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Airplane magnetos, contingency designs, and reasons ID will prevail

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Intelligent design will open doors to scientific exploration which Darwinism is too blind to perceive. The ID perspective allows us to find designed architectures within biology which are almost invisible to natural selection. Thus, the ID perspective is a far better framework for scientific investigation than the Darwinian perspective. What do I mean, and how will I justify my claim?

Let me illustrate my point with some anecdotes. I was piloting a small airplane in the spring of 2002. My airplane suffered a potentially serious systems failure during the flight. In piston powered aircraft, the electrical ignition system (called a magneto system) is life-critical. Aircraft engineers consider the magneto system so crucial that they design each engine with two redundant, independent magnetos. If one magneto fails, the other seamlessly takes over. In fact, these dually redundant systems are so effective that a pilot will not even know if one of the magnetos failed in mid-flight until he’s back on the ground doing a routine inspection of his airplane!

Well that’s what happened to me on my flight in 2002. My left magneto gave out and I continued flying using only the right magneto. There are no instruments on board to indicate if one of the magnetos fail. The failure is usually discovered after landing. The airplane flies just fine on one magneto as long as the other magneto is working. That is by design.

How did I eventually realize I had a left magneto failure? After I landed, I took a break, then prepared to take off again. I went through a routine procedure to check out the airplane’s airworthiness.

I started the engine and followed several procedures on my check list. I then got to the part on the checklist where I separately test the integrity of each magneto. I shut off one magneto and leave the other on.

“Engine 1800 RPM: check!”

“Right magneto: check!”

“Left magneto: Whoa! Holy smokes!”

The engine practically cut off during the left magneto check. There are no instruments to indicate a mid-flight magneto failure. Such system failures are detected after landing. Thus, I had previously been flying through the air blissfully unaware of the left magneto failure. “Ignorance is bliss”. Ha! As I came to the realization that I had been flying on only one magneto, I had visions of what might have happened had the right magneto also failed, visions of me having to fly the airplane with a dead engine, and visions of me gliding the airplane to a safe landing in someone’s backyard…(ah, but I digress)….

What does this have to do with biology and Darwinism? One way Darwinists conclude something is evolutionary junk, a vestigial feature, or an otherwise useless biological artifact is to apply “knock-out” experiments on an organism. If a piece of the organism is knocked out, and the organism still functions well and is otherwise “fit”, then the knocked-out piece is deemed useless, an evolutionary leftover, junk, or even bad design.

What’s wrong with such logic you ask? Well allow me to clarify. Imagine if one applies this line of reasoning to the architecture of a magneto-fired airplane engine:

We knocked out the left magneto system on Airplane X and determined the airplane flies just as well without it. We knocked out the right magneto system on Airplane Y and determined the airplane flies just as well without it. We conclude therefore from these knockout experiments that neither the left magneto nor the right magneto have any functional significance since the airplanes were clearly fit without them. Magnetos are therefore unneeded vestigial artifacts, junk, and evidence poor design, totally useless to the airplane. Furthermore this is further evidence that airplanes are made by blind watchmakers.

Think I’m kidding, and evolutionary biologists don’t make these kinds of obviously bad inferences?

See:
Minimal genome should be twice the size, study shows

“Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath.

“This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product.

When you knock out one gene, the genome can compensate by using an alternative gene.

But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead.

Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments.”

Knockout experiments have also been used to argue “junk DNA” is junk. This is out rightly bad science, but it persists because of Darwinist’s eagerness to close their eyes to design and paint various artifacts in biology as the product of a clumsy blind watchmaker rather than an intelligent designer.

The strategy of using several different means to achieve a particular goal where each of the individual means is sufficient by itself to achieve the goal is used in many engineered systems to ensure that the goal will be achieved, even if one or more of the means fail. For example, the space shuttle’s on-board inertial guidance system, consists of five redundant computers!

