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.
This is not the first time. A former FReeper, now banned, once linked me to a web site where he was the major "scientific" contributer. He had dozens of liks to articles that supposedly supported creationism or ID. I read the first linked article and it was clearly Darwinian. I had a lot of fun pointing this out.
There are lots of educated IDers who accept an old earth and the fact that evolution happened. They disagree about the mechanism. Some of them accept natural selection; they just believe variation is intelligent. I welcome proof of this, if it becomes available. It has certainly been investigated.
That's an interesting question. I have a nephew with schizophrenia. He has challenged me to prove his mind is malfunctioning. It's difficult to do this. He resisted medication for several years on the basis that his reality was as good as everyone else's. He's very smart and graduated from college with honors.
Understood. What I'm asking, then, is how you get from 'non-material' to 'supernatural'.With regard to ID theory, or me personally? As far as I know, IDers only postulate design, without reference to the designer.
I meant you personally, because you posed the problem as 'natural vs. supernatural' and seemed to place design on the 'supernatural' side.
Naturalism isn't identical with materialism.At dictionary.com, I found naturalism defined as: 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.
'Materialism' (essentially, the view that there is only 'material' stuff) is generally contrasted with 'idealism' (the view that there is only 'mindlike' or 'mental' stuff) and 'dualism' (the view that both sorts of stuff exist). (Here are a couple of sites I pulled up more or less at random that look like they do a decent job of explaining the differences: http://www.artsci.wustl.edu/~philos/MindDict/materialism.html, http://www.princeton.edu/~jimpryor/courses/intro/notes/mindbody-intro.html.)
Any of these may be compatible with 'naturalism' -- which in this context is, 'in relation to mind, the view that mental phenomena can be explained as part of the natural order and are empirically accessible features of the world'. (http://www.artsci.wustl.edu/~philos/MindDict/N.html)
For example, follow the first link and you'll find a claim that 'most contemporary naturalists' would favor the view that '[n]aturalism is ontologically neutral regarding materialism, and thus is logically compatible with ontological dualism'. (It's also compatible with idealism, though this article doesn't deal with that point).
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'. On your view, is anything non-material automatically 'supernatural'?
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.
Okay.
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'. (I pulled the latter from here rather than formulate it from scratch, but as I explain in my next paragraph, I don't think there's much riding on this point.)
. . . modern science rejects non-material explanations of phenomena a priori.
It does? According to whom? That's certainly not true in psychology, where behaviorism long ago lost whatever intellectual attraction it briefly had. At any rate, I would define 'scientific' with regard to epistemological method, not content.
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.
Either way, though, intelligence is regarded as the efficient cause of the lawful system in which the phenomenon in question occurs. 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.
But truly, the point of this article is that the researchers (the subject article of this article) have evidenced design (engineering) in biological systems.
Physical causation (evolution) is the presumption of the researchers which is disputed by this article. The evidence of design does not "prove" evolution as the cause.
IOW, analysts routinely embrace evidence while dismissing prejudices applied to or conclusions previously drawn from that evidence. Data does not come with "strings attached".
To the contrary (applying Occam's Razor) this article asserts the researchers' evidence points more directly to intelligent design as probable cause. On that point, I strongly agree. To assert evolution as the cause, the researchers would also have to have shown how information, autonomy, semiosis and complexity arose from non-life.
I'm a Forrest Gumpist. If matter can be particles and waves at the same time, then mind and matter can be the same thing at the same time.
To assert evolution as the cause, the researchers would also have to have shown how information, autonomy, semiosis and complexity arose from non-life.
(1) I don't think the original researchers were trying to prove anything at all about evolution; they were investigating how certain biological structures worked. (Their comments elsewhere indicate that they do in fact attribute the existence of those structures to evolution, but it doesn't appear to me that proving this was the aim of this article.)
(2) Even if that was their aim, they wouldn't have to demonstrate how anything arose from 'non-life' in order to show that something arose from 'evolution'. Evolutionary theory proper simply presumes the existence of life.
The point of the commentator, on the other hand, is that somehow, because the researchers used the language of control theory to describe the biological structure they were investigating, their work demonstrates that ID is correct and Darwinism isn't. That's not true; the use of those particular mathematical concepts shows nothing one way or the other about the origins of the phenomena under investigation, whether in predator-prey models or in the subject of these authors' research.
Thus, to demonstrate how this arose by evolution, they would have to propose how complexity emerged - and a type of complexification (Kolmogorov, self-organizing, physical, functional, etc.) That in turn requires establishing how semiosis emerged (language, encoding, decoding) which in turn requires establishing how autonomy arose and information itself.
