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 sory, but you are JUST missing the point we are making.
Perception of color is NOT "color"
Yes, all things emit (or reflect) radiation to give the appearance of color. But that means color is of itself, in existance, and it does not require man for it to be.
we are not discussing whether the chips are ideentical. In my example they are not. We are discussing whether they are perceived as the same color.
You are fond of envoking mathematics. Give me a mathematical description of the color green. What are the spectral characteristics of green? Be careful. You have asserted that pigments, such as Pantone chips, can have an objective color. What is the essential spectral characteristic of a green Pantone chip?
Fine. Define color in the absence of a perceiver.
A specific wavelength of moving particles.
Light waves also exist without a human to perceive them. Both light and sound can be described as having wavelengths, which are also objective.
But unless you are willing to assign a specific wavelength to the label green, the way we assign 440 hz as A below middle C, color is a perceived quality, like beauty.
What you did was rename the color. You did not change the property of it that makes it so.
So what is the Platonic wavelength of green?
I don't pretend to know it's wavelength. I do know that calling it by it's wavelength does not change the fact that it is green though.
Merely names.
In better words; show me an instance where the same wavelength as green cannot be green.
For the record: you shifted universals. I took that as a concession that you're no longer claiming green is a universal. If not, let me know, and we can discuss how loose the criteria for a universal can be.
Ever hear of a redshift?
That shift changes the length of the wave. Try again.
I know exactly what point you are trying to make, and you are wrong. color is not like 3 or pi. The definition of color can be arbitrarily limited to the concept of wavelength, but that has not been argued up to now. We have had arguments that color chips, such as Pantone chips, can be said to have color that is independent of the perceiver. Not just a recipe of pigment ingredients, but color.
It is possible, and commonly done, to make pairs of pigment chips that "normal" people will perceive as the same color, but which will appear different to color blind people. There are an infinite number of such pairs. The perception of color is an activity of the eye and brain. There is no possible way to define a shade of color objectively except as a measurable activity of the eye and brain.
Try brown or purple. With green, there is a frequency of light that is "green" but there is no frequency that is brown or purple. (I'm not denying the existence of the concepts, just pointing out some difficulties.)
"The definition of color can be arbitrarily limited to the concept of wavelength,"
"There is no possible way to define a shade of color objectively except as a measurable activity of the eye and brain."
Well, which is it?
You had been arguing until now that the mind was were color was.
In case you were wondering why I ask.
So your point is, although 'green' is a universal quality, 'greenness' cannot actually be associated with an object, because that color can be red- or blue-shifted; nor can 'greenness' be associated with a perception', and in fact 'green' is only another way of saying 'electromagnetic radiation of wavelength 540 nm'.
So what's monochromatic light of wavelength 541 nm? What about bichromatic light with two wavelengths, 539 and 541 nm? Are they not green? What if we take near-infrared light of high intensity, so that in a nonlinear medium it has harmonics of wavelength 540 nm?
I'm just trying to nail down this universal of yours. If it's a universal, it should be capable of precise delineation, right?
Both statements are true. An arbitrary definition is not objective.
Brown, I will say, is a perception. It is a blend (and confusion) in the mind of other colors.
Green has existed as long as radiation itself has.
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