Complex Specified Information Without an Intelligent Source

Meyer claims that specified complex information can only arise from an intelligent source, justifying that claim by citing a series of examples. One of those examples is computer code. In my previous post, I suggested that this was not an adequate example because of fundamental differences between computer code and DNA information. An obvious question is whether there is an example of specified complex information that is not derived from an intelligent source but solely from physical or chemical functionality. In this post I would like to offer just such an example.

The magnificent example of antibodies was presented by Dr. Craig Story in the December 2009 issue of Perspectives on Science and Christian Faith, Vol. 61, No. 4, p.221. (if you aren’t a member or don’t have a subscription, copies are available from the ASA office for $10 plus shipping and handling; contact asa@asa3.org.) In his article, Craig explains how the immune system works, focusing on the importance of the inherent randomness in the process. In this post, I would like to offer a physicist’s interpretation of his paper, with a focus on the information content. Craig has graciously reviewed these comments and corrected my errors in biology.

Stem cells in our bone marrow continuously produce a population of pre-B cells, so called because they are precursors to B cells, which manufacture antibodies when mature. These pre-B cells are all identical and have the same antibody gene DNA. This population therefore has a relatively low information content. All the complexity is within the cell and there is no diversity in the population of cells. As the pre-B cell population prepares to moves into the body, the cells undergo a transition into B cells. In the process, key segments of DNA in each cell are rearranged randomly to form a unique and novel DNA sequence. The process is described in detail in Craig’s paper. It is a constrained process so that the resulting antibody protein is always a particular folded configuration that may have affinity to an antigen, but the gene segments are randomly rearranged and joined to alter the magnitude of the affinity. The result is a population of B cells, each one of which is different in terms of its antibody DNA. This means that we have a transformation of a low information population of pre-B cells to a high information population of B cells, with reference to their antigen-binding abilities. The complexity has increased dramatically but we do not yet have specificity.

As a B cell moves through the body, it may or may not encounter an antigen with which it has affinity. If it does not, the B cell dies and that particular configuration no longer exists in the body. However, if an antigen appears with which a B cell has some degree of affinity, the B cell will attach to the antigen. In this case, that B cell will reproduce through cell division to create clones of itself. This process occurs throughout the population of B cells with the result that only B cells with some affinity to the environment of antigens survive. This is a basic level of specificity.

There is another level of specificity that Craig describes. A first-responder B cell usually will have a relatively small degree of affinity to an antigen. As this cell reproduces itself, an enzyme enhances the mutation rate of only the portion of the antibody genes that determines the affinity. In some cases, mutation rates can reach as much as one nucleotide per cell division. This means that the subpopulation of this particular B cell grows with a dynamic diversity of various degrees of affinity to that antigen. The cells with the strongest degree of affinity will preferentially attach to the antigens, leaving those with weaker affinity without antigens and therefore a death sentence. Over time, this subpopulation will be predominantly one with strong affinity to this particular antigen. This, in a nutshell, is why vaccines work.

In the bigger picture, this example shows how a homogeneous population of pre-B cells is transformed to a dynamically diverse population of B cells, with a tremendous increase in information content. This complex information then becomes highly specified by fine-tuning to match the antigens to which they are presented. The result is a high degree of specificity and complexity with no involvement of an intelligent designer as an immediate cause. This does not, of course, preclude the sustaining involvement of an Intelligent Designer at a metaphysical level.

Craig points out the critical role of randomness as a key characteristic of the cellular processes involved in the immune system. The random process of gene rearrangement is necessary to ensure a sufficiently broad range of binding specificities, such that some of them are almost sure to bind to one part of each pathogen. His example also illustrates clearly how highly complex and highly specified information is derived directly from a population of relatively low-information cells. Hence, the argument that Meyer makes that all complex specified information comes from an intelligent source does not withstand scrutiny.

