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.
Sweet:) It's like having the teacher pick you to answer... and getting it not only "right" but making yourself look like a smug smart-ass in front of your classmates :)
I love this feeling :p
If this is some kind of a test, and the question is: "Is there change [from?] outside of time?", my recorded answer would be: Yes. And No. It all depends on how you look at the problem. :^)
On the one hand, change needs time to "happen in." Outside of time, there is no change. But on the other hand, change qua change has no meaning. It suggests an endless progression of states with no point in view.
While this might pass as state-of-the-art scientific reasoning these days, personally I know very few human beings who would be willing to live by a rule like that. And in fact, don't. (What is the predictive value of a science that produces results that depart from the way humans actually live and think?) :^)
Good grief, is that what my old friend Rock-O told you? I could have sworn that his real beef with me was that I didn't hang around long enough to hear the eventual articulation of his existential being that he had taken a great deal of time to compose. But I did give him a fair hearing, considering then-present available resources. And so, it only seems fair that Rock-O return the favor and see the problem from my point of view, too. Fair is fair.
I suppose I disappoint Rock-O. I'm sorry for that, I didn't intend that result. Notwithstanding, it seems to me unreasonable that Rock-O should expect that I have an indefinite number of lifetimes, extended serially past-to-future, that could ever suffice to provide old Rock-O with an opportunity to "self-assert" in any way, shape, or form that I would even notice.
In short, dear tortoise, there seems to be some kind of fundamental disparity between humans and rocks. But I'm confident you have already independently discovered and confirmed this.
Prabably about as valuable as a religion that departs from the way humans actually lie and think
ooh, that should have been 'live and think'. Tends to happen when I put the word 'religion' in a sentence. Paging Dr. Freud.
So, translating this from pompous nonsense to English, the key feature of God is he just 'is'?
Sort of a supernatural slacker, eh?
That depends on what the meaning of "is" is.
Cf. Popeye.
Dear Heartlander, here you limn the contours of the great divide that qualifies and separates machines from living systems.
Yet today "everybody knows" that living systems are comprised of components that are "molecular machines." So I don't at all mean to detract from machines....
... which seem to come in two basic flavors: "natural" (e.g., self-organizing biological systems) and "built" (i.e., artifacts constructed from outside resources).
Machines comprise some of the greatest works of human genius in all fields, from the ancient past to the living present. They are a blessing to mankind, it seems to me -- but only just so long as they are our servants, and not our masters.
It seems machines come again in two more flavors: material and logical. One imagines the best-engineered machines optimize relations between the two "poles."
Machines are built, not born. You got a problem with a machine, go see its engineer/designer.
[My advice: Forget about any machines that disturb you. Just let 'em rust. :^) ]
Thanks so much for writing, H!
Astrophysicists these days have pegged the age of the universe at +-13.15 billion years. So about +13.15 years ago from some unknown First Cause -- nothing -- sprang big bang something the universe into being.
Several conclusions can be profitably and safely drawn from this.
Both animate and inanimate objects come from the same First Cause.
Both animate and inanimate objects have a beginning.
Judging by conditions in the first X billion years of the universe--inanimate objects have a longer pedigree than animate objects.
It is unknown as to whether organic chemistry came solely from inorganic chemistry--or whether some third party catalyst, God--played a role.
The ultimate end of all animate and inanimate objects is unknown to science because the ultimate end of the universe is unknown.
To the individual contemplating this sort of thing--life is short.
The people whose brains we think are malfunctioning don't think they are.
True. This is a very difficult case. I don't know the genesis of the problem of schizophrenia in general. Sense impressions are never false in themselves since sensation is an immanent activity (Whether there is falsity in the senses?). What is difficult to determine is the origin of the schizophrenic's apparent sensory perceptions. Is the schizophrenic truly hearing voices? This could be true in the case of possession diagnosed as schizophrenia. Is the sense of hearing defective? Do the voices originate in the imagination? I don't know. But at the very least, I would think that the schizophrenic would know that something is wrong with him, or know that most other people think so.
