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Author
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Topic: Biochemical complexity need not be irreducible
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Doubting Thomas
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Member # 1214
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posted 22. March 2004 16:56
I have always been fond of enzymes that have multiple functions or which can accomplish entire series of biochemical transformations. One such enzyme is 2,3-oxidosqualene cyclase (or lanosterol synthase). It has been a key component of sterol (triterpene) biosynthesis since at last as far back as the Eubacteria. It weights 83 kiloDaltons and consists of a chain of 732 amino acids.
This enzyme is highly conserved in nature, as one might expect from its vital function and the strict structural demands of its raw material and product. The human enzyme shows 36-40% sequence homology with the same enzyme in plants and yeast and 83% with the enzyme in rats.
This single enzyme possesses a large active site that accepts the linear polyolefin precursor 2,3-oxidosqualene and, in a single operation involving ten concerted (step-wise) modifications to covalent bonds, produces a molecule of the sterol lanosterol containing four rings and four asymmetric centers. (Subsequent enzymes produce cholesterol and the steroid hormones).
Here is a try at showing a graphic of this biochemistry:
=http://www.uky.edu/Pharmacy/ps/porter/squale1.gif If it doesn't show up you can paste it into the address line of your web browser.
The beauty of enzymes such as this is that its function is both elegant and not 'irreducibly complex'. The lesson we learn is that not everything wonderful and complex in Nature was necessarily designed.
[ 22. March 2004, 17:27: Message edited by: Doubting Thomas ]
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Micah Sparacio
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Member # 6
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posted 22. March 2004 18:59
DT,
I'm no biologist, so I'm just going to address what you state as the point of your post:
"that not everything wonderful and complex in Nature was necessarily designed."
I agree, though I'm not sure what intellectual work this analysis does.
First, I'm not sure that I know of anyone who states these two conditions as being sufficient for inferring designedness:
1. Object or event is wonderful
2. Object or event is complex
Therefore, object or event is designed
I'm sure such arguments are out there, but who takes them seriously?
Second, let's grant that condition 1 and condition 2 are a sufficient definition of designedness. Has anyone argued that these conditions necessarily imply design? Or, is the argument typically that these two conditions lead to a probablistic inference: that if the object or event meets condition 1 and 2, then it is probably designed.
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Rex Kerr
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Member # 632
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posted 23. March 2004 05:06
Also, the post seems to imply that anything that is designed must be irreducibly complex. But this is clearly not the case--I can break off a branch to use it as a club (design), but the transformation from vegetation to weapon is hardly IC.
That is a very neat enzyme, and it does suggest that we shouldn't be too hasty in assuming that just because a system appears IC now that there could not have existed a single-protein precursor that implemented the entire function. But this is not the same as a determination that lanosterol synthase is not designed.
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Art
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Member # 179
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posted 23. March 2004 08:34
FWIW, the perception of IC-ness based on the series of steps leading from substrate to product is an illusion (IMO). Lanosterol synthase and related enzymes really only do one thing - they catalyze the formation of a very transient and reactive carbocation that subsequently rerranges according to whatever geometric constraints the enzyme places on the intermediate.
A tangent that pops into my mind - enzymes are usually thought of as enablers, and it is this sort of positive action that frame hypotheses (design and otherwise). The carbocation intermediate that is formed by lanesterol synthase is highly reactive, and can form any of hundreds, if not thousands, of subsequent products in solution. What the enzyme does is limit - constrain to a very high degree - the options for rearrangement. In this way, we can view the enzyme as much as a "disabler" as an "abler".
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Doubting Thomas
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Member # 1214
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posted 23. March 2004 14:52
Micah Sparacio wrote:
quote:
I'm no biologist, so I'm just going to address what you state as the point of your post:
"that not everything wonderful and complex in Nature was necessarily designed."
I agree, though I'm not sure what intellectual work this analysis does.
First, I'm not sure that I know of anyone who states these two conditions as being sufficient for inferring designedness:
1. Object or event is wonderful
2. Object or event is complex
Therefore, object or event is designed
I'm sure such arguments are out there, but who takes them seriously?