How does this relate to biology and intelligent design? Let me quote geneticist Michael Denton in his book Nature’s Destiny:

It now appears that a considerable number of genes, perhaps even the majority in higher organisms, are completely or at least partially redundant. One of the major pieces of evidence that this it the case has come from so-called gene knockout experiments, where a gene is effectively disabled in some way using genetic-engineering techniques so that it cannot play its normal role in the organism’s biology. A classic example of this came when a gene coding for a large complex protein known as Tenascin-C, which occurs in the extra cellular matrix of all vertebrates, was knocked out in mice, without any obvious effect. As the author of a paper commenting on this surprising result cautions: “It would be premature to conclude that [the protein] has no important function …[as] it is conserved in every vertebrate species, which argues strongly for a fundamental role.” The protein product of the Zeste gene in the fruit fly drosophila, which is a component of certain multi-protein complexes involved in transcribing regions of the DNA, can also be knocked out without any obvious effect on the very processes in which it is known to function.

The phenomenon of redundant genes is so widespread that it is already acknowledge to pose something of an evolutionary conundrum. Although in the words of the author of one recent article, “true genetic redundancy ought to be, in an evolutionary sense, impossible or at least unlikely,” partially redundant genes are common. As another authority comments in recent review article: “Arguments over whether there can be true redundancy are moot for the experimentalist. The question is how the functions for partially redundant genes can be discovered given that partial redundancy is the rule.

And it seems increasingly that it is not only individual genes that are redundant, but rather that the phenomenon may be all-pervasive in the development of higher organisms, existing at every level from individual genes to the most complex developmental processes. For example, individual nerve axons, like guided missiles or migrating birds, are guided to their targets by a number of different and individually redundant mechanisms and clues. The development of the female sexual organ, the vulva, in the nematode provides perhaps the most dramatic example to date of redundancy exploited as a fail-safe device at the very highest level. A detailed description of the mechanism of formation of the nematode vulva is beyond the scope of this chapter, suffice it to say that the organ is generated by means of two quite different developmental mechanism, either of which is sufficient by itself to generate a perfect vulva.

It seems increasingly likely that redundancy will prove to be universally exploited in many key aspects of the development of higher organisms, for precisely the same reason it is utilized in many other areas–as a fail safe mechanism to ensure that developmental goals are achieved with what amounts to a virtually zero error rate.

Now, this phenomenon poses an additional challenge to the idea that organisms can be radically transformed as a result of a succession of small independent changes, as Darwinian theory supposes. For it means that if an advantageous change is to occur, in an organ system such as the nematode vulva, which is specified in two completely different ways, then this will of necessity require simultaneous changes in both blueprints. In other words, the greater the degree of redundancy, the greater the need for simultaneous mutation to effect evolutionary change and the more difficult it is to believe that evolutionary change could have been engineered without intelligent direction.

Denton describes what I call contingency designs. It should be hopefully obvious that contingency designs are exactly the kinds of designs that are hard pressed to be created via natural selection. How does one evolve a contingency design when the primary design functions just as well? If a creature mutates a failure into a life-critical primary system, it will more likely be selectively eliminated before it can evolve a fully functioning backup system!

ID’s explanatory filter is therefore a potentially more effective tool at identifying designs which elude Darwinian style tests (such as knockout experiments) for functionality. ID’s explanatory filter looks for possible functionality by identifying specified complexity in biological artifacts which may not evidence any immediate effect on the organism if the biological artifact is knocked out.

I will pursue this more perhaps in another post, but I point out, IBM may have unwittingly detected designs which would otherwise elude the fitness test. See:
Invasion of the IBM engineers

The ability of the Explanatory Filter to identify designs in biology which Darwinists would sooner perceive as an accident and which will elude “fitness tests” is another reason I believe ID will prevail as the proper scientific framework for investigating biology.

