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Life, Purpose, Mind: Where the Machine Metaphor Fails

cover story ann gauger on information.jpg

[This article is authored by Biologic research scientist Ann Gauger, whose work uses molecular genetics and genomic engineering to study the origin, organization and operation of metabolic pathways. She received a BS in biology from MIT, and a PhD in developmental biology from the University of Washington, where she studied cell adhesion molecules involved in Drosophila embryogenesis. As a post-doctoral fellow at Harvard she cloned and characterized the Drosophila kinesin light chain. Her research has been published in Nature, Development, and the Journal of Biological Chemistry. Dr. Gauger also appears in the upcoming film Metamorphosis.]

Over the last decade I've become convinced that in spite of our overflowing databases we don't understand much about biology. We're like students who have learned the Bohr model of the atom, and think we have grasped atomic structure. As a beginning, it's a decent approximation. But atomic structure goes way beyond this simple model.

In the same way, we're accustomed to talking and thinking about the cell as made up of machines (hardware), with DNA as the software program that somehow determines the hardware. This is an advance over imagining the cell as a few simple chemical reactions. But it's still radically inadequate, if not obsolete, when trying to capture the reality of what we're discovering in the biological world. We're in search of more adequate conceptual categories. And the outcome will make our current descriptions look utterly inadequate. What we want to do is to catch up to the evidence, and get beyond our own, quite limited ways of speaking of these realities.

In a recent essay Steve Talbott highlights the inadequacies of our current way of thinking and speaking about biology. He points out that organisms are more than the sum of their mechanisms. In fact, he rejects the machine metaphor as completely inadequate to describe living things. Living beings are adaptable and responsive to their environments, changing their behavior based on external cues and their own requirements. They are transformative, existing as entities that are much more than the molecules that compose them. They are not what they eat -- they make what they eat into themselves. Living beings are integrated wholes that come from other living things. And they are more than their DNA. DNA requires a functional cellular environment to be properly read and interpreted, just as a cell requires DNA to be able to sustain itself. In order to understand the whole picture you have to look at the cell from many points of view, not just a gene-centric one.

Everything in organisms is interconnected causally. Everywhere in biological systems, chicken and egg problems abound. For example, amino acid biosynthesis pathways are composed of enzymes that require the amino acids they make, ATP biosynthesis pathways must have ATP to make ATP, DNA is needed to make proteins, but proteins are needed to make DNA, and the list goes on. Indeed, the scope of the problem is difficult even to grasp.

Ultimately, cellular systems can be made only by -- wait for it -- cells. We can isolate ribosomes or nuclei or mitochondria or Golgi, and study their parts, but we can't build them, even though we know what they are made of. It takes a whole cell to make them. For example, ribosomes and spliceosomes, the large ribonucleoprotein particles that are essential for the processing and translation of messenger RNAs into protein, must be synthesized, modified, and partially assembled in particular regions of the nucleus, and then be exported to the cytoplasm for further modification and assembly. Literally hundreds of other proteins and RNAs are involved in these dynamic processes, enabling the many RNA-RNA, RNA-protein, and protein-protein interactions and rearrangements that are required, all the while proof-reading and removing stalled assemblages that may occur along the way.1

What kind of processes can produce such interconnected, self-reproducing systems? Can a bottom-up process like neo-Darwinism boot-strap its way to such causally circular beings?

Many biologists would answer yes, because after all, what else is there besides neo-Darwinism? Their prior commitment to mechanistic, reductionist thinking and materialist presuppositions prevents them from seeing the problem. In fact, this insistence on purely materialistic, bottom-up explanations goes back a long way.

I have a book of lectures given at MIT by the famous developmental biologist and geneticist, Edmund Wilson, in 1923. The book is called The Physical Basis of Life. Wilson acknowledged that we knew nothing about the origin or functioning of cells or the development of body plans, but insisted as an article of faith that there would be a purely physical explanation, based in chemistry.

