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Why isn’t ALL life extinct?

In another thread talking about engineers’ perspectives on the machinery of life the topic of entropy came up. Engineers have to deal with entropy in all their designs and the very best efforts at dealing with it only serve to slow it down and never stop it.

So one of my big questions isn’t why most cell lines sooner or later go extinct as that’s easily explained by entropy. Rather my big question is how a rare few of them have managed to persist for hundreds of millions or billions of years.

In computer design engineering we have to deal with users changing the software load in unpredictable ways. We ship the computer out with a software load we know works. It then “evolves” unpredictably as the computer is used and customized without or without the informed consent of the owner. Often that evolution of the software load results in a system that no longer functions. Without some recovery method that particular computer, which is analogous to a single cell line, would become extinct. The ways we address this problem are many, convoluted, and complex but I’d like to focus on a few in particular.

One method is called a “factory restore”. In this method a protected image of the known working software load from the factory is used to replace the evolved load. This is typically implemented by a user accessable trigger and an image stored on a protected segment of the hard disk or separately on a CD rom disk.

A somewhat less effective but largely successful method of recovery from disastrous software load “evolution” is employed by more recent versions of Microsoft Windows. It employs automatic trigger mechanisms that take a snapshot of the current state of the software such that if disaster happens the state can be restored to a previously known working state. This allows successful modifications wrought by evolution to “survive” without backtracking farther than absolutely required. It doesn’t always work because the images aren’t complete snapshots, which would quickly overflow the storage capacity of the disk, but rather carefully selected critical bits are saved that usually work to restore a known working state.

In other than inexpensive personal computers where cost isn’t so prohibitive (such as servers) both automatic and manually triggered backups of the software state are made to external, removeable media. In the most critical applications multiple backups are made and stored in physically separated locations such that a catastrophe, like a fire, in one location won’t destroy all the copies.

Now since in my experience many (if not most or all) designs we humans invent to solve engineering challenges end up having analogs found in the design of life I propose that a plausible answer to how life deals with the devastating effect of entropy is along the same lines used in computer systems. Periodic backups are made such that what random evolution hath wrought on the software load (DNA) can be undone back to a previously known working state. Evolution starts over but doesn’t start over from scratch. The details and triggers employed can only be imagined at this point in time but it doesn’t take much imagination for a computer design engineer. Experiments to tease out the methods and triggers, if they exist, seem like a reasonable line of inquiry.

It’s difficult to imagine how mutation and selection could invent a disaster recovery method such as this and that likely explains why there’s little if any research thrown at figuring out why most but not all cell lines eventually go extinct. This is where the ID paradigm becomes very valuable. Rather than limit the possibilities in the design of life to what is reasonable for a reactive process like mutation and selection to invent we extend our thinking to what is reasonable for a proactive process like intelligent design to invent.

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60 Responses to Why isn’t ALL life extinct?

  1. Yeah, Dave that is an excellent question. I’ve have argued on other threads that the so-called “deep time” necessary for TTOE and abiogenesis pose as much a problem as a solution. How likely is it that in “deep time” some asteroid or mutated evolved killer virus, or global warming or global cooling wouldn’t have obliterated life. Further according to the Wildlife Conservation Society 50K species of life go extinct every year. Wouldn’t we need pretty soon some new ones or else suffer ultimate extinction and annihilation.

    Also I don’t understand why TTOE proponents are so concerned about global warming, wouldn’t this pressure generate some new opportunity for mutating species?

    The other angle to this is that for every positive mutation (lions now run a time and half faster) a corresponding negative impact is felt by the zebras as they are driven out of existence and toward extinction. Which, when the zebras die out this would have an adverse affect on the lions. Either way, mutations positive or negative do not represent a net gain for an ecosystem because of the interdependence of the system. Those that are critical of human relations with nature seem to realize this.

  2. 2

    …my big question is how a rare few of them have managed to persist for hundreds of millions or billions of years.

    Some would say that the obvious answer is that they have not persisted for “hundreds of millions or billions of years” but rather orders of magnitude less. From this point of view it seems that an interesting research program would be to calculate the rate of degradation of the human genome and attempt by extrapolation to determine at what point in the past it would have been perfect.

  3. So one of my big questions isn’t why most cell lines sooner or later go extinct as that’s easily explained by entropy.

    The “canned” answer is the Earth is not a closed system. Meaning entropy need not apply.

    (don’t shoot the messenger!) ;)

  4. Take that answer boldly out of its can. You will not be shot.

  5. Joseph. Thank you for sharing this with me.

    http://www.worldnetdaily.com/i.....geId=56626

  6. Daniel,

    Try this experiment. Put a CD rom disk out in the sun. Check it every day to see if the information on it becomes more organized, less organized, or stays the same. Keep it up until something changes. Let me know which way it eventually changes. Since I’m an engineer who understands entropy I could tell you what’s going to happen but I think you need some personal experience in “open systems” with regard to entropy.

  7. Not even apples and oranges, DaveScot.

  8. “Rather my big question is how a rare few of them have managed to persist for hundreds of millions or billions of years.”

    They would persist if they were designed such that mutation of any essential elements would cause the mutant to die.

  9. …or disable it’s ability to reproduce.

  10. “The “canned” answer is the Earth is not a closed system. Meaning entropy need not apply.”

    “Take that answer boldly out of its can. You will not be shot.”

    OK, try this one. Add salt (maybe from that can you’re opening) to a pot of luke-warm water. How fast does entropy increase? Now add salt to a pot of water being boiled on a stove. Yes, it’s different. Entropy increases much faster. Adding energy to a system does one thing – it increases the rate at which entropy increases.

    The only way to decrease entropy in an open system is to add energy in an intelligent manner. This can be done by an “active” intelligence, or by pre-programmed intelligence (i.e. what you find in biological systems).

  11. SCheesman,

    This can be done by an “active” intelligence, or by pre-programmed intelligence (i.e. what you find in biological systems).

    Doesn’t that last bit kind of assume the consequent (that is, that “biological systems” are “pre-planned intelligence”)? Now, there’s a (theological) sense in which I believe that, but in terms of science. . . .?

  12. 12

    LarryNormanFan: Check your facts.

    I’m sure you are toting the current Darwinian line though. So you are probably right.