The antibody example is a beautiful illustration of the basic processes of evolution. It begins with the common ancestry of the stem cells that produce an ancestral population of pre-B cells that are essentially identical. Descent with random variability occurs in the generation of the B cells, which are all unique with respect to their antibody gene DNA. Natural selection describes the way in which B cells that do not bind to an antigen will die while those that do bind to an antigen proceed to reproduce clones. The random variability of the dynamically diverse population of antibodies ensures the formation, within a short period of time, of antibodies with affinity to virtually any antigen. The subsequent way in which those B cells acquire stronger affinity to that antigen is a type of adaptation. Darwin suggested that these basic processes, operating over a long period of time, could account for the origin of species. Little did he suspect that these very processes are active continuously in our bodies on a relatively short time scale to provide a vital line of immunological defense.

240 comments to Complex Specified Information Without an Intelligent Source

  • Charles Austerberry

    Dear Ide:
    In reply to Jon re. the typing monkey scenario you wrote:
    “As to your random number generator I see it as merely a variant of the fractal in that information and complexity are generated but specificity is not increased beyond that in the generator algorithm.”
    I think Jon would agree with you.  That seemed to be his point.  The monkeys are typing away randomly with respect to the English (or any) language.  They are generating information and complexity, but not specificity beyond that inherent in the typewriter itself.  The specificity is in the eye of the beholder, i.e. someone who can recognize English let alone Shakespeare.
    I agree that the analogy fails to match biology very well.  But, let’s imagine that meaningful (functional) words or sentences coming out of the typewriter are somehow preferentially copied (amplified).  Such words or sentences would increasingly represent a larger share of the total output of the word/sentence generating process.
    Again, I appreciate your point that imagining how the first biological code was able to be copied is a challenge.  My point here is, I think Jon sees the monkey scenario much as you (and perhaps we all) do.
    Cheers!
    Chuck

  • Ide Trotter

    Thanks, Chuck,
     
    I appreciate your support regarding the challenge of the first biological code but my understanding still struggles with the notion of “random” typing ever leading to anything meaningful.  I also seem to have a vague recollection of someone having supplied several chimps with typewriters and they wound up repetitively hitting just a few adjacent keys.  Don’t know if anyone can confirm this.
     
    All the best,
     
    Ide

  • Randy Isaac

    I’m glad to see that you’ve been continuing the conversation. I’ve been travelling on business out of the country and working on some projects with end of June deadlines so I haven’t been able to contribute lately. But most of all, I’ve been silent because I’m at a loss for words. Rare, to be sure! Ide, your response to my more recent comment simply leaves me speechless. Your interpretation of what I said seems to differ so widely from what I was trying to communicate that I don’t even know how to clarify it. Perhaps the blog format isn’t optimal for resolving such large differences in understanding. It would be good if you and I could sit down face to face and discuss it at length.

    So perhaps it would be best if I summarize this thread and move on to other topics, hoping we can return to this some other time.

    The focus of this post and thread is Meyer’s assertion that DNA information could only be generated by an intelligent agent because complex specified information can only be generated by an intelligent agent and living cells contain complex specified information. I have argued that his assertion is false for several reasons. The only one I will repeat here is the point of this particular post which is that antibody production is an excellent example of how the information in living cells changes and increases without an intelligent agent, through basic evolutionary processes. Meyer’s basic premise is therefore negated and his conclusion is not valid.

    Your point seems to be that specified information is conserved and must be somehow stored in the original cells or incorporated from the outside but careful observation shows that the relevant information, namely the required DNA sequence for high affinity to the set of antigens, does not exist either in the original cells or in the environment.

    As for the origin of life, you correctly point out that it is important that we make an inference to the best explanation. Would that be an intelligent agent or evolutionary processes? At this time, we have no observational evidence of any human intelligent agent generating any significant information necessary for living cells. Venter took genetic engineering techniques farther than anyone and showed that humans can synthetically duplicate a bacterial genome, modify it innocuously, and encourage another bacteria to incorporate it after 30 generations. That’s a far cry from generating any new information but even if we were to concede that someday well into the future humans will be able to create some synthetic cells, the result will not demonstrate that intelligent agents could have generated life in the first place, let alone that intelligence be required to create it. At best, it will show the elaborate fancy laboratory equipment that must be used by an intelligent agent to even imitate part of life. Such tools did not exist when life originated so we have no indication that an intelligent agent is even a candidate to be considered.

