Game on! A bioinformatician confronts Intelligent Design.
|January 16, 2012||Posted by vjtorley under Intelligent Design|
Professor Chris Hogue is a Canadian biochemist/bioinformatician who works on protein folding (among other things) at the National University of Singapore. Professor Hogue has recently started a new series on complexity and evolution on his Website.
It turns out that Hogue is highly critical of the Intelligent Design movement. But what makes his criticisms especially interesting for ID theorists is that they focus on the process of human design itself, which Hogue argues is indistinguishable from an incremental process of evolution.
In his first post on complexity and evolution, Professor Hogue begins with a short summary of his professional background:
As a mid-career scientist I spend my time teaching, building software, and researching topics on molecular assembly and evolution. My world of software gets more complex each year. I struggle to keep up with the latest methods, as does everyone, but I know that software grows in complexity one line of code at a time. So while I chase how complexity emerges in biology and software, I have a fascination with complex mechanical things created by the human design process. I will be posting articles and pictures here showing some of my collection of examples of human design at work. I hope to capture your interest with some better-known examples like the early stages of the Eiffel tower, and the earliest Harley-Davidson motorcycle which is still a functioning bicycle in every respect.
Hogue has some very interesting examples, too. His second post is about bottle corks and screw caps.
Hogue’s beef with Intelligent Design
Hogue explains the relevance of his examples of human design to the study of evolution:
The thread connecting these examples of human design is that each one is an analogy to biological evolution, from which evolution may be better understood by laypersons.
Is Hogue claiming here that human design is analogous to evolution, or that evolution analogous to design? In the passage above, Hogue appears to be making the former claim, but if he is doing so, then his conclusion, that by studying human design we can arrive at a better understanding of evolution, does not follow. Rather, the reverse follows: by studying evolution we can arrive at a better understanding of human design. That’s nice, but it won’t help laypeople wishing to get a better grasp of evolution.
If, on the other hand, Hogue wants to say that evolution is analogous to human design, then it would indeed follow that the study of human design processes can help us arrive at a better understanding of evolution. However, this analogy would also seem to imply that evolution itself might be an intelligently designed process.
Hogue appears to realize where his argument might lead, for he goes on to quickly disown this interpretation:
Now by posting new examples like this, I realize that they may all be stolen by the “intelligent design” (ID) creationists to argue against evolution. My view on ID follows that most clearly expressed in the 2005 court judgment from the Pennsylvania Kitzmiller v. Dover case: “The overwhelming evidence at trial established that ID is a religious view, a mere re-labeling of creationism, and not a scientific theory.”
I won’t waste time refuting the tired old “ID is religion” canard in this post, except to say that the fundamental difference between ID and religion is handily summarized here.
Now, at last, we get to the nub of Hogue’s quarrel with Intelligent Design theory. In his view, ID theorists badly misconstrue the process of human design, which is inherently slow and incremental, and never sudden:
My examples will show how ID concepts force the gerrymandering of human design history, and surround it with mystical borders to make their claims. The individual steps in human design are small, slow and absolutely require the intellectual imprinting of lessons by trial and error. Students who are led to think falsely about human design, or any complexity as having mystical origins are harmed by the diminishment of their own aspirations of creativity. We all need to understand how small steps and tools lead to human creativity and any object of complexity. I will reveal these small steps and show, where I can, the failures that led to success.”
Human creativity is always applied in small increments, as has been well stated by Thomas Edison and more recently by vacuum designer James Dyson. Complexity never gushes forth in a single setting. It accumulates, incrementally over time, and can be copied as a meme and reapplied. It is always more evolutionary than revolutionary.
Hogue concludes his post as follows:
Evolutionary processes have wonderful analogies in human design and I will go over many cases to show that complexity does in fact always arise from small steps. And when we take human design and shrink it down to the molecular level, as I myself have done, the human design process is indistinguishable from evolution. With an incomplete theoretical understanding of protein folding we lack the knowledge for de-novo design. So we apply our intelligence to choose the tool of evolution, and apply the force of selection accordingly.
