Functional information and the emergence of biocomplexity

Journal club time again 🙂

I like this paper: Functional information and the emergence of biocomplexity by Hazen et al, 2007 in PNAS, and which I hadn’t been aware of.

I’ve only had time to skim it so far, but as it seems to be an interesting treatment of the concepts variously referred to by ID proponents as CSI, dFCSI, etc, I thought it might be useful.  It is also written with reference to AVIDA.  Here is the abstract:

Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define “functional information,” I(Ex ), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA–GTP binding energy), I(Ex ) = −log2[F(E x)], where F(Ex ) is the fraction of all possible configurations of the system that possess a degree of function ≥ Ex . Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of function.

I thought it would be interesting to look at following the thread on Abel’s paper.  I’d certainly be interested in hearing what our ID contributors make of it 🙂

 

155 thoughts on “Functional information and the emergence of biocomplexity

  1. Allan- don’t blame me for your ignorance.

    I’m afraid I have to lay at least some of the blame for my ignorance of your position at your door, since I simply asked for clarification from you and that was your answer.

    Also I see you need proof of ID and that proves that you ain’t interested in science.

    So … you want evidence for non-ID evolution as the cause of biological complexity – you being such a scientist and all. Yet anyone suggests that, for symmetry, you support your made-up explanation of the same and they are “not interested in science”? You are a peculiar individual, to put it mildly.

    GA was sufficient- as I said it all depends on those starting conditions.

    So it’s common descent all the way from OoL, then? Good. We agree on something.

  2. damitall: Joe,think that’s an incorrect use of the word “know”

    When are you coming over to the UK, Joe?. I could pick you up at Heathrow, we could be in Cambridge in just over the hour, and I’ll try and line up some top-flight geneticists and cell physiologists to talk to, and labs to visit – Cambridge is stuffed with ’em both within and outside theUniversity.

    I’ll even try to line up some IDists, though they’re a bit thin on the ground in these parts

    Excuse me- but you don’t appear to know anything.

    As I said to refute ID just start presenting positive evidence that matter, energy, necessity and chance are all that is required- IOW actually grow a set, step up and support the claims of your position.

  3. Allan Miller: I’m afraid I have to lay at least some of the blame for my ignorance of your position at your door, since I simply asked for clarification from you and that was your answer.

    So … you want evidence for non-ID evolution as the cause of biological complexity – you being such a scientist and all. Yet anyone suggests that, for symmetry, you support your made-up explanation of the same and they are “not interested in science”? You are a peculiar individual, to put it mildly.

    So it’s common descent all the way from OoL, then? Good. We agree on something.

    Allan- we have direct observational evidence and plenty of experience with designers designing irredicible complex systems.

    If someone went onto a lab and designed a ribosome that would not be evidence for ID. However if someone went into a lab and demonstrated that blind and undirected chemical and physical processes can produce the ribosome, you would have driven a stake into ID- ID would be as good as dead as a ribosome is A) IC and B) contains CSI.

    And even baraminology is common descent all the way from the OoL…

  4. damitall: Joe,think that’s an incorrect use of the word “know”

    When are you coming over to the UK, Joe?. I could pick you up at Heathrow, we could be in Cambridge in just over the hour, and I’ll try and line up some top-flight geneticists and cell physiologists to talk to, and labs to visit – Cambridge is stuffed with ’em both within and outside theUniversity.

    I’ll even try to line up some IDists, though they’re a bit thin on the ground in these parts

    Hey- why aren’t those top-flight scientists publishing positive evidence for blind and undirected processes?

    Why can’t your geneticists refute our geneticists?

  5. Joe G: As I said to refute ID just start presenting positive evidence that matter, energy, necessity and chance are all that is required- IOW actually grow a set, step up and support the claims of your position.

    As I pointed out in the now closed GA thread, your concept of science is backwards. If ID is to be considered a scientific discipline, it must make testable hypotheses about objective, empirical evidence.

