds or the world outside my head is not a question for science so the null hypothesis does not apply.

    I can’t prove these things scientifically to a Descartesian skeptic hell bent to look foolish by pretending to be neutral.

    I don’t need to. I know they are only pretending not to know. As witnessed by the very fact that the choose to dialogue with me in the first place.

    That "personal acquaintance" is a religious belief, as is the conclusions you are drawing from what historical evidence there is.

    No more than my personal acquaintance with my wife is religious belief.

    Even though I draw the conclusion that she is not a figment of my imagination based on the evidence I have

    peace

  158. Comment by fifth monarchy man — July 2, 2010 @ 9:22 pm

  159. don provan Says:
    July 12th, 2010 at 4:34 pm

    Daniel Smith: If it were, it would have to be something in the objects themselves – which would necessitate that each thing in nature have a mind of its own.

    No, it could be something else in nature not in the objects themselves.

  160. Comment by don provan — July 12, 2010 @ 4:34 pm

  161. don provan Says:
    July 12th, 2010 at 6:40 pm

    fifth monarchy man: God’s existence like the existence of other minds or the world outside my head is not a question for science so the null hypothesis does not apply.

    You are free, of course, to ignore the null hypothesis, whether you claim it's because of a domain issue involving "science" or simply because you don't like it. I don't mind. Make up whatever logic system you'd like in order to support your personal opinions to yourself. But Daniel was saying that there's only one logical conclusion, and logical conclusions must stand up to the concept science calls the null hypothesis.

    No more than my personal acquaintance with my wife is religious belief.

    Not at all. I can meet your wife and confirm your relation with her empirically.

  162. Comment by don provan — July 12, 2010 @ 6:40 pm

  163. Daniel Smith Says:
    July 12th, 2010 at 7:15 pm

    Provan: No, it could be something else in nature not in the objects themselves.

    Define: "something else in nature outside of physical, natural objects".

    (Hint: you're getting warmer.)

  164. Comment by Daniel Smith — July 12, 2010 @ 7:15 pm

  165. Daniel Smith Says:
    July 12th, 2010 at 7:36 pm

    Provan: logical conclusions must stand up to the concept science calls the null hypothesis

    Not so Don. Logical conclusions are based on the rules of logic – not on scientific verification.

    Metaphysical reasoning has more in common with mathematical proofs than it does with scientific hypotheses.

    2+2=4 is always true whether anyone empirically verifies it or not.

    In order to show a logical conclusion to be wrong, you must show what part of it is illogical.

    Here's my statement again:

    Fact #1: Intentionality is solely the product of intellect.

    Fact #2: The objects we are talking about exhibit intentionality but are known not to have intellect.

    Logical conclusion: The intentionality we observe in these objects points to an intellect outside the objects themselves, and–since these objects comprise all of nature–the intellect must be outside of nature.

    I have stated two premises and a conclusion based on those premises. You can dispute the validity of the premises or you can show me where I am being illogical in my conclusion.

    Have at it.

  166. Comment by Daniel Smith — July 12, 2010 @ 7:36 pm

  167. don provan Says:
    July 12th, 2010 at 7:44 pm

    Daniel Smith: Define: "something else in nature outside of physical, natural objects".

    Your argument was that known objects in nature don't exhibit intentionality, therefore intentionality couldn't come from nature. I am simply pointing out that something unknown in nature could provide the intentionality, possibly something we wouldn't even consider an object. The point is that we don't know where the intentionality comes from, so we have no way of knowing whether it comes from something natural or something not natural.

  168. Comment by don provan — July 12, 2010 @ 7:44 pm

  169. Daniel Smith Says:
    July 13th, 2010 at 11:55 am

    don provan: The point is that we don't know where the intentionality comes from, so we have no way of knowing whether it comes from something natural or something not natural.

    We do know where observed intentionality comes from Don – minds.

  170. Comment by Daniel Smith — July 13, 2010 @ 11:55 am

  171. don provan Says:
    July 13th, 2010 at 3:10 pm

    Danel Smith: We do know where observed intentionality comes from Don – minds.

    Yet we do not know where the intentionality comes from in nature.

  172. Comment by don provan — July 13, 2010 @ 3:10 pm

  173. Daniel Smith Says:
    July 14th, 2010 at 8:43 am

    don provan: Yet we do not know where the intentionality comes from in nature.

    Don, intentionality can only come from a mind.

  174. Comment by Daniel Smith — July 14, 2010 @ 8:43 am

  175. don provan Says:
    July 14th, 2010 at 2:09 pm

    Daniel Smith: Don, intentionality can only come from a mind.