  13. 13

    “The only way to decrease entropy in an open system is to add energy in an intelligent manner. This can be done by an “active” intelligence, or by pre-programmed intelligence (i.e. what you find in biological systems)”

    Amen to that.

  14. Further to DaveScott’s:
    “Try this experiment. Put a CD rom disk out in the sun. Check it every day to see if the information on it becomes more organized, less organized, or stays the same.”

    Applying Kenneth Miller’s “evolutionary design” principle, put the CD in a rock polishing jar and “polish”. Then see how the information content improves when energy is added to this system.

    By contrast, intelligently designed CD disk polishing provides surfaces where the “bumps” risking above the polished surface are < 1 nm.

    Another method of “evolutionary design” is to place the CD in the oven set to about 232 C (450F) and add heat for several hours. Then test the increase in evolutionary “information” content.

    By contrast, “intelligently designed” controlled crystallization can provide surfaces with variations of < 1 atom in height.

  15. “Doesn’t that last bit kind of assume the consequent (that is, that “biological systems” are “pre-planned intelligence”)?”

    Well, yes it does, and that’s my own viewpoint, of course. I was expecting the reply that biological systems themselves decreasing entropy over time are in fact what RM+NS predicts.

    It is interesting, though to consider how biological agents decrease entropy, or at least do not increase it. They reproduce themselves, and they build structures usable by other creatures, and they may produce waste products or leave their own remains that may be useful for creatures that follow. One thing none of them do, though, is conciously modify their own programming. The only way that can happen is through random mutation, and intelligence is NOT involved there.

  16. CDs have a limited lifespan even when stored properly. So I think a better analogy would be to take a disc and duplicate it. Then take the copy and duplicate that and so on. Modern error corrections keeps the error rate to around 1 in 10^9 to 1 in 10^12 I believe. Check the information content after so many duplications.

  17. Daniel

    not even apples and oranges

    I agree. There is no demonstrated example of highly ordered macroscopic systems emerging by law and chance. It’s not my fault that the only demonstrated way for highly ordered systems such as computers and cellular machinery to beat the statistical improbability is by intelligent agents pushing matter and energy around to bring abstract thought into physical reality.

    Maxwell’s Demon is the classic thought experiment showing that no contraption can get a free lunch when it comes to energy being employed to defeat the increase of entropy. Are you familiar with it?

  18. Maxwell’s Demon is the classic thought experiment showing that no contraption can get a free lunch when it comes to energy being employed to defeat the increase of entropy. Are you familiar with it?

    If I remember correctly it deals with a closed system. However, life on this planet does not exist in a closed system. As I was taught in Biology 101, living things contend, for a while, against our internal, local entropy by inflicting increased entropy on our environment. As when one eats an apple, which is a highly organized set of chemicals, extracts what is needed (including energy) through the processes of digestion and excretes the much less ordered remainder in the form of fecal material.

    What is man, when you come to think upon him, but a minutely set, ingenious machine for turning with infinite artfulness, the red wine of Shiraz into urine?

  19. John Sanford in “Genomic Entropy and the Mystery of the Genome” cites numerous examples of evolutionist population geneticists asking the question Why are we not already extinct. See especially the appendix.

  20. Daniel

    re; Maxwell

    Yes, it’s a closed system. The caveat as I recall is that the demon needs intelligence to know when to open and close and the intelligence needs energy to operate which must come from outside the system.

    The earth as an open system doesn’t really seem relevant in any case. There’s enough energy in the earth to power life processes. One example is demonstrated by extremophiles that live deep underground and get their energy from oxidizing iron. The apple/fecal matter example is a good one that I’ve used myself to illustrate the same kind of order decreasing in one place (the apple) while elsewhere (new tissue in the apple eater) increasing but does that apply to iron eating bacteria? If we let the sun back in then we can look at plants which also take simple matter/energy gradients and construct much more highly ordered systems from it. Are the gradients of H2O, CO2, and minerals in the plant’s environment equivalent to the order in the plant tissue? I don’t think a good case can be made for that. Just like in Maxwell’s demon there has to be some kind of intelligent mechanism directing how the energy is applied. Maxwell’s demon comes up short in this case as the order it generates isn’t complex. It just creates a simple energy gradient. To get highly complex order from simple energy and chemical gradients there needs to be something else involved.

    Sewell’s paper Can Anything Happen in an Open System? discusses this in greater detail. I think it clearly shows that law and chance aren’t sufficient to concentrate the order represented in simple gradients into highly complex ordered forms. In other words you can’t just willy-nilly exchange thermal order for any other kind of order and this is exactly what is proposed by the open system rebuttal for entropic objections to life forming by law and chance alone. The order represented by information coded into the DNA molecule is not equivalent to the thermal order in the earth/sun system. Adding energy to a closed system in and of itself is not sufficient. Energy is a requirement but it’s not the only requirement. It must be directed.

    We can say that natural selection is equivalent to Maxwell’s demon in that it opens to allow beneficial change through the boundary and closing shut to prevent detrimental change from crossing the boundary and in that way increase order. Indeed, this is exactly what MET is based upon. Natural selection provides the direction required to translate one kind of order into another. This raises two further questions:

    1) Natural selection requires mechanism to operate where the mechanism is itself very highly ordered. What directed the formation of that? In other words it leads directly to the origin of life question.

    2) Are there no bounds on natural selection? Trial and error, which is essentially what chance & necessity is, is bounded by statistical mechanics. While anything is theoretically possible with chance & necessity merely being possible isn’t enough. There is a continuum of probability that needs to addressed ranging from physically possible, to physically plausible, to physically probable, to physically certain. Historic reconstructions of organic evolution ignore these in that if something is possible, even if the odds appear to be impossibly remote, that’s good enough to say it is plausible, probable, or even certain. The public is being gulled into believing the merely possible is a certainty. That’s what happens when a scientific theory becomes scientific dogma. Chance and necessity is a dogmatic truth so probabilities are ignored. No matter how much the probabilities are stacked against it chance and time and luck combined to overcome those odds. They must have overcome those odds because chance & necessity as the sole mechanism underlying organic evolution is a dogmatic truth.

    We ID proponents object to the dogmatism underlying this and believe that upon close inspection the emperor is wearing no clothes. Just being physically possible while ignoring what statistical mechanics tells us about the bounds of law and chance in any given circumstance is not good science. It’s ideological science.