    In this case, it means that instead of demanding that scientists disprove your speculations, you need to provide some objective, empirical evidence that anything other than known chemical and physical processes are taking place, come up with a testable hypothesis to explain your observations, and actually test your hypothesis.

    Unless and until some ID proponent does this, there is nothing to refute.

  6. Patrick: As I pointed out in the now closed GA thread, your concept of science is backwards.If ID is to be considered a scientific discipline, it must make testable hypotheses about objective, empirical evidence.

    In this case, it means that instead of demanding that scientists disprove your speculations, you need to provide some objective, empirical evidence that anything other than known chemical and physical processes are taking place, come up with a testable hypothesis to explain your observations, and actually test your hypothesis.

    Unless and until some ID proponent does this, there is nothing to refute.

    Patrick- as I told you in that thread you are wrong and ID, unlike your position, has testable hypotheses about objective, empirical evidence.

    Also you obviously didn’t understand my post because I explained evrything to you- the way to the design inference is through your position.

    IOW if your positiin had the science we wouldn’t be having this discussion.

    So far from being backwards, how I said it is the way science demands.

  7. I’ve got to the end of the paper.

    So, using their measure of Functional Complexity, they demonstrate that AVIDA, a program that uses Darwinian evolution to evolve virtual organisms, results in increases in Functional Complexity.

    So, where does this leave ID? Is this not prima facie evidence that Darwinian processes can do exactly what ID proponents say it can’t?

  8. Joe G:
    No, for the mere fact that AVIDA doesn’t have anything to do with Darwinian processes

    Well, it does, Joe. How can you possibly say that it doesn’t? Self-replicators with heritable variation in reproductive success within their environment?

  9. Joe G: Patrick- as I told you in that thread you are wrong and ID, unlike your position, has testable hypotheses about objective, empirical evidence.

    Excellent! Please describe that evidence and your hypotheses here.

  10. Elizabeth: Well, it does, Joe.How can you possibly say that it doesn’t?Self-replicators with heritable variation in reproductive success within their environment?

    Elizabeth- it has unrealistic parameters- when provided realistic parameters it does nothing.- That is in the Sanford paper

  11. Patrick: Excellent!Please describe that evidence and your hypotheses here.

    Patrick, I need to see your position’s evidence and hypotrheses first so I know what you will accept and you cannot back-peddle and flail away- everything I said is on my blog and I just have to go get it.

    OTOH your position has nothing- still.

  12. 1- Avida “organisms” are far too simple to be considered anything like a biological organism

    2- Avida organisms “evolve” via unreasonable parameters:

    The effects of low-impact mutations in digital organisms

    Chase W. Nelson and John C. Sanford

    Theoretical Biology and Medical Modelling, 2011, 8:9 | doi:10.1186/1742-4682-8-9

    Abstract:

    Background: Avida is a computer program that performs evolution experiments with digital organisms. Previous work has used the program to study the evolutionary origin of complex features, namely logic operations, but has consistently used extremely large mutational fitness effects. The present study uses Avida to better understand the role of low-impact mutations in evolution.

    Results:

    When mutational fitness effects were approximately 0.075 or less, no new logic operations evolved, and those that had previously evolved were lost. When fitness effects were approximately 0.2, only half of the operations evolved, reflecting a threshold for selection breakdown. In contrast, when Avida’s default fitness effects were used, all operations routinely evolved to high frequencies and fitness increased by an average of 20 million in only 10,000 generations.

    Conclusions:

    Avidian organisms evolve new logic operations only when mutations producing them are assigned high-impact fitness effects. Furthermore, purifying selection cannot protect operations with low-impact benefits from mutational deterioration. These results suggest that selection breaks down for low-impact mutations below a certain fitness effect, the selection threshold. Experiments using biologically relevant parameter settings show the tendency for increasing genetic load to lead to loss of biological functionality. An understanding of such genetic deterioration is relevant to human disease, and may be applicable to the control of pathogens by use of lethal mutagenesis.

