Intelligent Design

The Molecular Revolution’s unfulfilled promises of simplicity

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There has been a complexity explosion in biology – the fuse was lit in 1953 when the structure of DNA was discovered, but during the past two decades we have witnessed a dramatic expansion of data pointing to unanticipated levels of complexity. The hype surrounding the Human Genome Project suggested it would give us the blueprint of human biology and, as a consequence, would provide answers to our most probing questions.

“Mina Bissell, a cancer researcher at the Lawrence Berkeley National Laboratory in California, says that during the Human Genome Project, she was driven to despair by predictions that all the mysteries would be solved. “Famous people would get up and say, ‘We will understand everything after this’,” she says. “Biology is complex, and that is part of its beauty.””

In the early days of the revolution, the focus was on genes. This was regarded as the key that would unlock the mysteries of the cell. Genes were the providers of biological information, and the rest of the genome (98% of it) was deemed to be Junk DNA. Since this did not code for genes, the inference was made that it should be interpreted as an evolutionary artefact, unworthy of serious study.

[. . .]

The level of complexity rose higher and higher as it became apparent that the communication within the cell is not best modelled by signalling pathways but by networks of information flows. The discipline of systems biology was created to make sense of the complexity. The verdict appears to be one of partial success, for even the systems biology approach struggles with the levels of complexity that are found.

“In the heady post-genome years, systems biologists started a long list of projects built on this strategy, attempting to model pieces of biology such as the yeast cell, E. coli, the liver and even the ‘virtual human’. So far, all these attempts have run up against the same roadblock: there is no way to gather all the relevant data about each interaction included in the model.”

The author of this informative feature article on complexity is Erika Check Hayden. As more and more is known, biology does not conform to the reductionist expectation of ultimate simplicity, but instead it appears ever more complex.

“[A]s sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude. Delving into it has been like zooming into a Mandelbrot set – a space that is determined by a simple equation, but that reveals ever more intricate patterns as one peers closer at its boundary.”

The Mandelbrot set analogy has some value, but there is a danger to it. As Hayden points out above, the apparent intricacy is actually based on a simple equation. The complexity is in the eye of the beholder. Reductionism is entirely comfortable with the Mandelbrot set. But is biology really like this? The question deserves a much more rigorous analysis. Hayden refers to Davidson’s work in developmental biology and his claim to find simplicity and order. However, reductionism is not the only paradigm that incorporates simplicity and order. The concepts of complex specified information and irreducible complexity are entirely compatible with evidences of simplicity and order, yet are not explained by the reductionist approach. The domain surveyed by Hayden is home territory for the intelligent design paradigm. ID brings a perspective on biological information that takes us in a different direction to the Mandelbrot set analogy for biological complexity. The main problem for ID has nothing to do with relevance, but with its incompatibility with a materialist approach to science. But this also is a philosophical issue deserving of the widest possible discussion within the scientific community.

For more, go here.

24 Replies to “The Molecular Revolution’s unfulfilled promises of simplicity

  1. 1
    JPCollado says:

    Breathtaking indeed!!

  2. 2
    Nakashima says:

    Dr Tyler,

    I’m not a hearing a promise of simplicity, even in the hyperbole surrounding the genome project. Nor does reductionism promise simplicity of explanation either, only that the objects of one level are built out of the entities at a lower level. And that reductionism has so far been proven out. There is no elan vital. DNA is made of atoms. Information is copied by shifting about atoms.

    There is no evidence that the sequence of cytochrome C has existed eternally as disembodied ‘information’ in some Platonic ideal sense before becoming embodied in a cell, atoms moved into correct positions by an unknown force. Or the sequence of a bacteriophage virus. Or P. falciparum.

    The idea that there are many small RNA transcripts which are functional does not contradict the idea that much of the genome is useless junk. How many is many? 10,000? 100,000? That is still a small fraction of the junk genome.

  3. 3
    spot48 says:

    The main problem for ID has nothing to do with relevance, but with its incompatibility with a materialist approach to science.