Up until now, the materialist, reductionist method has been very successful, because cells can be ground up, probed, measured and tested in a way that life forces or agency can't be. But now molecular, cellular, and developmental biologists are drowning in a flood of data that we don't know how to interpret. We do not know, for example, how to read a genome from an unknown new species to say what kind of organism it will produce. We can only determine what other genomes it most closely resembles. In order to predict the nature and appearance of the organism with that genome, we would need to know -- just for starters -- the maternal and paternal contributions to the egg and sperm, the whole of the developmental path from egg to adult, plus the particular effects of any mutations within that genome on its phenotype, not to mention its environmental history.

When we rely only on a reductionist approach, we cannot see the organism as a whole. An extremely simple analogy, drawn from a human artifact, might help to see why. Imagine an elaborately knit sweater, maybe an Irish fisherman's. Someone who wants to understand the sweater finds a loose end and starts to pull. He keeps pulling and pulling, expecting to arrive at some causal knot, until the whole thing comes apart and is unraveled on the floor. The sweater as a functional whole depends on the way the wool twines together. To understand the sweater you have to look at the patterns in the whole, not just what it was made of. Pulling it apart destroys its essential nature. Now this is a very poor analogy, but scientists are often like that poor fellow tugging on the string.

I like to show a video to illustrate why we need to look top down as well as bottom up. It's a real-time visualization of a living cell, with various structures (organelles) highlighted one by one. Go here to see it.

These cellular components, and many others, function in a very crowded cellular milieu, somehow recognizing the molecules and structures with which they are supposed to interact. They send and receive signals, correct errors, and adjust their activity in a dynamic way according to the needs of the whole organism.

Notice the language of intentionality in the last paragraph: 'function', 'recognize', interact', 'signal', 'correct', 'adjust'. Such language is common in biological writing. Talbott points this out also, and explains why (emphasis added):

[Because] there is no possible way to make global sense of genes and their myriad companion molecules by remaining at their level, researchers have "simply bestowed upon the gene the faculty of spontaneity, the power of 'dictating,' 'informing,' 'regulating,' 'controlling,' etc." And today, one could add, there is at least an equal emphasis on how other molecules "regulate" and "control" the genes! Clearly something isn't working in this picture of mechanistic control. And the proof lies in the covert, inconsistent, and perhaps unconscious invocation of higher coordinating powers through the use of these loaded words -- words that owe their meaning ultimately to the mind, with its power to understand information, to contextualize it, to regulate on the basis of it, and to act in service of an overall goal.
Recognizing the implied intentionality in such language, several authors have called for biologists to abolish these words from their writing. According to them, anything that implies either teleology (being directed toward a goal or purpose) or agency (intelligence acting to produce an effect) is to be eschewed. After all, both teleology and agency have been discarded by modern biologists, along with vitalism. Yet teleological language persists. Maybe the reason such language is so common in biology research is because living things are directed toward a purpose. Maybe biological systems do reflect intelligent agency, because intelligent agents are the only known source capable of designing, assembling, and then coordinating so many interrelated sub-systems into a functional whole. And maybe, by acknowledging this, we can come to understand biology better.

Notes
1Staley JP, Woolford JL (2009) "Assembly of ribosomes and spliceosomes: complex ribonucleoprotein machines." Curr Opin Cell Biol. 21: 109-118. doi:10.1016/j.ceb.2009.01.003.


22 Comments

As an agnostic I reject neo-Darwinism and am just as offended as any theist at having philosophical materialism imposed upon science. If consciousness and purposeful creativity exist as aspects of reality, a deity may or may not participate in the process. However one doesn’t even have to be religious to be sceptical that “natural selection” (premature death or lessened fecundity) might somehow (???) organize random mutations (genetic accidents) into complex biological structures.

A Few Impertinent Questions about Autism, Freudianism and Materialism

http://30145.myauthorsite.com/

I'm a working biologist, on bacterial regulation (transcription and translation and protein stability) through signalling molecules, so I guess I have a different approach to this article that most would.

And yet I can confirm the following points as realities: we lack adequate conceptual categories for what we are seeing in the biological world; with many additional genomes sequenced annually, we have much more data than we know what to do with (and making sense of it has become the current challenge); cells are staggeringly chock full of sophisticated technologies, which are exquisitely integrated; life is not dominated by a single technology, but rather a composite of many; and yet life is more than the sum of its parts; in our work, we biologists use words that imply intentionality, functionality, strategy, and design in biology--we simply cannot avoid them.