    How do you know that? You're applying the same logic that led people to think the Sun must be a large bonfire because we did not yet know about fusion.

    And even so, what's the problem with nature having a mind?

  176. Comment by don provan — July 14, 2010 @ 2:09 pm

  177. angryoldfatman Says:
    July 14th, 2010 at 2:51 pm

    don provan wrote:

    And even so, what's the problem with nature having a mind?

    It would mean Intelligent Design is correct.

  178. Comment by angryoldfatman — July 14, 2010 @ 2:51 pm

  179. angryoldfatman Says:
    July 14th, 2010 at 2:53 pm

    As in "de facto Intelligent Design in Biology", which means you've talked yourself into a circle to the point where you're now supporting what you've been opposing.

  180. Comment by angryoldfatman — July 14, 2010 @ 2:53 pm

  181. don provan Says:
    July 14th, 2010 at 4:36 pm

    don provan: And even so, what's the problem with nature having a mind?

    angryoldfatrman: It would mean Intelligent Design is correct.

    Yes, if your definition of "intelligent" is "has a mind". It would also mean that Intelligent Design doesn't support a belief in God.

  182. Comment by don provan — July 14, 2010 @ 4:36 pm

  183. don provan Says:
    July 14th, 2010 at 4:42 pm

    angryoldfatman: As in "de facto Intelligent Design in Biology", which means you've talked yourself into a circle to the point where you're now supporting what you've been opposing.

    I don't think you understand what I'm opposing. Daniel claimed that intentionality must come from outside nature. Nature having a mind would confirm that his claim is wrong, just as I've been saying.

  184. Comment by don provan — July 14, 2010 @ 4:42 pm

  185. fifth monarchy man Says:
    July 14th, 2010 at 5:32 pm

    Not at all. I can meet your wife and confirm your relation with her empirically.

    Only if my wife chooses to allow your empirical confirmation.

    Like God she can choose to remain hidden from you or she can reveal herself. You have no legal way of confirming her existence empirically if she does not want you to do so.

    In the same way if God chooses to reveal himself to you empirically he will do so just as he has done many times in the past for other folks if not you are out of luck.

    Yes, if your definition of "intelligent" is "has a mind". It would also mean that Intelligent Design doesn't support a belief in God.

    Intelligent design is not about proving God’s existence. Everyone knows God exists.

    ID like any scientific hypothesis is about discovering how God acts in creation.

    It’s about “thinking God’s thought’s after him”

    peace

    Peace

  186. Comment by fifth monarchy man — July 14, 2010 @ 5:32 pm

  187. don provan Says:
    July 14th, 2010 at 5:54 pm

    fifth monarchy man : Only if my wife chooses to allow your empirical confirmation.

    Your wife's ability to obscure your relation from me has nothing to do with whether your belief in that relation constitutes a religious belief.

    Intelligent design is not about proving God’s existence. Everyone knows God exists.

    No, they don't.

  188. Comment by don provan — July 14, 2010 @ 5:54 pm

  189. fifth monarchy man Says:
    July 14th, 2010 at 6:58 pm

    Your wife's ability to obscure your relation from me has nothing to do with whether your belief in that relation constitutes a religious belief.

    I'll bite,

    What is it that makes my belief in God's existance a religious belief and my belief in my wife's existance not one?

    They seem to be the same to me.

    No, they don't.

    Yes they do.

    Denial is not an argument. You need to provide evidence for your claim.

    The very fact that you choose to live as if knowledge is possible is all the evidence I need to support mine.

    peace

  190. Comment by fifth monarchy man — July 14, 2010 @ 6:58 pm

  191. Daniel Smith Says:
    July 14th, 2010 at 7:55 pm

    don provan: How do you know that?

    Uh – we all agree on it! ;-)

    Seriously though, are you stating that intentionality can come from something that is not a mind?

    What is your evidence for this?

    You're applying the same logic that led people to think the Sun must be a large bonfire because we did not yet know about fusion.

    And you are relying on as yet undiscovered properties of nature to bolster a claim that God does not exist.

    Unfortunately for you Don, science is revealing the exact opposite. Science discovers intentionality on every level. Nothing seems to be random. Everything acts as if according to plan – even the tiniest particles of matter.

    And even so, what's the problem with nature having a mind?

    I don't think you've thought this through Don. Where would this mind be? What would it consist of? How would it operate? Where did it come from? Are you proposing that there are the equivalent of neurons firing somewhere in the cosmos? Are these neurons then somehow controlling all of matter?

    You're really grasping at straws here.

