Re: [asa] Molecular Biology and Design

From: Nucacids <>
Date: Thu Jan 01 2009 - 18:03:26 EST

Hi Bernie,


"Also, as far as engineering invading biology- that's sounds like compartmentalist thinking. There really is no compartment of engineering and another of biology."


Sure there is. That's why universities have biology and engineering departments and each field has its own set of journals. But I would acknowledge that to some extent, compartmentalist thinking can be arbitrary.


"Engineering invades everything, just like computer programming. It is more a matter of increasing knowledge overlapping many fields of study. Engineering is really just applied science."


There is some truth to this, as I am sure there is all kind of cross-talk between disciplines. But engineering concepts have deeply penetrated the core aspects of molecular biology, not some peripheral specialty, more so than other fields.


Historically, systems biology follows on from molecular biology, a science based on many concepts more closely linked to arithmetic and computation than to classical physics or chemistry. - Antoine Danchin


Viewed in the light of the theory of computation, the problem of biogenesis appears just as perplexing as it does through the eyes of the physicist or chemist. And the difficulties are not purely technical. Thorny philosophical problems loom too. Concepts like information and software do not come from the natural sciences at all, but from communication theory, and involve qualifiers like context and mode of description-notions that are quite alien to the physicist's description of the world. Yet most scientists accept that information concepts do legitimately apply to biological systems, and they cheerfully treat semantic information as if it were a natural quantity like energy. Unfortunately, "meaning" sounds perilously close to purpose, an utterly taboo subject in biology. So we are left with the contradiction that we need to apply concepts derived from purposeful human activities (communication, meaning, context, semantics) to biological processes that certainly appear purposeful, but are in fact not (or are not supposed to be). - Paul Davies


And here's a little excerpt from my book:


"To further evaluate whether the metaphors used by biologists are unlike the metaphors used in other areas of science, I searched three scientific databases for design terms in February of 2003. The first database is called Biological Abstracts, which includes 5500 biology and medical journals. The second database is called GeoRef, which includes 3500 geoscience journals. GeoRef was chosen because most scientists believe that life was spawned from geological processes. Finally, I searched the database, INSPEC, which provides access to the literature in physics, electrical engineering, electronics, communications, control engineering, computers and computing, and information technology. The results are shown in Table 3-I.


The first thing to notice from Table 3-I is that in every case, these design terms and concepts were far more common in the biological literature than the geological literature. Rather than clustering with geosciences, the number of hits from the biological database are more similar to the hits picked up from searching engineering and information science databases. In fact, almost 1.8 million hits were obtained from the engineering database with an average of 69,216 hits per search phrase. This is roughly the same picture the biological database presents, with a little more than 1.2 million hits and an average of 46,499 hits per search phrase. In stark contrast, the geological database returned only a total of a little over 39,000 hits and an average of only 1511 hits per search phrase. To ensure that these hits were not simply reflecting the size of the databases, the term "energy," was also searched, as this concept would be expected to be universally important in all sciences. In this instance, the engineering database returned 1,076,830 hits and the biological and geological databases were quite similar, with 230,280 and 199,059 hits respectively. While the biological database stored non-teleological terms such as "energy" only 1.16 times more often than the geological database, it stored the teleological terms over thirty times more often. Clearly, the biological research is using terms and concepts that look more like something from the engineering research literature than from the geological literature."


Bernie: "When did this happen? "scientists imported engineering concepts into biology""


If you go back to my original posting, the quote from Lewontin answers this:


"Many biologists in the late 1950s (I among them) regarded with a certain contemptuous hauteur the attempts of renegade physicists to illumine the relation between gene and protein by engaging in the sort of cryptanalysis that became so romantic as a result of the wartime triumphs of Bletchley Park. But Kay shows quite convincingly that, although these codebreaking techniques could not in themselves provide the right answer, the view of DNA as code and amino acid sequence as plaintext was absolutely essential in the very conception of the critical experiments at the beginning of the 1960s."


Earlier than this, physiology was influenced by a different set of engineering concepts:


To maintain a constant internal environment requires control mechanisms: sensors, effectors, information processing and feedback systems. These terms were imported into the language of twentieth century physiology from control engineering in the 1940s-but they do not belong to the language of physics (or, indeed, of nineteenth century physiology). - Paul Agutter


Jacob and Monod would later extend such concepts into the cell in the form of gene expression (the lac operon) in the 1950s and 60s.



- Mike Gene

  ----- Original Message -----
  From: Dehler, Bernie
  Sent: Thursday, January 01, 2009 2:13 PM
  Subject: RE: [asa] Molecular Biology and Design

  David C. said:
  "Bernie has a very valid question. But as far as I know, and I get this from my biochem books, molecular biology is based quite a bit on probability calculations. "


  That's a lot different. In the case of my question, I'm saying probability and statistics is not important when dealing with cosmological infinity. For example, if the probability is 1 in billion, what does that matter when dealing with infinity? You could still have infinite occurrences. A low probability means absolutely nothing when dealing with infinity.


  However, in molecular biology, you aren't dealing with infinities, but with gene mutations (some assumptions based in accordance with some data) over a finite time.


  Nucacids said:
  "And molecular biology was institutionalized when scientists imported engineering concepts into biology."


  Also, as far as engineering invading biology- that's sounds like compartmentalist thinking. There really is no compartment of engineering and another of biology. Engineering invades everything, just like computer programming. It is more a matter of increasing knowledge overlapping many fields of study. Engineering is really just applied science.


  When did this happen? "scientists imported engineering concepts into biology"


  I see it just as a maturing of science. It happened as soon as the knowledge was available. Until the knowledge was available, it didn't happen. Some day people will be able to design their own organisms by directly manipulating dna code on a computer and simulating the life-form before it is even real (like we do with computer chip designs today- simulating products and testing them before they are even built). This is not a matter of waiting for the day for software engineers and biochemists to do it- is a matter of getting the information to do such a thing. So I don't think it is a case of scientists saying "Hey, we should import some engineering concepts into biology." It just happens naturally as the data is available. We probably all agree to that, so sorry for going on-and-on.




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Received on Thu Jan 1 18:03:55 2009

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