At that point one is at the door of abiogenesis. After all, the point of their research is design evidence (complexification) not speciation. When one wanders beyond the boundaries of Darwin's theory, one must deal with the consequences.
Because of Occam's Razor, the commentator's deduction ("this" article) is more rational than the researchers'.
Indeed, it was not the objective of the researchers to prove a causation. That was a presumption on their part. The point of this article, is that the correct deduction is intelligent design.
Okay. We're agreed on that, then.
I agree that evolution theory does not address abiogenesis. But the subject of the researchers was the evidence of design (engineering) in biological systems.
Thus, to demonstrate how this arose by evolution, they would have to propose how complexity emerged - and a type of complexification (Kolmogorov, self-organizing, physical, functional, etc.) That in turn requires establishing how semiosis emerged (language, encoding, decoding) which in turn requires establishing how autonomy arose and information itself.
I think their point was merely that it's possible to apply a 'reverse engineering' approach to develop models of biological systems. Perhaps I've inadvertently overlooked part of their claim, but I see nothing in the claim as I've stated it that requires them to prove anything one way or the other about the origins of the systems being modeled.
[T]he use of those particular mathematical concepts shows nothing one way or the other about the origins of the phenomena under investigation, whether in predator-prey models or in the subject of these authors' research.I disagree. When presented with the evidence of design (engineering) in biological systems - in nature - the simplest conclusion is intelligent design, not evolution.
Well, I'm sure that argument has been beaten to death (from both sides) on many of these threads. My point here is simply that this conclusion, whatever its other merits may or may not be, can't be reached simply by noting that biologists can get useful results by employing concepts from control engineering.
"Advanced technologies and biology have extremely different physical implementations, but they are far more alike in systems-level organization than is widely appreciated. Convergent evolution in both domains produces modular architectures that are composed of elaborate hierarchies of protocols and layers of feedback regulation, are driven by demand for robustness to uncertain environments, and use often imprecise components. This complexity may be largely hidden . . ."
Yes. Which means that even if the origins of designlike structure had been the aim of the article at issue here, the researchers would not have needed to show 'how complexity emerged - and a type of complexification (Kolmogorov, self-organizing, physical, functional, etc.)' and, in turn, 'how semiosis emerged (language, encoding, decoding) which in turn requires establishing how autonomy arose and information itself'. It's already well established that the sort of control/feedback behavior in question here arises in a quite broad range of underlying 'substrate' systems; they don't need to prove anything about the origin of the underlying system in order to justify the use of the modelling techniques.
Attributing causation to evolution on either side is a presumption.
It is not a presumption to assert that a space shuttle is designed by intelligent beings. That is a historical "known".
It requires a religious belief in strong determinism to look at biological life and say "it evolved" and then look at a space ship and declare "it evolved". Yet that is what they are saying in this correlation.
It is much more rational to observe design evidence in biological life and declare it was designed, cause unknown, than to make that correlation. That is what the researchers should have done.
A classic example used by PatrickHenry as I recall is the presence of storks when babies are born. That is correlation, not causation.
If all they intended was to illustrate the usefulness of reverse engineering, they should have stopped right there and declared cause unknown leaving the remainder of the research (complexity, semiosis, autonomy, information) to other investigators.
Evolution is not based on presumptions. It is based on observation. ID has failed for two hundred years or more to demonstrate that variation is non-random or somehow anticipatory or non-blind.
All they are saying is that technology and biological life show a similar complexification. That is a correlation. Correlation is not causation.
Correct. So correlation between 'intelligence' and 'designlike structure' does not prove that the first is the cause of the second.
Attributing causation to evolution on either side is a presumption.
This statement is correct on the 'biology' side only if you're using the word 'presumption' to mean 'extremely well-established theoretical conjecture borne out by a century and a half of experimentation and other evidence'. That is not, of course, the generally accepted meaning of the word.
It is not a presumption to assert that a space shuttle is designed by intelligent beings. That is a historical "known".
Which, in large measure, is why we recognize it as 'designed by intelligent beings'. We know where it came from.
It requires a religious belief in strong determinism . . .
'Determinism', you say? Good; at least you acknowledge that the Darwinists aren't arguing in favor of 'randomness'.
. . . to look at biological life and say "it evolved" and then look at a space ship and declare "it evolved". Yet that is what they are saying in this correlation.
I may have misunderstood you here. Who says the space shuttle evolved?
It is much more rational to observe design evidence in biological life and declare it was designed, cause unknown, than to make that correlation. That is what the researchers should have done.
So far as I can tell, the researchers say nothing in this article about what 'caused' the complexity they're modelling through reverse engineering. The one arguing from correlation to causation is you -- that is, that intelligent design must be responsible for complexity everywhere because it's correlated with complexity in human artifacts.
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