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Reductionist Predictions Always Fail

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 Rod Dreher writes:

Time and time again, an experimental gadget gets introduced — it doesn’t matter if it’s a supercollider or a gene chip or an fMRI machine — and we’re told it will allow us to glimpse the underlying logic of everything. But the tool always disappoints, doesn’t it? We soon realize that those pretty pictures are incomplete and that we can’t reduce our complex subject to a few colorful spots. So here’s a pitch: Scientists should learn to expect this cycle — to anticipate that the universe is always more networked and complicated than reductionist approaches can reveal.

…Karl Popper, the great philosopher of science, once divided the world into two categories: clocks and clouds. Clocks are neat, orderly systems that can be solved through reduction; clouds are an epistemic mess, “highly irregular, disorderly, and more or less unpredictable.” The mistake of modern science is to pretend that everything is a clock, which is why we get seduced again and again by the false promises of brain scanners and gene sequencers. We want to believe we will understand nature if we find the exact right tool to cut its joints. But that approach is doomed to failure. We live in a universe not of clocks but of clouds.

Comments
Re my comment #16: For example, evolutionary biologists have proposed an evolutionary process by which the bacterial flagellum has evolved as the result of exaptation of structures and functions that were originally adapted to other circumstances. By contrast, Michael Behe (when pressed) asserted that the bacterial flagellum was created "in a puff of smoke". Is there an empirically testable process (i.e. a single step or series of steps) by which the bacterial flagellum can be shown to have become adapted to its function, and if so where can a clear and testable description of such a process be found?Allen_MacNeill
June 20, 2010
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Barry
clouds are an epistemic mess, “highly irregular, disorderly, and more or less unpredictable.”
Could clouds also be pressed into service as an analogy for fitness? I expect some real fitness landscapes to be very messy indeed.Ena Sharples
June 20, 2010
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Optimality, by itself, is no evidence for either evolution or ID. Indeed, both evolutionary biology and ID propose that most biological processes will be near optimal under most conditions (and this goes for rubisco, as well as for any other enzyme). The real question is how biological systems become optimal. Evolutionary biologists assert that this happens via natural selection, which be inferred from empirical studies of the genetic and phenotypic evolutionary transitions from non-optimal to sub-optimal to near-optimal function (and, of course, in the other direction as well). Until ID supporters provide empirically testable mechanisms for such transitions, it won't be considered to be a science.Allen_MacNeill
June 20, 2010
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ba77
though he has no chance of even explaining the origination of what he perceives to be sub-optimal design)
Out of interest, how do you explain it?Ena Sharples
June 20, 2010
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MacNeill's use of the rubisco enzymne, and the underlying implications of sub-optimal design for the rubisco, (though he has no chance of even explaining the origination of what he perceives to be sub-optimal design) is in fact a excellent example of the reductionist fallacy that materialists are gullible to fall prey to. For when taking into consideration the entire mosaic of the web of life here on earth we find rubisco is indeed optimal for its purpose of sustaining higher life forms above it which the rubisco is not aware of nor cares about: Rubisco is not an example of unintelligent design - David Tyler Excerpt: The analysis of Tcherkez et al. (2006) was significant for showing that Rubisco does not bear the marks of Darwinian tinkering and that research to genetic modify the enzyme to gain agricultural benefits can be expected to deliver only "modest improvements" in its efficiency of operation. "Further, [our hypothesis] raises the possibility that, despite appearing sluggish and confused, most Rubiscos may be near-optimally adapted to their different gaseous and thermal environments. If so, genetic manipulation can be expected to achieve only modest improvements in the efficiency of Rubisco and plant growth. Such improvement would be limited to the magnitude of the scatter apparent in the correlations (Fig. 3), if the scatter represents incomplete optimization (see above). [. . .] Such adaptation in response to the changing atmosphere and temperature appears to have been instrumental in enabling the expansion of the biosphere to its current size." Design theorists have drawn attention to three additional considerations: 1. A single-factor analysis of Rubisco is inadequate. The parameters considered to conclude the enzyme is poorly designed and inefficient are very limited. We should note that our perceptions of intelligent design are typically subjective, and most claims for poor design do not stand up to the test of time - further research leads to a greater appreciation of design (a good example being mammalian eye design). Furthermore, unintelligent design of architectures we deem sub-optimal should not be regarded as the only possible hypothesis. Multiple factors are likely to be relevant as chemosynthetic carbon fixation also makes use of Rubisco. It is employed by organisms living at hydrothermal vents and cold hydrocarbon seeps. 