    What we have is obvious intentionality in nature and no physical mind by which to explain it.

    THAT is why I say the mind must be supernatural.

  192. Comment by Daniel Smith — July 14, 2010 @ 7:55 pm

  193. don provan Says:
    July 15th, 2010 at 4:35 pm

    Daniel Smith: Seriously though, are you stating that intentionality can come from something that is not a mind?

    I am seriously pointing out that we do not know whether intentionality can come from anything other than a mind.

    And you are relying on as yet undiscovered properties of nature to bolster a claim that God does not exist.

    No, I'm pointing out that your claim that God does exist is based on the unsupported assumption that we know all possible sources of intentionality. I do not claim God doesn't exist. How many times do I have to repeat that?

    Unfortunately for you Don, science is revealing the exact opposite. Science discovers intentionality on every level. Nothing seems to be random. Everything acts as if according to plan – even the tiniest particles of matter.

    I have no idea what you're talking about, but for the purposes of argument I'll stipulate that this is true. You still have a problem narrowing down the possible sources of intentionality.

    I don't think you've thought this through Don. Where would this mind be? What would it consist of? How would it operate? Where did it come from? Are you proposing that there are the equivalent of neurons firing somewhere in the cosmos? Are these neurons then somehow controlling all of matter?

    Your argument fails because it depends on things we do not know. That failure is not redeemed by pointing out what we do not know.

    But do you have answers for those questions for God? Why would everyone else have to provide these details in order to satisfy you when you cannot provide them yourself? How are God's neurons controlling all of matter?

  194. Comment by don provan — July 15, 2010 @ 4:35 pm

  195. don provan Says:
    July 15th, 2010 at 5:03 pm

    Daniel Smith: What we have is obvious intentionality in nature and no physical mind by which to explain it.

    THAT is why I say the mind must be supernatural.

    Why shouldn't I interpret this as you saying, "We can't explain it, so it must be magic"? When you say it's supernatural, you aren't actually explaining anything, you're just saying it must be beyond explanation. But we really have no reason to think that's true.

    Besides, even if we agree it must be supernatural, that still leaves innumerable possibilities other than God, so it doesn't actually get you any closer to your proof, anyway.

  196. Comment by don provan — July 15, 2010 @ 5:03 pm

  197. angryoldfatman Says:
    July 15th, 2010 at 7:07 pm

    don provan wrote:

    I do not claim God doesn't exist. How many times do I have to repeat that?

    You don't really claim anything at all. You're like Mumbly the Dog trying to be a Critical Theorist.

    Oh wait, I forgot. If you actually make a claim, you can be refuted. Whereas if you become the figurative Jello that no one can nail to the wall, you can troll to your heart's content, while never being wrong.

    Of course, without making a definitive claim you can never be correct, either. A sort of gelatin Purgatory, as it were.

  198. Comment by angryoldfatman — July 15, 2010 @ 7:07 pm

  199. don provan Says:
    July 15th, 2010 at 7:26 pm

    angryoldfatman: You don't really claim anything at all.

    That is correct. I only impartially evaluate other people's claims.

    If you actually make a claim, you can be refuted.

    If I had anything I felt worth claiming, I would see the possibility of being corrected as a good thing.

  200. Comment by don provan — July 15, 2010 @ 7:26 pm

  201. Daniel Smith Says:
    July 15th, 2010 at 7:50 pm

    don provan: Your argument fails because it depends on things we do not know. That failure is not redeemed by pointing out what we do not know.

    Don, Don, Don, Don…

    YOU'RE the one making an argument based on things we don't know. You're argument is that we don't know if there is something else that can produce intentionality so we cannot say that it only comes from minds.

    (By this twisted logic, only an omniscient being could make a rational argument BTW.)

    MY argument is that the only known source of intentionality is minds – therefore wherever there is intentionality, there is a mind behind it.

    YOUR argument is based on what we don't know – mine is based on what we do know.

    It really is that simple.

  202. Comment by Daniel Smith — July 15, 2010 @ 7:50 pm

  203. don provan Says:
    July 16th, 2010 at 2:58 pm

    Daniel,

    OK, I guess we're done with this line of reasoning. You have it exactly backwards, but what else can I say? I'm the one taking into account that we don't know everything. You're the one trying to pretend that there can't possibly be another source of intentionality based on the fact that we do not know of any other one.

    If I were arguing that there must be another source for intentionality, then I'd be making a mistake. But I'm only arguing that there could be another source, and that's sufficient to refute your argument since it is based on there being no other source.

    Moving on…

    MY argument is that the only known source of intentionality is minds – therefore wherever there is intentionality, there is a mind behind it.