    By contrast, evolutionary processes are observed every day to significantly modify and often increase the information in living cells necessary for life. It happens in the antibody examples, it happens in the development of every organism and it happens in the reproduction of every individual of every species. No, we don’t know whether those processes are adequate for generating life from non-living origins. But from what we observe, it’s an excellent candidate worthy of intensive research. It seems that evolutionary processes are by far the best, if not the only, explanation to be inferred for the origin of life.

     

    Thanks for the great discussion. I hope to see you soon.

     

    Randy

  • Ide Trotter

    Randy,
     
    Happy 4th of July!  I’ve missed you.  I assume the “recent comment” you reference was that from June 20.  I’m sorry it rendered you speechless because I was looking forward to your response.
     
    I really don’t believe you should close out this thread at this point.   Here are the reasons.
     
    1)    You may now assert that “The focus of this post and thread is Meyer’s assertion that DNA information could only be generated by an intelligent agent because complex specified information can only be generated by an intelligent agent” but I joined because it was titled “Complex Information Without an Intelligent Source.”  And I will repeat, your argument fails to be convincing to me for two reasons.  First, the antibody case only comes into play after biologically functional CSI is in place.  The non-intelligent source for that CSI has yet to be identified.  Second, since I inquired no one has been able to describe how the CSI quantity is assessed before and after an antibody is formed or to establish unequivocally that any perceived increase is not just trafficking on preexisting CSI.
     
    2)    You keep saying “careful observation shows that the relevant information, namely the required DNA sequence for high affinity to the set of antigens, does not exist either in the original cells or in the environment.”  Maybe so.  So I ask the following. Who observed it quantitatively?  Where is it published?  And you may recall I offered to stipulate the point and set that argument aside if we could just focus on how the first biologically functional CSI came about.
     
    3)    You assert, “At this time, we have no observational evidence of any human intelligent agent generating any significant information necessary for living cells. Venter took genetic engineering techniques farther than anyone and showed that humans can synthetically duplicate a bacterial genome, modify it innocuously.”  I beg to differ.  That is exactly what Venter’s team did. They read a code of “significant information necessary for living cells” and “generated” it independently, letter by letter. I will grant that their intelligence did not invent the information but they clearly generated it. I also see no present reason to accept your assertion that “That’s a far cry from generating any new information.” New information is exactly what the inserted watermark was.  So I wonder if you missed my thought that “Given the growing indications of functionality for non-coding DNA and complex interactions with other features of the cell there may turn out to be a deleterious function.”  Only after study of competitive evolutionary striving for survival could it be demonstrated that the modification by incorporation of the watermark was “innocuous,” by which I presume you mean not functional. Whether functional or dysfunctional I would argue any effect would be significant.
     
    It seems to me that you have left too much on the table relative to the original statement of the thread to just declare victory and go home.
     
    Just my two cents worth.
     
    Ide

    • Randy Isaac

      Ide, no, I haven’t declared victory but admitted failure to write clearly enough to be understood. I really am so far behind in preparations for the annual meeting at the end of this month that I won’t be able to write again until August. I think your questions have all been answered previously.

      If you feel Venter offers evidence that intelligent agents can generate the information necessary for life, then it also constitutes evidence that such intelligence needs computer support and lab equipment to do so. When you show evidence that these existed 3.8 billion years ago, then perhaps an intelligent agent might be considered as a possible candidate for the origin of life.

      Yes, indeed the technical papers describe precisely the original state of the pre-B cells, the external influences, and the process by which the specified information is generated. In this example, as in the cosmos in general, specified information (not the abstract, or symbolic, kind that only comes from intelligent agents but the natural or functional kind) is generated by the interaction of components in complex systems through random processes within the laws of nature. That’s why I advocate this example so much. It is well studied and documented and shows explicitly how the specified information is generated without existing in the original state or coming from external influence or by an intelligent agent.

