Home » Intelligent Design » It doesn’t matter what we name them…

It doesn’t matter what we name them…

proteasome

…the “machines” of the cell will still be what they are: complex, sophisticated molecular systems, essential for the living state. Like the proteasome on the right, a sub-cellular machine that degrades proteins, among its other functions.

Oops, there I went and did it — used the “machinery” language that Massimo Pigliucci (CUNY) and Maarten Boudry (Univ. of Ghent) argue not only plays into the hands of ID advocates, but also misleads scientists themselves:

…if we want to keep Intelligent Design out of the classroom, not only do we have to exclude the ‘theory’ from the biology curriculum, but we also have to be weary [sic] of using scientific metaphors that bolster design-like misconceptions about living systems. We argue that the machine-information metaphor in biology not only misleads students and the public at large, but cannot but direct even the thinking of the scientists involved, and therefore the sort of questions they decide to pursue and how they approach them.

In their paper, “Why Machine-Information Metaphors are Bad for Science and Science Education” (open access), Pigliucci and Boudry argue that the careless use of convenient information-theoretic and machinery metaphors, to name and describe the parts of organisms, begs the question in favor of intelligent design. Moreover, they urge, such language misleads scientists themselves. Genes, for instance, are not “blueprints” for organisms, nor is “information” a theory-neutral descriptor of nucleic acid.

What Pigliucci and Boudry seem not to remember, however, is if they wish to blunt the perception of design, human semantic practices — i.e., the use of words like “machine” to describe cellular entities — should be not the real target of their critique.

Rather, the evidence itself should be. A proteasome, or a ribosome, or a spliceosome by any other name would be just as complex. And fascinating.

In the 18th century, Dr. Johnson knew:

I am not so lost in lexicography, as to forget that words are the daughters of earth, and that things are the sons of heaven.

Really, Pigliucci and Boudry should be arguing that the data of molecular biology be kept away from ordinary folks, or from scientists themselves. Lock up the journals; hide the evidence.

P.S. I’m not kidding. I once heard Lynn Margulis say that she hated seeing central metabolism flowchart posters or diagrams taped up on laboratory office walls, because “people always get the wrong idea.” The wrong idea about what?

  • Delicious
  • Facebook
  • Reddit
  • StumbleUpon
  • Twitter
  • RSS Feed

26 Responses to It doesn’t matter what we name them…

  1. 1

    Prediction: Their warnings will go unheaded for the simple reason that it is impossible to the discuss the subject without design language creeping in.

  2. Their wishes will not come true. The descriptions stem from the functions. No one can hide that.

    (by the way, it was nice to meet you at SMU)

  3. U. BiPed,

    Nice to meet you too. I wish the event had allowed more time for Q & A.

  4. 4

    Some of the protein complexes in the cell are “machines” in every sense of the term. They are in fact compound machines that utilize simple machines (levers, wheels & axles, ramps) that transform or redirect energy to perform work (very useful work). They are machines in every sense of the term and to call them anything other than that is misleading. Consequently, these protein machines are also regulated by software.

  5. When I was getting my psychology degree I encountered that too. A psychologist wrote that she thought that psychologists should not use terms like “choice, happiness, love” etc. Only narrowly defined jargon is allowed.

  6. 6

    What is amazing to me is that the “motors” in some cases are actually reconfigurations of electron orbitals. I don’t know much about it, but it seems to me that we could learn more about quantum mechanics by studying the force generated by such reconfigurations.

  7. It is way to late to stop,,,,

    Programming of Life (Amazon #1 in category ranking)
    Excerpt: Richard Dawkins wrote, “The machine code of the genes is uncannily computer-like. Apart from differences in jargon, the pages of a molecular biology journal might be interchanged with those of a computer engineering journal.” (River Out of Eden: A Darwinian View of Life, 1995, pg. 17)
    http://scienceintegrity.net/ProgrammingofLife.aspx

    Bioinformatics: The Information in Life – Donald Johnson – video
    http://vimeo.com/11314902

    On a slide in the preceding video, entitled ‘Information Systems In Life’, Dr. Johnson points out that:

    * the genetic system is a pre-existing operating system;
    * the specific genetic program (genome) is an application;
    * the native language has codon-based encryption system;
    * the codes are read by enzyme computers with their own operating system;
    * each enzyme’s output is to another operating system in a ribosome;
    * codes are decrypted and output to tRNA computers;
    * each codon-specified amino acid is transported to a protein construction site; and
    * in each cell, there are multiple operating systems, multiple programming languages, encoding/decoding hardware and software, specialized communications systems, error detection/correction systems, specialized input/output for organelle control and feedback, and a variety of specialized “devices” to accomplish the tasks of life.

