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.
The paper refers to a "null path." What is that? Is it something moving in a pure "second time" direction? Would it be similar to, say, how the shadow from a body moving vertically in 3D, wouldn't necessarily move or change much in 2D?
In the 5D theory, dynamics of the higher (5th) dimension vacuum manifest matter/energy in the 4 dimension block we perceive from inside it.
Personally, I like to consider the consortium's 5D theory in conjunction with Max Tegmark's Level IV Parallel Universe. Tegmark's cosmology is the only closed multiverse - all the others propagate to prior universes, multi-worlds (the cat is both alive and dead) and prior geometry (brane theory).
Tegmark's theory is that everything in four dimensional space/time is a mathematical structure "beyond" space/time. Or conversely, mathematical structures in 5D manifest all of 4D (geometry, matter/energy etc.)
I think the concepts are similar. It is not 4D type particles moving about in a 5th dimension but a vacuum. IMHO, what one sees as mathematical structures (which are non-corporeal, non-spatial, non-temporal), the other sees as dynamics of a vacuum (the geometry). To me, they are equivalent because I see mathematical structures as rooted in geometry.
Any hoot, something to think about...
Oh, it's a duzey, Alamo-Girl! Got it and read it. I thought this statement was simply fascinating:
"If we identify the orbit in the l/s plane with that of a particle, we have a realization of the old idea (often attributed to Wheeler and/or Feynmann) that instead of there being 1080 particles in the visible universe there is in fact only one which appears 1080 times."
That'll give us something to think about!
This 5D "two times" metric with signature [+(- - -)+] puts some flesh on the bones of our speculation about a fifth, "time-like" dimension. It is particularly interesting that Wesson says his work applies in both the induced-matter and membrane theory scenarios.
Thank you so much for steering me to this most interesting article!
Of course you have. If it isn't "objective", as per your assertion, then it must be "subjective." Either - or, as in the folowing:
the only possible source for "objective truth" and "absolute morality" is "beyond" space/time.
How do you know what the "only possible source" is unless you, yourself are omnipotent? This is an absolute statement that all knoweldge within space/time is non-absolute, thus this statement made within space/time is therefore non-absolute and contradicts itself.
You do not know, cannot know by the very definition of the term, that there is anything "beyond space/time" not withstanding your mystical experiences otherwise, since all your experiences take place within space/time.
we don't know what sound "is" from "beyond" space/time
This is non-sense, in the true sense (!) of the term. There is no "sound" outside or "beyond" space/time. You can give no evidence that there is. Sound is a perception, by definition. You can reify such concepts all you want, doesn't make it reasonable.
Max Tegmark, for instance, would suggest that sound is a mathematical structure "beyond" space/time which manifests "in" space/time - but we, from within space/time, cannot know that is the "objective truth" of the matter.
I suggest that Max sober up once in a while and look around him at reality. Just because somebody says something doesn't mean that it is reasonable argument, no matter who it is. Fallacy of Appeal to Authority.
Just because he makes the same errors in logic that you do doesn't mean his arguments carry any more weight. Fact is, neither you nor he can produce any evidence that anything exists outside the realm of space/time - by definition.
By the way, sound is the result of dragons interbreeding with Unicorns. Prove me wrong.
The following makes more sense.
"Whereof one cannot speak thereof one must be silent."
--Wittgenstein
Bye-bye, QM. Bye-bye relativity. Bye-bye Bell's inequality. Bye-bye the Copenhagen Interpretation.
Back to the drawing board.
Your presumption is that you must be right in your worldview and therefore whatever I or Max Tegmark say from a different worldview must comply or be deemed false by you.
My worldview cannot conform to yours nor would I ever wish it to, nor can I interpret it in terms of your worldview. Thus we have no foothold for further discussion.
The belief that there is no God is just as much a matter of faith as the belief that there is a God. If “faith” is defined as “belief lying beyond proof”, both Christianity and atheism are faiths. While this suggestion might seem astonishing to some atheists, it is not only philosophically correct but also illuminating in shedding light on the changed fortunes of atheism in recent years. The strength of the atheistic feeling has been directly proportional to that of its religious antithesis: with the weakening of religious faith in many parts of the West, especially Western Europe, there has been a concomitant erosion in the attractiveness of its atheistic alternatives. In the Western European context at least, a swelling public indifference toward religion has led to the loss of the potency of both poles of religious culture, Christianity and atheism.
In recent years there has been a growing recognition of the ultimate circularity of the great atheist philosophies of recent centuries. The explanation of the idea of God put forward by Feuerbach, Marx, and Freud have one all-important feature in common: they presuppose atheism. It is the fundamental assumption that there is not—indeed there cannot be –a God that prompts them to offer explanations of why perfectly intelligent human beings should think that there is a God to believe in. As there is no God, the origins of this idea must lie in the malfunctioning of the mind, the subtle influence of the human unconscious, or the complex social forces that shape our beliefs and values, often without our being aware of them. Yet when all is said and done, these explanations of religious belief start out from atheist premises and duly arrive at atheist conclusions. They are, in their own way, coherent: they are not however, compelling. They simply offer an atheist explanation of religious belief, in much the same way as Christianity offers a theistic explanation of the same phenomenon. They explain the observation on the basis of a preconceived standpoint; they most emphatically do not establish that standpoint in the first place.
How can this be? God is simply not an empirical hypothesis that can be checked out by the scientific method. As Stephan J. Gould and others have insisted, the natural sciences are not capable of adjudicating negatively or positively, on the God question. It lies beyond their legitimate scope. There is simply no water tight means of arguing from observation of the world to the existence or non existence of God. This has not stopped people from doing so, as a casual survey of writings on both sides of the question indicates. But it does mean that the “arguments” are suggestive and nothing more. The grand idea that atheism is the only option for a thinking person has long since passed away, being displaced by the growing awareness of the limitations placed on human knowledge and the need for humility in religious and antireligious advocacy.
The Twilight of Atheism
The Rise and Fall of Disbelief in the Modern World
by Alister McGrath p180-181
Oxford University, Oxford, England
Thank you so much for sharing that very interesting essay!
Hence the circularity of their arguments....
Thanks so much, ckilmer, for this illuminating extract from Alister McGrath!
No, you insist your worldview is the only right one.
I only ask how it is that you can be so sure you know what you "know" and how you know it. For which you have no answer.
I have "deemed" nothing false, (yet another Straw Man spurious charge against me) I just said I've yet to see any evidence.
As for my "worldview" - you don't know what it is, I have never revealed it.
As I have said I don't know how many times now:
Atheism would commit the Fallacy of Proving the Negative.
It is silly to define a position by saying what it is NOT.
As Stephan J. Gould and others have insisted, the natural sciences are not capable of adjudicating negatively or positively, on the God question.
Yes, precisely. And what I question is when someone tries to use the natural sciences, Quantum Theory in particular, to justify such a position "positively" - as in the case of asserting QM, The Uncertainty Principle, The Copenhagen Interpretation, Godel's Incompleteness Theorum justifies and supports Platonic Philosophical Realism. (That, after all was the subject and not the existence of God.)
There is simply no water tight means of arguing from observation of the world to the existence or non existence of God.
Then stop trying. I have never made any assertion about the existence of God, one way or the other. I only question the basis for assertions others have made, and on what basis, logically, they have made them.
IOW - stop putting assertions in my mouth that I haven't made.
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