  13. Joe G: Elizabeth- it has unrealistic parameters- when provided realistic parameters it does nothing.- That is in the Sanford paper

    What you said was that “AVIDA doesn’t have anything to do with Darwinian processes”. This is not true. It has everything to do with Darwinian processes. It is clearly not a realistic model of biology, but that is not to say that it has nothing to do with Darwinian processes. Darwinian processes are exactly what it consists of, and it therefore offers a proof-in-principle that Darwinian processes can result in an increase in Functional Complexity according to a definition that is extremely similar to that offered by Dembski.

    Now, you might want to argue that nonetheless, Darwinian processes couldn’t account for life as we observe it, but that would be a different argument. What this paper does is offer a direct rebuttal of Dembski’s inferential reasoning.

  14. Elizabeth- the parameters are too unrealistic to be called Darwinian.

    You can ignore that if you want but it doesn’t change the fact.

  15. Joe G: Patrick, I need to see your position’s evidence and hypotrheses first so I know what you will accept and you cannot back-peddle and flail away- everything I said is on my blog and I just have to go get it.

    OTOH your position has nothing- still.

    Let’s stipulate, ad arguendo, that your final statement is correct. We’ll ignore, for the sake of this subthread of discussion, 150+ years of scientific progress and literally hundreds of thousands of peer reviewed papers.

    That’s actually okay, because scientific theories must stand on their own merits. Disproving one theory does not automatically make a competing theory better supported. We can completely ignore modern evolutionary theory when discussing ID, because any flaws or limitations it may have are immaterial.

    So, what objective, empirical evidence did you have in mind when you made your claim that such existed? What testable hypotheses were you thinking of when you wrote “ID . . . has testable hypotheses about objective, empirical evidence”?

    Those terms are well understood by anyone familiar with scientific literature. Let’s see what you’ve got!

  16. Patrick: Let’s stipulate, ad arguendo, that your final statement is correct.We’ll ignore, for the sake of this subthread of discussion, 150+ years of scientific progress and literally hundreds of thousands of peer reviewed papers.

    That’s actually okay, because scientific theories must stand on their own merits.Disproving one theory does not automatically make a competing theory better supported.We can completely ignore modern evolutionary theory when discussing ID, because any flaws or limitations it may have are immaterial.

    So, what objective, empirical evidence did you have in mind when you made your claim that such existed?What testable hypotheses were you thinking of when you wrote “ID . . . has testable hypotheses about objective, empirical evidence”?

    Those terms are well understood by anyone familiar with scientific literature.Let’s see what you’ve got!

    Again with the equivocation that evidence for “evolution” = evidence for blind watchmaker evolution.

    You may me sick- congrats…

  17. Joe G: Again with the equivocation that evidence for “evolution” = evidence for blind watchmaker evolution.

    You may me sick- congrats…

    I’m engaging with you in good faith, per the rules of this blog. I have asked you, politely, to support claims that you have made. Please do so or retract those claims.

  18. Patrick: I’m engaging with you in good faith, per the rules of this blog.I have asked you, politely, to support claims that you have made.Please do so or retract those claims.

    All YOU have to do to make me retract my claims is to actually support the claims of your position without the sickening equivocation.

  19. Joe G: All YOU have to do to make me retract my claims is to actually support the claims of your position without the sickening equivocation.

    I made it clear in my comment that we are assuming that your claims about modern evolutionary theory are correct, for the purposes of this subthread of discussion. We can completely ignore all of that science.

    Now, let’s stretch our arms out and take a moment to enjoy the freedom of this rhetorical green field we’ve created.

    Relaxed? Ready to go? Great, now please support your claims that “ID . . . has testable hypotheses about objective, empirical evidence.”

  20. Patrick: I made it clear in my comment that we are assuming that your claims about modern evolutionary theory are correct, for the purposes of this subthread of discussion.We can completely ignore all of that science.

    Now, let’s stretch our arms out and take a moment to enjoy the freedom of this rhetorical green field we’ve created.

