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.
Lucky I don't type with my jaw ... it couldn't reach the keyboard from the floor, which is where it dropped when I read your #515....
That only follows if one includes some significant additional qualifiers to the assertion.
I suppose we could argue about what constitutes a "pattern," but suppose we limit it to a simple description of "predictable behavior."
In that sense, we know that patterns exist outside our minds. You know rockets: do you think that the pogo effect is something that our minds created? Or is it a pattern that actually occurs ... and which our minds figure out how to describe?
I think it's pretty clear that the pattern of a pogo effect (or whatever sort of fugoid mode you want to describe) is simply there, regardless of whether the human mind chooses to comprehend it.
Alas, doc, you're undone by the fact that you could describe your squorg in terms we can understand.....
How widely would you cast your net in defining "perceivers" of color? Seems to me that the ability of certain atoms to resonate in response to specific wavelengths of electromagnetic radiation carries along with it all of the basic elements of "color."
I guess then, the caveat would apply to all assertions thus far made on the subject.
If the definition is learned while young they will define it the same. If colour perception changes after the learning process, what you say is correct.
If we consider how a child learns colour we can see why it is necessarily so. A child learns by asking what colour an observed object is and memorizes the label for that colour. When light reflects from an object, unless the two observers, and there needs to be at least two, are in dramatically different physical positions relative to the light source and observed object the wavelength meeting the two observers will be very close to exactly the same. What happens to the perceived light after hitting the eye is irrelevant, assuming the eyes are more or less consistent.
The child is generally taught primary and secondary colours only, simply to get them accustomed to recognizing the category of colour. As long as the teacher consistently calls a specific 'range' of wavelengths a particular colour the child will learn to associate the 'perceived' colour by that label. Gradation in colour recognition occurs later and most people vary in their definitions only.
If my wife and I observe a blue-green object we always differ on the amount of green we see in it, not because our perception is necessarily different but because we choose different points along the continuum separating green and blue.
If my perception of a specific colour is red when the wavelength is green, which is how she sees it, and my perception of another colour is green when the wavelength is red, as she sees it, we perceive different colours but our labels will still correspond. Of course it is doubtful if the difference would ever be this dramatic and most problems with color are within a specific range so differences can be and are noted.
Well, there's computable and computable.... The n-body problem can be approached brute-force, but at the same time there's no closed-form solution to it that we're aware of. (Even the general three-body problem has only one "integral of motion.")
Given that there are different levels of computable, I'm not sure that we can really put "knowable" into a nice neat box that is one-to-one with "computable."
Oh my...what a penetrating insight, r9etb. Thank you, dear man!
"There is no finite description of the phenomena that elicit color perception, and there is no list of wavelengths or combinations of wavelengths that elicit the sensation of color, nor is the same combination of physical phenomena seen as the same by all observers."
There's that word again. "perception"
It has to exist to percieve it. Whether it is the TRUTH is argueable. Color IS, however, and this means that despite tricks our mind may be lead into to think of it, it still IS.
You can take a drug to make you feel happy. This does not mean happines doesn't exist, it means happiness can be counterfeited, which in essence proves it is a universal, as it has a reflective property in our perceptions. Same with colors.
"If it can't be tested, it can not be part of science."
Test "evolution" :p
You can use it to explain things, but that does not mean you can observe it.
Same goes for where our socks go in the laundry. I could explain it by saying "the dryer tore it apart and stuck it in the lent remover" but I can't observe it, so how would it be scientific?
I don't think I'm trying to do that. I think that knowable things contain all computable things but not vice versa. I think that all things is the union of knowable things and unknowable things. The unknowable set may be the null set. (Use quotation mrks appropriately.)
As usual, there you sit on that larded list-o-broken-links like Jabba the Hut, giving no indication by way of any well-reasoned commentary that you understand a thing that you've linked to, or what relevance it has to any discussion underway. And still, you babble on, acting like you're holding court, as you summon your other ego-inhebriated evo-trolls to their battle stations, to spit their venom and post their own lists-o-broken spam links as they evade their painfully obvious inability to cogently defend their silly positions with objective science.
