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.
I'm curious about your step one. It seems to violate a central dogma of molecular biology. What is the mechanism for communicating specific needs to the genome, and at what stage of reproduction does this occur?
Noble prizes all around for the people who can demonstrate this.
The significant differenence between ID proponents, and evolutionists is that the former will *admit* that their position is based upon faith, while the latter *pretends* that theirs is not.
Both are looking for evidence to support their faith, but the faith exists regardless.
I believe in Intelligent Design. I believe the Bible is the inspired word of God. I also believe that the Bible has numerous factual components to it, and numerous metaphorical elements to it.
When the Bible says the world was created in 7 days, I am willing to reserve judgement as to whether this means 7x24 hours, or 7 periods. When the Bible says there is a God, or that Jesus was born, lived, and died on the cross for our sins, I take it as historical.
The former is really irrelevant.... 7 days.. 7 periods..what does it matter to me or anyone? The latter, that is ESSENTIAL to all of us. It not only affects our eternity, but has been demonstrated to impact our lives as we live them.
So, if you want to believe that God created life by inspiring the evolution of creatures over 7 periods in which things went from darkness to life, fine... I can deal with it.
But remember, your faith is no better than mine, and it is focused on the portion of the Bible that really has no impact on any of us.
My faith, on the other hand, is focused on the part that impacts me directly every day and hopefully impacts others in a way that is positive for everyone I engage.
The significant differenence between ID proponents, and evolutionists is that the former will *admit* that their position is based upon faith, while the latter *pretends* that theirs is not. . . . But remember, your faith is no better than mine, and it is focused on the portion of the Bible that really has no impact on any of us.
Evolutionary theory isn't based on 'faith' in the common religious sense of the term. (Nor is it 'focused' on any 'portion of the Bible', although of course it has some relevance to the scientific plausibility of some interpretations of the first two chapters of Genesis.) It works as science in general works: by proposing testable hypotheses and then testing them, and modifying or dropping them when disconfirming evidence is found. To whatever extent evolutionary theory can be called 'faith' in some other sense, it is indeed 'better' (in the sense of 'more clearly formulated and better confirmed by repeated experiment and observation') than the religious sort.
Why not adopt the more plausible explanation for various phenomena? Would the discovery of canals on Mars be better explained as the work of intelligence, or natural formation? Most alleged evidence for evolution is ambiguous, like the seven archaeopteryx fossils. Is the archaeopteryx a "missing link," or simply an extinct species?
Rather, you've got to show the specifics of where the current theory is incorrect; and after that, you've got to provide the scientific basis for why design is a better explanation.
Why can't we search for the most plausible explanation given our current state of scientific knowledge and understanding of natural phenomena? Why should evolutionary theory be the default explanation of the origin of species?
IDers simply postulate design as an explanation for apparent design. Well yes -- but on what basis would you objectively demonstrate that?
On what basis would the discovery of a spoon on Mars objectively demonstrate the existence of extraterrestrial intelligence? It's a matter of probability, not certainty.
What criteria could separate between "designed" and "naturalistic" phenomena?
How do you know that a Dunkin Donuts has been designed and that a rainstorm is a natural phenomenon? We recognize the work of an intelligent agent when we observe a thing that was built to serve a purpose, and which could not have arisen by the action of natural forces alone. No one would argue that a Dunkin Donuts is the work of intelligent design. So why, when we observe design of staggering complexity, like the human body, something infinitely more complex than a Dunkin Donuts, do we assume that it arose by the action of natural forces alone?
It would be hard enough to overcome "science's" existing animosity to ID, even with those criteria. Without them, ID doesn't stand a chance.
I'm of the opposite view. Intellectual revolutions begin with philosophers whose ideas are later adopted by academics and, in turn, students, eventually becoming common knowledge many decades later. The philosophical turning point came in the form of two books, Michael Denton's Evolution: A Theory in Crisis, and Philip Johnson's book, Darwin on Trial, 20 and 10 years ago, respectively. What remains now is for these ideas to spread through academia, as is now beginning to happen. It's hard to say exactly when ID theory will become common knowledge, since most people reject evolutionary theory already.
No one would argue that a Dunkin Donuts is the work of intelligent design.
Dunkin Donuts managers everywhere are hoping you intended to include the word 'not' somewhere in this sentence. They may not speak for their customers, however.
No one would argue that a Dunkin Donuts is [not] the work of intelligent design. So why, when we observe design of staggering complexity, like the human body, something infinitely more complex than a Dunkin Donuts, do we assume that it arose by the action of natural forces alone?
You seem to be presuming here that the operation of intelligence is a supernatural force. A Dunkin Donuts is the work of a human intelligence, but that fact alone doesn't imply that human intelligence is supernatural (or 'non-natural' in any other sense). So in order to reach the conclusion you're suggesting, you need the additional premise that intelligence is (or ca be) supernatural.
If there's evidence of this already, why do you need ID? Wouldn't the existence of human intelligence already be the proof you want?
I read the paper a while back. The authors make no argument for design; actually, the describe how designed systems look different. The actual system is much more complicated than a designed version; but it is adequate.
It depends upon whether you consider human thought to be a supernatural phenomenon or a natural phenomenon. Intelligence is the act of the mind, which is ultimately spiritual or non-material in nature (although there exists some connection between the mind and the brain). This can be proved negatively, by demonstrating that a materialistic account of thought is internally contradictory and false, leaving only the non-contradictory, non-material explanation.