Hogue is very cleverly trying to “re-frame” the whole issue of design vs. evolution. If the two processes can’t be distinguished, then there can be no evidence in principle that would count in favor of Intelligent Design and against neo-Darwinian evolution. (And I take it, from Hogue’s avowed incrementalism and his open expression of admiration for Richard Dawkins in his post, that it is the neo-Darwinian variety of evolution that he believes in.)
I shall argue below that Hogue’s argument is fundamentally flawed; nevertheless, it is a well thought-out position, which demands a thoughtful response from the Intelligent Design movement. I look forward to hearing the views of other Uncommon Descent contributors, who have had extensive experience in designing artefacts, on Hogue’s claims about the design process.
Hogue’s example: replacing corks in wine bottles
Synthetic cork in a bottle. Courtesy of Wikipedia. Photo by Daily Dog.
In his second post, entitled, Reason vs Ritual: The Slow Demise of Cork, Professor Hogue described the long process which led winemakers to replace the corks in wine bottles with a steel cap. Corks are liable to cork spoilage, which taints the wine in about 2% of all corked bottles. The new steel cap has a special polymer coating that provides the gas permeable qualities of cork and allows the wine to age while preventing it from being spoiled by metallic components.
Obviously, a fair bit of trial and error was involved in finding a bottle cap that best matched the taste found in untainted cork-sealed bottles, which wine connoisseurs agreed was matchless. But does that mean that human design is fundamentally no different from evolution? Not at all. The reason for the trial and error experiments was twofold: first, a significant number of intelligent agents were quite vocal about their preference for the taste of untainted cork-sealed wine; and second, human scientists are utterly unable to predict the taste of wine from a knowledge of the trace compounds leaking into it from the cork or cap. An omniscient Designer, or for that matter, a Designer from an alien civilization with a much more advanced technology than our own, would not be held back by the second obstacle, which merely proves that we’re not as clever as we sometimes like to think. As for the first reason: I have to say I don’t think that a strong cultural bias in favor of corked wine is a particularly good analogue for natural selection. (I might add that a solitary Designer of the first living cell on Earth wouldn’t have had to deal with this problem either; hence it cannot be regarded as inherent to the design process.)
What do other bioinformaticians think of Hogue’s argument?
I recently received an email from a bioinformatician who gave me his opinion of Hogue’s claims about human design. He commented:
I am mystified by Hogue’s argument. Does he not see that all his human designed analogies are examples of intelligent design at work. We do not improve Harley-Davidson motorcycles via an evolutionary process. Having worked in the aircraft engine industry early in my engineering career, there was always an enormous amount of (intelligent) evaluation, (intelligent) analysis, (intelligent) discussion and meetings, followed by (intelligently derived) goals, followed by (intelligent) description of the goals in the form of blueprints and functional information, followed by (intelligently) designed tools to make those changes, etc., etc.
It seems patently obvious to me that Hogue’s thinking is what some folks back home would describe as ‘bass ackwards’ ……. it is human intelligent design that shows that biological life is also an example of intelligent design, rather than biology revealing that human design is merely evolution sans brains, in action. What a joke!
Incremental doesn’t mean random
A chemist who contacted me regarding Hogue’s post pointed out another flaw in his logic: even if human innovation is always incremental, as he claims, that doesn’t make it random. The chemist remarked:
I do not think that because human innovation happens in incremental steps that this is somehow analogous to evolutionary theory. Human innovation is not purely random “trial and error” because the human being is selecting which trials to do and assessing the errors. I do not see how one can grant that much to a naturalistic process. As you stated, human innovation is always directed with an end in mind. These are not random trials and errors, but ones that are leading to a final goal.
