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 the false dichotomy that the ID movement is trying to transcend. Evolutionary theory may correspond with factual evidence or not. ID theory may correspond with factual evidence or not. All IDers are asking is for a judgment regarding which theory best explains the available data.
Paley's watchmaker was never more than an allegory. The string theory is also allegorical. We call these things theory in the sense of being a best guess, not because they contain a god.
Sorry you were offended by his comments, BB. Next time I go to post something from that site, I'll be sure to not include the Editor's commentary if it contains potentially flammable material. (truth be told - I find his commentary refreshing, informative, and funny)
So it caused itself? Or did it arise by a mechanism inferior to itself, thus contradicting the principle of causality, that the effect cannot be superior to, or exceed, the cause?
Well, that's the rub though. In many cases, IDers are coming to the table with nothing except demands that they be listened to. By that standard, pretty much anybody should be able to demand a hearing from "science."
Those on the "science" side have a variety of reasons for not wanting to discuss "design" in the first place. The lack of some objective basis on which to discuss ID simply makes it easier for them to dismiss the concept out of hand. (We cannot dismiss, btw, the fact that some on the "science" side are ideological, rather than scientific, in their rejection of the idea.)
The second step in gaining "respectability" would be for the ID contingent to develop a set of "design markers" -- properties that can (to some extent) distinguish between "designed things" and naturalistic phenomena. The SETI folks face a very similar problem -- it might be helpful to the ID community to see how they're approaching it.
The first step, though, is I think still not well-defined: what is it that ID proponents hope to gain from this debate? I think there are all kinds of competing goals, and some of them have nothing at all to do with science. It seems to me that if the ID proponents are going to challenge science on the matter of life, then those goals first need to be identified and understood.
The first, and most important, question is this: why do IDers feel it necessary to conduct a debate with scientists?
It'd be interesting to see how some of the folks on this thread will answer the question.
Also gets to what "irreducible complexity" means -- a system so complex, it can not arise through mere random dynamics; it's probability of having happened without a designer is so exceedingly low, as to be in all effect zero.
Probability is ignored by hard-line orthodox marxists evolutionists, yet actual physics and chemisty can't ignore it.
There is a confusion between what is possible and what is probable. There is a confusion between what chemical process we know by pure scientific method is occuring and how it could have happened, that is to say -- many evolutionists seem to think that because we have identified and know to some detail a process, therefore that process and its component parts could have arisen through random dynamics in the absense of a designer. That second confusion seems like a specific instance of the first, but I take it to be unique. Unique because it can be held by people who well know the difference between probable and exceedingly improbable.
Three grand confusions. The third is that if we NOW don't know what a system of thing -- the male nipple -- does, it is a mistake if assuming a designer or just another random circumstance if designer-free.
It was a mind-croak to them.
Because evolutionary theory looks like bad science. I don't see much of a connection between the evolutionary theories that I'm aware of and the factual evidence. Either evolution happened gradually or in great leaps. The lack of fossil evidence contradicts the former, and the lack of a plausible mechanism contradicts the latter.
IDers simply postulate design as an explanation for apparent design. For example, what would be a more "scientific" explanation for the discovery of a spaceship on Jupiter, the existence of extra-terrestrial intelligence or random chance? Similarly, it seems to me that design is a better explanation of "irreducible complexity" and order in nature than random chance, particularly since we know through reason the existence of God. (The notion of "spontaneous order" seems nonsensical to me, as it seems to violate either the principle of sufficient reason or the principle of causality).
In essence, then, you're proposing ID as a strictly scientific approach to the problem, which is certainly a valid thing (though not a universal goal among those who get collected under the "ID" banner).
But if you're going to approach ID from a strictly scientific standpoint, then you've signed yourself up for providing more than just an inability to "see much of a connection." 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.
IDers simply postulate design as an explanation for apparent design.
Well yes -- but on what basis would you objectively demonstrate that? What criteria could separate between "designed" and "naturalistic" phenomena? 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.
As I recall, Junior has already made that observation, about a year or so ago. :^)
The table.
Sounds like something that I would have said, considering a literal translation of Grandpierre...
True. Designed that table is too!
When did quantum mechanics become accepted? When the older generation of mighty scientists retired (and they were truly mighty -- smart and genius, too).
Social structures can inherit old theories and wrap them in layers of instutionality of all sorts -- people's careers and institutions tied to a given way of looking at the world. They -- as history shows again, and again and again -- become very jealous of a certain way of looking at the world. Not only reactive -- but resistive -- lossey.
I think you miss a part of their posting. Read it again real closely.
Selection pretty much always plays a negative role. The source of variation as always been been a subject of research. I would like to see some research that clearly demonstrates non-random variation.
"What criteria could separate between "designed" and "naturalistic" phenomena?"
I think, as was mentioned before, that the roll of probability should be more played up by IDers when discussing with the hard-liners of the darwin cult.
In every other aspect of science (and technology) chances play an inseperable roll in the research.
Put more focus on the mathematics of it rahter than the mechanisms themselves.
Cute post, but I must correct your tagline if you're going to want to be properly mocking ID.
"Bible" is ALWAYS capitalized. Look it up in your grammar book.
Welcome to FR, hope you have thick skin if you're going to remain a darwinist on this thread.
Contact PatrickHenry if you want on the evo ping though.
Oh, please don't get me wrong, Michael_Michaelangelo -- I didn't mean to suggest that posters of threads here ought to be in the censorship business. Personally, I like to see as full and complete a public record as possible captured in real time. Especially since many of our collaborators here are first-rate thinkers and experts in their fields.
On the other hand, I can relate to your observation that stuff like this is often funny. [In present circumstances, not to a Darwinist, though.]
Believe it or not, I lurk more than I post. And that's probably because there is a certain type of post around here that is so totally "out of control" that one does not dare to put one's foot in.
And those are precisely the most hilarious, laugh-out-loud, cry-till-it-hurts threads at FR, bar none.
And a day without laughter is like a day without sunshine: One just progressively "wilts."
So here we have two putative "public goods": (1) a [putative] standard of truth; and (2) the [putative] requirements of human sanity. :^) How to reconcile the two, in the proper balance that best conduces to the well-being of human life -- and that of the wider sphere in which humans operate?
That is the open question that no censorship policy will help answer.
But on the other hand, as a poster/sponsor of a thread, it probably wouldn't hurt anything plainly to point out the polemical or propagandist aspects of the work you're posting. JMHO FWIW
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