“The functional sequences of amino acids within amino acid ¬sequence space should be extremely rare rather than common.”
The final prediction listed in this appendix relates directly to the research work done by Doug Axe in the BioLogic Institute. The argument is that the arrangement of amino acids in functional molecules like proteins should be rare, that is, the protein’s function is very sensitive to changes in the amino acid sequence. The inference is that it could not have been achieved by chance mutations of individual amino acids and therefore could only have been arranged by an intelligent designer. Axe has reported on a significant amount of work that shows the arrangement of amino acids is indeed highly tuned and specific to its function.
The question is not whether such a sequence is rare, but whether this truly reflects the work of an intelligent agent rather than natural selection operating on a large population of possibilities. The ID claim builds on Dembski’s explanatory filter and relies on probability calculations to show that no random event could achieve such a configuration in the lifespan of the universe.
However, the great difficulty of all probability calculations for living molecules is that neither the intermediate steps nor the process mechanisms are adequately known to calculate a trustworthy probability. The history of biochemistry has been that transformations from one state to another that seem incredibly improbable, turn out to be highly probable when we understand the details of the process. One example of that was discussed in a previous post, namely the antibody example. The transition from a state of a population of identical pre-B cells to a state of highly specified complex B cells with high affinity to relevant antigens would be calculated to have impossible odds of occurring if we knew nothing about the mechanisms driving that transition. Now that the details have been elucidated over the last few decades, we see how random rearrangement processes and natural selection make that transition highly probable.
I would suggest that all of Meyer’s probability calculations in this book, as well as any others relating to the development of biomolecules, suffer from this deficiency. A proper probability calculation requires detailed knowledge of the initial state and the process by which the system moves to the next state. It must also reflect the size of the population of the initial state. Instead, Meyer makes calculations of the type that assume the initial state is a set of disconnected nucleotides which then inexplicably and randomly assemble themselves into a functional protein. It is no wonder the result is impossibly low. Nature doesn’t work that way. Most origin of life researchers are not looking for evidence of the incredibly improbable event. Rather, they seek the understanding of the precursor populations that could predictably migrate to the next step. At the present time, no one knows enough about the intermediate steps to either claim understanding of such evolution or of claiming that such evolution could not have occurred.
Axe may well find that the sequences are rare with respect to sensitivity to changes in individual amino acids but that still doesn’t give us much information about the probability of its evolution. Larger scale mixing, matching, and borrowing of sections of amino acids are known to occur in many processes that form proteins. This means that the opportunity space for generating new proteins is enormous, making it extremely difficult to ascertain what actually happened in the evolutionary past. But it makes it even more difficult to show that such evolutionary changes couldn’t have happened. In light of current evolutionary thought of how proteins evolved, one might even predict that many, if not most, amino acid sequences in proteins are rare. They were unlikely to have evolved by changes in one amino acid at a time. This prediction does not seem to be fruitful in elucidating a unique prediction of ID.
Randy seems to fault Meyer for making “calculations of the type that assume the initial state is a set of disconnected nucleotides which then inexplicably and randomly assemble themselves into a functional protein.” While this may be a valid criticism at some point along the developmental chain it seems impossible to conceive of there never having been an initial set of disconnected nucleotides. If natural processes are at the root of life there must have been a transition from the laws of chemistry to biological processes at some point. While the laws of chemistry govern there are three fundamental issues to be addressed. 1) Natural synthesis of the nucleotides. 2) Separation, purification and isolation of a pool of sterioisomers of the nucleotides. 3) Polymerization to lengths of biological interest. If another sequence is conceivable it would be interesting to hear suggestions as to what that might be.
Superimposed on that is the requirement that the first nucleotide polymer of potential biological length must somehow not have been merely randomly assembled but have specified encoding. Add to that the interesting observation that one potentially biologically active entity rarely seems able to act on its on but requires other differing entities to function and it seems that Meyer’s assessment of the improbability of occurrence has much more scientific merit than Randy’s attempt to dismiss it.
Ide,
we all agree that biological systems are incredibly complex and marvelous in their intricate operation. Everyone also agrees that no one, ID or otherwise, has solved the question of how these came to be. My point is a rather simple one. No credible probability of the formation of a biological system or one of its components can be calculated unless the process is thoroughly understood in detail. On what basis can I make such a statement? Start with quantum mechanics. A probability distribution of how a quantum system might change over time can only be done if one knows the Hamiltonian to a very high degree of accuracy. Similarly in classical mechanics, the probability distribution of an ensemble can be calculated only if one knows the details of physical processes of the components. In chemistry, calculating the reaction rates or probabilities of reaction of a set of reactants requires a detailed understanding of the reaction path. The same is true in biology. Once the reaction paths are known, the probabilities can be calculated.