I had noticed the same flaw in Hogue’s reasoning. Even if human innovation is always incremental, it is nevertheless often directed at long-term goals (e.g. putting a man on Mars, or making a computer that can win at Jeopardy) while Darwinian evolution is never directed at anything long-term.
There are a few modern evolutionists who have recently challenged the neo-Darwinist dogma that mutations occurring in organisms are random. (A good article to read in this context is Stephen Talbott’s Evolution and the Illusion of Randomness in The New Atlantis, Fall 2011.) As far as I know, however, Hogue is not one of these pioneers, so I shall assume that his version of evolution is substantially Dawkinsian. That being the case, there remains a fundamental difference between the incremental progress in human design, and the incremental change envisaged by neo-Darwinian evolution: the former is directed at a long-term goal, while the latter is not.
Code may grow incrementally, but never randomly (Update)
A series of codons in part of a messenger RNA molecule. Image courtesy of Wikipedia.
It is an undeniable fact that the notion of a code is a concept of fundamental significance in biology. All known life-forms have the same genetic code. Professor Hogue argues in his post that “software grows in complexity one line of code at a time,” which may be true, generally speaking. However, as a doctor friend of mine remarked, there is zero probability of randomly generating any significant “line of code”. That, he added, is the point that Intelligent Design theory repeatedly makes.
Codons, like individual letters, have no intrinsic meaning, but are merely symbols. In order to gain meaning, the symbols need to be combined in specified sequences, giving rise to “words” which possess a limited assigned meaning. These are then combined together to produce specified sequences of words, or “sentences,” that can convey even more meaning. This may take place as an incremental process, but it is always an intelligently guided process.
The chemist who contacted me highlighted a further underlying assumption on Hogue’s part: the truth of reductionism. In his original post, Hogue wrote:
Evolutionary processes have wonderful analogies in human design and I will go over many cases to show that complexity does in fact always arise from small steps. And when we take human design and shrink it down to the molecular level, as I myself have done, the human design process is indistinguishable from evolution.
The chemist who contacted me made the following observation on the above passage:
This is reductionism. I suppose if you broke down anything to the molecular level, it is all indistinguishable. It would all be a bunch of atoms interacting together. But this reasoning is like saying a book is just composed of a bunch of letters, and each book is indistinguishable from the next (at the molecular level or alphabetical level).
I’d like to add a comment of my own: if the human design process does turn out to be “indistinguishable from evolution” at the molecular level, as Hogue claims, wouldn’t this constitute striking positive evidence for Intelligent Design?
The astronomical odds against proteins forming by undirected processes
A further criticism I would like to make of Professor Hogue’s post is that although he alludes to protein folding, he fails to mention the astronomical odds against a functional protein of any kind arising by random processes, as well as the complete failure of scientific proposals to date for a non-random origin of proteins on the primordial Earth. Amino acids display no inbuilt bias for forming functional proteins. These and other difficulties are discussed by Professor John Walton in a short video on the mathematical problems associated with naturalistic proposals for the origin of life, available online at Evolution vs. Probability – Origin Of Life Math – Prof. John Walton. However, Professor Hogue glides over all these problems when he writes:
With an incomplete theoretical understanding of protein folding we lack the knowledge for de-novo design. So we apply our intelligence to choose the tool of evolution, and apply the force of selection accordingly.
This is what is popularly referred to as begging the question. Commenting on the last sentence in the quote from Hogue above, the chemist whom I contacted wrote:
His last sentence reminds me of Darwin’s example of dog breeding in Origin of Species, which is not analogous to evolutionary processes because it is directed.
Incremental design might be a good thing, even for an Intelligent Designer of life
Recently, in computer programming circles, the popularity of Incremental design seems to have been growing. James Shore and Shane Warden make a persuasive case for the merits of this kind of design in their book, The Art of Agile Development: Incremental Design and Architecture (O’Reilly, 2008), from which I shall quote the following excerpt:
Incremental design applies the concepts introduced in test-driven development to all levels of design. Like test-driven development, developers work in small steps, proving each before moving to the next. This takes place in three parts: start by creating the simplest design that could possibly work, incrementally add to it as the needs of the software evolve, and continuously improve the design by reflecting on its strengths and weaknesses.
