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Author
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Topic: Wheels of Life
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Mike Gene
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Member # 149
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posted 21. June 2003 01:03
SPINNING WHEELS
Biologist Robin Holliday published an interesting essay in the June 2003 issue of BioEssays [1]. In this essay, Holliday notes that the wheel has been one of the most important inventions (designs) of man, where even to this day, we store our high tech information on discs. Holliday then implicitly argues that if life was designed, we might expect to see such a useful device implemented in biology:
quote:
Since the wheel has become so important for human motility and diverse other purposes, one would think that it might also be used by animals in a variety of contexts.
Holliday then claims that no wheels are found in biology and asks:
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So how do the creationists explain why an all-powerful deity did not on any occasion design an animal incorporating the enormously advantageous rotary motion of wheels? [2]
Holliday asserts that “creationists” have no answer for this question and then explains how Darwin’s theory of natural selection provides the explanation:
quote:
The wheel is a manufactured object that can only function when it is complete. One cannot use a quarter or a half of the wheel; indeed they would be an impediment to any animal. Therefore one cannot evolve a wheel in multiple stages, in the way that one can evolve an eye, a brain or a limb. So there can be no selection of advantageous mutations in the case of the wheel, because they simply do not exist.
The problem with Holliday’s argument is that wheels do exist in biology – they exist at the nanotech level.
The classic example is the bacterial flagellum where the motor proteins form a ring that spins. For some reason, Holliday dismisses this example:
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The flagellae of motile bacteria that have a rotary propeller-like movement contain a single structural protein called flagellin, but could scarcely be regarded as wheel-like.
Yet as biologist Sutherland Maciver, from the University of Edinbergh notes:
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Bacteria invented the wheel! The bacterial flagellum is a helical structure that drives the cell through the media like a propeller. The structure is rigid and turned by a rotatory motor at the base where it connects to the bacteria's body. The rotary motor consist of several wheel-like discs one of which the M-ring (and/or possibly the S-ring) interact with the C-ring and studs to rotate the whole structure. The rotary motor is very like a stepping motor! [3]
In fact, even Richard Dawkins acknowledges the bacterial flagellum as a wheel. [4]
Yet the flagellum is not the only wheel inside the cell. Another classic example is the ATP Synthase, which is considered the smallest rotary engine in nature. One paper describes this complex as follows:
quote:
The rotor portion is proposed to consist of a wheel of at least nine copies of subunits c, epsilon and a portion of gamma as a spoke, and another portion of gamma as a crankshaft. [5]
This motor has even inspired nanotechnologists. [6]
If we return to Holliday’s argument, in a sense, he is correct. If our inference to design stems, at least in part, from the analogies between life and technology, we should expect to see wheel-like structures incorporated among the machinery. Holliday notes, “Paley’s watch had cog wheels, but living organisms have no wheels…” Yet as I wrote a few years back, “In fact, I will now make a prediction: If the cell is designed, we will find that they look more and more like Paley's watch.” [7] Thus, from an design perspective, I would predict that the flagellum and ATP synthase represent only the tip of the iceberg.
To follow up this prediction, I poked around the literature and found another interesting example.
MCM (or mini-chromosome maintenance) protein complexes are essential in the initiation of DNA replication in eukarya. They function as helicases that unwind the DNA. However, there are aspects of MCM function that are confusing in this role. For example, the MCMs are not located at the sites of DNA replication. Ronald Laskey and Mark Madine have proposed an intriguing hypothesis that resolves many of these odd features.[8] They propose the ‘rotary pumping model,’ where the MCMs act as rotating wheels that thread the DNA strands into the sites of replication:
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We suggest that the existing data are far more consistent with an alternative model, namely that the MCM proteins are indeed rotary motors, but that they translocate DNA along its axis by helical rotation, causing it to unwind at distant, fixed replication forks (Fig. 2). This is analogous to a helical threaded ‘bolt’ rotating through ‘nuts’ (see below), and there are several precedents for such a rotational translocation of DNA. We envisage two steps, both using the same postulated rotary function. First, MCM complexes would load onto DNA at the origin of replication and move away from the origin by rotation along the helical thread of the DNA. In this way, MCMs would disperse along the unreplicated DNA….. Second, the dispersed MCMs would be anchored to an immobile nuclear structure and the identical rotary action would be repeated. Now only the DNA would be able to rotate, and this action would effectively pump DNA back towards the origin of replication (Fig. 2). This would provide a simple and efficient mechanism for spooling large quantities of DNA through ‘anchored’ sites of replication.
Given that there is growing evidence that DNA replication occurs in fixed protein factories, I expect this model to pan out. This would highlight just how artificial-like life is at its core. Here we’d have protein wheels being loaded on the DNA in their proper orientation and spinning down the DNA until they reached a proper location where they become anchored at fixed sites. Now, as they spin, they begin to thread the DNA back into replisome factories. And it’s worth mentioning that the same MCMs also license the DNA for replication [9].