    This statement contains within it everything one needs to know to understand why ID can’t succeed as the basis for a scientific theory or research program.

    The initial promise of ID was that it would generate empirically testable (falsifiable) hypotheses (here, I mean the sorts of testing that involves actual data and experimental observation, not parlour tricks with computational models). As a practicing biologist and a convinced theist, I eagerly set about trying to develop such hypotheses. The trouble I always ran into is that any ID hypothesis one might develop will have a supernatural component, the intelligent designer. The rules for God’s decision-making process in design are not available for scientific inquiry and, by definition, not constrained by natural laws. The supernature of the designer is the crux of the “incompatibility” David refers to in the above quote. By its very nature, science is an enterprise that involves use of the rational faculties of the human mind operating on the deliverances of the senses to understand the causal relationships between material things. It is in this respect a very limited enterprise, that can only make pronouncements about material things and the relationships between them (only part of the larger world we inhabit). Unfortunately, the causal relationships ID hypotheses inevitably seek to test are relationships between God’s (supernatural) mind and the material world.

    This is why ID can’t succeed, expressed in terms of David’s quote above: There is certainly an incompatibility between ID and the scientific enterprise, which is only able to study material things and the relationships between them. But this incompatibility actually means that ID is not relevant to the formulation of hypotheses that can be tested by the scientific enterprise. No worries, though, science isn’t the only discipline that marshalls the faculties of the human mind for the rigorous investigation of the world around us. Practitioners of other disciplines (eg. Philosophy or Theology) have a substantial responsibility, not only to provide us with an understanding of those things in our world not available to scientific inquiry, but also to remind us of the limits of science and of their respective disciplines.

  4. 4
    bornagain77 says:

    Spot, what you are advocating is called methodological naturalism and it is simply false to say materialism owns exclusive rights to how hypothesis in science may be formed:

    Materialism compared to Theism within the scientific method:
    http://docs.google.com/Doc?doc....._5fwz42dg9

    In fact I hold the “hypothesis” of the Genetic Entropy model for all biological adaptations to be the true principle for all biology that explains all the data we have, and it is derived directly from principles of science, Conservation Of Information and Entropy, whereas evolution has no foundational basis in science in which to appeal for its hypothesis of complexity generation. In fact ID presupposes exactly what Darwin did for the origin of life,,,

    “There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one;” Charles Darwin (Origin of Species)

    ,,, and if you put any evolutionists on the spot now as to the origin of life they will tell evolution does not deal with this. Well isn’t it convenient that Darwin is allowed to postulate a creator at whatever point he wants in Origin, yet when ID points out the limits to evolution, all of the sudden ID is not science because it shares a same premise as Darwin himself felt no pains to invoke.

  5. 5
    jerry says:

    “The trouble I always ran into is that any ID hypothesis one might develop will have a supernatural component, the intelligent designer.”

    What you say above is nonsense. There are thousands of ID hypotheses that have nothing to do with a designer let alone a supernatural one. If you are what you say you are, a biologist and a theist, then we can have an honest discussion.

    First of all what ID says is that there is unlikely any natural mechanism for the creation of all complex novel capabilities in life forms. That is certainly one thing that can be tested without any supernatural component. We might not have all the data available at the moment but biologists are working continually to supply the data that would support that proposition or not. The construction of irreducible complex systems over time should be something that would be open to validation in various families or orders of organisms. The study of genomes should eventually reveal what has happened and if in fact some hurdles can be breached or not.

    There also appears to be limitations built into organisms on how much they can change. Where are these limitations located and what would it take for natural processes to overcome them and why are they there in the first place. For example, why do not certain species gradually get older over time before they die. It would seem that ability to resist death longer would be heritable. Similarly there are many other limitations. Darwinian processes would not predict these limitations so why are they there? This may or may not end up supporting ID but it could so would be research that ID would be interested in that the materialist would be inhibited from doing if it was identified as friendly to ID.