To be specific, when you first create a design element — whether it’s a new method, a new class, or a new architecture — be completely specific. Create a simple design that solves only the problem you face at the moment, no matter how easy it may seem to solve more general problems.
This is difficult! Experienced programmers think in abstractions. In fact, the ability to think in abstractions is often a sign of a good programmer. Coding for one specific scenario will seem strange, even unprofessional.
Do it anyway. The abstractions will come. Waiting to make them will enable you to create designs that are simpler and more powerful.
The second time you work with a design element, modify the design to make it more general — but only general enough to solve the two problems it needs to solve. Next, review the design and make improvements. Simplify and clarify the code.
The third time you work with a design element, generalize it further—but again, just enough to solve the three problems at hand. A small tweak to the design is usually enough. It will be pretty general at this point. Again, review the design, simplify, and clarify.
Continue this pattern. By the fourth or fifth time you work with a design element — be it a method, a class, or something bigger — you’ll typically find that its abstraction is perfect for your needs. Best of all, because you allowed practical needs to drive your design, it will be simple yet powerful.
Throughout most of the four-billion-year history of life, living things have evolved at a fairly slow pace. This fits the pattern of incremental design. I would suggest that this may have been a good thing. Living things are multi-layered entities, and from a design perspective, the most important thing would be to make sure that organisms’ lower-level functions worked reliably in as wide a variety of circumstances as possible, and that in the event of a sudden environmental change, that they were able to mutate in a way that wuould maximize the chances of their progeny being able to cope with the sudden change. A long period of testing might have involved a lot less work for the Designer than the formidable task of coming up with perfect organisms up-front, at the dawn of life. If the Designer tends to work in a way that involves the least effort, one might therefore expect incremental design to be the norm in the evolution of life. From an Intelligent Design perspective, however, this evolution would still be directed at certain long-term goals: for example, the evolution of eukaryotes, of animals, and of sentient and sapient beings, as well as the less complex life-forms needed to support these beings.
When incremental design doesn’t work
So far, I have assumed that an incremental process is easier to implement than an up-front one. But occasionally there may be formidable biological hurdles where the desired outcome cannot be achieved without a more radical kind of design, because it is so immensely improbable. In this case, a one-off act of up-front design may be more practical.
An early trilobite, Paradoxides davidis. Image courtesy of Wikipedia. Copyright Sam Gon III.
I would suggest that the Cambrian explosion of 530 million years ago is a fairly clear example of up-front design. For it is here that we find a striking exception to Hogue’s claim:
Complexity never gushes forth in a single setting. It accumulates, incrementally over time, and can be copied as a meme and reapplied. It is always more evolutionary than revolutionary. And when it appears revolutionary, there are piles of failed, discarded or recycled prototypes behind the curtain. (Italics mine – VJT.)
Tell me, Professor Hogue: where are the failures from the Cambrian explosion? Where are the discarded or recycled prototypes? And why wouldn’t regard the emergence of 30 phyla over the space of 20 million years as a gushing forth of complexity? I won’t press my point here, except to recommend that you look at this Website: Darwin’s Dilemma.
Is human innovation always incremental?
But is Hogue correct in claiming that human innovation is always incremental? His appeal to Thomas Edison, who stated that “Genius is one per cent inspiration and ninety-nine percent perspiration,” is authoritative; but in the opinion of one prominent American scientist, Edison was a bumbling inventor:
His method was inefficient in the extreme, for an immense ground had to be covered to get anything at all unless blind chance intervened and, at first, I was almost a sorry witness of his doings, knowing that just a little theory and calculation would have saved him 90 percent of the labor. But he had a veritable contempt for book learning and mathematical knowledge, trusting himself entirely to his inventor’s instinct and practical American sense.