    Cells Are Like Robust Computational Systems, – June 2009
    Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,”We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail.”
    http://www.sciencedaily.com/re.....103205.htm

    Systems biology: Untangling the protein web – July 2009
    Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says. “The simple pathway models are a gross oversimplification of what is actually happening.”
    http://www.nature.com/nature/j.....0415a.html

    Simulations reveal new information about the gateway to the cell nucleus
    Excerpt: “There are whole machines in living cells that are made of hundreds or thousands of proteins,” says Schulten, “and the nuclear pore is one of those systems. It’s actually one of the most magnificent systems in the cell.”,,,Hundreds to thousands of NPCs are embedded in the nuclear envelope of each cell,”…
    http://www.psc.edu/science/2006/schulten/

    Life Leads the Way to Invention – Feb. 2010
    Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “ In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale.
    http://creationsafaris.com/cre.....#20100226a

    Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon – Charles H. Bennett
    Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,,
    http://www.hep.princeton.edu/~.....501_03.pdf

    Astonishingly, actual motors, which far surpass man-made motors in ‘engineering parameters’, are now being found inside ‘simple cells’.

    Articles and Videos on Molecular Motors
    http://docs.google.com/Doc?doc.....#038;hl=en

    Michael Behe – Life Reeks Of Design – 2010 – video
    http://www.metacafe.com/watch/5066181

    And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system.

    “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.”
    James Shapiro – Molecular Biologist

    etc.. etc.. etc..

  8. 8

    From #4, I suppose I should add that the “software” that regulates the protein machines is “software” in every sense of the term.

  9. 9

    I argued with a guy once who kept insisting that calling cellular components “machines” was just an analogy, and that no evidence for ID actually existed. I almost lost my mind.

  10. Actually, I taped the metabolism chart mentioned above, printed in A2, to the wall in my kids’ bedroom. Before they got the wrong idea, I also explained to them that compared to the small molecules depicted (like fructose) the machines that actually do the steps-by-step changes in the flowchart are as big as the entire poster. And each machine is purpose built and different from the others, unless they have the same name.

    I hope they don’t get the wrong idea…

  11. Alex:

    It really is too late.

    In the IOSE Intro-summary page, Fig. I.2 (b) has a link to the big detailed wall-chart. Part (a) allows us to compare it with the reaction and units diagram for an oil refinery.

    This is as complex and integrated as any known engineered chemical reaction system. the difference is, the living cell does it in a tiny dot, instead of a sprawling industrial plant.

    J S Wicken is apt:

    ‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [[originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [[“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65.]

    GEM of TKI

  12. Let us reduce the NAMES to their components describing only THINGS and STUFF or even further using only 1′s and 0′s. The MEANINGS of the SYMBOLS will still produce an image of a MACHINE in the mind of the hearer. No matter how they change the word the meaning remains.

  13. The last barrier evolutionists needed to overcome to deny a Creator was to prove that the appearance of design we see in nature was not so. They thought they had achieved this with Darwin’s molecules to man hypothesis of evolution by natural selection acting on random mutations.

    The problem for them now is that life is not as simple as it once appeared to be. A self replicating cell in not just a glob of chemicals that evolutionists originally believed it to be.

    Science has proven their hypothesis untenable. Not only is the complexity of life mind boggling but the supposed molecules to man evolution is no where to be seen, in spite of the vast amount of experiments carried and the millions of dollars spent in the effort in the last 150 years.

    Evolutionists are so desperate that even Dawkins will make such absurd statements as: “Evolution has been observed. It’s just that it has not been observed while it’s happening.”

    Huh! As far as I know I can only observe that which is happening in front of my very own eyes. What I observe in nature cries out for design, design everywhere, design that ultimately requires a Designer.

  14. It would seem as if at least one person was taking notes on May 14.

    IIRC, Stephen Meyer wasn’t very willing to defend the machine metaphor. In fact, he pretty much conceded that it is not a good argument for design.

