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.
Can you give me a coherent reason why matter and spirit cannot be manifestations of the same underlying reality. If physics can cope with wave/particle duality, why is it necessary for philosophy to insist on an either/or solution?
Can you give me a coherent reason why matter and spirit cannot be manifestations of the same underlying reality. If physics can cope with wave/particle duality, why is it necessary for philosophy to insist on an either/or solution?
AquinasFan, would you mind pinging me on your reply to this question? It's relevant to our earlier exchange about whether 'mind' is automatically going to count as 'supernatural'. (For the record, I'm basically with js1138 on this issue but I think it makes better sense to regard 'mind' as more fundamental than 'matter'.)
Been to ARN.Org much? Where there are Pro ID *scientists* who regularly take part in the discussions? Have you heard of Mike Gene or Bill Dembski?
I think most of the problems in philosophy arise from overextending metaphors. The concept of matter is my prime case. The supposed properties of matter have been truncated by philosophers and theologians who visualize matter as interacting billiard balls.
Ultimately, I would have to abide by my bishop's decision.
If your bishop tells you that killing your children isn't murder (perhaps because they are possessed by the devil) then what?
What if there are two conflicting bishops? The whole spiritualist outlook seems like a formula for conflict.
Leibniz thought of them as non-interacting billiard balls or monads.
I'm not sure philosophers or theologians would do much better to visualize matter as interacting complex wavefunctions either.
I think most of the problems in philosophy arise from overextending metaphors. The concept of matter is my prime case. The supposed properties of matter have been truncated by philosophers and theologians who visualize matter as interacting billiard balls.
That's a good point that brings up another: it's hard to settle on a meaning of 'materialism' without first settling on a meaning of 'matter'. If our understanding of 'matter' expands to the point that we regard it as including 'mental' properties, there will be a lot more 'materialists' than there are now.
This is the key question ID has to answer before it can cross the dividing line between philosophy and natural science. "Irreducible Complexity" seems to be an attempt at an answer, but the irreducible keeps getting reduced--we have yet to see an example of IR in the real world.
If ID produces a set of intellectual tools by which design can be distinguished from apparent design, it can become an expirimental science with the possibility of verifiable results. Until then, it will remain a pursuit better suited to philosophers than to biologists.
That is true to a certain extent, however, the occurrence of resistance to change in the past does not mean it is happening now. It is simply not an argument.
It was just a note that more than one answer can be correct.
""Bible" is ALWAYS capitalized. Look it up in your grammar book. "
I left it uncapitalized because in that context it simply means 'book' therebye including faiths other than Christian. I will correct it because your point is valid. Thanks.
"Welcome to FR, hope you have thick skin if you're going to remain a darwinist on this thread. "
I've argued against YECs for a couple of years so my skin is fairly thick. My concern is not having enough time to devote to fully answering posts.
"Contact PatrickHenry if you want on the evo ping though."
Thanks. I've been on PatrickHenry's list for a few weeks.
You are assuming that there are no brain defects that could change your fundamental understanding of reality. This assumption would have to ignore clinical experience.
I understand there is a problem of measurement here: who decides who is sane and who is insane. But in this case the majority rules, even if there is no way to prove the majority is right.
Unrelated to the problem of demon possession, there is a famous case of an artist who lost his color vision due to a brain injury. It is possible, of course, for colorblind people to understand the concept of color, but this artist lost his memory of color and his ability to understand the concept of color. He was unable to imagine color in any way.
There are countless syndromes like this in which a brain deficit or injury results in the inability to understand or imagine what is lost.
If the true locus of consciousness is not the physical brain, then brain injuries should be perceived as a loss in the same way that loss of a limb is perceived. But this isn't the way it works. Brain disfunctions frequently "close," leaving the individual without the ability to perceive the loss.
you: You are assuming the conclusion. There is nothing in the paper that shows purpose, only use. Things may be used for various purposes; leather's first use may be holding cows together, but that doesn't stop it from being ant food later.
1. [n] the quality of being determined to do or achieve something; "his determination showed in his every movement"; "he is a man of purpose"
2. [n] what something is used for; "the function of an auger is to bore holes"; "ballet is beautiful but what use is it?"
3. [n] an anticipated outcome that is intended or that guides your planned actions; "his intent was to provide a new translation"; "good intentions are not enough"; "it was created with the conscious aim of answering immediate needs"; "he made no secret of his designs"
Perhaps it is the inference of intent which is unsettling, i.e. does design + purpose suggest intent? To me, it does. To others, it may not.
I'm pleading ignorance here. Would you explain further?
But since we can't get inside other people's heads, it seems that we're up against the limits of our ability to know anything here with certainty.
Brain disfunctions frequently "close," leaving the individual without the ability to perceive the loss.
The ability of the mind to receive sensible forms depends on the proper functioning of the body's sense organs, so this would not contradict an essentially non-material theory of sense cognition.
The ability of the mind to receive sensible forms depends on the proper functioning of the body's sense organs, so this would not contradict an essentially non-material theory of sense cognition.
(Aside: for similar reasons, it also wouldn't tell against the practice of prescribing chemical medication to treat psychological disorders. So the current practice of 'doping' students -- whatever else is wrong with it -- doesn't imply, as you suggested in an earlier post, that the psychologists who do so are necessarily materialists.)
LOL. Two of your dictionary definitions include will or intention. So you are saying that intention=intention.
I didn't make myself clear. The natural law is "the first line of defense." Murder is always wrong. So, with regard to the Yeats case, there would be no need for me to seek the counsel of my bishop to determine my course of action. The case with Joan of Arc is different, since the command to undertake a war against England wasn't intrinsically evil. Whether such a course of action was prudent, or commanded by God, would have been difficult to determine.
Parenthetically, the fact of my children's possession is irrelevant. Murder is always wrong.
What if there are two conflicting bishops? The whole spiritualist outlook seems like a formula for conflict.
I am always obligated to act according to my conscience, but I am never permitted to do anything that is intrinsically evil. Since I am obligated to act according to my conscience, I am obligated to inform my conscience as best I can.
Bishops' opinions frequently differ, particularly regarding the prudence of particular courses of action, i.e., the application of principles to particular circumstances. In normal disciplinary matters (not doctrinal matters), I'm obligated to abide by the decision of my bishop, unless his command violates my conscience or the natural law.
Disclaimer: Opinions posted on Free Republic are those of the individual posters and do not necessarily represent the opinion of Free Republic or its management. All materials posted herein are protected by copyright law and the exemption for fair use of copyrighted works.