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.
Maybe you should ask the rock.
The word "illusion" needs a context, given it by the fifth dimention, consciousness. Do the first three dimensions exist in form outside of time? Can time exist outside of consciousness?
1) Jesus, said "my sheep know my voice". If you form a relationship with the one true God and you keep that relationship active, you don't normally have a problem, recognizing His voice from anyone's elses.
2) God also prohibited spiritism, i.e. the seeking out and communicating with spirits other than Him. One of the ways people get in trouble is by playing around with spiritism.
"NOPE. I strongly doubt it."- Betty Boop
I agree, rocks don't have conciousness. However, had people not praised Jesus, the very rocks would have cried out. That would have been interesting to see. So if God so desires, rocks apparently can be made to speak.
All axioms can be negated theoretically, not just some.
And yet can anyone provide evidence to the contrary of existence itself? The possibility of disproof is, in this case, both a logical and actual absurdity. Such evidence would have to exist to be evident.
Therefore existence itself is a brute fact. It does not admit any proof or disproof.
Since scientific knowledge includes knowledge of things that are not demonstrable, the disjunction you set up with falsifiability is only partially applicable and does not extend to the entire scope of what concerns "science."
In other words, the suppressed premise: not both p and q. Affirmation of only one side of your disjunct between disprovable and not/disprovable is logically exclusive. To escape such a fallacy on merely logical terms, both terms of the disjunct are possible or they are incongruous. But we cannot say that existence is incongruous with science.
If you really want to do logic, you can't hide from metaphysics :)
(I know ckilmer, for one, understands the point first made by Aristotle how it is that some first principles are not demonstrable.)
I have. I got no reply. :^)
Ontology in the classic sense is the science or study of being (Life). I am using it in its Leibnitzean refinement: "Ontology [is] the science of something and not nothing, of being and not-being, of the [particular] thing and the mode of the thing, of substance and accident." Further, I want to look at the problem at the most global level -- that of the evolving Universe itself: What is it that changes ("accident"), and what stays the same ("substance")?
Of course, it will almost certainly be pointed out that this is a philosophical, metaphysical approach that many feel is inappropriate in scientific applications. But I just tsk-tsk all that. For I have noticed that there are "schools" of science in the sense of the philosophical schools, whose "cosmologies" are implicit (though buried) in the way the science is being done. In the case of metaphysical naturalism, for instance, I think we are looking at a frank instance of a philosophy being conducted under the color/cover of science. To say that "all that there is" is "matter in its motions" is without doubt evidence of a philosophical commitment. Or so it seems to me. FWIW.
Thanks so much for writing, bvw!
No, it is an illusion and wouldn't even be an idea.
Can there be change outside of time? If not, then according to Goedel there wouldn't be change either. Nor would there be cause and effect.
"possible, but not all possibilities are equally worthy of investigation. Just because something is complicated or appears to have been designed, doesn't necessarily make it so."
Let me simply put here before I continue that I appreciate your civility and this discussion is indeed enjoyable on my part.
This "possibility" aspect is exactly what some of my newer posts on the subject regard. Think of it this way: statistically, what are the chances of life forming on its own? Now, if there was any sort of guidance in the creation of life, how much more likel would it be?
This by far does not PROVE ID, but it does make an arguement for it in a mathematical POV. It's the same as saying "I have a chance of getting to Jamaica this year." While it isn't impossible to do so without one, buying an airplane ticket would make the chances rise greatly.
Again, this does not prove anything, but simply points out that by what is possible, either is considerable. What is probable (by mechanism alone) is ID. What is probable (by directly observable occurances) is abio-genesis and evolution.
We are yet to find a way of distenguishing between intended design and inherent random events.
All the world's a stage and life is just a metaphor for chemical acts.
– (From: As Matter Resembles It)
The one thing we all should know about is ‘ourselves’ (our very being, morality, who and what we are, our consciousness, etc…) Science is currently trying to tell us about ‘ourselves’ in purely mindless mechanistic processes. I personally cannot reconcile a mindless beginning and mindless processes with who I am. Science is treading upon philosophy; morals, being, consciousness, and religion.
Yes, I know. The rock told me. Apparently the rock is pissed about something and not speaking to you, something about you not taking the rock seriously and refusing to recognize its feelings. I really think you and the rock should work this out.
I'll be sitting in for Dr. Phil all week.
This, too, is falsifiable. Or are we treating another animal here?
"Therefore existence itself is a brute fact. It does not admit any proof or disproof."
Would the same be said of God? No admittance of proof, no way of disproof. Does that make God a brute fact as well?
Taking a stab here at oversimplifying things:
Time can only exist in the realm of Conciousness.
The three standard dimensions can only exist if Time is present. This is how distance is established, by how long at a certain rate it takes to get from point A to points B, C, and D.
This means that without Timel; Hight, Width, and Depth do not exist. And without being able to percieve Time, you do not percieve existance.
This implies that Black Holes (Worm Holes, etc.)would be imperceptable to those that are in them, due to the bending of Time and Space and loss of perception.
In full circle, this means that Conciousness defines reality, not the physics there-in.
Can you explain why this statement says not? You include as a mark of scientific knowledge it's instrumental value, and when it is used instrumentally, it becomes non-falsifiable. You've also been saying that a mark of scientific knowledge is falsifiability. Perhaps its late.
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