Posted on 03/15/2005 2:41:19 PM PST by Michael_Michaelangelo
The Future of Biology: Reverse Engineering 03/14/2005 Just as an engineer can model the feedback controls required in an autopilot system for an aircraft, the biologist can construct models of cellular networks to try to understand how they work. “The hallmark of a good feedback control design is a resulting closed loop system that is stable and robust to modeling errors and parameter variation in the plant”, [i.e., the system], “and achieves a desired output value quickly without unduly large actuation signals at the plant input,” explain Claire J. Tomlin and Jeffrey D. Axelrod of Stanford in a Commentary in PNAS.1 (Emphasis added in all quotes.) But are the analytical principles of reverse engineering relevant to biological systems? Yes, they continue: “Some insightful recent papers advocate a similar modular decomposition of biological systems according to the well defined functional parts used in engineering and, specifically, engineering control theory.”
One example they focus on is the bacterial heat shock response recently modeled by El-Samad et al.2 (see 01/26/2005 entry). These commentators seem quite amazed at the technology of this biological system: In a recent issue of PNAS, El-Samad et al. showed that the mechanism used in Escherichia coli to combat heat shock is just what a well trained control engineer would design, given the signals and the functions available.
This is no simple trick. “The challenge to the cell is that the task is gargantuan,” they exclaim. Thousands of protein parts – up to a quarter of the cell’s protein inventory – must be generated rapidly in times of heat stress. But like an army with nothing to do, a large heat-shock response force is too expensive to maintain all the time. Instead, the rescuers are drafted into action when needed by an elaborate system of sensors, feedback and feed-forward loops, and protein networks.
Living cells defend themselves from a vast array of environmental insults. One such environmental stress is exposure to temperatures significantly above the range in which an organism normally lives. Heat unfolds proteins by introducing thermal energy that is sufficient to overcome the noncovalent molecular interactions that maintain their tertiary structures. Evidently, this threat has been ubiquitous throughout the evolution [sic] of most life forms. Organisms respond with a highly conserved response that involves the induced expression of heat shock proteins. These proteins include molecular chaperones that ordinarily help to fold newly synthesized proteins and in this context help to refold denatured proteins. They also include proteases [enzymes that disassemble damaged proteins] and, in eukaryotes, a proteolytic multiprotein complex called the proteasome, which serve to degrade denatured proteins that are otherwise harmful or even lethal to the cell. Sufficient production of chaperones and proteases can rescue the cell from death by repairing or ridding the cell of damaged proteins.
The interesting thing about this Commentary, however, is not just the bacterial system, amazing as it is. It’s the way the scientists approached the system to understand it. “Viewing the heat shock response as a control engineer would,” they continue, El-Samad et al. treated it like a robust system and reverse-engineered it into a mathematical model, then ran simulations to see if it reacted like the biological system. They found that two feedback loops were finely tuned to each other to provide robustness against single-parameter fluctuations. By altering the parameters in their model, they could detect influences on the response time and the number of proteins generated. This approach gave them a handle on what was going on in the cell. The analysis in El-Samad et al. is important not just because it captures the behavior of the system, but because it decomposes the mechanism into intuitively comprehensible parts. If the heat shock mechanism can be described and understood in terms of engineering control principles, it will surely be informative to apply these principles to a broad array of cellular regulatory mechanisms and thereby reveal the control architecture under which they operate.
With the flood of data hitting molecular biologists in the post-genomic era, they explain, this reverse-engineering approach is much more promising than identifying the function of each protein part, because: ...the physiologically relevant functions of the majority of proteins encoded in most genomes are either poorly understood or not understood at all. One can imagine that, by combining these data with measurements of response profiles, it may be possible to deduce the presence of modular control features, such as feedforward or feedback paths, and the kind of control function that the system uses. It may even be possible to examine the response characteristics of a given system, for example, a rapid and sustained output, as seen here, or an oscillation, and to draw inferences about the conditions under which a mechanism is built to function. This, in turn, could help in deducing what other signals are participating in the system behavior.
The commentators clearly see this example as a positive step forward toward the ultimate goal, “to predict, from the response characteristics, the overall function of the biological network.” They hope other biologists will follow the lead of El-Samad et al. Such reverse engineering may be “the most effective means” of modeling unknown cellular systems, they end: “Certainly, these kinds of analyses promise to raise the bar for understanding biological processes.”
1Tomlin and Axelrod, “Understanding biology by reverse engineering the control,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0500276102, published online before print March 14, 2005.
2El-Samad, Kurata, Doyle, Gross and Khammash, “Surviving heat shock: Control strategies for robustness and performance,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0403510102, published online before print January 24, 2005. Reader, please understand the significance of this commentary. Not only did El-Samad et al. demonstrate that the design approach works, but these commentators praised it as the best way to understand biology (notice their title). That implies all of biology, not just the heat shock response in bacteria, would be better served with the design approach. This is a powerful affirmation of intelligent design theory from scientists outside the I.D. camp.
