Does “Soft Machines” present arguments for Intelligent Design?

I’m normally pretty pleased when my book Soft Machines gets any kind of notice, but a recent rather favourable review of it leaves me rather troubled. The review is on the website of a new organisation called Truth in Science, whose aim is “to promote good science education in the UK”. This sounds very worthy, but of course the real aim is to introduce creationist thinking into school science lessons, under the guise of “teaching the controversy”. The controversy in question is, of course, the suggestion that “intelligent design” is a real scientific alternative to the Darwinian theory of evolution as an explanation of the origin and development of life.

The review approvingly quotes a passage from Soft Machines about the lack of evidence for how the molecular machine ATP synthase developed as evidence that Darwinian theory has difficulties. Luckily, my Darwinian credentials aren’t put in doubt – the review goes on to say “Despite the lack of hard evidence for how molecules are meant to have evolved via natural selection, Jones believes that evolution must have occurred because it is possible re-create a sort of molecular evolution ‘in silico’ – or via computer simulation. However, as more is discovered about the immense complexity of molecular systems, such simulations become increasing difficult to swallow.” This is wrong on a couple of counts. Firstly, as Soft Machines describes, we have real experiments – not in-silico ones – notably from Sol Spiegelman, that show that molecules really can evolve. The second point is more subtle and interesting. Actually, there’s a strong argument that it is in complex molecular systems that Darwinian evolution’s real power is seen. It’s in searching the huge, multidimensional conformational spaces that define the combinatorially vast number of possible protein conformations, for example, that evolution is so effective.

The review signs off with a reiteration of a very old argument about design: “In the final chapter, ‘Our nanotechnological future’, Jones acknowledges that our ‘…only true example of a nanotechnology…is cell biology…’. Could that lead to an inference of design? “ Maybe, like many scientists, I have brought this sort of comment on myself by talking extensively about “Nature’s design principles”. The point, though, is that evolution is a design method, and a very powerful one (so powerful that we’re seeing more use of it in entirely artificial contexts, such as in software engineering). However, design doesn’t necessarily need a designer.

“Truth in Science” may present itself as simply wishing to encourage a critical approach to evaluating competing scientific theories, but a little research reveals the true motives of its sponsors. The first name on the Board of Directors is Andy Mckintosh, Professor of Thermodynamics and Combustion Science at Leeds University. Far from being a disinterested student of purported controversies in evolutionary theory, this interview reveals him to be a young earth creationist:
“So you believe in a world created about 6,000 years ago, cursed on account of sin, then devastated by Noah’s Flood?
“Absolutely. There’s nothing in real science (if you take all the assumptions into account) to contradict that view.”

I don’t have a problem if people want to believe in the literal truth of either of the creation stories in Genesis. But I don’t think it is honest to pretend that a belief which, in reality, is based on faith, has any relationship to science, and I think it’s quite wrong to attempt to have these beliefs insinuated into science education in publicly funded schools.

16 thoughts on “Does “Soft Machines” present arguments for Intelligent Design?”

  1. I wonder if there is a risk that your emphasis on the superiority of biological machines over mechanical ones could be misinterpreted as a sort of vitalism. Perhaps you should clarify that there is no *fundamental* reason why mechanosynthesis and diamondoid designs cannot work, merely that certain designs you have seen appear to have practical flaws and limitations (if that would fairly represent your views).

  2. Hal, I think it is safe to say that anybody raised under a religious point of view can still interpret the world through that point of view even after becoming an agnostic or atheists. To be fair, the social impact and development timelines of MNT have been compared to Christian “end times” prophecies of doom and gloom, and there is some truth to that. It is also true that almost all religions make life out to be something special, scientists learning how to manipulate natural nanotechnology might get a (false or otherwise) sense of the superiority of life that could be characterized as “vitalism”.

  3. I missed the book in the Bible where Organic Chemistry and London Forces are discussed. Perhaps when (flesh and blood) humans were deciding which books written by other (flesh and blood) humans to include in the Bible, back in the middle-ages, they should have included imput from a chemist? Same goes for the Koran (written by a single flesh and blood human) and any other works penned by humans.

    Inspiration and vision is not synonomous with God. To believe that any “prophets” can know the mind of a being as powerful as God with absolute certainty is itself a sin. Andy Mcintosh is a child hopefully not successfully exporting his brand of thermodynamics to too many impressionable young adults.