    Relaxed?Ready to go?Great, now please support your claims that “ID . . . has testable hypotheses about objective, empirical evidence.”

    In that case I will just assume ID’s claims are correct….

  21. Joe G: In that case I will just assume ID’s claims are correct….

    “That which can be asserted without evidence, can be dismissed without evidence.”
    ― Christopher Hitchens

    You’ve made the claims that there is objective, empirical evidence that is explained by testable hypotheses of intelligent design. Please document that evidence and describe those testable hypotheses. Until you do so, there is no reason to take your claims seriously.

  22. We can completely ignore all of that science.

    What science would we be ignoring?

    What is the science that demonstrates blind and undirected chemical processes can produce any bacterial flagellum?

    What would the hypothesis be?

  23. Patrick: “That which can be asserted without evidence, can be dismissed without evidence.”
    ― Christopher Hitchens

    You’ve made the claims that there is objective, empirical evidence that is explained by testable hypotheses of intelligent design.Please document that evidence and describe those testable hypotheses.Until you do so, there is no reason to take your claims seriously.

    Right- that is why I dismiss your position’s claim- evidence free

  24. You’ve made the claims that there is objective, empirical evidence that is explained by testable hypotheses of intelligent design.

    Yes, just as archaeology, forensic science and your position claim to be able to determine design from nature, operating freely, ID does also.

    And as with archaeology and forensic science ID says that when agencies act they tend to leave traces of their involvement behind- traces like IC and CSI.

    And to refute any given design inference ID says just demonstrate that blind and undirected processes can account for it- just as Newton said.

  25. Joe G: Yes, just as archaeology, forensic science and your position claim to be able to determine design from nature, operating freely, ID does also.

    And as with archaeology and forensic science ID says that when agencies act they tend to leave traces of their involvement behind- traces like IC and CSI.

    No one has yet ever provided a rigorous definition of CSI, as described by Dembski, nor has anyone shown any example calculations that would allow a third party to apply that metric. If you intend to use CSI as evidence for your position, you must rectify those problems.

    And to refute any given design inference ID says just demonstrate that blind and undirected processes can account for it- just as Newton said.

    Once again, you have the process backwards. You are claiming that something other than known chemistry and physics is required for life. It is up to you to support that claim.

    You have gone further and claimed explicitly that “ID . . . has testable hypotheses about objective, empirical evidence.” Thus far you have provide no support whatsoever for those claims. Please demonstrate the good faith that Elizabeth expects from all participants here by documenting the evidence you claim exists and detailing your testable hypotheses.

  26. Again CSI has more rigour than anything your position has to offer.

    And I do not have the process backwards- you are sadly mistaken.

    YOU need to have evidence for the claims of your position, and you do not.

    ID’s testable hypothesis is the same as for forensic science and archaeology. Did you miss that part?

    What are your position’s testable hypotheses so we can compare.

  27. Joe G: ID’s testable hypothesis is the same as for forensic science and archaeology. Did you miss that part?

    So when will you be testing it? What are you waiting for?

  28. Joe G:
    Again CSI has more rigour than anything your position has to offer.

    Please provide a rigorous mathematical definition of CSI, as described by Dembski, and some example calculations to support this claim

    And I do not have the process backwards- you are sadly mistaken.

    YOU need to have evidence for the claims of your position, and you do not.

    Again, for the purposes of this subthread of discussion, we are accepting ad arguendo that modern evolutionary theory is completely incorrect. That, of course, does nothing to support whatever claims you are making. Those must stand or fall on their own.

    ID’s testable hypothesis is the same as for forensic science and archaeology. Did you miss that part?

    Are you asserting that life was designed by humans? Human agency is what forensic science and archaeology investigate.

    What are your position’s testable hypotheses so we can compare.

    If you’re really interested in modern evolutionary theory, there are numerous textbooks and hundreds of thousands of publicly available peer-reviewed papers with which you can educate yourself. That’s neither here nor there. The point is that you have made the claims that “ID . . . has testable hypotheses about objective, empirical evidence.” Please support those claims or have the intellectual honesty to retract them.