2. Photorespiration, the consumption of oxygen to produce a sugar that ultimately forms carbon dioxide during a series of reactions, may not be a mark of inefficiency, but the process may be useful to the plant. The null hypothesis for Design theorists is that processes have functionality. This hypothesis is not without some support: the process of photosynthesis is not just to capture CO2 and release oxygen because nitrate assimilation in plant shoots depends on photorespiration, as Rachmilevitch et al (2004) have shown. 3. Ecological considerations should be included in the analysis. If design is relevant to understanding the way plants work, we should consider not only the benefits to the organism (which limits the horizon for those with a Darwinian perspective) but also the biosphere as a whole. Rubisco's ability to capture CO2 increases with increasing CO2 content in the atmosphere, so its efficiency rises in a CO2-rich atmosphere. However, increasing oxygen levels in the atmosphere will reduce Rubisco's ability to capture carbon. So a negative feedback mechanism exists to regulate the relative concentrations of oxygen and carbon dioxide in the atmosphere. This is another example of design affecting the Earth's ecology - for more on this, go here. http://www.arn.org/blogs/index.php/literature/2010/01/21/rubisco_is_not_an_example_of_unintellige My question for you MacNeill is why did you use this example of rubisco without the caveat of "thank goodness it is inefficient"? You knew this refutation was issued several months ago. so why do you refuse correction to your stance? notes: "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist As well, Physicists find many processes in a cell operate at the "near optimal" capacities allowed in any physical system: William Bialek - Professor Of Physics - Princeton University: Excerpt: "A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,," http://www.princeton.edu/~wbialek/wbialek.htmlbornagain77
June 20, 2010
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Upright
Why not just retract a calculated but failed insinuation?
What, this?
In your first post, you insinuated that simplifiying can lead to misunderstanding.
But it can, can't it? You'd not argue with that?
To illustrate this you compare a actual picture that does not show the internal structure to an idealized picture that does.
You are more then welcome to provide such a picture of internal structure. When you find one that looks anything like the image at the top of the blog please let me know! But you'd agree that there is a significant different to the lay person when seeing the two types of image, right? And it seems that if it's anything, the image at the top is reductionist. Mechanical. So an image of the actual structure would be more apt for this blog, would it not?Ena Sharples
June 20, 2010
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Also, I just spent about 20 minutes trying to find a TEM of the basal attachment of a bacterium, but all I could find were the kinds of schematic diagrams shown at the top of this blog. Either there are no actual TEMs of individual bacterial flagella (a distinct possibility, as their fine structure has been worked out mostly via electron scattering and crystallography, not transmission electron microscopy), or such TEMs are only to be found in the technical literature. As to the distinction between clocks and clouds, of course biological organisms are clouds. This, however, means that a great deal of the fine structure of biological organisms (like the fine structure of clouds) is the result of stochastic processes. That is, a cloud viewed as a single entity exhibits regular structure and function. This is why we can classify them as cirrus, cumulus, stratus, etc. However, this overall regularity is the result of the mass action of a very large number of very small particles, which viewed individually act as purely stochastic "Newtonian" particles. That is, although the cloud as a whole exhibits teleomatic changes over time (to use Ernst Mayr's word for purely physical processes with predictable cause-and-effect relationships), each individual particle moves and collides with others in essentially random patterns. So, once again we find that biological processes exhibit predictable patterns of "behavior" (i.e. change over time), but these are grounded in stochastic processes that have irreducible random components. Ergo, the "complexity" of clouds (as compared with clocks) is due to their massively greater stochasticity, rather than greater organization at the level of fine structure. Therefore, it seems to me that asserting that biological systems, if they are more like clouds than clocks, are much closer to the evolutionary model of reality than the ID model. Clouds evolve (i.e. change over time) as the result of purely "natural" processes which do not require any "intelligence" or "design" at all, whereas clocks (at least the kind that are manufactured by humans) are designed for an intended purpose by intelligent agents. Thanks for clarifying this distinction, Barry! I couldn't have said it better myself...Allen_MacNeill
June 20, 2010
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Ena, "Perhaps I could ask a different question." Why not just retract a calculated but failed insinuation?Upright BiPed
June 20, 2010
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Ena, the image is for teaching and understanding. If such images are applicable to understanding the functional structure of the flagella, then they are applicable to understanding the fuctional structure of the flangella. It just that simple.