  4. Hal and Nanoenthusiast, I know that people have interpreted my kind of view a vitalism, but this is a complete misunderstanding. What dictates the kinds of solutions biology has found, through evolution, is not any special mystique of life, but simply the nature of the physics that operates on the nanoscale. There is no reason why similar kinds of principles shouldn’t be executed using synthetic materials, and indeed I have called for a research program to do just this (especially here, in a piece later published as Jones, R.A.L. (2005) “Biomimetic nanotechnology with synthetic macromolecules” Journal Of Polymer Science Part B-Polymer Physics, 43 3367-3368 )

  5. I think there are a few additional restrictions that nature had to deal with that nanotechnologist do not have to deal with. First of all, in reality, the vast majority of the universe *is* a low-temperature vacuum. It is obvious that evolution would not produce self replicating machines on the cold side of an asteroid for any number of reasons. Not the least of which is that evolution requires fortuitous collisions of hundreds and thousands of atoms to self-assemble into a functional system, none of that can happen in a low-temperature vacuum because there is not enough energy and there are not enough lose molecules to bump into each other. Life is the result of the chaos in fluids, because chaos is the only thing that can make anything complex before intelligent life arrives on the scene. Only after intelligence emerges can that sterile, low-chaos environment of the vacuum be fully explored for potential productive nanosystems. The fact that nature never used that environment is not proof that it can’t be used by man. It may be that such machines are indeed impossible, but with the current state of nanoscience you can not say so with any certainty if they are or not possible.

    In short, nature had to use the chaos of self-assembly because, at the time, there was no one around to perform directed-assembly. Now that there are intelligent agents, i.e. people, around; the full potential (great or small) of directed-assembly at the nanoscale can be discovered.

  6. That’s a very interesting line of thought. Broadly you have to be right that to get evolution to work you need to be not to cold, and not too hot either. But cold and hot here are relative, relative some characteristic energy scale, which for biology is set by typical energies of things like hydrogen bonds and hydrophobic interactions. But, I wonder, there are other types of interaction and excitation which have quite different energies. Underneath the other question you raise is the whole vexed issue of teleology. Undoubtedly having an intelligent designer raises the possibility that you can design things for a wide range of purposes, but this isn’t actually inconsistent with using evolution to achieve those goals.

  7. “Undoubtedly having an intelligent designer raises the possibility that you can design things for a wide range of purposes, but this isn’t actually inconsistent with using evolution to achieve those goals.”

    But then why do bad things happen to good people?

  8. The kind of intelligent designer I had in mind here was a scientist doing the sorts of experiments Sol Spiegelman did, or for that matter the kinds of things Angela Belcher does to get macromolecules to optimally adsorb to a semiconductor surface. Here one essentially has a test-tube of molecules to be evolved, and you impose, from the outside, the selection pressure that gives you the result you want. This isn’t that different, I suppose, from doing dog-breeding on the molecular scale, if you see what I mean. I’m not getting drawn any further on what my own religious position is!

  9. One thing I wonder about synthetic macromolecules is, how do you know if you have created something truly synthetic? Obviously, if you make something that is not found on Earth then it is synthetic by Earth standards. Now, if what you have created in the lab is something that nature could, under a different set of circumstances, produced on its own; how do you know it is not currently being used by living systems on a planet a thousand light years from here? In fact, I think the whole field of biomemetic nanotechnology could give us much needed insight on extra-terrestrial biology centuries before we are able to explore distant star systems. The tools and techniques developed may also help to fill in gaps in the ‘molecular fossil record’ of our own planet.

  10. “I’m not getting drawn any further on what my own religious position is!”

    That’s fine. *I* would need to witness a genuine miracle before *I* would ascribe to the entities Spiegelman and Belcher, the rank of Deity.

  11. Nanoenthusiast, I think your comment is spot on. Biomimetic nanotechnology ought to give us a new window into exobiology, by broadening our conceptions of living systems to include systems based on different chemistries to life on earth, and systems that are optimised for different physical environments.

  12. Richard, I recently found this article that I think is very interesting with regards to our previous posts.
    It seems as though an organism has been found that is completely independent of the sun for its energy needs; it instead gets its energy from radiation.

    These types of discoveries are interesting because of what they might mean for the search for extra-terrestrial life. However, you must be careful in making extrapolations from them. The bacteria in the article most likely evolved in another environment and then gradually adapted to life in these rocks. It is not clear if the extreme environments where life is found on Earth (like the mine in the article and the area immediately around hydrothermal vents) can nurse the creation of life to begin with. It is suspected that the Jovian moon, Europa, may have an ocean of liquid water and hydrothermal vents teeming with life. For all we know, this type of environment may be sufficient for life to exist; but not to evolve in the first place, thus making the entire moon barren. In this respect, the field of biomimetic nanotechnology could be better suited at demonstrating under what conditions the molecular evolution that is the needed for life to start can occur compared to field discoveries on Earth.