    There is much more so your statement is nonsense. ID is fully compatible with everything done today in biology and in the history of biology. What ID adds is possible alternative conclusions to the findings of the materialist biologist. Ones he is obliged to reject because he is a materialist. So contrary to your assumption it is the materialist who is limited, not the ID scientist who can accept or reject all materialist conclusions depending upon if they are supported by the data or not. The materialist must make certain conclusions or else he will be ostracized from the current academy.

  6. 6
    spot48 says:

    Okay folks, the quality of exchange here is making me sleepy.

    I am familiar with the term “methodological naturalism” and appreciate your great confidence that Intelligent Design hypotheses do not involve a Designer(!). Also, I appreciate how much impact saying things like “simply false” and “nonsense”, But, just to make things interesting, you should really try to spend a few minutes thinking about how to engage my point rather than responding with free word association and making unsupportable claims in favor of your position.

  7. 7
    spot48 says:

    Okay folks, the quality of exchange here is making me sleepy.

    I am familiar with the term “methodological naturalism” and appreciate your great confidence that Intelligent Design hypotheses do not involve a Designer(!). Also, I appreciate how much impact saying things like “simply false” and “nonsense” seems to produce. But, just to make things interesting, you should really try to spend a few minutes thinking about how to engage my point rather than responding with free word association and making unsupportable claims in favor of your position.

  8. 8
    jerry says:

    “Also, I appreciate how much impact saying things like “simply false” and “nonsense” seems to produce. But, just to make things interesting, you should really try to spend a few minutes thinking about how to engage my point rather than responding with free word association and making unsupportable claims in favor of your position.”

    You are following a familiar pattern. You make a false claim and then when called on it say that no one is engaging you. You have restricted ID to a world it does not inhabit and because we will not play in your straw man world you complain.

    I will say it again. Nothing in ID is relevant to the supernatural. So to bring it up it to engage in a false premise. Maybe one that you want to impose but which has nothing to do with ID. So I suggest if you want to have a conversation engage ID on what it is about not your stereotype which is something mainly just in your mind.

  9. 9
    bornagain77 says:

    Here is a cool video of a Mandelbrot set zoom

    Mandelbrot, Much bigger than the universe! deep zoom 2^316
    http://www.youtube.com/watch#!v=2tRdLD6vh3g

  10. 10
  11. 11
    bornagain77 says:

    Link wouldn’t take. but it works if you cut and paste the address.

  12. 12
    spot48 says:

    I will say it again. Nothing in ID (as in, Intelligent Design of the natural world) is relevant to the supernatural.

    If a person keeps saying things like this do they eventually begin to believe them? What other stake does a proponent of ID have other than demonstrating that there is, ultimately, an Intelligent Designer?

  13. 13
    jerry says:

    “What other stake does a proponent of ID have other than demonstrating that there is, ultimately, an Intelligent Designer?”

    Good science. Certainly modern evolutionary biology can not justify a lot of its claims.

    If it was designed it had to have an intelligent designer. There is nothing in ID that will tell you who, what, why, when or how the design was accomplished, just that it was very likely designed. Maybe sometime in the future, some of these other issues can be addressed.

  14. 14
    Adel DiBagno says:

    If it was designed it had to have an intelligent designer.

    IF there is no evidence for the existence of an intelligent designer OR if one has no idea about the properties of such a designer, then there has been no intelligent design.

  15. 15
    spot48 says:

    BTW, a reprint of someone else’s response at UD re: the aim of ID, apropos:

    Phillip Johnson:

    “We are taking an intuition most people have (the belief in God) and making it a scientific and academic enterprise. We are removing the most important cultural roadblock to accepting the role of God as creator.”

    William Dembski

    “ID is three things: a scientific research program that investigates the effects of intelligent causes; an intellectual movement that challenges Darwinism and its naturalistic legacy; and a way of understanding divine action.”

    and

    “The Designer of intelligent design is, ultimately, the Christian God.”

  16. 16
    Upright BiPed says:

    spot,

    You’re whistling past the graveyard.