Let me suggest other candidate wheels. First, there is the rho transcription terminators used by eubacteria. These hexameric protein complexes help to extract the RNA transcription products. While no one has proposed rotary movement for the rho terminators, they are thought to be quite similar to the F1 component of the ATP synthases, where three of the six subunits hydrolyze ATP in a sequential fashion in a manner that tracks with rho’s movement across the RNA [10]. Also, it has been found that the RNA is threaded through the hole of the hexamer [11].
Secondly, there is the FliI component of the bacterial flagellum. It has been recently shown that FliI forms an ATP-dependent ring structure [12] and is thought to sit at the very base of the flagellum. FliI is also thought at act as the intermediary between the cytoplasm and the embedded protein secretion apparatus, recruiting flagellar proteins. Since many flagellar proteins are probably unfolded as they enter the secretion apparatus, one can envision FliI acting much like the MCMs, snagging and threading the amino acids chains into the apparatus as it spins.
What all these proposed wheels have in common is that they form ring structures and handle polymers in an ATP dependent fashion. I’ll label these machines as the molecular threaders. In a sense, cells do have “cog wheels,” only they are more sophisticated than Paley’s watch.
1. Holliday, R. 2003. Creationism and the wheel. BioEssays 25: 620-621.
2. Holliday conflates creationism with ID and assumes the designer must be an an all-powerful deity
3. http://www.bms.ed.ac.uk/research/others/smaciver/Teaching/Locomotion%2034.pdf
4. http://www.dslnorthwest.net/~danwilcox/wheels.htm
5. Engelbrecht S, Junge W. 1997. ATP synthase: a tentative structural model. FEBS Lett. 414: 485-491.
6. http://www.sciam.com/article.cfm?articleID=000988D5-647B-1C75-9B81809EC588EF21
7. http://www.idthink.net/biot/dif/index.html
8. Laskey, RA & Madine, MA. 2003. A rotary pumping model for helicase function of MCM proteins at a distance from replication forks. EMBO Reports 4: 26-30.
9. http://www.idthink.net/biot/dna/index.html
10. Stitt, BL. 2001. Escherichia coli Transcription Termination Factor Rho Binds and Hydrolyzes ATP Using a Single Class of Three Sites. Biochemistry 40: 2276-2281.
11. Burgess BR, Richardson JP. 2001. RNA passes through the hole of the protein hexamer in the complex with the Escherichia coli Rho factor. J. Biol. Chem. 276: 4182-4189.
12. Claret L, Calder SR, Higgins M, Hughes C. 2003. Oligomerization and activation of the FliI ATPase central to bacterial flagellum assembly. Mol Microbiol. 48:1349-55.
[ 21. June 2003, 01:15: Message edited by: Mike Gene ]
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Rex Kerr
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posted 21. June 2003 05:21
I wonder whether the same sense of wheel is being used throughout the different quotes. Without having checked all three sources, it's difficult for me to judge.
My impression is that Holliday is thinking of a large round thing with a central (fixed) axis, enabling translational motion by rotation of the round thing while leaving the axis fixed. At least this is what is normally meant by the "invention of the wheel".
Maciver appears to be using "wheel" to mean only rotory motion, and I'm not sure what Dawkins said. Likewise, the ATP synthase quote appears to be using "wheel" to describe the shape. It seems a little odd to have a single component being both spoke and crankshaft, for instance.
Do you think my assessment of the difference in terms is accurate, and if so, is it relevant to Holliday's argument?
Also, one might think of a similar argument, namely: large-scale wheels cannot be formed by recruitment of ever increasing numbers of small functional units. So, although one can generate both linear and rotary motion on the molecular level, large-scale linear motion is accessible to evolution (given small units with linear motion, e.g. single muscle cells) while rotary motion of a large-scale structure is not.
It also puzzles me if Holliday picked out the wheel as compared to fire or shotguns or a laser or metal blades or cell phones. There are lots of very useful human inventions that are not found in nature. Wouldn't all of these make the same point as the wheel? Many of these do not have molecular analogs--for instance, there are no molecular lasers as far as I know. If his point is invalid, it seems that it is not (only) finding molecular-scale rotary structures that disproves it; there must be something more general to say about the distinction between human technology and what is found in nature.
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Pim van Meurs
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posted 21. June 2003 11:45
This post was totally useless and thus deleted. In the future, Pim, please be more thoughtful when you click the submit button.
I agree, Rex had reaised most of my comments already although at that time I had not read them. The anology of 'wheel' whether used in a literal or figurative sense is still useful describing the flagellum.