  29. Please provide anything rigourous taht your position has to offer- and the evidence to support it.

    And if you are going to take the chicken-way out then I can just declare ID is right.

    Also I see you don’t understand science- look up the word “extrapolation”

    And STOP with your equivocation already- there isn’t anything pertaining to blind and undirected processes

  30. Joe, please try to stay on topic. I know you think there isn’t any good evidence for whatever you think that some of us think there is good evidence for, but let’s try to be specific.

    Thanks.

  31. OK, the topic of this thread is “functional complexity”. Let’s try to stick with it.

  32. Elizabeth-

    The issue/ question is:

    Can functional information arise via blind and undirected physical processes?

    How can we test the claim?

  33. Joe G:
    Elizabeth-

    The issue/ question is:

    Can functional information arise via blind and undirected physical processes?

    How can we test the claim?

    No, Joe, the question for you is what other than known chemistry and physics do you claim is necessary in biological systems? The further question is how do you support your claims that “ID . . . has testable hypotheses about objective, empirical evidence.”

    Until you provide the evidence you claim exists and the hypotheses you claim explain it, there is literally nothing to discuss and no reason to take your assertions seriously. Please either support your claims or demonstrate the integrity required to retract them.

  34. Joe G:
    Elizabeth-

    The issue/ question is:

    Can functional information arise via blind and undirected physical processes?

    How can we test the claim?

    By running AVIDA, as in the paper, and seeing whether there is an increase in Functional Complexity.

    Turns out there is.

  35. Elizabeth: By running AVIDA, as in the paper, and seeing whether there is an increase in Functional Complexity.

    Turns out there is.

    LoL! AVIDA does not use realistic parameters- why do you keep ignoring that?

  36. Patrick: No, Joe, the question for you is what other than known chemistry and physics do you claim is necessary in biological systems?The further question is how do you support your claims that “ID . . . has testable hypotheses about objective, empirical evidence.”

    Until you provide the evidence you claim exists and the hypotheses you claim explain it, there is literally nothing to discuss and no reason to take your assertions seriously.Please either support your claims or demonstrate the integrity required to retract them.

    Patrick- again you are confused- Your position makes the claim that livuing organisms arose from non-living matter via blind and undirected processes. However that claim has never been supported.

    That said I rpovided an testable hypothesis wrt ID. Don’t blame me for your problems.

  37. Joe G: That said I rpovided an testable hypothesis wrt ID. Don’t blame me for your problems.

    I must have missed that. Please provide both the objective, empirical evidence you claim exists and the testable hypotheses you claim explain it.

  38. Patrick: I must have missed that.Please provide both the objective, empirical evidence you claim exists and the testable hypotheses you claim explain it.

    Yup, obvioulsy you have missed quite a bit during your life.

    And why are you still dragging this thread off-topic?

  39. Joe G: Patrick- as I told you in that thread you are wrong and ID, unlike your position, has testable hypotheses about objective, empirical evidence.

    Also you obviously didn’t understand my post because I explained evrything to you- the way to the design inference is through your position.

    IOW if your positiin had the science we wouldn’t be having this discussion.

    So far from being backwards, how I said it is the way science demands.

    Well joe, if ID “has testable hypotheses about objective, empirical evidence”, you shouldn’t have any problem with calculating the “CSI” in a banana, and describing who, when, where, how, and why bananas were designed and created. And yes, ‘why’ does apply to ID since you IDiots claim that there’s a purpose behind everything.

    What’s the matter joe, can’t your “position” stand on its own? Why is your “position” through another “position”? And do you really think that your “position” would be automatically supported or proven simply by refuting another “position”?

    Hmm, I claim that Fifi the pink unicorn designed and created this universe and many other universes, and everything in them. Prove me wrong, joe, and demonstrate that there’s more testable scientific evidence for your “position” than for my “position”, and demonstrate that if my “position” is wrong that your “position” is thereby automatically right.

