Programs, cells and letting God be God (A concluding reply to the Smithy)
|April 30, 2010||Posted by vjtorley under Intelligent Design|
I would like to thank Dr. Sullivan for his recent post, Nature, Artifacts, Meaning and Providence which has helped to clear the air enormously. In his closing comments, Dr. Sullivan calls for calm in the debate over life’s origin, and urges that the origin of life should be examined dispassionately, in an atmosphere free from theological bias. He is of course quite right, and in this post, I intend to engage him on precisely those terms. What I propose to do is address some general issues raised by Dr. Sullivan in his latest post on ID.
Life – an agreed definition?
While our views on the formal conditions for something’s being alive are somewhat divergent, I think we can now agree on the finalistic conditions.
In his his recent post, Nature, Artifacts, Meaning and Providence, Dr. Sullivan made some highly pertinent criticisms of the finalistic definition of life that I originally proposed, viz. that a living thing is a thing with a good of its own. This was followed by a helpful clarification (see UPDATE 2) by Professor Feser of an alleged difference I had pointed out between his way of talking about immanent causality and Dr. Sullivan’s. After reading their comments, I hope that Dr. Sullivan, Professor Feser and I can all agree on the following finalistic definition of life, which is adapted from a remark made in an earlier post by Professor Feser:
A living thing is a natural entity characterized by causal processes occurring within it, which can only be understood as terminating within and benefiting the organism considered as a whole.
Now I’d like to discuss the formal conditions for being alive. Dr. Sullivan has no quarrel with the second and third conditions I proposed (a nested hierarchy and embedded functionality), but he queries the legitimacy of describing the cell in terms of a program. To him, this terminology might be all right if it were merely metaphorical, but the literal usage strikes him as problematic. Now, cells of course do not understand “meaning,” and I would not say that “what happens in the generation of an organism is the application of meaning, according to grammatical rules, to transmit semantic content” (to quote Dr. Sullivan’s words), because this characterization overlooks the mechanics of generation. Instead, I would say that semantic content is indeed transmitted, but that this is accomplished by a chemical process, just as computers (whose programs embody semantic content) actually perform their calculations by means of processes at the electronic level. I would also claim that if scientists want to properly understand how cells work, then the only appropriate way to do so is to speak in terms of a program contained in their DNA. In other words, scientists need to employ the notion of semantic content to grasp how living things work. Now that is surely a very odd fact.
Is the “program” in the cell a real program?
The answer, I would maintain, is: yes, and it’s as literally a program as the nose on your face is literally a nose. There’s no metaphor here.
Both Dr. Sullivan and Professor Feser have queried my terminology here, so I’d like to cite a few scientifically respectable sources for my claim.
Let me begin with the late Daniel Koshland, Jr. (1920-2007), former editor of the journal Science, a long time professor of molecular and cell biology at UC Berkeley, and author of an oft-cited essay entitled, The Seven Pillars of Life, in Science 22 March 2002: Vol. 295. no. 5563, pp. 2215 – 2216, DOI: 10.1126/science.1068489. I shall quote a key extract:
What is the definition of life?… I think the fundamental pillars on which life as we know it is based can be defined. By “pillars” I mean the essential principles – thermodynamic and kinetic – by which a living system operates…
The first pillar of life is a Program. By program I mean an organized plan that describes both the ingredients themselves and the kinetics of the interactions among ingredients as the living system persists through time. For the living systems we observe on Earth, this program is implemented by the DNA that encodes the genes of Earth’s organisms and that is replicated from generation to generation, with small changes but always with the overall plan intact. The genes in turn encode for chemicals – the proteins, nucleic acids, etc. – that carry out the reactions in living systems. It is in the DNA that the program is summarized and maintained for life on Earth.
Here’s software developer Bill Gates (who is incidentally an atheist): “Human DNA is like a computer program but far, far more advanced than any software ever created.”(The Road Ahead, Penguin: London, Revised, 1996, p. 228.)
When Bill Gates says something like that, I pay attention.
I’d also like to quote from an article by Alex Williams, a creationist who spent most of his professional career working as a botanist for the Australian government, and who is currently a Research Associate at the Western Australian Herbarium, specializing in the taxonomy of grasses. The article is entitled, “Astonishing complexity of DNA demolishes neo-Darwinism,” and was published in the Journal of Creation 21(3), 2007 (pages 111-117). It is available online at http://creation.com/images/pdfs/tj/j21_3/j21_3_111-117.pdf . Here’s a short extract:
The traditional understanding of DNA has recently been transformed beyond recognition. DNA does not, as we thought, carry a linear, one-dimensional, one-way, sequential code — like the lines of letters and words on this page. And the 97% in humans that does not carry protein-coding genes is not, as many people thought, fossilized ‘junk’ left over from our evolutionary ancestors. DNA information is overlapping – multi-layered and multi-dimensional; it reads both backwards and forwards; and the ‘junk’ is far more functional than the protein code, so there is no fossilized history of evolution. No human engineer has ever even imagined, let alone designed an information storage device anything like it. Moreover, the vast majority of its content is metainformation — information about how to use information. Meta-information cannot arise by chance because it only makes sense in context of the information it relates to.