Furthermore, I suggest that to maintain that all of biology is solely a product of selection and genetic decay and time requires a metaphysical conviction that isn't troubled by the evidence. Alternatively, it could be the view of someone who is unfamiliar with the evidence, for one reason or another.

But for those who will consider the evidence that is so obvious throughout biology, I suggest it's high time we moved on.

To me as an ardent Theist, life doesn’t just whisper “design” it vigorously shouts it loud and clear! This notion that the deity is somewhat illusive and discrete in presenting his creative works is wholly a projection of the Atheist. The complexity is an advertising billboard, writ large as to call mankind to its senses! I do appreciate that methodological naturalism has made the world a saner place; that being objective is a path to balanced enquiry. Yet, one must also concede that no human being is purely objective; that try as we may, we do take sides, on various issues. When the ultimate question is put forward, “is life a product of an intelligence?” the answer will inevitably polarize people. It’s like the controversy about global warming; some will and some won’t accept the notion. The idea that a human being can be totally objective when it comes to life’s design accreditation, Darwin’s Theory or I.D, I think generates a lot of dishonesty and self deception.

Fundamentally, the likes of Richard Dawkins – hates the “Judaeo-Christian God:” yet he denies his bias using spurious excuses. Such ones, in all my blogging battles, have Theophobia. Its an irrational fear, which I think has come about through the very unappealing unfortunate image of the Churches of Christendom. Unfortunately, I can sympathise; Isaac Newton had a profound disdain for the Churches – yet was an ardent Theist.

The investigator, who does not care either way who the designer is, will accept I.D. The one who has an issue with God – will never accept I.D. Others just don’t want to appear as the outsider and want to keep their institutions free from ill repute. When the issue is deeply personal, its implications personal, how can anyone pretend to be objective?

Thanks for all the kind comments.

If you haven't already, I encourage you to read Talbott's piece at The New Atlantis for more examples of the "wholeness" of being. Here's the link in case you missed it.

http://www.thenewatlantis.com/publications/the-unbearable-wholeness-of-beings

Dear Casey Luskin; et al,

I just had an idea hit me. The only reason the materialists immediately jump to the supernatural when intelligent design is obvious is that human intelligence can in no way do what "Nature" (sarcasm here for those of you who miss it) has done on its own. Since human designers cannot even come close, the only recourse is to posit the supernatural.

So the materialist make a strong case for theism being the only other game in town, hence creation and evolution are mutually exclusive!

We own Dr. Kehl a big favor.

If one were to ask a neo-Darwinist to distinguish life from non-life could they do so without using the supernatural concepts of self-awareness and purpose? I think not.

In fact, I think that “purpose” is actually the fundamental driving force of their flawed evolutionary theory. Survival is purpose. The competitive aspect of natural selection implies that the being doing the competing is self-aware (I am) and is purposeful (I want to be).

Furthermore life itself is distinguished form non-life through the attributes of growth, metabolism, response and ultimately reproduction. I would argue that none of these basic life processes can be described or defined without using the concepts of purpose and self-awareness (and information).

The purpose of reproduction is an acknowledgement of another unique attribute of naturalistic life that helps to to demonstrate these supernatural concepts . . . death. Death results in no immediate physical change to the natural “ingredients” of the body (nor the coded information for that matter). The only change at the instant of death is the loss of self-directed purpose (I want to be) and awareness (I am).

Maybe the simple answer to the question “What is the purpose of life?” is actually that life IS the purpose, (at least for those living organisms that don’t have a soul . . . but that’s another topic).

Bottom line is that any evolutionary biologist who claims that “purpose” is unnecessary for the defense of their theory disregards fundamental realities of both the theory and the phenomena it attempts to explain.

I would like to thank Dr. Gauger for a wonderful and thought provoking essay.
The discussion of the power of reductionism- and its possible short comings- occurs in discussions of physics as well.
http://scienceweek.com/2005/sw050916-6.htm

It must be OK to question basic assumptions, or it's not likely you are doing science.
But does the current state of evidence justify such questioning?
It seems a somewhat contentious issue. Should I be surprised?