I cited the example of antibody production as an illustration of how our idea of probability changes as we understand the process. Prior to the 70’s, the observation that a population of identical pre-B cells was transformed into a highly specified set of B cells with antibodies to the specific antigens in the body was not understood. It seemed to be a most improbable development. Now that we understand the details of the process, we see that it is actually a highly probable process. I merely suggest that we must have a lot of humility about what we know and we don’t know when it comes to the origin of biological systems. Until we discover the detailed processes, we simply don’t know whether the probabilities are high or low. We cannot draw any conclusions from an argument from incredulity, unable to perceive how something might have developed.
Randy
Randy,
I find that all very interesting but it takes us away from the central challenge I thought you were trying to address. That was, “Complex Specified Information Without an Intelligent Source.” I agree with you that detailed mechanistic understanding is what is ultimately needed. I wonder if you will agree that a detailed mechanistic understanding is still missing from our understanding of “evolution.”
Regarding “pre-B cells was transformed into a highly specified set of B cells” you say “Now that we understand the details of the process, we see that it is actually a highly probable process.” And I say my prior post showed that the highly probably process did not demonstrate production of additional CSI. It is not clear from your response whether you agree with that or not.
Now, back to the topic. I’m not asking to see a specific answer to the source of CSI in ANY biological system. Nor am I seeking an answer as to why we came to be here. I’m simply asking if there has ever been the simplest, bare bones demonstration of the production of CSI from random imputs “Without an Intelligent Source.” I’ve asked this question quite a few times in many venues and haven’t found anyone who can come up with the demonstration. But many, and apparently you are among them, think it has been done somewhere. I’m from Missouri. Show me.
Ide
Ide,
I’m sorry I didn’t make it clear that, yes, I believe that everywhere around us we see the generation of CSI without intelligent agents. The case that Meyer tries to make that all CSI can only be generated with the aid of an intelligent agent is not convincing. He has no theoretical basis, uses inductive reasoning, supplies examples that I believe are not relevant, and has overlooked examples of CSI generation without intelligent agents.
I do think the antibody example is one of the simplest and finest examples. You did not find it compelling while I think your objection was not relevant. My schedule is overbooked for the next few days but I will explain this in more detail after a few days. I think this is better discussed in the post of that example and I will comment there.
Randy
Randy,
I got your response to the other post that this is the place to address the origin of CSI issue. I’ll transfer the pertinent part of your response from there.
“I believe that everywhere around us we see the generation of CSI without intelligent agents. The case that Meyer tries to make that all CSI can only be generated with the aid of an intelligent agent is not convincing. He has no theoretical basis, uses inductive reasoning, supplies examples that I believe are not relevant, and has overlooked examples of CSI generation without intelligent agents.
I do think the antibody example is one of the simplest and finest examples. You did not find it compelling while I think your objection was not relevant.”
This gives us plenty to chew on. Let me restate my last, “I’m not asking to see a specific answer to the source of CSI in ANY biological system. Nor am I seeking an answer as to why we came to be here. I’m simply asking if there has ever been the simplest, bare bones demonstration of the production of CSI from random inputs “Without an Intelligent Source.” I’ve asked this question quite a few times in many venues and haven’t found anyone who can come up with the demonstration. But many, and apparently you are among them, think it has been done somewhere. I’m from Missouri. Show me.”
It should be a very interesting exercise. I’m essentially out of time for now as well with travel and meetings until the middle of next week, too, so take your time.
Ide
Randy,
I think you are making the probability calculations more difficult than they really are. Actually, the chemical reaction of polypeptide formation is very well understood: dehydration synthesis. Also, the thermodynamics and the kinetics are also very well understood. In addition, it is well know that there are no thermodynamically favored combinations of one amino acid to another vis peptide bond formation (lysine bond with equal propensity to arginine, glycine or any other amino acid). Hence, the use of simple probability applications is quite appropriate. I would be interested in knowing why, given our very good understanding of these chemical principles, you assert we somehow can’t evaluate probabilities of particular polypeptide sequence formation?
Second, you keep assuming that the antibody forming system in the body is a result of a non-intelligent system – isn’t that begging the question? How do you know that this system came about by a non-intelligent mechanism?