  17. 17
    spot48 says:

    Upright,

    I completely agree with you. I thought it would be possible to engage this bunch in actual dialog, but it appears you only get to have open and cordial conversations if you already agree with everything ID stands for. Now that I realize the views of an actual experimental biologist who is also a Christian theist is uninteresting in this graveyard, I will probably go whistle elsewhere.

  18. 18
    Upright BiPed says:

    Spot, twisting someone’s meaning to fit your line of thought is not exactly cordial conversation. Neither is applying your thumb to the scale of reason.

    “The initial promise of ID was that it would generate empirically testable (falsifiable) hypotheses (here, I mean the sorts of testing that involves actual data and experimental observation, not parlour tricks with computational models).”

    What exactly is the testible hypothesis which has been generated for the unguided emergence of information processing in an organic substance?

  19. 19
    spot48 says:

    Upright,

    I will humour you with a response to the above. Sounds like what you are asking for is a testable hypothesis regarding abiogenesis. Miller and Urey, so many years ago, provided one of the early examples of just such an hypothesis, and performed a series of experiments to test it. Whether their results were conclusive or not is beside the point, which is that they provided a testable hypothesis and produced experimental support for it that has been available for scrutiny by the scientific community.

    This, by the way, can be found in any biology text that hasn’t been edited by the Kansas School Board, so you shouldn’t have trouble finding reading material if you are confused about what a testable hypothesis is. Once you have read up, provide me a similar example from the extensive peer-reviewed ID literature in experimental biology.

  20. 20
    Upright BiPed says:

    spot,

    MU (as interesting as it was) is hardly a testible hypothesis to answer the question I asked. IF we had synthesized every molecular component of a living organism it would not even begin to suffice for the coordinated organization which is inherent in all living systems. Perhaps you were just not aware of that.

    And the question I asked comes directly from you yourself. You seem to want to deride ID because you don’t think it has produced a testible hypothesis to support its claim – which makes me wonder if you understand that the hypothesis is based upon observed effects (exactly like the Big Bang), and rationally follows from our universal experience with those observed effects, as well as the fact that the current paradigm is unable to account for the effects in any way whatsoever.

    So the question follows from your own comments, and your response here has been to suggest experimental results which haven’t even a chance at answering the issue at hand.

    So again, I ask the question that you yourself feel must be answered. But I ask it of you yourself instead.

    What is the testible experiment that has inanimate chemicals producing information content and processing? And please explain how these experiments show that the rise of this phenomena happens without any agent involvement whatsoever, for that would certainly negate ID.

  21. 21
    spot48 says:

    Upright,

    This excuse of never being satisfied with the answer to your question permits you to dodge providing an answer to mine.

    As you probably know, the Miller Urey experiment launched decades of subsequent hypothesis-driven research whose aim was to provide a compelling naturalistic explanation for abiogenesis (the generation of information bearing systems is part and parcel of this, given that these are one of the essential features of living things). Again, whether this work was actually compelling is neither here nor there. What is important for the sake of this dialog is that the work proceeded by advancing testable hypotheses and then doing experimental work, which was made available for the scrutiny of the scientific community.

    So now how about your example (and make it something substantial, if you would)?

  22. 22
    Upright BiPed says:

    Spot,

    This excuse of never being satisfied with the answer to your question permits you to dodge providing an answer to mine.

    Perhaps you need to reread my comment. It addresses your accusation that I am never satisfied with your answers, as well as the accusation that I am dodging your question. Actually my comment so directly addresses both these accusations that it’s difficult to understand why you made them. In any case, I’ll be more than happy to go through it again.

    Let’s start with the accusation that I am dissatisfied with your answer:

    ID makes an inference from observable molecular evidence that life could not have spontaneously arisen as the product of purely undirected natural processes. By “natural processes” it is meant those that can be quantified and tested by the physical laws we see in operation across the universe (Newtonian Mechanics, Einstein’s Relativity, Maxwell’s Electromagnetic Field, Quantum Mechanics). ID posits that agency input is necessary, along with the physical properties of matter, in order to explain the effects observed within the cell. Those effects include the rise of sophisticated biological organization by means of information processing. There are no physical properties of matter that can even conceivably originate these effects which we observe. This inference is based upon our universal experience with these effects, as well as with the entire range of our experience with matter itself. By “universal experience”, it is meant that no one has ever produced a single exception to these observations, regardless of what their metaphysical predisposition is or was.