    Actually, what we've really seen is that the only known source of intentionality is brains, physical, biological brains, not "minds". When you invoke a supernatural non-brain mind that could be the source of intentionality, you are inventing something just exactly as hypothetical and unsupported by evidence as the non-brain non-mind I've suggested.

  204. Comment by don provan — July 16, 2010 @ 2:58 pm

  205. Daniel Smith Says:
    July 17th, 2010 at 4:05 pm

    Don,

    If you're going to base your argument on what "could be" then I guess you're right – we're done with this line of reasoning. My argument is based on the known, yours is based on what "could be".

    Actually, what we've really seen is that the only known source of intentionality is brains, physical, biological brains, not "minds".

    That's the materialist bent on it – that the mind is nothing more than the brain. You know as well as I do that that line of reasoning leads to all sorts of explanatory problems. You know also that what's known about the brain does not explain what's known about the mind. Beyond that though – we see intentionality IN THE PHYSICAL CONSTRUCTION OF THE BRAIN!!

    When you invoke a supernatural non-brain mind that could be the source of intentionality, you are inventing something just exactly as hypothetical and unsupported by evidence as the non-brain non-mind I've suggested.

    First, you did not suggest a "non-brain non-mind", you suggested a "non-brain natural mind". (Remember this: "And even so, what's the problem with nature having a mind?")
    Second, I'm just following the evidence to a reasonable conclusion.
    The evidence is this:
    Mind is the only known, observed source of intentionality.
    Nature has no known or observed mind controlling it.
    Nature exhibits intentionality as if it were controlled by a mind.

    That's the evidence. The logical conclusion is that there is a mind outside of nature. The illogical conclusion is that there is an undiscovered mind inside nature.

    So let's recap – your argument is based on an appeal to what could be true (but is unknown at the present time) and mine is based on a reasonable inference from the known evidence.

  206. Comment by Daniel Smith — July 17, 2010 @ 4:05 pm

  207. don provan Says:
    July 17th, 2010 at 8:20 pm

    Daniel Smith: If you're going to base your argument on what "could be" then I guess you're right – we're done with this line of reasoning.

    I'm not making an argument, I'm just explaining to you what's wrong with your argument.

    My argument is based on the known, yours is based on what "could be".

    "The Sun is a big bonfire" was a similar argument based on what was known in the 19th century.

    That's the materialist bent on it – that the mind is nothing more than the brain.

    Not at all. It's simply what we know, exactly what you claim to be basing your argument on. We do not know that there are any minds which are not connected to physical, biological brains.

    Beyond that though – we see intentionality IN THE PHYSICAL CONSTRUCTION OF THE BRAIN!!

    Exactly. So this one thing we know absolutely and for sure: whatever caused the brain cannot be a mind in the sense of any mind we know.

    You are inventing something we do not know — a non-physical, non-biological mind — and pretending you can infer its existence based on what we know about minds we have seen.

  208. Comment by don provan — July 17, 2010 @ 8:20 pm

  209. Daniel Smith Says:
    July 18th, 2010 at 6:32 pm

    You are inventing something we do not know — a non-physical, non-biological mind — and pretending you can infer its existence based on what we know about minds we have seen.

    I'm not "inventing" anything Don. I am making a reasonable inference based on what is known.

    A) There is ample evidence that our own minds are not purely physical. Our minds understand and comprehend things that have no connection to physical objects – even things that do not exist. We understand the Pythagorean theorem for example, though it only applies to a perfect triangle (something that does not physically exist anywhere.) Yet we are able to comprehend both triangles and the many concepts of mathematics. If our minds were purely physical, how do you explain the ability to understand concepts that don't physically exist? Where is the physical connection Don? Explain how the physical brain "knows" things that don't exist.

    B) There is also ample evidence that a supernatural mind pre-existed our own. Again take mathematics as an example: We did not invent mathematics, we discovered it. We are still discovering how the entire universe is based on, and explicable via, mathematics. This fact alone points to a mind that pre-exists and transcends the universe. Explain the existence of a math-based universe Don – without referencing a mind that comprehends mathematics. Is this another unknown, as yet undiscovered, property of matter?

  210. Comment by Daniel Smith — July 18, 2010 @ 6:32 pm

  211. don provan Says:
    July 18th, 2010 at 8:31 pm

    Daniel Smith: I'm not "inventing" anything Don. I am making a reasonable inference based on what is known.