Larry
Larry,
It seems I may have chosen the wrong term, or else failed to qualify it correctly. You are quite correct that we have a very good understanding of the chemical principles behind the formation of peptides, in the sense of their production in the body. What I meant to say is that we need a much better understanding of their formation in the evolutionary sense. That is, what was the precursor to any particular peptide? How did that peptide come to exist in the first place? Most ID probability calculations assume the precursor was a set of disconnected nucleotides that must randomly aggregate in the right sequence to form the peptide. If that were true, we would all agree the probability is so low that it would never occur. But to calculate an accurate probability, we must know what the precursor actually was.
This is where the force of the irreducible complexity argument comes into play. The idea is that no possible precursor can be identified from which a peptide, for example, can be generated with modifications that have a reasonable probability of occurring. So Behe claims that a biomolecule doesn’t function when a subunit is removed. And Doug Axe shows that a protein is so sensitive to the modification of a single amino acid that it could not have a precursor from which it could have formed.
The problem is that neither Behe nor Axe nor anyone else can confidently claim to have identified all possible precursors and all possible processes from which a biomolecule can be generated. To pick one precursor, like a disassociated set of nucleotides, and one process, like their random assembly into a protein, and calculate a probability from that assumption will inevitably lead to a virtually zero result, but one that is totally meaningless.
Biochemists have learned enough in the past few decades to know there are many ways in which new biomolecules can be generated. They also know there are likely many processes yet to be discovered. The research challenge is to find out what precursors and what processes in fact were responsible for any given biomolecule. Claiming that some arbitrary precursor and process have too low a probability and therefore an indeterminate intelligent designer must have done it, doesn’t cut it. And no, claiming that the information sequence of the biomolecule is a positive indicator of such an intelligent designer does not rescue such a claim.
Your second question was how do we know the antibody system came about by a non-intelligent mechanism. First of all, let me clarify that I’m not addressing how “this system came about” from the sense of its ultimate origins. What I am addressing is how a highly specified, complex population of antibodies is generated from a population of pre-B cells that are different from the antibodies and are all identical in their DNA sequence. That is, this is a continuous process of generating CSI. This process occurs in many millions of cells throughout the body. I think it is rather clear that no physical intelligent being has access to these cells inside our bodies to manipulate the process and determine the DNA sequence necessary to generate the right antibodies. Even more to the point, the rearrangement of the DNA segments is through processes that are not influenced by a desired outcome. That is, there is no feedback loop or mechanism that can modify the rearrangement process. It is truly random at that point.
Randy
Randy,
I’m still confused by your line of argument. You must agree that at some point there was no “precursor” other than at least two monomeric nucleotides. Each must be either levo or dextro. Then the possible paths branch. To get things started the two form a dimeric peptide. There are four possibilities. The dimer can be all levo, all dextro, or one of the two mixed optical isomers. Or another nucleotide could appear before the polypeptide formation initiates, etc, etc, etc, ad nauseum. It seems to me that Larry is saying that at this stage “the use of simple probability applications is quite appropriate.” I think that is the case as well. You don’t seem to be addressing this point in the process. Neither Larry nor I yet grasp your reasoning for seeming to ignore this starting point for the process. It must have existed. If so why doesn’t it provide the basis for Meyer’s statistical calculation?
Ide
Ide,
The reason is that Randy is not addressing the precursor to the precursor to the precursor… to the nth degree. He is simply addressing a key proposition that appears to be advanced by ID, that CSI can only be generated by direct intelligent action. He is giving a limited counter-example to that (apparently) generalized claim of ID.
Now, in my brief summary perhaps I have trivialized the ID argument. I will simply pose it as a question. Can new compex specified information be generated in a system without the direct action of an intelligent source? If the answer is no, then Randy’s example potentially provides a counter-example (or else needs to be shown why it isn’t a counter-example). If the answer is yes, then ID’s argument fails as a general principle and thus can’t be relied upon as a conclusive indicator of intelligence.
One more comment about “direct” versus “indirect” action of intelligence. Randy has implied, although maybe not stated in these words, that the production of CSI in this example has no appearance nor any functional reason to imply the *direct* action of intelligence (i.e. no non-natural agent acting on the cells to create a specified population of antibodies). He doesn’t say that there isn’t (or wasn’t) intelligence, just that we don’t have any reason to suspect direct interaction in this example. Your response doesn’t seem to commit one way or the other, but rather tries to take it back to a much earlier precursor that isn’t under discussion in the example.
You may say, “Wait a minute, we didn’t say ‘direct’ intelligent action was necessary. There could have been indirect action, or direct action of intelligent design at a much earlier stage that provided a complex machine that now generates antibodies naturally.” But that just moves the action of intelligence back to a point in our scientific understanding that is less understood, where it can’t be proved conclusively one way or the other, and doesn’t address the question. If CSI can be generated at any stage by natural forces, then how can ID make the unqualified assertion that all CSI is the result of intelligence?