  21. Daniel (con’t)

    Getting back to the focus of the article. From an engineering perspective the molecular machinery in a living cell is highly ordered and finely tuned. Many small machines and information processing systems all interdependently entwined cooperate to accomplish a task – metabolism and replication. Random mutation in this system is equavalent to throwing gold dust into a gold watch. There’s a tiny chance that a dust particle will land somewhere where it improves the mechanism, a good chance for most particles landing somewhere where they make very little difference, and a good chance they’ll land somewhere that makes the watch inoperable.

    Natural selection operates on the entire watch. In the rare case where a particle lands somewhere good in order to keep that particle it must also keep the other particles that fell along with it. It’s the accumulation of the other particles over time that makes things go extinct. The genome eventually becomes overwhelmed by the accumulation of slightly detrimental changes. This is more or less Haldane’s Dilemma. An excellent book on the topic of genetic entropy is Cornell geneticist John Sanford’s Genetic Entropy & The Mystery of the Genome. I personally think he cherry picks the literature to establish a background random mutation rate orders of magnitude greater than commonly accepted rates in order to justify such a high rate of entropic decay that life couldn’t have been around more than 6000 years. That aside, given more commonly accepted background mutation rates, his thesis remains intact. Instead of 6000 years with a high mutation rate, the genetic entropy problem still remains given a lower mutation rate over millions of years. Extinctions are quite handily explained by this. What isn’t explained is how extinction is avoided by a lucky few.

    If we accept at face value that organic evolution occured over hundreds of millions or billions of years, and we take at face value descent with modification from one or a few common ancestors is true, then it appears there must be some mechanism at work that can sweet genomes clear of accumulated detrimental modifications. A problem of exactly the same nature happens in computer systems and mechanisms to sweep detrimental changes clear have been implimented to address it. Unless we view the molecular machinery of life as an engineered system and look for mechanisms in it that seem implausibly remote for chance & necessity to have invented we’re crippled. A paradigm shift is needed in the way life is viewed. ID is that paradigm shift. Mike Gene in the book The Design Matrix: A Consilience of Clues delves into why we need to stop pretending that cellular machinery is the unquestionable result of reactive chance & necessity and start looking at it as the result of proactive design. I’m less than halfway through the book and will write a review of it when I’m finished but so far it almost exactly matches my thoughts on the matter.

  22. DaveScot:

    Natural selection operates on the entire watch. In the rare case where a particle lands somewhere good in order to keep that particle it must also keep the other particles that fell along with it.

    Two points of enhancement:

    1 – I contend that, because almost all mutations in the active DNA are deleterious, if there are any more than one mutation in active DNA, any beneficial mutation will be counterbalanced by multiple deleterious mutations. I belive that the fastest pace of mutations in active DNA that natural selection can filter is 1 per generation.

    The number of deleterious mutations experienced per person is quite high as pointed out by a recent article on LiveScience about the genetic differences between identical twins. I suspect, in honesty, that this article would suggest that the mutation rate is much nearer to Sanford’s than it is to the current scientific expectation.

    2 – Not only does the “beneficial mutation” need to overcome any other mutations in the system, it must stand out even thought the organism that received it received an “average” allele mix. Each allele is better or worse than the otehr alleles, as such they add noise to the system of detecting the beneficial mutation. I do not believe that in a 20,000 gene mix, a “slight improvement” of a single point mutation can in any way be detected. This is the signal to noise problem.

  23. DaveScot: An eloquent and challenging two-part essay. I doubt that I can say anything in response that you haven’t already heard many times, but I feel that it’s incumbent on me to respond since you addressed me personally.

    I wish I were up to speed on some of the topics you covered, but I’m not, so I can only remark on a few points.

    1. As you noted, the apple example of nutrition that I gave does not apply directly to other metabolic transformations, as in iron-eating bacteria or photosynthesis-powered plant growth. You said, “To get highly complex order from simple energy and chemical gradients there needs to be something else involved.” Certainly. The biologist would answer that the “something else” is the metabolic pathways that each organism possesses – ultimately encoded in each organism’s genome.

    2. Regarding the origin of life, that is certainly a daunting problem. But it’s early days in our understanding of life, so it’s a reasonable bet that progress will be made in good time. Much too early to give up and say it’s not a soluble problem.

    3. Statistical mechanics. It’s not clear to me how this relates to natural selection. Does subatomic uncertainty set bounds on our ability to continue productive work on atoms, molecules, macromolecules, and so on up the ladder of complexity?

    4. You said that extinctions need to be explained, and you think that “genetic entropy” is the explanation. Maybe in some cases, but the prevailing view among scientists is that a race of organisms can’t survive to reproduce if it’s unable to cope with environmental changes. Note that those iron-eating bacteria and the photosynthetic machinery mentioned above appear to have survived and prospered for eons, presumably because neither encountered an insurmountable environmental obstacle in its history on the planet.

    5. “A paradigm shift is needed in the way life is viewed.” All fertile paradigm shifts are welcome! Our ability to solve problems depends on how we frame the questions.

  24. Daniel

    Statistical mechanics. It’s not clear to me how this relates to natural selection. Does subatomic uncertainty set bounds on our ability to continue productive work on atoms, molecules, macromolecules, and so on up the ladder of complexity?

    That’s quantum mechanics you’re referring to. Statistical mechanics applies to large populations of particles where the unpredictability of individual particles at the quantum scale disappears. Bulk collections of particles behave predictably.

    You said that extinctions need to be explained, and you think that “genetic entropy” is the explanation. Maybe in some cases, but the prevailing view among scientists is that a race of organisms can’t survive to reproduce if it’s unable to cope with environmental changes.

    That’s still explained by entropy. As the slightly deleterious mutations accumulate it reduces the ability of the organism to adapt to environmental change by the normal method of recombination bringing recessive alleles into dominance. Entropy weakens the gene pool and it’s a diverse gene pool that makes organisms robust in the face of environmental stress. This is why inbreeding is generally bad and cross breeding is generally good (hybrid vigor).

    Note that those iron-eating bacteria and the photosynthetic machinery mentioned above appear to have survived and prospered for eons, presumably because neither encountered an insurmountable environmental obstacle in its history on the planet.