    No, you're simply inventing the non-biological mind in exactly the same way I am inventing my two explanations: a naturally occuring mind and something that is not a mind yet can create intentionality. If anything, my naturally occuring mind is more logical, since we do know naturally occuring minds exist — our own, for example — but we have absolutely no examples at all of supernatural minds. None.

    B) There is also ample evidence that a supernatural mind pre-existed our own.

    OK, for the last time: your examples show that something created mathematics, but not that what created it was a mind. You are simply guessing at that, and then insisting without any logical justification that your guess is correct and all other guesses are wrong.

  212. Comment by don provan — July 18, 2010 @ 8:31 pm

  213. Daniel Smith Says:
    July 19th, 2010 at 8:52 am

    Don, there's a big difference between a "guess" and a "reasoned proof".

    What I have cited is a reasoned proof – Aquinas' fifth way to be exact.

    It's no guess.

  214. Comment by Daniel Smith — July 19, 2010 @ 8:52 am

  215. don provan Says:
    July 19th, 2010 at 12:37 pm

    Daniel,

    OK, in the case, mine are also reasoned proofs. Now that we've renamed them, you still have the same problem: your reasoned proof only works if there are no competing, similarly derived reasoned proofs. But there are.

  216. Comment by don provan — July 19, 2010 @ 12:37 pm

  217. Daniel Smith Says:
    July 19th, 2010 at 6:55 pm

    don provan: OK, in the case, mine are also reasoned proofs. Now that we've renamed them…

    I have not "renamed" anything Don (though you have.)

    Go and learn what a reasoned proof is, then come back and present your argument in that form.

  218. Comment by Daniel Smith — July 19, 2010 @ 6:55 pm

  219. don provan Says:
    July 19th, 2010 at 7:33 pm

    Daniel Smith: Go and learn what a reasoned proof is, then come back and present your argument in that form.

    The world around us is innudated with intentionality, therefore nature must have an inherent, internal source of intentionality.

  220. Comment by don provan — July 19, 2010 @ 7:33 pm

  221. Daniel Smith Says:
    July 20th, 2010 at 9:14 am

    The world around us is innudated with intentionality, therefore nature must have an inherent, internal source of intentionality.

    You have stated an assumption. There is no justification given for the "inherent, internal source". Try again.

  222. Comment by Daniel Smith — July 20, 2010 @ 9:14 am

  223. don provan Says:
    July 20th, 2010 at 5:41 pm

    Daniel Smith: You have stated an assumption. There is no justification given for the "inherent, internal source". Try again.

    It's no different than your assumption that intentionality can only come from a mind.

  224. Comment by don provan — July 20, 2010 @ 5:41 pm

  225. Daniel Smith Says:
    July 21st, 2010 at 5:18 pm

    don provan: It's no different than your assumption that intentionality can only come from a mind.

    It's quite a bit different actually.

    My premise – that intentionality can only come from a mind – is based on what we know.

    Your conclusion – that the source of intentionality must be physical – is based on your belief that there is nothing beyond the physical.

  226. Comment by Daniel Smith — July 21, 2010 @ 5:18 pm

  227. Daniel Smith Says:
    July 22nd, 2010 at 7:35 pm

    For Don Provan:

    Intentionality: n., pl., -ties.

    1. The state of having or being formed by an intention.
    2. Philosophy. The property of being about or directed toward a subject, as inherent in conscious states, beliefs, or creations of the mind, such as sentences or books.

  228. Comment by Daniel Smith — July 22, 2010 @ 7:35 pm

Leave a Reply

You must be logged in to post a comment.

  • Featured Books


    The Design Matrix: A Consilience of Clues by Mike Gene
    Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body

    Catalyzing Inquiry at the Interface of Computing and Biology

    System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

    The Plausibility of Life By Marc W. Kirschner and John C. Gerhart

    Agents Under Fire by Angus Menuge

    Life's Solution by Simon Conway Morris

    Information Theory, Evolution and the Origin of Life by Hubert P. Yockey

    The Fifth Miracle by Paul Davies

    Nature, Design, and Science by Del Ratzsch

    Origination of Organismal Form by Muller & Newman

    Biased Embryos and Evolution by Wallace Arthur

    Rare Earth by Peter Ward and Donald Brownlee

    The Privileged Planet by Guillermo Gonzalez and Jay Richards

    The Way of the Cell by Franklin Harold

    The Volitional Brain by Benjamin Libet

    Evolution in Four Dimensions by Eva Jablonka & Marion Lamb

    The Evolution-Creation Struggle by Michael Ruse




Telic Thoughts is proudly powered by WordPress
Hosting provided by TopSoftware4Download.com .

Entries (RSS) and Comments (RSS).