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.
Give me a specific example of an animal that responds to color without being able to see it? My first impression is that you are making this scenerio up.
The point of a universal is that it exists - whether or not I or anyone else can perceive it is beside the point.
If one is a Nominalist then universals do not exist. There is no objective, universal "green" - it is a figment of a Normalist's imagination.
To an animal with different color pigments, there are colors which exist even though you can't see them. To a human with different color vision, there are also colors that exist even though you can't see them. In fact, by your definition, there are as many objective colors as there are possible visual pigments; which is close to an infinity of colors. Out of this infinitiy of objective colors people and most organisms can see only three, or two, or just one.
And ultimately, it all comes down to a function where we have intensity of light on one axis and frequency on the other. But even that function can be shifted, for example, by the Doppler effect.
It's not a very good example of a universal.
And what make human life "a good in itself?" You're going to have to appeal to something objective for your claim to have any meaning. Anything less than an objective basis will collapse into relativism, and most likely utilitarianism.
But suppose I were to make the counter-claim that "making 'better' children" was the highest good? The objective basis for my claim would be that I can see all around me, using the evidence in favor of evolution, that this is the objective definition of "good." It's straightforward to show how this claim leads to utilitarianism.
I would dispute that "green" is a qualia. . . I can however communicate a precise shade of green by pointing to it.
Which works only as long as the person to whom you're communicating it is experiencing it at the time you point. Be that as it may, we're not disagreeing about anything worth arguing over; you can feel free to rewrite my post substituting the phrase 'experienced quality' for 'quale' (that's the singular' 'qualia' is the plural').
I addressed that above somewhere, beginning with something like, "'the first line of defense' is the natural law..."
I can present you with two entirely different mixtures of frequencies which to your eyes look like emerald green. Which of the two mixtures is 'the color itself'?
How about "pi" or "threeness"? Did pi exist before it was named? Did threes exist before anyone learned to count?
No, of course not. I'm not an essentialist.
"I know what green is."
And for all the rest, you didn't show me.
Bad scientist! ::swats with a nespaper::
If you "know" you can demonstrate it.
All you can demonstrate is that the mind can be fooled. Those are called "illusions"
By spinning a top, it does not become "green" it is still black and white.
Green exists as a universal form, whether you percieve it that way or not is up to you.
It can be argued that if you and I were to swap brains, "green" would become some other color to both of us. This is due to "perception"
"Your" green is not de facto "my" green. HOWEVER: There is a "green" out there that we both percieve AND identify as such. There is a universal idea of "green" just as there is a universal idea of "chair"
Neither. Thanks for playing :)
I had been musing on the industry standard numbering for colors which printers and artists use and happened upon your post at that very moment...
I'll take that as a concession.
This is simply untrue. The pigments used for Pantone colors may have an objective reality, but the spectral characteristics of pigments is very complex, and many alternate mixes would produce the same match by humans.
Our perception of color is entirely subjective. People with differences in their retinal receptors see colors differently. There are people with "color blindness" in only one eye, and they are able to describe the perceived differences.
you: No, of course not. I'm not an essentialist.
If circles did not exist, then why pi?
Well, for one thing, if you wish to call "man" an animal, I will allow it for this discussion. (Seeing as I cannot know what an animal thinks)
I know a guy who is color-blind to blue. He knows a beautiful day when he sees it out his window though. He's reacting to the appearances without reacting to color. But how does he know its beautiful? It's gray to him!
Presumably it fails to communicate its unpleasantness to every conceivable predator.
This is a common anti-evolution argument that goes as follows, "Since adaption 'x' does not work in every situation faced by species 'y' evolution is a crock...". The argument misses the point that the benefit of the adaption is still apparent in other situations, and as long as the cost of the adaption is less than its overall probabilistic benefit natural selection will tend to preserve it. Nature doesn't insist on perfection, most of the time good-enough is good-enough.
I mention this based on long experience discussing theproblem of universals online and elsewhere.
Whatever scientists call "matter" isn't what Aristotle called "matter." Aristotle's "matter" can't be further reduced.
You have demonstrated that philosophers are capable of multiplying entities beyond necessity. Greenness probably corresponds to a behavior of the brain that can be mapped to a specific location. In that sense, and that sense alone, it is objective.
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