    Alternatively, you could start the evolution process in one medium and make a sharp change to another, radically different one. Depending on the types of mediums used and the types of transitions used, you could make things that probably have no natural analogue

  13. My apologies, Nanoenthusiast, that your post got lost in my spam filter. These findings of life in extreme environments are very interesting and significant. Have you ever read “The deep hot biosphere” by Thomas Gold? Very unorthodox, even heretical, but certainly thought provoking.

  14. This is my first post here – I’ll have to spend some time reading through the archives. I remember reading Drexler’s Engines of Creation (another book which the creationists attempted to latch onto) on holiday with my wife – easily one of the most exciting books I have read!

    Those of us campaigning against them in the UK such as the BCSE ( ) , which I am a member of, have had reasonable success in countering the attempts of “truth” in science to sneak ID and creationism into the UK science classroom.

    A Government minister from the department for education made the following statement in Parliament:

    “Neither intelligent design nor creationism are recognised scientific theories and they are not included in the science curriculum, the Truth in Science information pack is therefore not an appropriate resource to support the science curriculum.”

    They are now clearly running around desperately trying to gather any possible sources of credibility to help build a “controversy” that simply isn’t there. Thanks for helping to debunk this particular claim!

    Ian Lowe.

  15. Richard Jones
    “But I don’t think it is honest to pretend that a belief which, in reality, is based on faith, has any relationship to science, and I

    think it’s quite wrong to attempt to have these beliefs insinuated into science education in publicly funded schools.” end Quote

    It’s interesting to see you make that statement. Let’s have a look at just who is operating on a belief by faith system here.
    Your intent in the statement above was to first;
    infer that anyone operating on a belief based on faith was unscientific and thus unworthy of serious consideration.
    infer that you do not operate on a belief based on faith and are thus worthy of serious consideration.

    So let’s have a look at the basis of your evolutionary belief and see what it is really based on.

    1) Have you or any other observer ever seen complex machines come into existence by anything other than inteligent design?
    2) Have you or any other observer ever seen complex machines evolve into a more complex form?
    3) Have you or any other observer ever seen biological complexity form from base chemistries in any natural environment envisionable for the early earth?

    If you have empirical evidence for any of the above then your foundational belief is scientific. However, if you do not have empirical evidence then you are operating on a faith based belief system just as creationists do.

    Richard Jones
    “Firstly, as Soft Machines describes, we have real experiments – not in-silico ones – notably from Sol Spiegelman, that show that molecules really can evolve.” end Quote

    It would appear that your definition of evolution is based on the results obtained by Spiegelman which in reality infers a one way street of complexity changing to simplicity as is noted in the excerpt below;

    In a classic experiment, Sol Spiegelman … showed what happens to a molecular replicating system in a test tube, without

    any cellular organization around it. The replicating molecules (the nucleic acid templates) require an energy source, building

    blocks (i.e., nucleotide bases), and an enzyme to help the polymerization process that is involved in self-copying of the

    templates. Then away it goes, making more copies of the specific nucleotide sequences that define the initial templates.

    But the interesting result was that these initial templates did not stay the same; they were not accurately copied. They got

    shorter and shorter until they reached the minimal size compatible with the sequence retaining self-copying properties. And

    as they got shorter, the copying process went faster. So what happened with natural selection in a test tube: the shorter

    templates that copied themselves faster became more numerous, while the larger ones were gradually eliminated. This

    looks like Darwinian evolution in a test tube. But the interesting result was that this evolution went one way: toward greater


    Unfortunately his experiment began with an existing functionally complex mechanism for which you nor he have any empirical evidence for cause of its origin and the experiment itself did not show the aspect of the evolutionary theory thats truly in question, which is “can evolutions proposed mechanism of mutation and natural selection form greater complexity from less complexity”. The only thing that Sol really showed was that left to natural action “existing complexities become less complex” just as the laws of thermodynamics would expect.

    The fact is you also operate on a belief system with a foundation of faith and I am left asking “who’s faith is more realistic to believe in, you or a creationist.” At this point I would take the creationists side simply because they admit in a faith based belief while you deny yours and bash them for theirs.

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