      Carry on,

      Randy

  • Ide Trotter

    Randy,
     
    I do appreciate the demands on your time and am thankful you have been able to participate here as much as you have.  I am about to go off DSL myself, into a remote mountain valley in CO for about a month where I am thankful to have dial up and too cheap to go for satellite.  So after July 15 I’ll be in recess.
     
    Perhaps Chuck can come back before then and assist with accessible references to the “technical papers describe precisely the original state of the pre-B cells, the external influences, and the process by which the specified information is generated” you refer to.  However, I’ve been reflecting on our continuing inability to converge to a mutual understanding.  It may not depend on the specific papers at all.   It may depend on our differing use and understanding of “generate” vs. “create.”
     
    In my previous post I tried to help by explaining with regard to Venter’s accomplishment, “I will grant that their intelligence did not invent the information but they clearly generated it.”  Perhaps you didn’t have time to reflect on the difference I hoped to communicate and I might have been clearer if I had said they “regenerated it.”  In the sense I intended the Venter team did not originate the DNA code but drew on extensive preexisting CSI, and their own considerable intelligence, to reproduce it.  I think I see a correspondence to what you are saying about the antibody case. I see your “original state of the pre-B cells, the external influences, and the process by which the specified information is generated” as possible the same thing I have been saying all along.  That the antibody example does not “invent” but “generates” based on preexisting information.  I wonder if that makes sense to anybody but me.
     
    However it seems to me we remain quite far apart with regard to, “the external influences, and the process by which the specified information is generated. In this example (the antibody case), as in the cosmos in general, specified information (not the abstract, or symbolic, kind that only comes from intelligent agents but the natural or functional kind) is generated by the interaction of components in complex systems through random processes within the laws of nature.”  I continue to argue that cosmic dynamics produce near infinite quantities of complex “information”  “by the interaction of components in complex systems through random processes within the laws of nature”  but not a smidgen of new CSI.  I see absolutely no analogy between the copying, processing, rearranging and error introducing procedures studied in evolutionary molecular biology and the workings of general relativity and quantum mechanics in the prebiotic universe. 
     
    I look forward to your eventually finding time to help me see how you are able to find them so similar.
     
    Have a great annual meeting.  Sorry I won’t be able to make it.
     
    Ide

  • Charles Austerberry

    Ide mentioned that it might be helpful if I could provide links to freely accessible sources of information regarding the adaptive immune system.  Previously I provided links to articles about the evolution of the adaptive immune system, but not to articles about how the system (as it now exists in humans) works. PubMed Central has many free recently-published articles on various details of the system.  However, perhaps what’s needed is background information to help us connect basic well-established dots, rather than the latest research that adds the newest dots to the picture.  I recommend the university-level textbook resources provided by PubMed Books.
    One book made available there is titled Immunobiology.  I’ll start with a few references from that text.
    Chapter 4 is key, because it describes how the diversification occurs.  Here is a link to the introduction to that chapter:
    http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=imm&part=A435
    It’s the first section of that chapter that is most relevant:
    http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=imm&part=A436
    Chapter 7 is also important, because it describes the negative selection process that eliminates or inactivates potentially self-reactive lymphocytes.  Here is the introduction to chapter 7:
    http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=imm&part=A797
    Here is a link to a highly relevant section of Chapter 7 (section 7-17):
    http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=imm&part=A842
    Finally, Chapter 10 has a discussion of immunological memory, which develops when lymphocytes are activated by encounter with foreign antigens.  The relevant section is at:
    http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=imm&part=A1372
    Of course, there are links to lots of other pages in the text, and PubMed books has other books with information on the topic.  But perhaps the portions referenced above can provide a good start.
    Cheers!
    Chuck
     
     
     
     
     
     