Very well said, Jon. That’s precisely correct. Thank you.
As another illustration, in any chemical system, one cannot simply compute the probability that the initial set of reactants will produce the final synthesized product without knowing each step of the reaction and the intermediate products. Indeed, take it back far enough, and any chemical reaction on this earth can be traced back to a random ensemble of baryons. Can one calculate the probability that these baryons would produce the beauty of, say, marble? I think that without knowing the intermediate steps, that probability would be impossibly low. But when we learn how stars form and become supernovas and how planets form, we gradually realize that the probability isn’t so low after all.
The same is true in biomolecules. Their formation must be understood at every step. Without that, any probability calculation is wrong.
Randy
Hi guys,
A couple of thoughts and questions: First, Meyer (and the rest of the ID writers) have formulated their argument in a modus pollens fashion, with their major premise being that CSI is always the result of an intelligent agent. Randy, et.al. seem pretty confident that they have undermined this premise, and hence the ID argument, by asserting that the g.o.d. of the immune system is a counter example (no direct intelligent agent as cause for this CSI). Therefore, ID argument fails. Okay – fine. One could make the same modus pollens argument about marbles: all marbles in this bag are white; this marble is from the bag, hence it is white. One black marble will show the argument to be false. Of course, there may be 1,000,000 white marbles in the bag and only one black marble – so that the vast majority of the marbles are white – but this fact is inconsequential to the point that the arguement in the MP form is defeated – and this is what Randy is pointing out. However, it seems to me that an unwarranted corollary is being drawn, namely, that therefore most of the marbles are black (if not ID then natural forces explain all of the complexity of life). Perhaps you have not stated it plainly as such, but isn’t that what is believed? In fact, I have seen that if one doesn’t automatically attribute a naturalistic mechanism to a thorny problem (e.g., origin of life) that one is “giving up on science.”
Two questions: Would the ID argument be more palatable if it were not presented in an MP format, say “the most likely (not only) cause of CSI is intelligence (leaving the possibility for the black marble)” Second, is the same high bar and rigorous skepticism that is applied to ID theory also applied to the theory of non-intelligently generated genetic mutation along with Natural Selection as the cause of CSI employed by the critics of ID? If this is the case, could you point out peer-reviewed articles that are thusly critical?
Larry
Larry,
Nice try, but no cigar. I presume you mean modus ponens arguments of the type “If P, then Q; P; therefore Q.” Meyer says, “If CSI increases, then an intelligent agent was the source; the development of living organisms constitute an increase in CSI; therefore an intelligent agent was the source”. You are correct that this can be invalidated by showing that an intelligent agent is not always the source of an increase in CSI. And that’s just what the antibody example does. But no, Larry, this is not the rare example. It’s just one of the easiest and most elegant ones to explain and understand. In my opinion, every single living cell that has existed in the last 3+billion years is an example of increased CSI without an intelligent agent. In fact, no example has yet been shown of a living system that was generated by an intelligent agent, notwithstanding all the genetic engineering experiments.
Neither Meyer nor Dembski nor any other ID advocate has put forth an argument of why CSI can only come from an intelligent source. There is no theory to back it up. The only support offered is a set of examples and the conclusion is obtained through inductive reasoning. However, all the examples offered are rather trivial in complexity compared to a living organism, and virtually all can be shown to involve abstract reasoning, a known indicator of intelligence. DNA-based systems do not involve abstraction and there is no reason it requires an intelligent source. Meyer believes he can extrapolate from examples like computer code to DNA information. The only rationale he offers is that both are identical in being CSI. Yet, he himself notes there are two types of CSI though he fails to note that the two types need not have the same source.
Regarding your last two questions, I repeat what I said in my posts. CSI that involves abstraction necessitates the involvement of an intelligent agent. CSI that does not involve abstraction may or may not involve an intelligent designer. Living cells do not involve abstraction and may or may not come from an intelligent agent. The design process of reproduction with modification followed by differential reproductive success is a marvelous design agent that seems adequate to explain all living cells though the details have not yet all been filled in. Living cells are highly unlikely, if not impossibly so, to be designed by a physical intelligent agent. To assert that a physical intelligent agent existed throughout the last 3+ billion years with the ability to do the planning and bioengineering necessary to create life, and yet not leave a trace of its existence, is well beyond incredible. Yet, the alternative, a supernatural designer, is vigorously opposed by the ID community as a smear tactic against ID. It seems that design without an intelligent designer (except at a higher level of explanation) can be inferred as the best explanation.