    Beyond this intractable evidence, the inference to design is propelled forward by several other factors; two of which are (a) the fact that the opponents of theory (try as they might with virtually unlimited resources) cannot produce even a conceptual means to produce the effects in question and thereby falsify ID, and (b), the fact that the gap in the explanatory power of the opposing theory is ever increasing under new discovery. In other words, the more we discover and catalog about the intricacies of the molecular world, the higher the bar becomes for explaining it by purely unguided processes.

    Now against this backdrop, you suggested UM as an experimental test of the opposing theory. The output of that theory is, of course, that we may assume a purely unguided origin of life. Your suggestion strictly implies that by this experiment and others like it we have found a plausible pathway to explain the effects we see inside the cell.

    How is it that you could even make such a suggestion? Regardless of any hyperbole one might want to adorn UM, the simple fact is that UM showed that a portion of the raw organic compounds found in living systems can be synthesized in an intelligently directed apparatus. However, it is virtually impossible to construe UM as an experiment that tests the rise of sophisticated organization by means of information processing – given that there was no information processing even associated with the experiment. If this leads you to conclude that I will forever be dissatisfied with your response, then you would be 100% accurate in that assessment. It’s a little like saying you’ve tested the software on your computer by making sure the circuit breaker in garage is turned on.

    And how is it exactly that you made this presentation? You said:

    I will humour you with a response to the above. Sounds like what you are asking for is a testable hypothesis regarding abiogenesis. Miller and Urey, so many years ago, provided one of the early examples of just such an hypothesis, and performed a series of experiments to test it.

    Again, the synthesis of a few raw compounds is not a test that substantiates a theory which must explain what is observed inside the cell. You may want to suggest that UM was just the start of a series of experiments which have substantiated the theory, but I would simply remind you that no one has ever even attempted to show the rise of information processing in a cell. No one can even conceive of such an experiment.

    Even you seem to understand this, although you want to posit such experiments as a test of the theory anyway. Perhaps this is illuminated by your own comments. Twice in your past two posts you made statements about the results of these tests:

    Whether their results were conclusive or not is beside the point

    Again, whether this work was actually compelling is neither here nor there.

    It seems a little odd that someone would come to UD to accuse ID of being without tests, and then carelessly offer experiments as a mark of achievement for the opposition (which do not even test the opposing theory against what must be explained). Then compound it by reminding us that these tests are not sufficient in light of the evidence. It’s hardly a compelling argument.

    As for your accusation that I am dodging your question, I will address that accusation now. Again, I suggest that you reread my comments, and do so with the idea that you might process the information/ideas contained within them. I stated:

    You seem to want to deride ID because you don’t think it has produced a testible hypothesis to support its claim – which makes me wonder if you understand that the hypothesis is based upon observed effects (exactly like the Big Bang), and rationally follows from our universal experience with those observed effects,

    It would follow from this statement that we are examining a historical event – perhaps even a one-time-only historical event. The reference to the Big Bang was intentional. The Big Bang was a one-time-only event in the history of the universe which has been theorized upon the basis of its observable effects. It is safe to say that we will not be creating an infinitely small, dense, and hot singularity and testing it to see if it results in the beginning of space and time. Given that, are you then suggesting that the Big Bang Theory “can’t succeed as the basis for a scientific theory or research program” (?)

    Biological ID is based upon the sum of all experimental data that has ever been created relevant to biological life. There is no experimental data that does not have the earnest potential to impact the ID hypothesis. So, beyond the fact that there is absolutely nothing known by mankind’s means of experimental investigation (that could not affect the design hypothesis) what exactly is it that you are looking for?