That’s just a short quote to whet the reader’s appetite. The author goes on to describe how DNA instantiates coding techniques that are more efficient than anything dreamed of by human computer programmers, with the same code having layers upon layers of meaning. His discussion of meta-information is also well worth reading. More recently, Alex Williams has published an update on his research at http://creation.com/astonishing-dna-complexity-update .
It was Williams’ article that alerted me to what ID was all about, a few years ago. I could finally understand the scientific evidence that living things had been designed by an Intelligent Creator. Living things contained programs that were cleverer than anything we could design. To not infer a Designer for these programs would be an act of intellectual blindness.
Finally, I’d like to cite Dr. Don Johnson, who has a Ph.D. in chemistry and a Ph.D in computer and information sciences, gave a presentation entitled Bioinformatics: The Information in Life for the University of North Carolina Wilmington chapter of the Association for Computer Machinery, on April 8, 2010. Dr. Johnson’s presentation is now on-line at http://vimeo.com/11314902 . Both the talk and accompanying handout notes can be accessed from Dr. Johnson’s Web page at http://scienceintegrity.net/ . Dr. Johnson spent 20 years teaching in universities in Wisconsin, Minnesota, California, and Europe. Here’s an excerpt from the presentation blurb:
Each cell of an organism has millions of interacting computers reading and processing digital information using algorithmic digital programs and digital codes to communicate and translate information.
I’d like to quote a brief excerpt from Dr. Johnson’s presentation:
“Somehow we have a genetic operating system that is ubiquitous. All known life-forms have the same genetic code. They all have the same protein manufacturing facilities in the ribosomes. They all use the same types of techniques. So something is pre-existing, and the particular genome is the set of programs in the DNA for any particular organism. So the genome is not the DNA, and the DNA is not the program. The DNA is simply a storage device. The genome is the program that’s stored in the storage device, and that depends on the particular organism we’re talking about.”
On a slide 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.
To sum up: the use of the word “program” to describe the workings of the cell is scientifically respectable. I would like to add that although I used the term “master program” in a previous post, it matters little for my purposes how many programs are running in the cell; what matters is that they are well co-ordinated. In the absence of this co-ordination, they would be unable to accomplish their respective tasks smoothly and harmoniously, as they would be liable to interfere with one another.
I believe that the question of whether the program contained in the DNA of cells is a real program needs to be turned on its head. The program in DNA is a paradigm of what a good program should be like. The question we should be asking ourselves is: do our poorly written human programs, which are but a pale imitation of the Real Thing, deserve to be called programs in the true sense of the word? In other words, the shoe is on the other foot. If the program in our DNA is not a program, then nothing is.
Future directions for science
If living cells embody programs which are far superior to anything written by our own scientists, then the future direction of science is clear: we have to reverse-engineer the cell. This is part of a grander project, which Dr. Steve Fuller has written about: the endeavor to reverse-engineer the Divine plan. Let me add that I do not believe that this project is tied to a mechanistic conception of life; rather I see it as a simple consequence of the fact that the Universe was designed to be understood. In so doing, we are “thinking God’s thoughts after Him,” as Newton put it.
As I see it, the atheistic denial of a Designer of nature is therefore a “science-stopper.” When scientists unthinkingly accept the common prejudice that Nature is blind, they stop looking for reasons why nature might do things in a particular way that may appear scientifically puzzling. Instead of digging deeper, they conclude that the organism they are looking at is a “kludge” or that its DNA contains “junk.”
The intellectual impetus behind ID is the conviction that the design we see in nature is intelligible to rational human beings who are prepared to look at nature with an open mind.
What does my “program argument” prove, anyway?
Both Professor Feser and Dr. Sullivan raise the legitimate question of whether my argument from “There is a program in our DNA” to “DNA was designed by an Intelligent Being” begs the question, in terms of its teleological assumptions. Let me say at the outset that I would not use this argument on a dyed-in-the-wool skeptic who denied the existence of teleology in living things. When arguing with such a skeptic, I would cite the ID argument made in Dr. Stephen Meyer’s Signature in the Cell. It is a simple fact that the DNA in the cell exhibits two properties: Shannon complexity and functional specificity. Thus we can describe it as containing specified information. The best explanation for the vast amount of specified information found in even the simplest living things is an intelligent designer. In the absence of such a designer, the likelihood of laws of nature and/or chance events generating the amount of specified information found in the cell is astronomically low. Dr. Meyer’s argument is solid and scientifically respectable, and can be used against any skeptic. It appeals to probabilities, not because it contains mechanistic assumptions, but because it seeks to engage skeptics on their own turf.