First, if the mind reduces to matter in motion, then no thought can be more or less valid than any other thought, since both would have to be the result of indifferent, determined, natural forces. But my theory that "the mind is essentially spirit," and the opposing theory that "the mind is essentially matter," would both equally be the result of blind natural forces and would both have to be equally true (whatever truth means under a materialist rubric.) Yet both cannot be true. So the assumption must be false.
Secondly, materialism cannot account for the phenomenon of consciousness. What part of the body simultaneously experiences various thoughts, emotions and sensations? What is the self? Is it a thought --a bunch of chemicals? If so, there would be as many selves as discrete thoughts. Is the self a scanning mechanism in the brain? If so, there would be as many selves as acts of scanning, etc., ad infinitum.
Thirdly, if my mind is a machine, then it can be defective. How then can I know with certainty at any moment that my mind is not malfunctioning?
If there's evidence of this already, why do you need ID? Wouldn't the existence of human intelligence already be the proof you want?
Yes, in the sense that it demonstrates the possibility of a spiritual being as the cause of existing things, as human beings are the proximate cause of Dunkin Donuts stores. But it remains to be seen whether species arose by a supernatural act or by natural forces.
Doh!
Perhaps he was referring to the Zlotnick-Avida Seminary in Johannesburg, South Africa.
It depends upon whether you consider human thought to be a supernatural phenomenon or a natural phenomenon. Intelligence is the act of the mind, which is ultimately spiritual or non-material in nature (although there exists some connection between the mind and the brain).
Understood. What I'm asking, then, is how you get from 'non-material' to 'supernatural'. Naturalism isn't identical with materialism.
If there's evidence of this already, why do you need ID? Wouldn't the existence of human intelligence already be the proof you want?Yes, in the sense that it demonstrates the possibility of a spiritual being as the cause of existing things, as human beings are the proximate cause of Dunkin Donuts stores. But it remains to be seen whether species arose by a supernatural act or by natural forces.
How, if at all, does the outcome affect the conclusion that the entire cosmos, natural selection and all, is the product of a supernatural intelligence? What I'm getting at here is that even if I were to grant (which I don't) that ID is 'scientific', it still doesn't seem to do the job some of its proponents want it to do. Surely the mainstream IDers don't want to claim that God didn't make e.g. rocks.
Well, that's probably due to your outlook. But it seems to me that a direct solution to a problem is more likely than an indirect solution to a problem without using a design.
First, not my step one. Second, dogmas are not science. Third, finding the mechanism presupposes you are allowed to look for it. And last, you are very generous with your noble prizes.
With regard to ID theory, or me personally? As far as I know, IDers only postulate design, without reference to the designer.
Naturalism isn't identical with materialism.
At dictionary.com, I found naturalism defined as:
Philosophy. The system of thought holding that all phenomena can be explained in terms of natural causes and laws.I assume that "all phenomena" includes non-material phenomena like human thought, et. al., in which case, I find it hard to distinguish naturalism from materialism.
Philosophy. The theory that physical matter is the only reality and that everything, including thought, feeling, mind, and will, can be explained in terms of matter and physical phenomena.Are you trying to say that modern "science" is based on naturalistic assumptions and not materialist ones?
How, if at all, does the outcome affect the conclusion that the entire cosmos, natural selection and all, is the product of a supernatural intelligence?
I think ID theory just leaves it as evidence of "intelligence" or design, and leaves it at that. So, for example, under ID theory (as far as I know), apparent design in nature that could not plausibly arise by natural forces alone would be classified as the result of design or intelligence as its proximate efficient cause.
What I'm getting at here is that even if I were to grant (which I don't) that ID is 'scientific',
Define "scientific." This is important, since modern science rejects non-material explanations of phenomena a priori. Thus, reasonable beliefs, such as the belief that thought is an essentially non-material activity, are excluded as possible explanations for psychosomatic phenomena, mental illness, etc.
it still doesn't seem to do the job some of its proponents want it to do.
Like what? Prove the existence of God? I don't think that's the explicit objective of IDers. At least they claim that their goal is to demonstrate intelligence as the proximate efficient cause for the origin of species, although it's not a great logical leap from design to the Designer.
Surely the mainstream IDers don't want to claim that God didn't make e.g. rocks.
I'd distinguish the origin of rocks from the origin of species in that intelligence seems to be the remote efficient cause of rocks, while natural forces would be the proximate efficient cause of rocks; while intelligence would be the proximate efficient cause of the origin of various species.
God is certainly the efficient cause of all existing things. The debate regards the proximate efficient cause of the origin of species, the proximate cause of the origin of life, etc.
Our commentator's conclusion is a remarkable one: a scientific theory is being declared wrong on the grounds that the phenomenon it seeks to explain exists in the first place.
Good points.
Drum hit.
It isn't. For 200 years prior to Darwin, ID was the default explanation.
Darwinism was resisted by science for 80 years, until 1940, until all the alternative explanations failed for one reason or another.
Among the alternatives studied during these 80 years were Lamarkianism, saltation, finalism. Efforts were made to detect any evidence of non-randomness in mutation.
Don't keep repeating the lie that Darwinism was cooked up to destroy religion and was accepted by science without a fight. Even as we speak there are serious disputes over the mechanisms of variation.
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