    Play it out in your head: ID is the hypothesis that an act of agency input is necessary to explain the existence of sophisticated organization by means of information processing. Do you want ID to create molecular information processing by an act of agency input? Would that do it for you? Or, do you want ID to try creating molecular information processing by unguided means, and fail?

    Which is it?

    I’ll tell you which it is…it uninformed. It’s ignorant of the theory and of the limitations placed upon historical science. And it also completely evades the reality that the competing paradigm implies that unguided origins it is a repeatable phenomenon (because it is based upon nothing more than the natural unguided processes at work in the cosmos) but then cannot even conceptually provide a means to test their hypothesis without doing exactly what they suggest did not happen. It’s a boilerplate argument that not even a Darwinian bench-warmer should exercise, much less an educated person.

    In the meantime, ID moves forward without a single scientific observation that contradicts its theory. Perhaps that is why you feel the need to keep a thumb on the scale.

  23. 23
    spot48 says:

    In the meantime, ID moves forward without a single scientific observation that contradicts its theory.

    Which makes sense, because based on your description of ID in the post above, the theory is insulated from disconformation. The little voice of conscience in your head may have told you that you still haven’t given me an example of an experimentally testable hypothesis generated by ID.

    BTW, you have lost the point of our dialog, which was to trade examples of experimentally testable hypotheses generated by biological theories. The reason whether it is of no consequence whether Miller and Ureys’ experiments or others in that series of experiments are convincing is because they were only offered as an example of what an experimentally testable hypothesis might look like. I hoped this example would kind of “prime the pump” in your brain and help you come up with a similar example from ID.

    I’m pretty sure you won’t give me an example. Let me offer a vocabulary lesson that may help you in your future conversations here (with others, I am done):

    Main Entry: ob·scu·ran·tism
    Pronunciation: \äb-skyur-n-ti-zm, b-; äb-skyu-ran-\
    Function: noun
    Date: 1834

    1 : opposition to the spread of knowledge : a policy of withholding knowledge from the general public
    2 a : a style (as in literature or art) characterized by deliberate vagueness or abstruseness b : an act or instance of obscurantism

    ob·scu·ran·tist \-n-tist, -ran-tist\ noun or adjective

    spot, over and out.

  24. 24
    Upright BiPed says:

    Spot,

    Closing your eyes and ears to information is hardly a novel defense. Trying to quickly close the exchange so that you may claim victory is no more compelling than ignoring the information in the first place.

    Yet, what exactly was the part of my comment which you chose to ignore??

    Biological ID is based upon the sum of all experimental data that has ever been created relevant to biological life. There is no experimental data that does not have the earnest potential to impact the ID hypothesis. So, beyond the fact that there is absolutely nothing known by mankind’s means of experimental investigation (that could not affect the design hypothesis) what exactly is it that you are looking for?

    Play it out in your head: ID is the hypothesis that an act of agency input is necessary to explain the existence of sophisticated organization by means of information processing. Do you want ID to create molecular information processing by an act of agency input? Would that do it for you? Or, do you want ID to try creating molecular information processing by unguided means, and fail?

    Which is it?

    I’ll tell you which it is…it uninformed. It’s ignorant of the theory and of the limitations placed upon historical science. And it also completely evades the reality that the competing paradigm implies that unguided origins it is a repeatable phenomenon (because it is based upon nothing more than the natural unguided processes at work in the cosmos) but then cannot even conceptually provide a means to test their hypothesis without doing exactly what they suggest did not happen. It’s a boilerplate argument that not even a Darwinian bench-warmer should exercise, much less an educated person.

    – – – – –

    Only a truly talented ob·scu·ran·tist could then turn around and say ID is insulated from the evidence. Only a ob·scu·ran·tist could ignore the stated limitations, then claim their opponent fails to address the issue.

    Please allow me to offer a little literacy study for you as well:

    pr?-j?k’sh?n: a psychological defense mechanism whereby one “projects” one’s own thoughts and motivations onto someone else (usually another person, but psychological projection onto animals and inanimate objects also occurs).

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