My argument that living things instantiate programs, and that neither the laws of nature nor chance are reliably capable of creating programs, leaving intelligence as the only reliable explanation of the programs we find in living things, is an argument that would appeal to anyone with an open mind. The argument does appeal to an immanently teleological feature of organisms: life instantiates programs. In that sense, it is indeed Aristotelian. But the argument does not require an explicit avowal of Aristotelian teleology. It simply invokes a commonly used way of talking about DNA, which many scientists feel increasingly comfortable with, and it proceeds from that starting point. Thus it appeals to a way of talking which is implicitly teleological, and then appeals to the elegance and perfection in the cell’s programs as evidence of a Higher Intelligence. As scientists make further discoveries of the beauty of the cell’s code in the years to come, I believe that this argument for a Designer of the cell will gain strength.
Beyond “either-or”: let God be God
In his post, Dr. Sullivan makes a plea for thinking that goes beyond “the dichotomy that God is either the blind watchmaker that winds up the universe at the big bang and then lets it unspool according to blind laws, or that he has to enter into the world and tinker around with particles in order to make things come out as he likes.”
I agree. The Judeo-Christian view is that God continually upholds nature, sustaining it in being by his Word. No living thing could survive even for an instant without God. God is infinitely more than a watchmaker.
But we know that life had an origin at some point. How did it originate? In my original response to the Smithy) , I was somewhat harsh in my criticism of the view that the laws of nature alone, combined with just about any old set of initial conditions, could have generated the first living thing. The language I used was rather judgmental, and I’d like to apologize for any offence caused. I have reflected on Dr. Sullivan’s arguments in his recent post, Nature, Artifacts, Meaning and Providence and have modified my own views somewhat. What I’d now like to do is make a short list of all possible origin-of-life scenarios, and briefly discuss the theological implications of each.
As I see it, the first living thing could have been generated by one of three processes:
(a) the laws of nature alone, with no need for a specific set of initial conditions, because any set of conditions would generate a living thing somewhere in the universe;
(b) the laws of nature, combined with a very specific set of initial conditions;
(c) an act of intelligent intervention, which may or may not have been followed by other acts of intervention.
Can anyone think of any others?
I have discussed something like scenario (a) previously from an ID perspective, in a short post of mine:
Because ID is agnostic regarding the Designer’s modus operandi, it allows for the possibility that scientists might one day discover bio-friendly laws, which, when combined, constitute a “magic pathway” leading from simple substances to complex life. But these laws would themselves have to be highly specific (e.g. relating to particular molecules), extremely numerous (perhaps numbering in the tens or hundreds of thousands), and in some way sequential (so that together, they would make up a series of stepping stones leading to life and complex animals). In short, they would be quite unlike any laws discovered to date, as the laws we know are general, relatively few in number, non-sequential and information-poor.
On this view, the laws of the universe are designed for life, but not for any particular life-form such as ourselves. Our own individual existence could still be planned, however, by God choosing a particular set of initial conditions at the moment of the Big Bang, which He knew would eventually give rise to us.
What ID tells us here is that if you want laws that will generate life under any set of initial conditions, they would have to be very, very specific. Life has a high degree of specified complexity. A simple set of laws won’t do the trick.
Scenario (b) has been discussed by Professor Michael Behe in The Edge of Evolution (The Free Press: New York, 2007, pp. 231-232). In essence, Professor Michael Behe’s proposal is that God set up the universe at the beginning of time with an extremely finely tuned set of initial conditions, so that all He had to do was press “Play,” as it were, and the universe then unfolded naturally, resulting in the first living organism. On this view, God designed the initial conditions, with a view to producing the first living thing.
The design implications of scenario (c) are too obvious to require spelling out.
Summing up, it seems to me that all three scenarios are ID-compatible. Scenario (a) would appear quite congenial to theistic evolutionists, and perhaps (b) as well. Scenarios (a) and (b) require no act of supernatural intervention within the cosmos to create life, but of course they require intelligence to design a cosmos that can generate life.
What does ID have to say about these scenarios? ID should remain “above the fray,” as it is concerned with science rather than theology. What the scientific discipline of Intelligent Design can tell us, however, is that the design of life, by whatever process, requires a great deal of specificity – whether in the laws of nature themselves, the initial conditions of the universe, or in an act of Divine intervention resulting in life.
I’d like to conclude by thanking Dr. Sullivan for a lively exchange. Dr. Sullivan’s concluding comments can be found here. I am grateful for the opportunity this exchange has afforded me to sharpen my own views on the origin of life.