  • Charles Austerberry

    The publisher of Roitt’s Essential Immunology (11th edition) has a very helpful website that provides free information.  I especially recommend the animations and tutorials associated with each chapter, and also the Encyclopedia of Life Sciences (ELS) articles.  For example, the ELS article titled “Immune System” gives a concise overview.
    The web site is: http://www.roitt.com

  • Ide Trotter

    Thanks, Chuck, I knew I could count on you.  But that is an overwhelming amount of info.  Would it be too much to ask if you could direct me to any sections that deal specifically with the information issue?  What I’m looking for is some concrete demonstration that what is going on is more than “copying, processing, rearranging and error introducing procedures” that actually creates new code, not just transformed code.  To my original list I probably should add and not deleting or importing preexisting code.
     
    Ide

  • Charles Austerberry

    I think the following section probably zeros in on the question as well as any.
    http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=imm&part=A436#A449
    Note that there are four mechanisms creating the diversity.
    The two combinatorial diversification mechanisms described in the text probably exemplify what you mean by “processing” or “rearranging” or “transforming” existing code.  The other two mechanisms, junctional diversification and somatic hypermutation, probably constitute what you mean by “creating new code, ” because those non-combinatorial diversification mechanisms actually create new complex information.  The combinatorial mechanisms diversify by creating various combinations of existing informational (coding) portions of DNA sequence.  Of course, the natural selection that follows is also important because it makes the information specific, but that comes in other chapters.  Let me know when you have questions about the specificity issue.  Until then, perhaps it’s best to focus on the generation of complex information via the four diversification mechanisms.
    Cheers!
    Chuck

  • Ide Trotter

     
    Thanks Chuck and with apologies for the delay in responding. 
     
    This reference is the closest yet to what I have been looking for.  For the benefit of other readers it is a section titled,”The diversity of the immunoglobulin repertoire is generated by four main processes.”  It classifies two of the processes as “consequences of the recombination” and a third as “due to the different possible combinations.”  To may way of thinking neither combination or recombination produces new code or CSI.
     
    The fourth, “somatic hypermutation,” initially sounded more promising.  However, Wikipedia, my easiest source, describes somatic hypermutation (SHM) as follows:

    “Experimental evidence supports the view that the mechanism of SHM involves deamination of cytosine to uracil in DNA by an enzyme called Activation-Induced (Cytidine) Deaminase, or AID.[6][7] A cytosine:guanine pair is thus directly mutated a to a uracil:guanine mismatch.”
     
    I read this to say it is exactly as I have suspected.  All these antibody development process really depend on the preexisting code.  In the forth or SMH case some process simply makes a C to U swap.  Different code, yes, but clearly not “new” in the sense of a new order independent of any preceding order. I hope you will agree with this interpretation?
     
    Thanks again for the reference.
     
    Ide

    • Charles Austerberry

      Dear Ide:
      Here I just want to note that while activation-induced deaminase indeed converts one pyrimidine (cytosine or 5-methylcytosine) into another pyrimidine (uracil or thymine, respectively), the range of possible outcomes is really quite large and to a great degree “independent of any preceding order.”  Here’s why:
      1) The U:G or T:G mismatch is a type of DNA damage that is then repaired by error-prone DNA repair.  It’s the DNA repair process that actually causes the sequence change (mutation), and the range of possible errors (DNA mutations) resulting from the repair is quite large.
      2) Given the nature of the genetic code, even if the range of possible mutations via DNA repair errors were quite limited (for example,  always replacing a C:G basepair with a T:A basepair), such transitions can have a variety of effects on the encoded amino acid sequence depending upon the affected triplet codon and the position of the base (1st, 2nd, or 3rd) that is changed within the codon.
      I’d be happy to explain the details more if you wish, but perhaps first it would be best to review the three separate posts I wrote earlier today that probably appear farther down in the post list.
      Cheers!
      Chuck

 

February 2010
M T W T F S S
« Jan   Mar »
1234567
891011121314
15161718192021
22232425262728

Email Notification for Posts