    Excellent point. I addressed it here before as it occured to me as well. The advantages enjoyed by bacteria are 1) very small genomes which far more often than not are perfect copies of the parent and 2) very large populations. Moreover since they don’t have sexual recombination in the equation any deleterious mutations are instantly fixed in all the cell’s descendants and beneficial mutations are instantly fixed as well. This allows selection to act on individual mutations and to act rapidly. P.falciparum (a eukayote with a 23mb genome) didn’t go extinct in billions of trillions of replications over the last 50 years because 49 out of 50 replications are perfect genetic clones of the parent. But it replicates in such large number that there’s always enough trial balloons for selection to choose from in case there’s a need to adapt or die. In organisms with large genomes and small populations like birds and mammals there is little chance of any germ cell being free of random DNA copy errors. In other words perfect DNA replication is the rule for bacteria and small genomed single-cell eukaryotes while perfect copies are the exception for larger genomed organisms.

    In organisms with large genones where asexual reproduction is possible and practiced (such as cloning of a commercially valuable variant of a food crop species) there’s something call “senescence” that becomes a problem after a number of generations. That’s because the clones have big genomes and each generation isn’t quite a perfect copy of the parent. Slightly deleterious mutations accumulate and the variant strain loses its vigor, most often manifesting as slow growth and susceptability to disease. At that point the clonal variant must be abandoned and a new variant with the valuable commercial properties is sought by artificial selection from a sexually reproduced population. Expensive measures such as cryogenic preservation of an early generation of the clonal strain are employed to get around the senescence problem but even cryogenic preservation doesn’t last forever so at best it’s a temporary solution.

    The same senescence mechanism in clonal copies is what eventually kills us too if nothing else gets us first. Somatic cells in our bodies don’t replicate by sexual means so slightly deleterious mutuations pile up as they replicate asexually. It causes us to eventually die of old age. This explains the so-called the “Hayflick Limit”. If nothing else kills a cell line with a big genome a number of generations (that varies by species) defined by an empirically determined “Hayflick Limit” number of generations will cause that line to go extinct. Some large genomed species have either no or very large Hayflick limits. Pines are good example, a redwood being a well known example. Some of these live to be 5000 years old if they are lucky enough to not succumb to disease and other causes of premature death. Shorter Hayflick limits (52 clonal generations in humans) are hypothesized in organisms with faster metabolisms as an evolved means of avoiding cancer. Obviously it’s not a perfect solution.

  25. Somatic cells in our bodies don’t replicate by sexual means so slightly deleterious mutuations pile up as they replicate asexually. It causes us to eventually die of old age. This explains the so-called the “Hayflick Limit”. If nothing else kills a cell line with a big genome a number of generations (that varies by species) defined by an empirically determined “Hayflick Limit” number of generations will cause that line to go extinct.

    Good old Lenny Hayflick! Believe it or not, I’m so old that I can remember the excitement when his 1965 Exp Cell Res paper came out.

    Current thinking is that telomere shortening sets the limit.

  26. Daniel

    Shortening telomere lengths is what is proposed as the evolved mechanism to avoid cancer I mentioned in shorter Hayflick Limits. The Hayflick Limit is nothing more or less than the observation that some cell lines aren’t immortal. Digging a little deeper you’ll find that the mortal cell lines are all large genomes and further that the mortality is explained by genetic entropy. This leads us back to the original question of how some rare large genomes have managed to avoid genetic entropy for geologic spans of time. Something appears to be working to wipe the genome clean of near neutral deleterious mutations which natural selection can’t effectively deal with in large genomes.

    Keep in mind the average survival time of species in the fossil record is about 10 million years. That’s millions of generations. The HeLa cell line (a human cancer cell line) has been alive since 1951. HeLa cells divide roughly once per day. In 60 years that’s 22,000 generations removed from the ancestral cells. It doesn’t even approach the number of generations we’re talking about where the effects of genetic entropy become overwhelming. As far as I know HeLa cells are the longest observed large genomed cells. Since they’re grown on culture plates as single cells and they have a modified human genome I think we can reasonably presume that most of their genome, which normally produces whole humans, is unused. In that regard they’re probably more like a small genomed organism that just happens to have a lot of truly junk DNA. It won’t matter to the cell if the junk DNA decays by genetic entropy so they can now enjoy the same benefits of large population size and small genomes to defeat, or at least drastically slow down, genetic entropy.

    Consider the cells in your body. Ostensibly every one of them is the most recent incarnation of an unbroken cell line going back at least to some Cambrian chordate individual 500 million years ago – a hundred million generations. Most of the lines starting from that ancestor are extinct. Was it just luck that yours survived and you’re here today to wonder about it? Maybe. The thing of it is that “luck” isn’t a very satisfying explanation. You’ve heard of “God of the Gaps” I’m sure. Is “God of the Gaps” any more or less scientific than “Luck of the Gaps”? I don’t believe there’s any difference at all. Luck, or chance or randomness or whatever you care to call it, is just a replacement for “God” to bridge gaps in knowledge and is just as much a “science stopper”. Whether you choose to credit things as “God dunnit” or “Chance dunnit” both are equally vacuous in their ability to make predictions. To coin a phrase, chance evolution is creationism in a cheap tuxedo.

  27. bFast
    “1 – I contend that, because almost all mutations in the active DNA are deleterious, if there are any more than one mutation in active DNA, any beneficial mutation will be counterbalanced by multiple deleterious mutations. I belive that the fastest pace of mutations in active DNA that natural selection can filter is 1 per generation.”

    Affirming your points, Sanford in Genetic Entropy, explains why harmful mutations accumulate faster than “natural selection” can filter them, and that they swamp “beneficial” mutations.

    (Technically, if several harmful mutations occurred on the same DNA strand, “selection” would delete both if it could delete either.)

  28. DLH, that said, Sanford takes a huge bite when he dejunkifies all DNA without scientific proof. As such, his argument is ignored. If Sanford used the modern understanding of what constitutes active DNA, even if that understanding is in error, he would make a far more convincing case. The case is still there to be easily made, it does not need the level of science-rejection that Sanford chooses.

  29. bFast
    Before dismissing Prof. John C. Sanford, consider that his life work has dealt with mutations and genetic changes. (He invented the “gene gun”.) He knows more about mutations and genetic changes than most biochemists discussing the issues.