One wonders what makes scientists study cells. Is it a mechanistic drive to save themselves from a hostile environment? (Pretty slick labs to do that in.) The very study indicates purposefulness.

I don't mean to pile on Dr. Kehl here and in fact I do appreciate the fact that he’s willing to come and post in this forum. Nonetheless, his understanding of intelligent design is flawed.

Dr. Kehl, you compare intelligent design (ID) to "Cargo Cults" claiming that like Cargo-Cults, ID is "un-supported by objective evidence." Your argument has a major flaw, and it is refuted by the very quote you provide from Ann Gauger when she writes:

because intelligent agents are the only known source capable of designing, assembling, and then coordinating so many interrelated sub-systems into a functional whole

Here’s the flaw: Well-coordinated interrelated sub-systems that combine into a functional require a goal-directed process to originate, and if intelligent design is a goal-directed process (which it is), then ID IS supported by objective evidence.

Unfortunately, your rebuttal then misrepresents Ann Gauger's thesis, as you then you write: "Dr. Gauger’s thesis seems to be: if scientists cannot explain an observable phenomena then the explanation must come from the supernatural."

Where did Dr. Gauger appeal to the supernatural? If you notice, she didn’t. She appealed to intelligent agency.

Appealing to intelligent agency is different than appealing to the supernatural. Intelligent agency is a much more limited causal inference, and it IS scientific because we have much observation-based experience with how intelligent agents design things, and we observe that they produce interrelated sub-systems that combine into a functional whole. No other cause we observe in nature can do this. So ID is supported by objective evidence.

In closing, your discussion of Cargo Cults is irrelevant because ID is nothing like Cargo Cults. Gauger’s argument does not "invent an explanation". Rather, it uses known causes we understand from observations of the world around us (i.e. intelligent agency) as an explanation. Thanks.

Sincerely,

Casey

Kehl said, "Since nobody knows the origin of life one cannot say “Maybe biological systems do reflect intelligent agency, because intelligent agents are the only known source capable of designing, assembling, and then coordinating so many interrelated sub-systems into a functional whole.” If you don’t know, you don’t know. Don’t invent an explanation."

If you don't know, why do you rule out intelligence? The cargo cult recognized the cargo came from intelligent agents. That puts them ahead of the evolutionist who believes living "cargo" spontaneously arose on its own.

Kehl writes;
If you don’t know, you don’t know. Don’t invent an explanation.

So, I suppose Kehl would have us believe that natural selection acting on random mutation is not an invented explanation.

Speaking for myself, "believing" in such a proposal requires more faith than critical thinking (a form of thinking which excludes circular reasoning) permits.

Kehl is misconstruing Gauger’s suggestion in the crudest possible way. The suggestion is NOT that we don’t know how the processes of life work, so therefore, God did it. Her suggestion (building on Talbott's article), rather, is this: the more and more we discover of life, the more it exhibits the work of an intelligence vastly exceeding our own, and the less it submits to reductionist stories left over from the nineteenth century.

It does NOT look like something cobbled together from natural selection acting on random mutations along the DNA molecule, or cooked up from simple chemical reactions in a warm pond.

In this and many other cases, intelligence can be inferred from the evidence. It’s not an argument from ignorance. Even though we are just beginning to understand what's going on inside cells, what we do know bespeaks intelligence. The fact that the aborigines made a mistake about the American cargo doesn’t gainsay that.

In fact, the Cargo cult example doesn’t even establish the point Kehl wants to make. While the aborigines were mistaken about the identity of the agents who brought them the cargo, they were right to recognize the product of intelligent agency based on its advanced technology.

If the reductionist mindset makes it impossible for someone to tell the difference between an argument from ignorance and an inference to design, then that’s another strike against reductionism.