My original point was that materialist philosophy cannot provide a coherent account for the general reliability of our senses.
As I've mentioned on other threads, I am (mathematically and philosophically) a Platonist -- meaning, roughly, that I believe there is an objective, eternal order of timeless 'ideas' and that the truths of (at least) mathematics and logic are truths about this objective order. I believe that we grasp these truths through what is usually called a priori reasoning. (Both Plato and Aristotle believed this, by the way, and of course so did St. Thomas Aquinas.) I'm also a theist, and I locate this objective, eternal order in the 'mind of God'. (Kurt Goedel has been mentioned a time or two in this thread; my views are similar to his. I should also mention that I have a graduate degree in mathematics.)
I mention these things not because I expect you to find my opinions fascinating or because I'm trying to persuade you of them, but because you need to know them in order to understand why I am not on the side of the IDers.
Obviously it's not because I think they should be 'materialists'. Obviously it's not because I object to their belief in God. I object to ID for the same reason every other Darwinist does: it's an incompetent hash of a theory.
The theory of evolution by natural selection is a simple, beautiful, powerful, elegant answer to a deep question that really need not be asked in terms of 'design' at all. It's a theory that describes how complex, finely adapted structures can develop algorithmically in a system that doesn't 'look ahead' and deliberately attempt to bring about specific results.
Note carefully: it's the system itself that doesn't 'look ahead'. The theory says not one single word about whether or not there's an eternal God who looks at the entire process timelessly and 'all at once', any more than the theory of gravitation does. (The laws of physics don't 'look ahead' either.) If the theory is sound, all an Aquinist needs to reconsider is whether God made there be horses by saying 'Let there be horses' or by saying 'Let there be a physical spacetime universe in which natural selection occurs and generates really nifty creatures including (as I know in My Infinite and Timeless Wisdom it will in fact do) horses'.
The theory isn't merely brilliant in an abstract sense; it also works. There is no question whatsoever that a system with certain properties will exhibit evolution by natural selection; this fact has been verified by rigorous mathematics and computer simulation time and again. There is also no question that the biological systems we see around us today have the properties that allow a system to exhibit natural selection; genes fit the bill wonderfully. And there is plenty of empirical evidence that natural selection at the genetic level is sufficient to account for the vast richness of biological structure we see around us today; PatrickHenry maintains a very nice page of links that will take you to much of that evidence.
The IDers simply do not understand this theory -- or, if they do, they understand it only intermittently and forget their understanding when they sit down to theorize. Again, I object to ID not because it isn't 'materialistic' or because it's 'theistic', but because it is an incompetent hash of a theory.
For example, William Dembski, their court mathematician, simply cannot work through a calculation without implicitly presuming that the only alternative to 'design' is 'randomness'. To borrow a famous example, we would all agree that a Boeing 747 is much more likely to be the product of 'intelligent design' than of a tornado passing through a scrapyard. Dembski's computations presume that these are the only two possibilities; he never once manages to consider the probability that a complex structure evolved algorithmically, even though the algorithmic theory is the one he imagines himself to be refuting.
Nor do his mathematical arguments (which, to the extent that they are sound, are not his) support his philosophical/metaphysical conclusions. I won't go into detail here because my purpose is not to refute ID but simply to explain why a nonmaterialist Platonistic theist like me still thinks ID is crap. (I did post once on this subject recently in another thread, and I can direct you to my post if you're interested. But you're probably better off skipping me altogether and going to http:www/talkorigins.org.)
That's enough for one post. I hope the foregoing helps you understand why I'm asking some of the questions I'm asking.
True
2. That there exist permanent, unchanging laws by which the Universe works
True
and these laws can be discovered (not invented) through experimentation.