    May I strongly recommend that you review his scientific publications on the issue, NOT tar him with his popular book. See especially his recent publications. (But don’t publicize them until Sanford does.)

    I also strongly urge you to read up on recent developments in Junk DNA.

    I expect Sanford et al. to be discovering treasure that others have dismissed as “junk” – and to have a few patents filed before his discoveries are publicized. I expect you will find it instructive to review Sanford’s position.

  30. Is Prof. Sanford still at Cornell or has he been “expelled” by the Darwinian storm troopers? I would guess that it’s not that easy to ostracize someone with such an impeccable and brilliant history of achievements.

  31. Sanford is still officially a
    “Courtesy Associate Professor”.

    Wikipedia’s “editors” try to dismiss Sanford and he comments on the ostracization in his book.

  32. DLH, thanks for the links. Wow. The Wikipedia article says that Sanford believes that the age of the earth was between 100,000 and 10,000 years. Is it true that Sanford is a young earth creationist or is that a propaganda smear, courtesy of the “unbiased” Wikipedia editors?

  33. DaveScott
    Back to “Why Isn’t All Life Extinct?”

    Following along the lines you have been describing, I have been thinking on how to formally develop this. e.g., with the following methodology:

    Design Detectability:
    Design by Intelligent agents may be detectable by other intelligent agents.

    Discoverable design principles:
    The design principles used by some intelligent agents may be recognizable and discoverable through reverse engineering by other intelligent agents.

    Extrapolating Design Principles:
    Design principles used by some intelligent agents may be similar to those used by other intelligent agents.

    Thus:
    Identify Human Design Principles
    Identify all the design principles used by human engineers to preserve designs.

    Extrapolate to biotic design principles
    If biotic systems are designed, then some or all of these human design preservation methods may have been used by an intelligent designer to design biotic systems.

    Then formulate these design principles to systematically
    Describe biotic systems, and to:
    Predict biotic features and processes.

    By reverse engineering, this leads to a high level ID design principle of:
    Preserve the Design.

    Thus I propose that it would be fruitful to:

    1) Assemble and classify those design principles relating to preserving the design.

    2) Compare these preservation principles to biotic systems.

    3) Use those preservation principles to predict further features of biotic systems.

    E.g.
    Robust design.

    Information coding.
    Coding efficiency.
    Coding redundancy.
    Coding recovery.
    (Solomon Codes etc.)

    Error detection.
    Error correction.
    Redundant systems.
    Multiple copies.
    Parallel operations.

    Storing default configurations.
    Restoring default configurations
    Testing for process completion.
    Restarting on process failure.
    etc.

    We should probably develop these and then start another thread addressing them.
    (This is a small part of what I want to write this up as part of a larger ID theory. However, you appear to have more expertise along these lines, and possible more time to do so.)

  34. Mapou
    That is irrelevant here – go read his book – and help improve Wikipedia and ResearchID.

    Focus on the topic at hand of why life still exists and what design principles and theory we can develop from it.

  35. For the record, at the Kansas science hearings in 2005, Sanford said that he believed the earth was between 5 and 100,000 years old.

    As to his position at Cornell, he said this:

    when the GeneGun technology was developed, I was able– I was very blessed and able to take a lot of revenue from that. It was a very financially-rewarding invention which eventually let me leave Cornell. So right now I’m a courtesy professor at Cornell with an office there, but I’m not on a paid– a paid faculty. And I’m presently in the process of writing books.

  36. The transcripts of the science hearings were definitely not falsified – the transcripts were created by a court reporter hired by the state Board of Education, which sponsored the hearings.

    And, for what it’s worth, I was there and heard the entire conversation.

  37. bililiad: Of course DLH is right. Whether someone believes the Earth is 6,000 or 60 billion years old is irrelevant to the question of how seriously they should be taken.

    I’m sorry but I have to disagree that it is irrelevant. I am an unapologetic Christian and I respect YECs but I consider the young earth hypothesis to be no more valid than the flat earth hypothesis. It’s a ridiculous belief, in my opinion.

    I don’t take a lot of physicists seriously precisely because they believe in the possibility of time travel which I consider to be pure crackpottery. Likewise, my respect for a creationist scientist immediately takes a dive when I find out that he or she believes in a young earth. I am 100% pro-ID and pro-science as long as we go about it with an open mind and are willing to go where the evidence leads us, not where we think the evidence should lead us. And the evidence clearly says that the earth and the universe are billions of years old.

    My Bible does not instruct me to park my brain in a closet when I read it, sorry. It plainly says, “seek and you will find”. So I guess my point is this. YECs are not doing either Christianity or ID a service in my opinion. They make Christians look stupid in the eyes of the enemy and the world at large.

    Sorry to be so brunt but I always tell it like I see it.

  38. Mapou
    What we want to focus on here is a theory of Intelligent Design that
    1) can detect evidence of such intelligent design

    2) is a better description of biotic systems, and

    3) is a better predictor of biotic systems.

    (- whatever a person’s beliefs or interpretations of the data on how old the earth is, or how old life has been around.)

    Please do NOT denigrate others for their beliefs. We want to uphold the unalienable freedom of speech and conscience. (Otherwise there are plenty of opportunities behind the great firewall where you may find comrades.)

    If you hold to life being 1 billion years old, all the more important to focus on the topic of this thread.

    Why isn’t ALL life extinct?
    Why are you able to talk about it?

    Please contribute constructively and don’t waste our time.
    Address the topic, the data and the hypotheses in DLH 33, and DaveScott’s comments above.

    PS Do to others what you would want them to do to you!

    Please review ID Assumptions – “Beliefs

    Scientists and engineers working with intelligent causes have various worldviews and religious beliefs. The only assumption on their beliefs are the assumptions 1 through 8 above in examining intelligent causes.

    I want to see an objective ID theory that could be supported across the full range of YEC. OEC, agnostics – and even atheists.

    You are free to express your beliefs in your own public web page etc. Lets here focus on the task at hand.

  39. DLH: Please contribute constructively and don’t waste our time.

    All right. I will not waste your time anymore. Neither will I let you waste mine. I will come back and offer my support for ID when the ID movement can gather enough gonads to denounce the crackpottery of the YECs and distance itself from them. Good luck to you all.