Remember the Cargo-Cults of WWII? http://en.wikipedia.org/wiki/Cargo_cult && http://www.damninteresting.com/john-frum-and-the-cargo-cults/

Aborigines of the South Pacific had made contact with American troops and became the recipients of comparatively high technology. After the Americans departed, the Aborigines sorely missed the wonderful items brought to them by the C-54 cargo planes. As long as they used the American rifles to kill as many Japanese as possible, the C-54 largess continued to flow.

Of course the war ended and the Americans departed -- and the largess stop. The Aborigines were totally mystified. So they did the best they could. They invented a whole new religion, invented and built sacred icons, made up a whole mythology complete with prayers, all in hopes that the cargo would start to flow again. Of course, all prayers to the Cargo gods went unanswered.

Moral of the Cargo-Cult story: inventing explanations un-supported by objective evidence is a futile pursue. Specifically, Dr. Gauger’s thesis seems to be: if scientists cannot explain an observable phenomena then the explanation must come from the supernatural (which, to the scientist, is no explanation at all). There are many phenomena that science cannot explain -- there are also many phenomena that were originally unexplained but eventually gave way to investigation.

Since nobody knows the origin of life one cannot say “Maybe biological systems do reflect intelligent agency, because intelligent agents are the only known source capable of designing, assembling, and then coordinating so many interrelated sub-systems into a functional whole.” If you don’t know, you don’t know. Don’t invent an explanation.

Great points, and story, though I think that the ending could have been a little more developed for the non-ID reader/believer.

Thank you for taking the time to write this, and keep it coming and developing. Let's move some mountains.

Good analogy, David. And the complexity of cells is certainly millions of times greater than that of the CPU!

Very good article that sums up quite nicely the increasingly overwhelming problem facing anyone who insists on clinging to a materialist, reductionist view of the world. I have said this before, but this article brings to mind once again what seems totally obvious to me: it is only a matter of time (one or two decades, I would guess) before it will be impossible for anyone who knows anything about biology to continue to believe that living things were not engineered. As Michael Behe says so eloquently, "Life reeks of design." When that happens, materialism will no longer be a tenable philosophical position, and we will see a new birth of spirituality among not just ordinary people, but among the intelligentsia as well. It will be very interesting to see what form that spirituality takes.

How ironic is it that science, the very club the materialists have tried to destroy theistic religion with, is now destroying their materialist religion.
Materialism simply cannot explain the incredible complexity and functional information found in living systems; not even the simplest ones.

This article is a welcome one -- it seems like a vindication of irreducible complexity. I realize that Talbott's article is not from a technical journal, but I sense there are indeed more and more scientific papers coming out that support a teleological ID position.

Coming form the mind of an MIT biologist, this article is a beautiful essay technology and the purpose of life. Bravo!

In the modernist project, the goal was to have neatly defined and separated fields of study. Thus, if there was a challenge to the materialist paradigm in science (evidenced or metaphysical), it was sectioned off into philosophy, theology or another field of study. Eventually all of those items that you've hidden under the rug start to overflow and make the room look rather messy.

When we rely only on a reductionist approach, we cannot see the organism as a whole. An extremely simple analogy, drawn from a human artifact, might help to see why.
Reminds me of the phrase "Cannot see the forest for the trees."

Yeah, I fully agree with this article. Not just because I’m a Theist, but because it manifests humility in the face of the sheer volume of data, I imagine, flooding the senses when one were in a position of directly examining biology. I’m no expert, although I did study a little electronics. As a parallel, to me the current Intel CPU architecture, and the descent to the 22nm scale, seems impressive. And as pointed out, nothing really can exist without reliance on other systems to exist in tandem. A 22nm processor needs a whole raft of technologies fully operational for its inception let alone its production. Also, beyond its technical wizardry, one has to step back and view the larger picture and contemplate the purpose of such a piece of engineering. There are market forces, geo-political variables that dictate its commercial success. Technology today is not the product of a single mind, as back in the days of Edison; they are products of a whole array of minds – beavering away – for their own and group interest. If one could imagine a single mind capable of visualising the whole flow of the global economy, one would attribute to such an individual divine prowess. In biology, it’s currently inadmissible to do the same. Still, surely, now, none would entertain chance as a credible agent in all this - organizational enterprise?