You'd agree then that it's important to also explain at the same time that the real structures look nothing like the illustrations?Ena Sharples
June 20, 2010
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Mr Arrington, I just found this recent gem of a Dr. Craig talk. He goes into a little detail of the reductionist fallacy around the 27:00 minute mark in defending the fine-tuning argument: William Lane Craig - Arguments of God's Existence and Response to the New Atheists - Gracepoint Berkeley (2010) http://www.vimeo.com/11170354bornagain77
June 20, 2010
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Upright
To illustrate this you compare a actual picture that does not show the internal structure
Perhaps I could ask a different question. If you were given an actual picture of internal structure and an idealized image such as can be found at the heading of this blog, would the values of CSI (or FCSI) be different if you had only the picture to calculate them with?Ena Sharples
June 20, 2010
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BTW, the link in comment #2 ( http://en.wikipedia.org/wiki/File:Chlamydomonas_TEM_09.jpg ) isn't to a TEM of a bacterial flagellum. It's a TEM of the flagellum (technically, "undulapodium") of aChlamydomonas, a unicellular eukaryote ( a green alga, to be precise).Allen_MacNeill
June 20, 2010
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Ena, the image is for teaching and understanding. If such images are applicable to understanding the functional structure of the flagella, then they are applicable to understanding the fuctional structure of the flangella. It just that simple. In your first post, you insinuated that simplifiying can lead to misunderstanding. To illustrate this you compare a actual picture that does not show the internal structure to an idealized picture that does. I hope that helps.Upright BiPed
June 20, 2010
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Clocks, like all machines, are precise, regular, and limited in function. Biological entities are imprecise, irregular, and multifarious in function. To be as clear as possible, biological structures and functions differ from human machines in a quality that could be called "stochastic mass action". That is, they work fairly regularly most of the time because many (but not all) of their parts are massively redundant. There is an irreducible random component in all biological systems which makes necessary this kind of "mass action" that accomplishes biological functions. A very clear example of this is the "mechanism" by which photosynthetic organisms add carbon dioxide to ribulose 1,5 bisphosphate (abbreviated RuBP) in the Calvin cycle. The enzyme that accomplishes this is ribulose bisphosphate carboxylase oxidase, usually referred to as "rubisco". Rubisco is an astonishingly inefficient enzyme. Most enzymes can catalyze several thousand to several hundred thousand reactions per second. Rubisco, by contrast, can only catalyze the addition of about three carbon dioxide molecules to RuBP per second. Photosynthetic organisms get around this extraordinarily inefficient mechanism by producing huge quantities of rubisco. Most plant biologists estimate that rubisco is the most abundant protein in the biosphere. This abundance compensates for the low efficiency of rubisco in carbon fixation. The point here is that the relative inefficiency of biological "machines" such as rubisco is almost always compensated for by "massive redundancy". The schematic diagrams of bacterial flagella, drawn like engineering designs, illustrate the "average" arrangement of such structures. In any given bacterium, the actual structures only approximate this ideal structure. However, given large numbers of "approximations" of the "ideal" structures, biological processes proceed with fairly high efficiency. This model of biological efficiency — that irreducible randomicity is compensated for by massive redundancy – is, of course, the underlying organizing concept in evolution by natural selection. An irreducibly stochastic generator of phenotypic variation (the so-called "engines of variation"; see http://evolutionlist.blogspot.com/2007/10/rm-ns-creationist-and-id-strawman.html for a list) is coupled with a probabilistic "filter" that preserves and reproduces only those phenotypic variations that on the average