(Thomas Edison: Life of an Electrifying Man. Biographiq. 2008. p. 23. ISBN 1599862166.)
Who, you might ask, would say such a presumptuous thing about the man who invented the phonograph, the motion picture camera, and the first long-lasting electric light bulb, and held over 1,000 American patents? Edison’s critic was none other than the Serbian-American inventor, Nikola Tesla (1856-1943), pictured at the top of this post, of whom Ben Johnston wrote in the Introduction to his 1982 edition of Tesla’s work, My Inventions: The Autobiography of Nikola Tesla (Hart Brothers):
Nikola Tesla is the true unsung prophet of the electronic age; without whom our radio, auto ignition, telephone, alternating current power generation and transmission, radio and television would all have been impossible.
Tesla himself had a very different way of inventing things from Edison’s “one per cent inspiration and ninety-nine percent perspiration.” As he put it in his autobiography:
I am credited with being one of the hardest workers and perhaps I am, if thought is the equivalent of labour, for I have devoted to it almost all of my waking hours. But if work is interpreted to be a definite performance in a specified time according to a rigid rule, then I may be the worst of idlers. Every effort under compulsion demands a sacrifice of life-energy. I never paid such a price. On the contrary, I have thrived on my thoughts. (Italics mine – VJT.)
(Chapter 1 : Early Life.)
No perspiration here, it seems. From an early age, Tesla had a photographic memory and could visualize an invention in his brain in precise form before moving to the construction stage. In the first chapter of his autobiography, Tesla goes on to describe his method of invention, which he first came upon at the age of seventeen:
…I observed to my delight that I could visualize with the greatest facility. I needed no models, drawings or experiments. I could picture them all as real in my mind. Thus I have been led unconsciously to evolve what I consider a new method of materializing inventive concepts and ideas, which is radically opposite to the purely experimental and is in my opinion ever so much more expeditious and efficient. The moment one constructs a device to carry into practise a crude idea he finds himself unavoidably engrossed with the details and defects of the apparatus. As he goes on improving and reconstructing, his force of concentration diminishes and he loses sight of the great underlying principle. Results may be obtained but always at the sacrifice of quality.
My method is different. I do not rush into actual work. When I get an idea I start at once building it up in my imagination. I change the construction, make improvements and operate the device in my mind. It is absolutely immaterial to me whether I run my turbine in thought or test it in my shop. I even note if it is out of balance. There is no difference whatever, the results are the same. In this way I am able to rapidly develop and perfect a conception without touching anything. When I have gone so far as to embody in the invention every possible improvement I can think of and see no fault anywhere, I put into concrete form this final product of my brain. Invariably my device works as I conceived that it should, and the experiment comes out exactly as I planned it. In twenty years there has not been a single exception. Why should it be otherwise? Engineering, electrical and mechanical, is positive in results. There is scarcely a subject that cannot be mathematically treated and the effects calculated or the results determined beforehand from the available theoretical and practical data. The carrying out into practise of a crude idea as is being generally done is, I hold, nothing but a waste of energy, money and time. (Italics mine – VJT.)
Two electric induction motors. The induction motor was first invented by Nikola Tesla in 1883. Image courtesy of Wikipedia. Author: Zureks.
Tesla’s method of inventing was thus diametrically opposed to the incremental, experimental method employed by Edison. It is quite true that if we look at the history of the electric light bulb, for instance, we will find a pattern of incremental improvement. Tesla’s inventions, however, were quite different. Here is how he describes his invention of the induction motor in chapter three of his autobiography:
One afternoon, which is ever present in my recollection, I was enjoying a walk with my friend in the City Park and reciting poetry. At that age I knew entire books by heart, word for word. One of these was Goethe’s “Faust.” The sun was just setting and reminded me of the glorious passage:
The glow retreats, done is the day of toil;
It yonder hastes, new fields of life exploring;
Ah, that no wing can lift me from the soil
Upon its track to follow, follow soaring!