My major point concerns defining the boundary between what is biologically designed and what is not designed. In order to gain some insight into this, let's turn to see what intelligent design has to say about this point.
My heavily bookmarked copy of Michael Behe's Darwin's Black Box, written primarily for the scientifically untrained lay person, leaves the distinct message that virtually everything in the living cell is either IC or is in some other vaguely defined way designed. For instance, in the reply to my first post in the ATP synthase string the responder makes the flat-out statement that the ATP molecule is IC! I guess the 'logic' there is that removing a phosphoanhydride group from ATP by breaking a covalent bond means you no longer have ATP! By his argument, every biochemical is IC. But ATP can't be IC, at least by Behe's definition on pp. 39-40:
quote:
By irreducibly complex I mean a single system (italics mine) composed of several (italics mine) well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system (italics mine) to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. ... Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to work on.
Behe clouds the design issue as follows on p. 205:
quote:
MAKING DISTINCTIONS - Just because we can infer that some biochemical systems were designed does not mean that all subcellular systems were explicitly designed. Further, some systems may have been designed, but proving their design may be difficult. ... Detecting design in the cilium might be a piece of cake, but design in another system might be borderline or undetectable. It turns out that the cell contains systems that span the range from obviously designed to no apparent design. Keeping in mind that anything might have been designed...
On preceeding pages in the same chapter (9), Behe states (p. 196) as follows:
quote:
In order to reach a conclusion of design for something that is not an artificial object...or to reach a conclusion of design for a system composed of a number of artificial objects, there must be an identifiable function of the system. ... In considering design, the function of the system we must look at is the one that requires the greatest amount of the system's internal complexity.
And on p. 193: quote:
What is "design"? Design is simply the purposeful arrangement of parts. With such a broad definition we can see that anything might have been designed.
For the purpose of the enzyme in question, lanosterol synthase, it obviously fails Behe's IC requirement of having 'several well-matched interacting parts.' Or does it? An analysis of the various functions of different amino acids and hydrophobic domains in the enzyme show it to be a multi-purpose, 10-step molecular machine in a single package. An argument could be made that the 'several well-matched interacting parts' are actually present, internal to the structure of the enzyme.
Here's Behe again:
quote:
there must be an identifiable function of the system. ... In considering design, the function of the system we must look at is the one that requires the greatest amount of the system's internal complexity.
And on p. 193: quote:
What is "design"? Design is simply the purposeful arrangement of parts. With such a broad definition we can see that anything might have been designed.
Here he is basically stating that lanoesterol synthase is a designed product if we make the assumption that 'parts' can be amino acid residues in a peptide chain and sterically-constrained hydrophobic domains within the tertiary structure of the enzyme that allow it to bind 2-oxidosqualene in the correct conformation for producing lanosterol.
quote:
Second, let's grant that condition 1 and condition 2 are a sufficient definition of designedness. Has anyone argued that these conditions necessarily imply design? Or, is the argument typically that these two conditions lead to a probablistic inference: that if the object or event meets condition 1 and 2, then it is probably designed.
We're back to 'implying,' 'inferring,' and probability theory. Meaning nowhere.
My impression after reading DBB is that the average lay person would come away with the impression that anything biological and complex would have to be the product of dsesign. This is the familiar Argument from Personal Incredulity (Richard Dawkins, The Blind Watchmaker p. 38). Indeed, it is difficult to look at lanosterol synthase and postulate how it might have evolved (along with the sterol biosynthesis pathway) rather than being the product of design. This is the familiar Argument from Design (Ibid, p. 4). Lanosterol synthase is Paley's watch in miniature.
My conclusions are that the definitions of and tests for design in biology are insufficient and too vaguely defined to be of practical use. Until someone can demonstrate design to me conclusively, I'll remain skeptical. That's more of an agnostic viewpoint rather than an atheistic one.
[ 23. March 2004, 14:57: Message edited by: Doubting Thomas ]
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