Sure, they referred to evolution a couple of times, but the statements were incidental and worthless. Reverse engineering needs Darwinism like teenagers need a pack of cigarettes. Evolutionary theory contributes nothing to this approach; it is just a habit, full of poison and hot air. Design theory breaks out of the habit and provides a fresh new beginning. These commentators started their piece with a long paragraph about how engineers design models of aircraft autopilot systems; then they drew clear, unambiguous parallels to biological systems. If we need to become design engineers to understand biology, then attributing the origin of the systems to chance, undirected processes is foolish. Darwinistas, your revolution has failed. Get out of the way, or get with the program. We don’t need your tall tales and unworkable utopian dreams any more. The future of biology belongs to the engineers who appreciate good design when they see it.
It’s amazing to ponder that a cell is programmed to deal with heat shock better than a well-trained civil defense system can deal with a regional heat wave. How does a cell, without eyes and brains, manage to recruit thousands of highly-specialized workers to help their brethren in need? (Did you notice some of the rescuers are called chaperones? Evidently, the same nurses who bring newborn proteins into the world also know how to treat heat stroke.) And to think this is just one of many such systems working simultaneously in the cell to respond to a host of contingencies is truly staggering.
Notice also how the commentators described the heat shock response system as “just what a well trained control engineer would design.” Wonder Who that could be? Tinkerbell? Not with her method of designing (see 03/11/2005 commentary). No matter; leaders in the I.D. movement emphasize that it is not necessary to identify the Designer to detect design. But they also teach that good science requires following the evidence wherever it leads.
Please note my numerous uses of (and corrctions of others') analogies then.
Maybe the fault lies not in the interpreter, but the open-endedness of the analogies in the first place. Just because somebody else can see a fault in your logic, doesn't mean they are wrong, it could mean your logic isn't perfectly communicated.
Because [consciousness] is intangible, ought we to ignore it? If we must ignore it in order to satisfy the scientific method, then what would be the status of either evolutionary theory or design theory?
I would certainly say that consciousness should not be 'ignored' by science, and I hasten to add that I don't think it is ignored. However, I don't see that this issue, though fascinating in its own right, has any special bearing on natural selection vs. intelligent design, which concerns not the existence or nature of consciousness but the possible role of intelligence in the generation of complex systems.
So long, everyone. Thanks for the interesting chat.
Darwinist theory doesn't seem to have much to say about it. Darwinists such as Pinker, Dawkins, Wilson, Lewontin, et al., seem to regard consciousness pretty much as an "illusion." But if they have to speak of it at all, they say it is an epiphenomenon of brain activity. Moreover, according to Wilson, evolution itself works to generate "useful illusions," such as moral theory (a construction of illusory mind or consciousness alone). What is the evidence that Nature is really in the business of producing illusions? Or is this just another ad hoc gap-filler that preserves one's preferred cosmology intact (e.g., Darwinist evolutionary theory, materialism, metaphysical naturalism, etc.) -- to make it "all come out right in the end?"
My larger point, however, was that both Darwinist theory and design theory are both products of mind, or consciousness. If mind is fictional, what can we say of its products? Both Darwinism and ID are constructions, or "designs" in their own right, and both seek to fill in the evidentiary gaps of their preferred theoretical approach. The great challenge to Darwinist evolution is the fact that it depends on a history of the biota, which is no longer available to direct inspection. Sure there are a zillion fossils. But like the shedded skin of a cobra, what can fossils tell you about the creatures that they once were? Can one really construct a genetic history from dead crusts -- other than a very superficial one, based on appearances, resemblances?
I would argue that there is an aspect of design involved with Darwinist theory: Its theorists have perceived what they consider to be a pattern in nature, and then go on to fill in the gaps of the evidentiary record with whatever appears to fit. The deeper ontological structure of Nature is ignored.
And yet the evidence or by-products of design are there in nature, and can be observed.
Evolutionary theory likewise is not a phenomenal object in the sense that it is not a direct production of nature. It is a conceptualization; that is, it is an immaterial entity that purports to be a universal rule of nature. In this regard, I do not perceive any real difference in its status as compared with design theory:
Math is entirely a priori, that is, a product of our noodles and can neither be proved nor disproved by appeal to empiricism.
For sure!
(Hey what does onotological mean in the sense that you used it?)
For Lurkers: under the Aristotle view, the mathematician invents the math - under the Plato view, the mathematician discovers the math, e.g. pi exists and was only discovered.
I don't know how to say this, but you get all worked over an unsolved, and perhaps unsolvable, problem, as if talking about it and finding just the right words would solve it.