The Explanatory Filter may very well succeed in identifying places to look for design which may have otherwise been easily overlooked. I will post on this more, but in the meantime in case you’ve missed it, here is my essay on a related topic: How IDers can win the war

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Comments
Farshad @9: “I removed Part X and it still works fine, therefore Part X is junk” is an argument from ignorance. Moreover, second-guessing of any aspect of any design without knowing the design's specifications and constraints is a demonstration of ignorance and presumption. One must know what the goal was/is to be able to legitimately evaluate or criticize a design.j
June 14, 2006
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The complementary sequence of bases - every A matches with a T, every G matches with a C - allows a double strand of DNA to be regenerated from a single strand. When DNA is replicated the strands are separated and one DNA polymerase complex goes to work on each of the resulting strands, making them double again. If something happens to one of the strands - let's say two thymines next to each other happen to stick together and make a thymine dimer that has to be cut out or excised - the resulting hole can be filled in because DNA polymerase detects the two adenines opposite the hole, and knows to fill it in with two thymines. So there's redundancy right off the bat. Diploid organisms have an extra layer of redundancy: if both strands of DNA on one chromosome are damaged, (DNA damage from ultraviolet light, etc.), there is still a homologous chromosome with a hopefully identical, or at least similar, sequence. When it comes to DNA repair by recombination, in the event of a double-stranded break the two chromosomes are brought together and do some sort of horizontal action (real technical, I know...) that allows DNA polymerase to make new strands for the broken piece of DNA from the sequence on the other chromosome. When it comes to backups: http://blog.tmcnet.com/blog/tom-keating/technology-and-science/dna-backup-surprises-scientists.aspPatrick
June 14, 2006
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The examples you have been discussing of junk/not junk are fine, but the vast bulk of DNA people refer to as "junk" fall into a different category. It is placed in that category based largely on how it is observed to be preserved (or not preserved) across individuals in a populuation or between closely related species. What we call "junk" typically mutates with abandon. It's rearranged, chopped up, and heterogenous across individuals. The information contained therein decays rapidly. Every now and again a chunk of it is co-opted for something useful, but by and large this isn't the case. Some of it's of viral origin. Some of it is the result of the proliferation of endogenous viral-like genetic elements. Again, every now and then something is plucked out as useful, but this appears (so far) to be the rare exception. The genomes of most higher eukaryotes are shifting ephemeral sands with the occassional nugget of conserved information. This may be the manifestation of a complex design paradigm, but it is one so entirely alien and unfathomable to us that, even if we *knew* it was designed that knowledge would be of little practical value. We began in biology by assuming everything we saw had a functional purpose. It's been a long hard-fought road to come to terms with the notion that many things simply don't. The "mistake" of claiming something is not functional when it is does happen, but it's a rare thing and one that can be remedied easily enough when additional info comes to light. The notion that a design paradigm would fill a "blindspot" in current biological thinking is, in my opinion, of far more rhetorical substance than actual substance. When you're down on the front lines, there's ultimately very few systems that are deemed nonfunctional. Even if every one of those turn out to have been a mistake, it's still a sliver of a fraction of biology. So it's not so much a blindspot as a bad pixel. The only significant chunk deemed useless (with regards to our genome)--repetitive/viral DNA,etc--can be pretty clearly seen to have, except for those rare circumstances mentioned above, no apparent function beyond making new copies of themselves. We even can find host molecular components whose job appears to be to hinder them from making still more copies. Not only are they useless; they also appear downright counterproductive. Strangely enough, the only folks in biology that still hold steadfast to the notion that everything is there for a functional "purpose" are your good friends the darwinian fundamentalists. How's that for irony?