result in continued function. Or, as the guys with whom I used to work on road construction used to say, "you ain't building a swiss watch". The roads we drive on, like the biological systems of which we are composed, are only approximations of what could be called "ideal designs". The dispute between evolutionary biologists (EBers) and ID supporters (IDers) is between EBers who see biological systems as being constructed and operated "from the bottom up", with irreducible random/stochastic variation woven in at all levels, and IDers who see biological systems as being designed "from the top down", with no genuine random/stochastic variation at all. This dispute between "incommensurate worldviews" is a very old one in western culture (see http://evolutionlist.blogspot.com/2006/02/incommensurate-worldviews.html for more). Personally, I don't really see much hope for a resolution of this dispute, given its long-standing nature and wildly divergent underlying assumptions.Allen_MacNeill
June 20, 2010
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Upright, Is a flagellum a clock or a cloud then? And I would note that the clue is in your own words.
the same idealized images that are in all the science books that biology students are taught from.
Students should learn about things in such a manner, in the first instance. If they choose to go on to study in more detail they'll quickly learn that those images were idealized images not fully representing the item in question. And that things are somewhat more messy then their first textbook makes out. We both know that the real thing looks nothing like the image at the top of this blog post.
He then links to the same image (showing none of the internal structure) as you have done
There are similar images of internal structure, and *none* of them look like the image at the top of this blog. If you can link to such an image, then please do so.
He obviously then hopes no one notices how desperate he sounds.
I think you've misunderstood my intent. I'm not making any claim one way or the other about the design or otherwise of the bac flag, I'm saying that in the context of this blog post we're both commenting on, is the bac flag a cloud or a clock? Does your answer in fact depend on what image you look at?Ena Sharples
June 20, 2010
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Ena, Are you channeling Mark Perakh over here? Professor Perakh, unable to answer ID arguments, foamed at the mouth about the header image on this page. It was an eloquent argument to be sure. It went something like this: creationists like Behe and Dembski are liars, so they use the same idealized images that are in all the science books that biology students are taught from. He posits the warning that idealized images (like the ones which appear in all the science books in order to help students understand the structure) is likely to give someone the idea that there is a recognizable structure. He then links to the same image (showing none of the internal structure) as you have done, and then goes on to say that all flangella are unique (with their individual irregularities) just as all other organisms are individually irregular. He obviously then hopes no one notices how desperate he sounds. It was interesting to see a scientist ignore detail. Apparently, there was too much of it.Upright BiPed
June 20, 2010
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You might say that the flagellum is the Haeckel's embryo of ID.Adel DiBagno
June 20, 2010
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gingoro, Barry, I think trying to make things simple cuts both ways. For example, if you look at the top of this blog you see an image of a flagella. Looks like a machine alright, I'll give you that. Must have been designed. Yet if you look at an actual picture rather then an idealized version it looks rather different, as can be seen here http://en.wikipedia.org/wiki/File:Chlamydomonas_TEM_09.jpg So is the flagellum a clock or a cloud? It seems to depend on what picture you look at.Ena Sharples
June 20, 2010
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Good post Barry. Yes many subjects are complex and not well understood and trying to make them simple is often an error as it makes them too simple. Dave Wgingoro
June 20, 2010
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