False (and if one claims objectivism is not a blind faith note the internal contradiciton)
Since scientific method is the means of guaranteeing objective truth,
Like how scienctists have proved global warming? No, forget global warming, evolution is a far, far better example. There is not evidence that bacteria evolved into multi-celled sexual producing organisms. Yet there are those, who speaking in the name of the scientific method, not only insist that this happened but it is so certain this happened all debate should end on the possibility of this happening.
God exists. Can He prove Himself to you? Yes. Will you let Him? No. Why? Because if He should prove Himself, you will no long be able to believe that you can be your own god.
Tell me about your relationship with Dr. Freud.
Eliza.
Postulating the act of apprehension as an essentially spiritual activity makes certain knowledge possible in principle, because the act of sensation would be a non-material (spiritual), immanent activity involving the reception of forms. In the act of apprhension, the form (the organizing principle) of the object becomes one with the subject. There is no "gap" between the knower and the thing known.
A thorough account of this process is very difficult, and the greatest philosophical minds disagreed about the details of the process. Nevertheless, thought must be spiritual in essence, because the opposing view is internally contradictory.
The Aristotelian and the Thomistic positions agree on a number of points with regard to the process of knowing:This much is fairly clear. The solution to the discrepancies between the Thomistic and Aristotelian accounts discussed in part II of Sense Cognition: Aristotle vs. Aquinas is much more difficult, but is worth reading. I'm glad you brought up this point, because this is something that I need to study.(a) that, in the case of material composites, the form of that which is knowable and can become actually known (i.e., the form of the quod) must be received in the knower, separated from or without its matter (i.e., the matter to which it is united in the quod);
(b) that the knower is potentially a knower by having the power to receive forms in this way, and becomes actually a knower when its cognitive œ power is actualized by their reception;
(c) that the received form which actualizes a cognitive power is the quo or that whereby the knower actually knows the knowable and makes it actually known;
(d) that the sensible forms of the material composite to be known are received in a cognitive power that is corporeal, whereas the intelligible forms of the material composite to be known are received in a cognitive power that is incorporeal, and
(e) that this radical difference between the phantasm as the quo of sense cognition and the concept as the quo of intellectual cognition explains why the phantasm is the indispensable means of our knowing singulars and the concept is the indispensable means of our knowing universals.
How do you distinguish the validity of voices telling you to kill a few people (Andrea Yeats) or many people (Joan of Arc)?
First of all, the natural law is written on our hearts. We all know that murder, theft and adultery are wrong. But our intellects and wills can become clouded, weak, or ill-formed, weakening the strength of conscience.
The case of Andrea Yeats is straightforward. If, right now, I heard voices telling me to kill my children, I would know with certainty that they were demonic, a defect of my imagination or some other disorder, since murder is always wrong.
But killing is not always wrong. So the case of Joan of Arc is much more difficult. It might be analogous to the case of me hearing voices telling me to begin a war against Syria. Such a war may be just, but are the voices of divine or demonic origin? That would be very difficult to determine. The proper thing for a Catholic to do would be to seek out spiritual counseling, which Joan did. Her personal virtue would be perhaps the most important criteria for evaluating the authenticity of her visions.
To settle the question, they sent her to Poitiers, to be questioned by a commission of theologians. After an exhaustive examination lasting for three weeks, the learned ecclesiastics pronounced Joan honest, good, and virtuous; they counseled Charles to make prudent use of her services.Nevertheless, the judgments of individual theologians and bishops regarding private apparitions are fallible (as was the English tribunal's judgment of her), but the bishop's subject is obligated to obey the bishop. Ultimately, I would have to abide by my bishop's decision.
Juswt for the record, in the several years I've been following this debate on FR, I have yet to see an IDer who could give a coherent description of variation and natural selection.
And those who assert that variation is not blind have provided absolutely no evidence for an alternative.
Does that question interest you?
Just for the record, in the several years I've been following this debate on FR, I have yet to see an IDer who could give a coherent description of variation and natural selection.
I haven't followed the debate on FR, but I've never seen such an IDer anywhere else either.
Why do you ask?
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