Too often, your side digresses from a discussion about science into a discussion about religion, because your evo-paganism is threatened to its core by what science actually knows stripped of all the evo-religiosity, counterfeit "scientism", demonstrably false "evidence" peddling (e.g., von Zieten -- just your latest bad-boy example) and all the vain speculation that is fraudulently peddled as fact by your liberal mouthpieces in the MSM. Cowards and intellectual dwarfs -- the lot of you.
Though I have to say, this was a priceless admission for an evo like you from that "Theory of Everything" thread for the other day:
In the past, the great scientific work seemed to simplify the world, and describe it in ways that were relatively easy to understand. If I'm to understand anything more, there needs to be a new simplification, not this 11-dimensional beast that seems to be the most promising bridge between the Einsteinian and the quantum-mechanical world.
It's a bias -- and a hope -- built on my own limitations, but my suspicion is that deep down, and I mean way deep down, the universe is based on a few very simple rules.
Simple rule #1: You evolutionists need to prove you have the time to make happen what is statistically physically impossible to happen.
Simple rule #2: No amount of time exists to make happen what is statistically physically impossible to happen.
Simple rule #3: Without an ability to fulfil simple rule #1, and logically admitting the indisputable fact of rule #2, you must logically conclude that evolution is no "theory" at all, but is at best only a premise and a bias you can merely wish to be true.
Of course, arriving at simple rule #3 requires intellectual honesty in a search for truth in this matter, but too many on your side like Pontius Pilate have looked truth straight in the face and still vainly ask, "What is Truth?" There is none so blind as he who will not see the abundant and screamingly obvious evidence of the intelligent design of the universe which surrounds him.
Now there's the simple truth of the universe in a nutshell.
It's just up to you to summon the courage necessary to get past your own silly ego and smary sophist venom spitters on your team long enough to finally admit to what it is "way deep down" inside that I suspect your 5-senses already know.
This is equivalent to saying "existence is proof of intelligent design". Any existence, including a universe filled with nothing but big rocks and no humans. There could not be any existence (and "inception" is really irrelevant) that was not an algorithm. Any state with a Kolmogorov complexity is an algorithm, and I'm sure some would argue that even a state with no Kolmogorov complexity is an algorithm.
When I formulated the hypothesis years ago I used the "Euclid algorithm" (finding the highest common factor between two numbers) as my example. As I'm sure you know, that algorithm includes process, symbol, decision and recursive.
If we see such an algorithm either at the inception of the universe (or multi-verse) or at the inception of life - then it is proof of Intelligent Design. My hypothesis can be falsified by proving that such an algorithm can arise from nothing (universe or multi-verse inception) or from the physical laws/constants (life).
you:??? That does not follow short of contorting strict definitions with vague semantics. You'll need to explain it.
Some introductory information for anyone interested:
SPARE TIME. Descartes gave us co-ordinate geometry, with its three spatial dimensions. Einstein put time on an equivalent footing, creating 4-dimensional spacetime. String theory added six more spatial dimensions, and M theory added yet one more for a total of eleven (see Update 329). Now Cumrun Vafa of Harvard has added still another----an extra element of time---to make the existing theories more compatible with each other. Because of possible side effects, such as faster-than-light travel or questionable causality (time would not be measured sequentially along an axis but would spread out into a plane), Vafa's "F Theory" has not found many adherents yet. (New Scientist, 1 November.)
Two Timing Universe (starting at pg 247)
To recap it for any Lurkers:
tortoise: Unknowable in some context does NOT imply non-computable.
AndrewC: Unknowable, does not mean somebody else knows, but I don't. Unknowable, means precisely that, unknowable. It cannot be computed. I might argue that something knowable is not computable. For instance, I know I love my child. Compute it. In any case, if ~Q then ~P is the contrapositive of if P then Q.
I think the logic is...
If x is unknowable then x is not computable. The contrapositive would be If x is computable then x is knowable.
r9etb: I'm not sure that we can really put "knowable" into a nice neat box that is one-to-one with "computable."
AndrewC: I think that knowable things contain all computable things but not vice versa.
Thus, although everything is a mathematical structure in that cosmology - not everything is knowable, i.e. we can compute what we know - but we may know of something which we cannot compute (adding r9etb's insight here) - and we cannot compute what we do not know.
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