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.
Is green a figment of your individual imagination - or a universal?
I say it is a universal (except of course to the color blind men as RWP asserts cannot see that particular universal) - and thus, even with preschoolers, I could instruct them to color the grass green on handouts without having to first teach them to read the wrapper on the crayon.
See #258.
Indeed, "green" is a universal. Likewise "olive green" is a universal. "Hunter green" is a universal.
For some people, colors are easier to make the point about universals. But we could have also used "chairness" or "threeness" or "female" or "pi" or "triangle" to make the same point.
would you care to enlighten me, so the speak, with an objective definition of green that covers all cases in which people call something green in color?
Whether or not it's possible to give an objective, covering-all-cases definition of a range of experiential qualia -- or even of one such quale -- doesn't really address the question whether such qualia are universals. If that specific shade of green can recur identically in more than one context, it's a universal in the sense in which ontologists use the word. If not -- that is, if two occurrences of what seem to be the exact same color are really two different but 'exactly similar' qualia -- then that specific shade is not a universal. (Most modern nominalists would invoke trope theory or something equivalent at that point.)
No it doesn't. And you think about it.
But in real life, objects, including light emitters, are pretty complex. I can even construct a spinning object with "black and white" stripes that appears green, even in monochromatic light.
And, of course, green pigments are usually mixtures of non-green pigments.
Green is a construct of the eye and brain. The Benham Top demonstrates that color is encoded by the retina as a firing rate for neurons. When you induce the firing rate with a non-chromatic pulsating light source, you get the subjective sense of color. I've done this under carefully controlled laboratory conditions, using a monochromatic light source.
OK, doc ... tell me why murder is "wrong." Or tell me why something is "good."
The problem here is an equivocal use of the term matter.
I think this returns the discussion to the issue of posts #224 and #229.
But you sidestepped the question of what to do if a religious authority, say one that you have respected for a long time, says that a specific act of killing is not murder.
First of all, there is design. The question is whether the efficient cause of the design is remote or proximate.
Secondly, the theory may be simple, beautiful, powerful and elegant, but it doesn't accord with the facts, as far as I can tell. As far as I know, evolution happened either gradually or rapidly. The lack of fossil evidence contradicts the former, and the lack of a plausible mechanism contradicts the latter.
A question that I've been pondering recently is whether the existence of essences contradicts the theory that evolution is currently ongoing. It is because the intellect abstracts the essence of a cat indifferently from its particular notes that I am able to know that you and I are referring to the same thing when we refer to "cats." How could this essence be stable, and therefore knowable, if it were undergoing constant, gradual change?
I'm not sure I buy that. Your eye and brain may be fooled into perceiving "green" in some instances, but that sounds more like an instance of "aliasing," which is a well-known phenomenon in signal processing.
We could test your statement, and the control would be to see whether people with "normal" vision (however defined) would ever identify your "Platonic Green" as some other color. Dollars to donuts they won't.
The color green exists even when the man cannot see it. That is what makes it a universal. It exists even if no man could see it.
Before there was man, there was "greenness" "threeness" "pi" and so forth.
This is the same point of a tree falling in the forest. Did it make a sound if noone heard it?
I can however communicate a precise shade of green by pointing to it. The colors are actually numbered for graphic artists/printers for consistency - so I could speak or write a number to communicate a precise shade of green.
I do however strongly agree with you on the existence of qualia and its importance to philosophy, mathematics and science.
I thought we were discussing the moral implications of evolution? Since I maintain it has none, no discussion of the morality of murder would be relevant to a discussion of evolution.
But since you asked; murder is wrong because it terminates a human life, which is a good in itself.
Since we're talking about colors:
How does the poison arrow frog communicate to animals that are color blind that it is indeed poisonness?
We know animals avoid brightly colored animals as food in the wild, but not all animals can see color. If it is indeed only a matter of the brain, how come these other brains can preserve their own lives?
Peter Kreeft agrees, for the same reason.
You may want to qualify that with "Murder is wrong because it terminates a human life while not necessarily preserving another."
Killing can be right, as long as it is to preserve another life.
I know what green is. Green is a word people use to describe a perceived property of objects. Aside from the fact that my definition is off the cuff and is probably flawed, there is no other meaning of green, as a color. The notion that there is a Platonic green is just stupid.
there is no wavelength that is green. There is not even a range of wavelengths that can absolutely be called green. And worse yet, not everyone has the brain structures required to form the perception of green. Green requires some rather specific activity in the brain. There is no green "out there."
First of all, there is design. The question is whether the efficient cause of the design is remote or proximate.
The theory of natural selection doesn't need to be posed in terms of design, however. And if it is, the sense of 'design' at issue is a pretty specific sense -- something like 'looking forward in time and deliberately producing a specific result selected at an earlier time'. Assuming that God is eternal and 'acts timelessly', this sense of 'design' arguably may not apply to God either.
Secondly, the theory may be simple, beautiful, powerful and elegant, but it doesn't accord with the facts, as far as I can tell. As far as I know, evolution happened either gradually or rapidly. The lack of fossil evidence contradicts the former, and the lack of a plausible mechanism contradicts the latter.
Well, I'll leave you to follow up on the evidentiary issues. Again, PatrickHenry's homepage is the place to start.
A question that I've been pondering recently is whether the existence of essences contradicts the theory that evolution is currently ongoing. It is because the intellect abstracts the essence of a cat indifferently from its particular notes that I am able to know that you and I are referring to the same thing when we refer to "cats." How could this essence be stable, and therefore knowable, if it were undergoing constant, gradual change?
That's a fascinating question on several levels. I have my own views (about this and about the theory of universals generally) but they would take us fairly far afield here.
If you're interested, you might enjoy reading Brand Blanshard's Reason and Analysis, which in its latter chapters develops an account of universals that at least indirectly addresses your question.
I understand "vision" perfectly well.
It's "color" that I'm disputing.
Not the "perception of" but the "color itself"
Do keep up if you'r going to dog me.
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