  40. I can see, perhaps, how an objective ID theory might eventually span theists, agnostics, atheists and people of other philosophical persuasions, but I can’t see how any objective ID theory could encompass both a 4.5 billion year old earth and a 6,000 year old earth. There are too many details about when and in what order things happened for these two to be reconciled.

  41. My Bible does not instruct me to park my brain in a closet when I read it, sorry. It plainly says, “seek and you will find”.

    Why should I trust a Bible that says “Seek and you will find” if it also says that G-d formed Adam from the dust of the earth, that Adam gave birth to Seth, who gave birth to…etc, that birds were created before reptiles, etc? Are only some portions trustworthy?

    It goes both ways. YECs would criticize you for not taking the Bible seriously and making it look like “foolishness”.

    So I guess my point is this. YECs are not doing either Christianity or ID a service in my opinion. They make Christians look stupid in the eyes of the enemy and the world at large.

    The mind of the flesh cannot understand spiritual things; they are foolishness to it. So guess again if you think “Christianity” will ever appear “smart” to anyone other than Christians.

  42. Mapau:

    I respect YECs but I consider the young earth hypothesis to be no more valid than the flat earth hypothesis. It’s a ridiculous belief, in my opinion.

    From #32:

    The Wikipedia article says that Sanford believes that the age of the earth was between 100,000 and 10,000 years

    Sanford seems to be saying that his science, biology, would be extremely challenged by an age greater than 100,000 years. This is somehow fundimentally different than the theologian that delclares that the Bible says that the earth is 6000 years old — God said it, I believe it, That settles it. Sanford is not the only biologist who is suggesting that his scientific understanding challenges a 4 billion year old biology. Peter Borger has said the same thing on ISCID’s brainstorms. I think PB’s view is that anything beyond 1 million years is highly unlikely.

    If scientists are seeing this quandary, I don’t think their view should be rejected out of hand. I fully agree that anyone who places Biblical authority above scientific discovery is making a huge mistake. However, these guys are coming to this conclusion from studying their discipline. I respect their consern and believe that their issues, entropy, need to be reconed with.

  43. Not to mention, there was a time when all the best science, scientists, thinkers, facts and evidence showed conclusively that the universe had no beginning.

    Let’s not put on our dogmatic hats just yet. Follwo the evidence where it leads but always be open to new evidence that may lead you away from where you currently stand.

    YEC includes very bright minds and very knowledable scientists who’d probably love to debate you on the age of the earth/universe. So let’s just say there is more than one opinion on those matters within the ID camp, as it includes both ID evolutionists and ID creationists.

    If Gonzalez is free to develop an Old Earth ID PP hypothesis, Sanford should also be allowed to develop a Young Earth Genetic Entropy hypothesis.

  44. Mapou

    Encourage you to explore the data on biotic systems themselves, (whatever the age of the earth or the universe, or a person’s beliefs thereto.)

    Have a good sabbatical.

  45. Jack Krebs at 41
    I think that an ID theory for biotic systems could easily span this range.

    Similarly, if we look at the anthropological principle and focused on the parameters describing the fine tuning of the universe, I could also see that spanning that range.

    Its the interpretation of geological features and the “age” of the earth and universe that appears to be particularly where the divergences appear to lie.

  46. Jack Krebs:

    I can see, perhaps, how an objective ID theory might eventually span theists, agnostics, atheists and people of other philosophical persuasions, but I can’t see how any objective ID theory could encompass both a 4.5 billion year old earth and a 6,000 year old earth.

    I personally don’t see ID as a theory, I see it as a metatheory, a framework. Within this ID framework are a bunch of theories: IC, SC, etc. (Each of these theories is a falsifiable entity.) As such, the ID framework can quite easily encompass both a 4.5 billion and 6,000 year old earth. The specific theories within the framework may or may not suggest an age. Sanford’s theory of the entropic effects on DNA fit far more comfortably within a young earth than within an old. Neither IC nor SC make any comment about the age of the earth.

  47. But eventually the ideas of IC, SC, etc, need to gain specificity that they don’t have now, and when they do they will need to address issues of not only how but when and where – and those questions will have to address the age of the earth and the time sequences for both the geological history of the earth and the biological history of life on earth.

  48. bFast
    I expect Sanford will quantify genetic entropy based on the evidence available.

    That should stand on its own based on measured statistics of mutations etc.

    Some could then take the results and interpret them as to relating to the age of biotic systems.

    The idea of metatheory vs specific theories is worth exploring. In some ways that parallels “evolution” as a parallel meta theory.

    Jack Krebs
    I do not see how the specificity of IC needs to depend or tie into the age of the earth. It appears valid which ever age.

  49. Atom: “YEC includes very bright minds and very knowledable scientists who’d probably love to debate you on the age of the earth/universe. So let’s just say there is more than one opinion on those matters within the ID camp, as it includes both ID evolutionists and ID creationists.”

    This does seem to be the case, and it continues to be a source of puzzlement to me. Some very smart people (in particular scientists) can ignore mountains of evidence for the ancient age of the earth in favor of Scripture. The explanation has to be in the psychology of religious belief (realizing that “religious” belief also applies to Darwinism). By far the most reasonable interpretation of the geologic, radioisotope dating and fossil evidence is for an earth age of billions of years. Scripture as literally interpreted describes creation as occurring in near historic times. If there is fervent belief (or emotional need to believe) in a literal interpretation of the Bible, a major cognitive dissonance is created. This is stressful and painful, generating a strong desire to resolve the inner intellectual conflict. The result is to preserve the emotionally most important belief (fundamentalist Christian) and very cleverly find some other interpretation however strained for the scientific evidence.

    Unfortunately, it would seem that YEC scientists are committed ideologues as much as fanatic atheistic Darwinists, and will determinedly interpret or ignore evidence in such a way as to fit their preconceptions. We all have these tendencies, but hopefully try to maintain at least some form of objectivity and open mindedness to contrary evidence.

    It is clear that YEC to some extent discredits ID in the media and in the scientific arena. I wonder whether this matters, however, since any flavor of ID regardless of who espouses it would invite the same scorn and ridicule even without YEC advocacy. There actually may be some benefit because some of the YEC thought has generated strong legitimate scientific arguments for ID (such as Ray Sanford, assuming he is actually a YEC advocate).