  40. <blockquote?Well joe, if ID "has testable hypotheses about objective, empirical evidence", you shouldn't have any problem with calculating the "CSI" in a banana,

    That doesn’t even make any sense- as I have said you have no clue wrt CSI, and it shows.

    And do you really think that your “position” would be automatically supported or proven simply by refuting another “position”?

    No- however if you have a position that relies on the refutation of another, then said refutation would be support for that position, especially in a scenario when there are only two options.

  41. Joe G: LoL! AVIDA does not use realistic parameters- why do you keep ignoring that?

    Because your question (rightly) was: “Can functional information arise via blind and undirected physical processes?” not: “Can functional information arise via blind and undirected physical processes if those processes use realistic parameters?”

    AVIDA is a system by which blind (the genomes are randomly mutated without any bias towards greater fitness) and undirected (they are selected entirely post hoc depending on how well they convert input into output within their virtual environment) processes give rise to an increase in functional information

    Therefore any argument that says this cannot happen is falsified.

    Now, it may well be that there are other valid arguments (perhaps the ribosome is unevolvable) for ID, but the argument that “blind and undirected processes” (specifically Darwinian processes) cannot result in an increase in functional complexity is clearly falsified in principle by this paper.

  42. Joe G:
    Elizabeth-

    The issue/ question is:

    Can functional information arise via blind and undirected physical processes?

    How can we test the claim?

    Is there “functional information” in a raw diamond, the wind, a volcano, a tsunami, a drop of sulfuric acid, a solar flare, a birth defect, a corpse, an ice cube, a toe hair, or a stalactite? If so, measure it, demonstrate how, when, where, why, and by whom or what it was designed, and show your work.

  43. Elizabeth: Because your question (rightly) was: “Can functional information arise via blind and undirected physical processes?”not: “Can functional information arise via blind and undirected physical processes if those processes use realistic parameters?”

    AVIDA is a system by which blind (the genomes are randomly mutated without any bias towards greater fitness) and undirected (they are selected entirely post hoc depending on how well they convert input into output within their virtual environment) processes give rise to an increase in functional information

    Therefore any argument that says this cannot happen is falsified.

    Now, it may well be that there are other valid arguments (perhaps the ribosome is unevolvable) for ID, but the argument that “blind and undirected processes” (specifically Darwinian processes) cannot result in an increase in functional complexity is clearly falsified in principle by this paper.

    Umm the claims of ID pertain to biology and AVIDA does not represent biological evolution.

  44. The whole truth: Is there “functional information” in a raw diamond, the wind, a volcano, a tsunami, a drop of sulfuric acid, a solar flare, a birth defect, a corpse, an ice cube, a toe hair, or a stalactite? If so, measure it, demonstrate how, when, where, why, and by whom or what it was designed, and show your work.

    Answer my questions.

  45. Joe G: Umm the claims of ID pertain to biology and AVIDA does not represent biological evolution.

    Dembski would disagree.

  46. Joe G:

    No- however if you have a position that relies on the refutation of another, then said refutation would be support for that position, especially in a scenario when there are only two options.

    But you haven’t established there are only two options. I count at least three:

    1) The current ToE is responsible for the biological variation we see
    2) Another currently unknown natural process besides ToE is responsible
    3) ID is responsible

    Merely disproving the current ToE does nothing towards establishing ID’s case. For that you need your own positive evidence, which ID doesn’t have.

  47. Thorton: But you haven’t established there are only two options.I count at least three:

    1) The current ToE is responsible for the biological variation we see
    2) Another currently unknown natural process besides ToE is responsible
    3) ID is responsible

    Merely disproving the current ToE does nothing towards establishing ID’s case.For that you need your own positive evidence, which ID doesn’t have.

    LoL! I was just making an example- and ID has plenty of positive evidence and it has been provided. OTOH we are still waiting on that elusive positive evidence for the blind watchmaker.

    Strange, that

  48. Joe,

    This is a courtesy note to let you know that I am discontinuing my participation in this discussion.

    Patrick

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