A glorious dream! though now the glories fade.
Alas! the wings that lift the mind no aid
Of wings to lift the body can bequeath me.
(translation by Bayard Taylor)
As I uttered these inspiring words the idea came like a flash of lightning and in an instant the truth was revealed. I drew with a stick on the sand the diagram shown six years later in my address before the American Institute of Electrical Engineers, and my companion understood them perfectly. The images I saw were wonderfully sharp and clear and had the solidity of metal and stone, so much so that I told him, “See my motor here; watch me reverse it.” I cannot begin to describe my emotions. Pygmalion seeing his statue come to life could not have been more deeply moved. A thousand secrets of nature which I might have stumbled upon accidentally, I would have given for that one which I had wrested from her against all odds and at the peril of my existence … (Emphases mine – VJT.)
(Chapter 3: My Later Endeavors – The Discovery of the Rotating Magnetic Field.)
Whence human creativity?
Tesla seems to have held contradictory views regarding the source of his creativity. He tells us in his autobiography that he realized at an early age that the appearance of clear images in his mind was always preceded by a vision of very unusual scenes, under highly peculiar conditions. (Tesla appears to have experienced synesthesia throughout his life.) The regularity of this correlation led him to believe that he was nothing more than an automaton, whose thoughts were entirely prompted by outside impressions, and it is clear from the final chapter of his autobiography that he was heavily influenced by the writings of leading biologists in his day, who maintained that life was a purely mechanical phenomenon.
On the other hand, Tesla also credited Divine Providence with saving his life and rescuing him from disaster on a number of occasions, which suggests that his conception of the universe was not entirely closed. Additionally, in chapter 5 of his autobiography (Wildside Press, Prime Classics Library, 2005 edition) we find a passage (which is curiously absent from this online version of his autobiography), where he attributes his creativity to God:
At this time, as at many other times in the past, my thoughts turned towards my mother’s teaching. The gift of mental power comes from God, Divine Being, and if we concentrate our minds on that truth, we become in tune with this great power. My Mother had taught me to seek all truth in the Bible; therefore I devoted the next few months to the study of this work.
(Chapter 5, p. 69, Wildside Press, Prime Classics Library, 2005.)
He then goes on to describe how he got an idea for wireless transmission as a result of noticing that in a thunderstorm, the release of electrical energy triggered precipitation. On this occasion, however, visualization of the solution did not come all at once, and he took a break from his work, returning to it in 1892. He then continues:
At this time I made a further careful study of the Bible, and discovered the key in Revelation. The first gratifying result was obtained in the spring of the succeeding year when I reached tensions of about 100,000,000 volts – one hundred million volts – with my conical coil, which I figured was the voltage of a flash of lightening (sic).
(Chapter 5, p. 71, Wildside Press, Prime Classics Library, 2005.)
In chapter 6 of his autobiography, Tesla acknowledged that belief in a “supreme power” or “dematerializing force” of some kind was a practical necessity, serving as “an ideal to govern our conduct,” and that a common conception of this higher power was “essential to the peaceful existence of humanity.”
Human creativity is a profoundly mysterious thing, which scientists are just beginning to explore. In the process, they will undoubtedly discover that some human activities are more automatic than we thought; but they will also discover that human beings are a lot more free and creative than we would have imagined possible. Never has human creativity blossomed so greatly in the course of history as during the last 100 years.
Professor Hogue’s proposal that human design resembles trial and error process has been examined and found wanting on a number of counts. That does not make it entirely without merit; but what I would argue is that the analogy goes the other way: evolution is like design, rather than design being like evolution. To the extent that evolution is like design, it is not a trial-and-error process.
I look forward to reading Professor Hogue’s future posts on the history of human inventions.
(H/T Professor Larry Moran (7 January 2012):
Chris Hogue on Complexity and Evolution )