  50. Magnan,

    Why does it have to be a strong emotional need to believe? Can’t a YEC just decide, in a perfectly rational way, that mainstream science is probably wrong and that he/she’d rather give the benefit of the doubt to someone/something they have never had fail them?

    I keep the story from Spetner’s “Not By Chance” in my head every time I hear someone disparage YECs as nuts:

    There was a time (as I mentioned before) when all science showed conclusively that the universe had no beginning. But this flatly contradicted Torah and so a group of rabbis met to resolve the matter. They eventually decided that the science must be wrong, since it was clear that there was a beginning of the Universe, according to Torah. The science came to the wrong conclusion, so was to be rejected.

    Spetner points out two things. First, they could have caved to pressure and re-interpreted Torah. But if they had done so, they would have had to admit they were wrong twice, as their original position was eventually vindicated.

    Now I don’t see how this faith in an ancient religious text (that has withstood over 2000 years of scrutiny and had many, many archeological details confirmed, again and again) or G-d is any less rational than faith in a group of human data collectors and their deductive/inductive reasoning. If I find that a text and a god are very reliable in daily life and that human data gatherers are much less reliable, isn’t it more reasonable to give the text/god combination the benefit of the doubt when there is a conflict?

    I think it would be irrational to do otherwise. Hence why I respect the YEC position, even if I see it as a religious and not scientific-evidence based hypothesis.

  51. Addendum:

    You wrote:

    Unfortunately, it would seem that YEC scientists are committed ideologues as much as fanatic atheistic Darwinists, and will determinedly interpret or ignore evidence in such a way as to fit their preconceptions. We all have these tendencies, but hopefully try to maintain at least some form of objectivity and open mindedness to contrary evidence.

    I think it is important to highlight this. If one is to hold a position contrary to scientific evidence then they should not hide or distort that evidence in any way. They should openly admit that there is evidence against their belief (as Woodmorappe does when he discusses Chimp/Human similarities) and maybe even attempt to solve those issues. But even if they cannot solve them, they can simply admit that the scientific, human data gathered argues against their theory, but their personally more reliable source of information confirms it. And they are free, and rational, to go with the evidence provided by the most trustworthy source, as demonstrated to them personally.

  52. I do not get this dialog at all! These scientists, Stanford and PB in particular, are simply stating that THE EVIDENCE FROM THEIR SCIENTIFIC DISCIPLINE does not fit with an old biology. They then go on to suggest an outside edge for the age of biology at 100,000 and 1,000,000 years. These number are not numbers that they are getting from some religious text! Why do we need to whipe them out as religious cooks, despite their solid scientific credentials?

    I have worked throught the case of young v. old earth. I come down with the majority on this one — the case for an old earth is strong. Yet these scientists suggest that genetic entropy is great enough that biology would have fried in 4 billion years. What’s the schtick here. Show them that they are wrong — with Stanford that’s easy, he has a book that clearly deliniates his position. Show that biology can withstand 4 billion years of entropy, or honestly declare that these scientists are bringing up a serious canundrum. Is biology 4 billion years old because the intelligent designer(s) have refreshed it over the eons? Maybe there is evidence of this. If so, then the earth really has old biology, and has a repeated force in opposition to entropy (intelligent agency) acting to maintain the quality of the DNA. There is no reason to slay our top scientists (Sanford certainly qualifies) because their data does not fit the current paradyme.

  53. “Neither IC nor SC make any comment about the age of the earth.”

    Both IC, SC as well as Behe’s Edge of Evolution only make sense in terms of an old universe and an earth of billions of years.

    Both Dembski and Behe’s ideas depend upon massive number of opportunities happening and failing. Dembski’s UPB is based on an old universe. Behe’s edge of evolution is based on zillions of reproductive events with no joy. Granted he was using recent single celled reproduction rates but the weight of the argument would have been vacuous unless it could be extended to multi-celled organisms and their evolutionary path of millions of years or greater.

    ID as it is practiced now it predicated on an old universe and old earth. To deny either then you make Dembski’s and Behe’s research meaningless.

    As far as extinction is concerned, are we really seeing any species go extinct because they are the result of deleterious mutations or the accumulation of them. I doubt it. We have a world full of species and if any of them are going extinct it is mainly due to human intervention reducing the gene pool of the populations and not from the species getting sick and passing on. In fact that is ludicrous. I am sure there are many examples that do not involve human intervention but I doubt if any is due to deterioration of the genomes. I also doubt the large numbers of species going extinct as quoted in a lot of popular sources. This is good political fodder that plays well with the squeamish and guilt ridden.

    I haven’t read Sanford’s book but if the ideas put forth in it say that species are accumulating bad mutations at alarming rates then we would be witnessing a never ending report from the scientific community of the effects on species. Since we do not see these expected effect, you would have to conclude that Sanford’s ideas are suspect.

    Wouldn’t the species that reproduced faster be more suspect to dying off than those who reproduced slower. It seems to me that the insects are doing just fine in my neighborhood.

    And as far as humans are concerned and those of you who believe in a young earth, are we now such a decrepit species physically and mentally from all these mutations or are we doing just fine compared to our ancient ancestors. I am not sure we have any Plato’s and Aristotle’s today but we have some really bright people in our midst.

    I think the answers to all these questions are obvious and I wonder what absurd science suggested these concepts. I will make a couple of conjectures about extinction. It is best explained by natural selection as it continually culls the gene pool of a population to less variety and eventually a species meets an environment it can’t handle. So it is the narrowing of the gene pool that is the culprit and not any accumulation of harmful mutations.

    Dave may be right that there is some built in mechanism yet to be found that will explain a defense against mutations accumulating and we will probably see when we examine genomes from millions of humans that there are not accumulating these supposed harmful mutations.

  54. bFast,

    I only bring up the general YEC case because that is what others are doing. I agree, if Sanford has a scientific YEC case from his data, more power to him.

    jerry,

    Dembski’s UPB does give enough opportunities as could have occurred in an old earth…but it does not require one. If the earth were young, then the UPB would still be a UPB; the true bound, however, would be orders of magnitude lower. If Darwinists can’t do it with 10^150 tries then they sure can’t do it with 10^50 tries.

    Either way, 10^150 would still be an upper bound, just one that is far too generous.