    I still like my ARN sig line:

    “Machines are not made of parts that continually turn over, renew. The organism is.” – Carl Woese

  15. Machine-information metaphors are not metaphors, they are accurate descriptions of biological reality.

    So, apparently it’s “bad for science” to describe things as they really are. This is a very strange notion.

    Paul, your stuff is the best, and I always know that when you post here I’ll get yet another insight, presented with superb and economical eloquence.

    I am jealous of your talent.

  16. following kf’s link, here is a flow chart that can be printed out that people can be put up in their child’s line of sight so they might actually get the ‘right’ idea about life instead of the wrong idea that they were an accident:

    Map Of Major Metabolic Pathways In A Cell – Diagram
    http://www.sigmaaldrich.com/im.....17_04_.pdf

    ,,, perhaps, besides inventing a completely new language of obfuscation so as to deny the overwhelming inference to design in the cell, we should also try to do away with microscopes and animators to so that children don’t get the ‘wrong’ idea???

    CELL TO CARBON ATOM – SIZE AND SCALE – Interactive Graph – Move cursor at the bottom of graph to the right to reduce the size:
    http://learn.genetics.utah.edu.....lls/scale/

    Ben Stein – EXPELLED – The Staggering Complexity Of The Cell – video
    http://www.metacafe.com/watch/4227700

    The inner life of a cell – Harvard University – video
    http://www.youtube.com/watch?v=mbcWGU8fpxA
    User’s guide to the video
    http://sparkleberrysprings.com.....fcell.html

    further notes:

    Building a Cell: Staggering Complexity: – Feb. 2010
    Excerpt: “All organisms, from bacteria to humans, face the daunting task of replicating, packaging and segregating up to two metres (about 6 x 10^9 base pairs) of DNA when each cell divides,” “,,,the segregation machinery must function with far greater accuracy than man-made machines and with an exquisitely soft touch to prevent the DNA strands from breaking.” Bloom and Joglekar talked “machine language” over and over. The cell has specialized machines for all kinds of tasks: segregation machines, packaging machines, elaborate machines, streamlined machines, protein translocation machines, DNA-processing machines, DNA-translocation machines, robust macromolecular machines, accurate machines, ratchets, translocation pumps, mitotic spindles, DNA springs, coupling devices, and more. The authors struggle to “understand how these remarkable machines function with such exquisite accuracy.”
    http://www.creationsafaris.com.....#20100202a

    “To grasp the reality of life as it has been revealed by molecular biology, we must first magnify a cell a thousand million times until it is 20 kilometers in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would see then would be an object of unparalleled complexity,…we would find ourselves in a world of supreme technology and bewildering complexity.”
    Geneticist Michael Denton PhD., Evolution: A Theory In Crisis, pg.328

    “The manuals needed for building the entire space shuttle and all its components and all its support systems would be truly enormous! Yet the specified complexity (information) of even the simplest form of life – a bacterium – is arguably as great as that of the space shuttle.”
    J.C. Sanford – Geneticist – Genetic Entropy and the Mystery Of the Genome

    As well, the virus is far more complex than many people have ever imagined, as this following video clearly points out:

    Virus – Assembly Of A Nano-Machine – video
    http://www.metacafe.com/watch/4023122

    The bacteriophage virus – A molecular lunar landing machine
    http://www.metacafe.com/watch/4205494

    etc… etc… etc…

  17. Actually Dr. Boudry is somewhat right when he says this,,,

    ‘but we also have to be weary [sic] of using scientific metaphors that bolster design-like misconceptions about living systems.’

    ,,, He is right we should change our terminology,,, we should in fact quit calling the machines that man builds ‘machines’ since they are but poor reflections of the staggering levels of engineering in the ‘true machines’ found in life:,,,

    Bacterial Flagellum – A Sheer Wonder Of Intelligent Design – video
    http://www.metacafe.com/watch/3994630/

    Evolution Vs ATP Synthase – Molecular Machine – video
    http://www.metacafe.com/watch/4012706/

    Molecular Machine – The ATP Synthase Enzyme – video
    http://www.metacafe.com/watch/4380205/

    ,,,, but just what do we call our proto-machines that we build in our factories so as not to confuse them with the marvel of ‘true machines’ that we find in cells, so as not to ‘mislead students and the public at large’??? Any suggestions Dr. Boudry???