As for your second question, I don’t know what it means. Yes, I think as much, if not much more skepticism has been shown toward evolution. You ask for references? I’d say the literature from the mid-19th century to the mid-20th century is filled with skepticism until the evidence finally became so compelling that few credible concerns remained.
Randy
P.S. Larry, let me just expound a little more on the ubiquity of examples of CSI increasing without an intelligent agent. All multi-cellular organisms are also great examples. Each one begins as a single cell embryo with a certain amount of CSI. The full grown organism has more CSI than the starting embryo. Through cell differentiation due to variations in gene expression,rather than changes in nuclear DNA, the development process is an increase in CSI, without the involvement of an intelligent agent. Truly, examples of increasing CSI without an intelligent source abound all around us.
Randy
Randy
Randy,
Thanks for the reply. Why do you assert that a physical intelligent agent that lived 3+ billion years ago is “more than incredible”? I mean isn’t “credibility” a matter of probabilities, and haven’t we already established that probabilities really can’t be applied if we don’t understand all of the mechanisms involved?
Could not a “Neo ID” scientist make the claim that 3+ billion years ago by some unknown mechanism (”unknown” in the same sense that the mechanism of how the first living cell came to be is unknown) a super-intelligent physical agent came to be and it was this agent that created some proto-cell with DNA needed to propagate life and evolve. This intelligent agent was soft-bodied, so didn’t leave any trace of its (their?) existence in the fossil record (which most everyone seems to agree is “incomplete”). The volumes of DNA which we see in the Cambrian animals were also in soft-bodied precursors and also didn’t fossilize. I know this theory would entirely break down if some one could show that such an intelligent creature could not have existed and done the engineering that I am suggesting – but until one actually does this, wouldn’t this be a viable theory, as no non-physical entities are invoked?
If you find this scenario incredible, I would like to know your reasons for thinking so.
Larry
Larry,
Richard Dawkins beat you to it. The intelligent physical agent was a giant flying spaghetti monster. Of course, it only exists in his imagination. Yes, this could be a very valid scientific hypothesis. But what good is it?
If it’s going to be a useful scientific hypothesis, there ought to be some means of distinguishing among alternatives. How would you propose to differentiate between the following causal agents?
1. Giant flying spaghetti monster
2. A leprechaun
3. A super-intelligent dolphin (yes, I once read Douglas Adams)
4. Self-organization of non-organic matter into organic matter
5. The Judeo-Christian God
We have zero evidence that either of the first three have ever existed; or if they existed, whether they existed at the right time; or if they existed at the right time, whether they had the causal power to create the first living cell. We do know that dolphins exist, but we have zero evidence that they existed 3+ billion years ago prior to the existence of living matter on this earth. Therefore, you could propose any of these three as a scientific hypothesis if you want (or a thousand others), but that is the end of it until some independent empirical, inferential, or theoretical basis can be discovered which provides evidence for or against them. If the hypothesis is science at all, it’s pointless and a dead end without further identification of the designer.
The self-organization of matter into living matter is a valid scientific hypothesis. Perhaps there are conditions in which matter could have organized into a simple protein, proto-RNA, or other structure that eventually developed into a complex cell. So far, as I understand it, the experimental evidence is against this, so it remains a matter for future discovery to either prove conclusively for or against. It is valid science, in that it’s subject to further human investigation. Whether or not it ever proves conclusive is an open question.
Finally, there is God. Is there independent evidence that He exists, that He existed 3+ billion years ago, and that He has the causal power necessary to create a living cell? I would argue, as I suppose would all Christians, that there is independent evidence of God’s existence. Not only in the Bible, but in our revelatory and relational experience with Him, we have sufficient evidence of His existence. According to His revelation, He was present at creation and was responsible for it (leaving the detailed scientific steps aside for a moment). And He certainly, according to our faith, has the causal power to do so.
So of the choices I presented above, I find #5 to be the most reasonable hypothesis. But is it scientific? ID rejects #4 as a purely materialistic conclusion, and strongly resists #5 because it’s a religious inference, and so try to avoid the two most plausible conclusions. So they try to suggest that there *might* be some unspecified non-materialistic, non-supernatural designer, in order to make ID sound more scientific. I frankly think it’s a bit of a shell game.
Now, again, it could be that God supernaturally “poofed” into existence the first living cell without precursors, or it could be that He worked through natural causes and materials to influence the natural development of the first cell; or He could have designed matter with the property of being self-organizing under the right conditions. I’m not sure how science could differentiate between these three hypotheses or others, but I’m open to suggestions.