Not going to happen. we can learn about the properties of the brain, and we might even be able to replicate the functionality of the brain in silicon. But even that would not solve the problem as you see it.
Actually js1138, I have seen a pretty good theoretical solution to the problems of life and consciousness that is premised on a universal evolutionary model based on physics and mathematics/geometry, in a manuscript currently being prepared for publication. I really do wish I could say more about it here, but I do not have the necessary permissions. When the time comes though, I'll be putting up billboards all over the place!
I meant you personally, because you posed the problem as 'natural vs. supernatural' and seemed to place design on the 'supernatural' side.
Oh, OK. In essence, intelligence, whether human, angelic, or divine, is spiritual in nature. So my Dunkin Donuts example was an analogy. If we see intelligent design in the existence of a Dunkin Donuts, why don't we see intelligent design in infinitely more complex organisms, such as the human body?
So is your question, how do I arrive at supernatural intelligent agency as the efficient cause of the human body versus natural intelligent agency as the proximate efficient cause of a Dunkin Donuts?
Given this limited line of reasoning, I suppose that it's logically possible that a natural, intelligent agent, other than God created the human body. The problem is that there are no likely candidates, outside the angels, as proximate efficient causes. But personally, I know with certainty through reason that there exists a Prime Mover, First Efficient Cause, Perfect Will and Perfect Being, who we all call God. It's unreasonable to believe that the Designer is other than God, and only God can be the proximate efficient cause of souls in particular, since only God can create a spiritual being from nothing.
Are you trying to say that modern "science" is based on naturalistic assumptions and not materialist ones?
No, I didn't intend my question to imply anything about modern science one way or the other. I was asking how you made the step from 'mind' to 'supernatural'. You replied with several arguments to the effect that the mind isn't susceptible to a materialistic explanation (a point with which I happen to agree, but that's neither here nor there). So now I'm asking why you seemed to identify 'natural' with 'material'.
Because by and large, the modern scientific enterprise excludes non-material explanations of phenomena a priori, particularly with regards to the origins of life and species.
On your view, is anything non-material automatically 'supernatural'?
Yes, going by the dictionary.com definition. No, going by your definition. Yes, going by the definition accepted, at least tacitly, by most biologists.
Define "scientific."
The usual. 'Of, relating to, or employing the methodology of science', where 'science' is understood as the 'the process of gaining knowledge based on making repeated observations about nature in controlled conditions (experimentation) and attempting to explain what causes those observations (theorizing) through constructing hypotheses that can be tested experimentally'.
Why doesn't this definition exclude evolutionary theory?
. . . modern science rejects non-material explanations of phenomena a priori.
It does? According to whom?
Me. It seems to be the consensus amongst scientists, at least in their published work. Why else are IDers being raked over the coals by the "evolution establishment?"
That's certainly not true in psychology, where behaviorism long ago lost whatever intellectual attraction it briefly had.
Well, someone should tell it to the doctors who are doping up children. Secondly, scientists in other disciplines would argue whether psychology represents a science. Thirdly, two of the three schools of modern psychology that I'm aware of, Behaviorism, Freudianism and Jungianism, are based on materialist presuppositions. Otherwise, modern psychology seems to me to be largely ad hoc, and studiously agnostic regarding its metaphysical foundation.
I found this claim on a communist website.
While it may have been the case that Freud represented the only materialist psychologist (or developmental psychologist) 70 years ago, this is certainly no longer the case. Vast strides have been made in this field, and most psychologists today are materialist.Either way, though, intelligence is regarded as the efficient cause of the lawful system in which the phenomenon in question occurs.
True.
In your example, intelligence is the proximate efficient cause of the natural forces producing the rocks; if speciation occurs through natural selection, presumably intelligence would also be the proximate efficient cause of the natural forces in that system as well.
True.
Goedel said this might not be possible. Goedel is not popular in AI circles, nor in math and science circles. Well, what should be expected of a man who proved that time is an illusion?
You are assuming the conclusion. There is nothing in the paper that shows purpose, only use. Things may be used for various purposes; leather's first use may be holding cows together, but that doesn't stop it from being ant food later.
I think it's pretty far off.
My point though, is that a materialist worldview makes it impossible in principle to know at any moment whether one can trust the the evidence of one's senses or one's thought at all. In reality, we can check the correspondence of our thought against the outside world, contradicting the above corollary of materialist philosophy.
I can't wait, unless it posits that the locus of consciousness is somewhere other than the brain.
What he said was more indirect. If we ever are able to prove all of math it can't be by logic, so if we do it, it would be something that logical machines can't do.
You can do that if you start by assuming that your brain is not malfunctioning. But what if it is?
The people whose brains we think are malfunctioning don't think they are.
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