  18. I hope they are successful. It will only add to the evidence of the inefficacy of natural evolution to account for the brilliant elegance that is rampant throughout the biosphere. Let’s call these extremely complex, specified, efficient solutions one of the following:

    Mistakes
    Kludges
    Jumble of molecules
    Bloopers
    Lucky gaffes (“lucky” could be added to all)
    Blind blunders
    Selected aberrations
    Convenient bungles
    Rats’ nest of godlessness
    .
    In the end, though, Mr. Nelson is right; it is not the diction that makes these “machines” ID-friendly, it is their complex, specified function. And since it is not human language that is causing these to be portrayed as ID-friendly, it can mean only one thing: natural evolution is a creationist!

  19. You guys have to stop this right now.

    I have it good authority- Oleg Tchernyshyov- that is all emergence- from the laws that govern this universe to just about everything else including the biocomplexity we observe.

    Stuff happens and things emerge as a result.

    So enough of this Intelligent Design already- it’s all emergence.

    Any questions?

    The answers will emerge in due time…

  20. From now on I will no longer be known as Collin. I will be Jumble of Molecules Number 57R-00C7612Z-99.

    After all, that’s all I am.

  21. What’s in a name? that which we call a rose
    By any other name would smell as sweet;

    Excerpt:

    In the play Romeo and Juliet, the line is said by Juliet in reference to Romeo’s house, Montague which would imply that he was bad and they should not be together.

    Juliet:

    O Romeo, Romeo! wherefore art thou Romeo?
    Deny thy father and refuse thy name;
    Or, if thou wilt not, be but sworn my love,
    And I’ll no longer be a Capulet.

    Romeo:

    [Aside] Shall I hear more, or shall I speak at this?

    Juliet:

    ‘Tis but thy name that is my enemy;
    Thou art thyself, though not a Montague.
    What’s Montague? it is nor hand, nor foot,
    Nor arm, nor face, nor any other part
    Belonging to a man. O, be some other name!
    What’s in a name? that which we call a rose
    By any other name would smell as sweet;
    So Romeo would, were he not Romeo call’d,
    Retain that dear perfection which he owes
    Without that title. Romeo, doff thy name,
    And for that name which is no part of thee
    Take all myself.

    Romeo:

    I take thee at thy word:
    Call me but love, and I’ll be new baptized;
    Henceforth I never will be Romeo.

  22. My copy of Programming of Life arrived today. I’ll be through it by Sunday unless the fish are really biting this weekend. :-)

  23. Hah-hah- My copy arrived last week!

    But I haven’t had the time to get through the book just yet- 3 chapters down.

    I liked what I read so much I ordered “Probabilities Nature and Nature’s Probability”- both liteand the scientific version- lite arrived yesterday.

    The first chapter oflite is the same as te first chapter of “Programming”.

  24. Collin @20.

    That’s really sad. I am sorry for you.

  25. The sole argument I hear in this thread is ‘it’s very complex, therefore NS can’t explain it, therefore it must have been designed’.

    I don’t understand the reasoning that says that NS cannot explain complexity. What is is that sets the limits on this? I know ID folk don’t accept that evolutionary algorithms generate complexity, but I don’t understand why this is. I’ve heard arguments that the fitness function contains the information required to build the solution, and that this is supplied by humans. But in NS, the fitness function is supplied by the natural environment, so I don’t see that this argument has any force in principle.

    Secondly, why assume that if NS cannot explain something, then design is the answer?

  26. Peepl:

    The sole argument I hear in this thread is ‘it’s very complex, therefore NS can’t explain it, therefore it must have been designed’.

    Selective “hearing”.

    Machines- if they weren’t machines, jst a complicated mass of goo, we wouldn’t infer design.

    But yes, if blind, undirected (chemical) processes could account for those machines we wouldn’t infer the were designed.

    It tkes two things to get to the design inference- complexity and specification- and only one to refute it- demonstrating lind, undirected processes can produce it.

    Peepul:

    I don’t understand the reasoning that says that NS cannot explain complexity.

    It’s a strawman.

    I don’t know why anti-ID folks always have to misrepresent ID and then attack that misrepresentation.

    Peepul:

    Secondly, why assume that if NS cannot explain something, then design is the answer?

    We don’t.

    Anything else you need help with?

Leave a Reply