A big problem I have with the notion of a lot of unused DNA is that 3 billion bases, even if every single base contained needed information, seems like an incredibly small storage space for the specifications of something as complex as a human being. Perhaps the rapidly mutating regions are simply softer data that changes more often by design. For instance, we really don't have a clue as to how instinctive behaviors are stored. Having instincts that are very malleable from generation to generation so that inheritance of acquired knowledge can happen rapidly would have great survival value as it would allow rapid adaptation to a changing environment. Until we know how instincts are stored I hesitate to call anything junk because there is just seemingly too little storage capacity in the genome to begin with. -ds great_ape
June 14, 2006
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I'm pretty attuned to the performance of the aircraft. 300 RPM on a motor that turns 2400 is lot when it's at the top of the RPM range. Remember that lift increases roughly as the square of the foil speed so 300 less RPM on the prop at close to full speed is a lot more loss of thrust than 10% reduction in total RPM would make you think if you're thinking linear. Since you seldom do anything except climb out of the dead zone on takeoff at full RPM you'll still get enough power for cruise speed but you'll need to increase throttle to get it. I'd certainly notice a degraded maximum rate of climb on takeoff. I might not notice a slightly different throttle position at cruise speed but I'd like to think I'd notice a loss of power if the magneto failed while I had constant throttle applied in any climb or level flight.DaveScot
June 14, 2006
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To what extent are redundant systems in living organisms really redundant? In the airplane example, I think we are talking about two or more *identical* systems, one of which can take over if one or more of the others fail. Do such systems exist in nature? I think not. It seems more likely that the "redundant" systems overlap to a degree but are not really identical. One system might rely on a different basic nutrient than the other system. This might be hard to detect in an experimental setup where all necessary nutrients and then some are supplied by the experimenter. It might well be that one of the redundant systems is much more efficient under one set of environmental conditions, whereas the other system performs much better under a (perhaps slightly) different set of conditions. If so, it is easy to see how such a collection of "redundant" systems could be maintained by selection, if both sets of conditions occur sufficiently often in nature. Can anyone give an example of truly (i.e. identical) redundant systems in nature?

Eh? Two kidneys, two lungs, two ears, two eyes, 32 teeth, 4 fingers... seems like a lot of redundancy. Granted at reduced performance if there's a loss but that's typical of redundant systems where the parts operate in tandem. -ds Raevmo
June 14, 2006
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Would any airplane backup system work with Sal's analogy? The emergency landing gear extension system on most jets is a dusty handle under a seldom-opened panel in the floor of the cockpit. It is more primitive than the regular hydraulic gear extension system and the landing gear works fine without it.russ
June 14, 2006
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"Actually Gil, you can tell if a magneto fails in flight. RPM will drop for no reason. In addition to two magnetos there are two spark plugs in each cylinder each fired by a separate magneto. Two spark plugs results in better combustion and more power. If one magneto fails then only one plug is firing in each cylinder. That’s why your pre-flight magneto test is to note an RPM drop when you switch from BOTH to LEFT or RIGHT. At least that’s how it worked in the Cessna 172’s that I rented." Yes, Dave. But as I recall, that drop in RPM is only a few hundred RPM. The airplane will still fly on one magneto (one ignition system), even if performance is somewhat degraded.russ
June 14, 2006
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Actually Gil, you can tell if a magneto fails in flight. RPM will drop for no reason. In addition to two magnetos there are two spark plugs in each cylinder each fired by a separate magneto. Two spark plugs results in better combustion and more power. If one magneto fails then only one plug is firing in each cylinder. That's why your pre-flight magneto test is to note an RPM drop when you switch from BOTH to LEFT or RIGHT. At least that's how it worked in the Cessna 172's that I rented.

I have a better story than a magneto failure. I rented a plane where the airspeed indicator was in MPH instead of KNOTS and I didn't notice. When I was flying it I noticed that the airspeeds weren't what I expected for rotation, stall, etcetera so I cut the difference in half between what my experience told me the airspeed was and what the airspeed indicator reading was and used the compromise to set up the plane for various flight modes. When I came back (it was a cross country solo while still in training) and told my instructor he didn't know whether to be more impressed that I knew the aircraft well enough to know that the indicated airspeed was wrong or upset that I didn't notice it was MPH instead of KNOTS as it was clearly labeled on the face of the instrument. DaveScot
June 14, 2006
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Many designs contains part that seem to be useless at first glance, but their job is to make your design fail-safe. For example take an electronic circuit board and remove some capacitors and the board may still seem to work fine. The reason is that some capacitors are only used for power decoupling and their job is to provide energy when a particular IC draws a high amount of instantaneous current. The decoupling capacitors will guarantee that your device will not behave in an erratic way under certain conditions.
"I removed Part X and it still works fine, therefore Part X is junk" is an argument from ignorance.