  55. ID as it is practiced now it predicated on an old universe and old earth.

    I’m sure many ID adherents would disagree with that statement, for the reasons I mentioned above.

    If blind-processes can’t produce the results in 15 billion years they sure can’t in 10,000 years. ID concepts such as IC and CSI are just fine in either Old Earth or Young Earth settings.

  56. Atom,

    I am sure that anyone who thinks the world was created 6,000 years ago would have to believe everything was created de novo so concepts that discuss progress or lack of progress over time are meaningless in such a short time scenario. To even present ideas that rely on process or deep time in this scenario has no meaning. Why would anyone bother paying attention to it.

    Thus, the only framework that makes sense discussing these ideas is one in which deep time is considered the likely scenario. ID is used to refute things that might have happened in deep time but really couldn’t. Thus, ID needs deep time to have any relevance. If you said well IC couldn’t have happened in 6 days except by an intelligent intervention no one would pay any attention to you. You are stating the obvious. Because no one believes that natural process work in that short of time. They only work in deep time. But to prove it couldn’t happen in 4 billion years, that is a conclusion that makes one sit up and take notice.

    Neither if you said well if it could not have happened in 4 billion years so that makes the 6,000 year old earth more likely. No one would pay any attention to you either. It would be a non sequitur unless there were a multitude of processes that ID ruled out that happened in deep time and not just this one. There are thousands of other processes that are best explained by 4 billion years with which ID has no quarrel and says could be best explained by natural means. In fact ID would point to a non intelligent source for these processes due to laws and chance. No the only purpose of ID is ruling out things that could not have happened in deep time by natural mechanisms and has no relevance to short time scenarios.

    If you want to bring up things like forensics or arrow heads, go right ahead but the only thing of real interest to ID is how life progressed over billions of years.

  57. To YEC critics:

    WE SHOULD NOT ABANDON OUR BIG TENT PHILSOPHY.

    Just as ID deserves a place at the table of mainstream science, legitimate diverse opinions within the ID camp deserve to be heard. When the subject of intelligent design is examined from several distinct vantage points, intellectual laziness gives way to subtlety and sophistication. My own experience has been enriched because, through the years, others have tugged away at my own biases and prejudices.

    From the YEC’s I learned about “uniformitariasm,” an assumption about modern science that has never really been verified. From the agnostics, I have learned about the utopian dream of elevating artificial intelligence to the status of mind. Thanks to the anti-Darwinists, I can more fully appreciate the pretensions and excesses of the scientific establishment. Thanks to the Darwinist sympathizers, I now have a better understanding about RV+NS, its capacities and its limitations.

    While diversity of opinion provides intellectual stimulation, a corresponding unity and solidarity provides a vital sense of mission. We know that ID is an empirically-based science, and the world will soon know it—in spite of our adversary’s proclivity to publicize lies to the contrary. To me, it is foolish to throw YEC’s to the wolves on the grounds that keeping company with them will cause others to misunderstand us. Some of us have become downright paranoid about this. We can’t afford to allow an activist Pennsylvania Judge or some whacked out professor in Louisiana to inhibit us from developing naturally as legitimate cultural phenomenon, even if part of that development includes intermittent discussions about religion. We have our own built in mechanism to limit inappropriate references and verbal eruptions of piety. Anyway, I agree with Atom, who has pointed out that our adversaries do not need an excuse to militate against us. Any pretext will do.

    I like surprises, and this blog offers a lot of them. Some of the administrators are awesome with respect to their knowledge of science. Others are better at framing ID’s social implications and introducing themes about the relationship between philosophy and science. A few are quite good at reporting on the ramblings from the other side. Somehow, we have found a way to navigate through a dozen or more threads simultaneously without losing much continuity. As a wise man once said, “if it ain’t broke don’t fix it.

  58. Atom (#51): “Why does it have to be a strong emotional need to believe? Can’t a YEC just decide, in a perfectly rational way, that mainstream science is probably wrong and that he/she’d rather give the benefit of the doubt to someone/something they have never had fail them?”

    I would hold to my comments in #50. It is not rational to ignore the overwhelming preponderance of evidence in this case. The main categories of evidence (just the tip of the iceberg) are:

    - Thousands of feet of sedimentary rock looking mostly to have been deposited slowly by presently observed geologic processes, and by those processes requiring hundreds of millions of years, cumulatively billions of years.
    - Radioactive isotope dating (using known decay rates) of lava layers, volcanic ash, etc., dating the immediately superposing and underlying sedimentary layers.
    - Such dating correlating with sedimentary deposition rates in many cases
    - Fossils found in corresponding sedimentary layers, indirectly dated via the radiometric means mentioned.
    - Plotting the forms and types of organisms indicated by the fossils versus their dating mostly obtained as above clearly showing a very general picture of progressive elaboration and diversification with time over hundreds of millions and even billions of years.

    It seems to me the only way this data can be logically reconciled with the YEC belief structure is to propose that the world as physically discovered in the summary above was recently created with all these built in correlating indicators of great age. It must have been to test men’s faith in Scripture. It is true that there is no way to logically disprove such a conjecture, but is it reasonable from an objective (non faith-based) point of view?

    StephenB suggested that it is important to maintain the “big tent” philosophy for ID. As I mentioned, I think it is a mixed call, significant negatives and a few positives.

  59. magnan,

    One could also say that human data gatherers (overwhelmingly atheist/agnostic scientists) probably have the whole picture wrong and misunderstand the processes that lead them to such ages. Materialistic agenda-driven science consistently gets the picture wrong in regards biological evolution, so would it really be a total shock if their uniformatarian/Darwinistic beliefs color their presentation and interpretation of the “facts” in other areas of science?

    I’m not arguing for YEC, I’m just saying it isn’t like the consensus hasn’t been completely wrong before. (See global cooling, phlogiston, eternal universe, and NDE to name a few)

    As for my main point, think of the individual. If they trust in a god (small g, it could be whatever they put their trust in) and that “god” has empirically shown itself unfailingly trustworthy, why should they put their trust instead in oft-mistaken and unreliable hypotheses of human data gatherers?

    I’d say it would be irrational to discount personal empirical experience in favor of popular consensus. In the YEC’s case, they may be doing the most rational thing.

  60. I guess it just isn’t rational to continue this discussion.

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