Software is even more packed with apparently useless code called error handlers. The usual state of affairs is no errors so removing them isn't noticed except in special circumstances. -ds Farshad
June 14, 2006
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Hello Salvador, Why do you think life's designer might have created redundant genetic pathways for the generation of a nematode vulva? Do you have any thoughts about what general criteria the designer might have used to determine which genetic functions ought to be reduntant? If the designer was really good at what he does, would redundancy really be necessary? ThanksMichael Tuite
June 14, 2006
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"The Explanatory Filter may very well succeed in identifying places to look for design which may have otherwise been easily overlooked." Can you explain what you mean by 'look for design', isn't that what the explanatory filter does?Chris Hyland
June 14, 2006
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Scordova, there has been a lot of chatter on ISCID's BrainStorms ("Can some aspect of Darwinism be falsified") along the same lines. Dr. Peter Borger is suggesting, similar to you, that redundant genes creates a significant problem for NDE. My understanding is that he is intending to publish his findings farely soon. In the chatter over there, is also a proposal that I have made that certain kinds of error correction algorithms are not evolvable by NDE. Though we have not been able to confirm that such mechanisms exist, it does produce an interesting hypothesis, and an interesting channel to explore. Let me put a little meat on those bones. One of the easiest ways of making error correction code is to have three copies of the code. If an error happens in one of those copies, you can tell which is the error by "voting" -- the correct value will be represented in two out of three. Such an error correction system is a very logical reason to have redundant genes. Further, if there is no similar scheme, the redundant genes should no longer be protected by natural selection, and therefore they should mutate to mush in very few million years. The problem with NDE developing such an error correction scheme, however, is that the scheme would need to be developed with one gene first. (Once it is established with one gene, having the system spread to others sounds believable.) The problem with developing such a scheme with one gene first is that there is painfully little for natural selection to latch on to. Once you have multiple copies of the same gene, either being able to get the job done, the likelihood of a deleterious mutation actually affecting an individual organism becomes enormously small. If the individual organism is not affected, how on earth can selection say "you're not fit to live" when the only system that is not yet there is the system that says "let's correct for any error"? Alas, this is a catch 22 situation. If specific gene error correction exists, it is unevolvable by NDE. If redundant genes exist without error correction, then they are not protected by natural selection, and should mutate to mush in very few million years.bFast
June 14, 2006
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But Mr. Cordova, Even if a system is redundantly complex and thus could not have been produced directly, however, one cannot definitively rule out the possibility of an indirect, circuitous route, right?Mung
June 14, 2006
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Chance and necessity in the evolution of minimal metabolic networks.
Evolution by devolution. I wonder what the original E.coli devolved from.Mung
June 14, 2006
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The correct term for what you're talking about is "genetic interaction". The evolution of genetic interactions by gene and genome duplication is a contemporary focus of the study of cellular networks. There are real questions and challenges here that evolutionary theory has yet to address. But come on, the claim that scientists somehow don't think of these things is silly.nilekim
June 14, 2006
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Sal, excellent post. I have been thinking along the same lines recently -- i.e., that knockout experiments on individual components are poor ways to identify redundancy and/or compensation. Thanks for beating me to the punch and taking time to put down your thoughts. It would be great if you worked up your lengthy post into a brief essay that could be accessible where the issue could see the light of day for a while, rather than being buried in a few days in the UD blog archives.Eric Anderson
June 14, 2006
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Awesome article! An informative read.Atom
June 14, 2006
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