[ 21. June 2003, 18:14: Message edited by: Pim van Meurs ]
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Mike Gene
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Member # 149
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posted 21. June 2003 12:24
Rex,
I think of a wheel as a round thing that rotates continuously around an axis. Whether the axis must be fixed or can also revolve doesn’t seem significant to me. Large scale wheels employ fixed axles to anchor the spinning wheel in a fixed position. Cells use other means of localizing their wheels and thus can actually use the wheel to turn the axle.
Nevertheless, many people, not involved in this debate, independently recognize the wheel-like features of the flagellum and ATP synthase:
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In addition many bacteria move using a structure called a bacterial flagellum. This is quite different than the flagella found in eukaryotes in that it has a rotating base like a wheel that supplies torque to the rest of the flagellum.
http://old.jccc.net/~pdecell/cells/basiccell.html
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The prokaryotic flagellum rotates around its base, much like a wheel.
http://www.colorado.edu/epob/epob1220moreno/PROKARYOTES.htm
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The anchor of the bacterial flagellum is an "axle-and-wheel" arrangement which allows the flagellum to rotate like a propeller.
http://www.biology.lsu.edu/introbio/spring/spring2003/1002/SMP/Outlines/1002.Outline1B.html
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Flagella are inserted through the cell walls of bacteria. At their base can be found wheel-like structures.
http://www.bmb.leeds.ac.uk/mbiology/ug/ugteach/icu8/introduction/bacteria.html
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Cilia and eukaryotic flagella function to move whole cells or to move materials across or into cells. Prokaryotic flagella are not only constructed very differently that those of eukaryotes, but operate by truly rotating - nature's only example of the wheel!
http://www.science-projects.com/CC101D4.htm
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There are 12 copies of the c subunit, organized in a ring. The current causes the ring to rotate, like a water wheel, while the protons are delivered from one side of the membrane to the other. This rotary motion drives the "mechanical" proteins called gamma and epsilon.
http://svik.life.smu.edu/images/atpsynth/ATPtext.html
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Boyer has called ATP synthase a molecular machine. It may be compared to a water-driven hammer minting coins. The F o part is the wheel, the flow of protons is the waterfall and the structural changes in F 1 lead to three coins in the ATP currency being minted for each turn of the wheel.
http://www.nobel.se/chemistry/laureates/1997/press.html
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ATP synthase, an enzyme in the membrane uses the concentration gradient to phosphorylate ADP: Protons coming back along the gradient act like water turning a mill-wheel!
http://niko.unl.edu/bs101/notes/lecture7.html
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New research has dramatically refined our picture of a protein machine that functions like a waterwheel, harnessing the energy of “falling” hydrogen ions instead of falling water. Amazingly, this bio-machine includes a rotating shaft….These experiments reveal the remarkable mechanical similarity between this Lilliputian bio-machine and the rotating water wheels used for centuries by humanity to harness the energy of falling water.
http://www.ascb.org/newsroom/pb99/yasuda.html
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Circular motion also occurs in the proteins which rotate bacterial flagellae, another important enzyme system which is driven by the proton motive force. It is apparent that the wheel has been in continuous use for at least 2000 million years.
http://www.bmb.leeds.ac.uk/illingworth/oxphos/atpase.htm
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The enzyme ATP synthase spins like a wheel to convert energy into ATP for storage. High-speed imaging reveals the details of the rotation.
http://www.biomedcentral.com/news/20010420/03/
It is also worth keeping in mind that rotary motion inside the cell was once considered an absurd idea:
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"Initially, people thought the rotary mechanism was a crazy idea," says John Walker of the MRC Dunn Human Nutrition Unit in Cambridge. His deduction of part of the enzyme's structure backed up the theory -- and finally won him a share of the 1997 Nobel Prize for Chemistry.
The sceptics were silenced by earlier work from Kinosita's group, which showed the ATP motor turning for the first time. "It had major impact -- seeing is believing," says Walker.
http://www.nature.com/nsu/nsu_pf/010419/010419-3.html
I mention this because revisionism is common. That is, as we begin to uncover the many ways in which cells reflect technology, while initially viewed with surprise, years later, many react with a “yawn” as if such features were supposed to fall out of non-teleological entities.
As for the other analogs you mention, I don’t think it’s simply a question of making superficial comparisons. In this case, I envision the cell as an artificial construct that entails coordinated movement. This vision is behind my prediction: “I will now make a prediction: If the cell is designed, we will find that they look more and more like Paley's watch.” If we consider the coordinated movement inside the cell, there is either linear movement or rotary movement. Concerning the latter, the wheel is a circular device that is well-suited to couple rotary motion to work. The advantage of a rotary motion device is that it can carry out such work indefinitely with minimal rearrangement of the surrounding structural architecture. Yet the cell is also very good at coordinating internal structural rearrangements, as its order is dynamic. Thus, the advantage of the wheel inside the cell may be minimal and restricted to certain functions. This is one reason why I propose the molecular threaders. The rapid threading of polymers is something a wheel could do very well.
Pim,
The purpose of my essay is to push the artifact-like nature of life to its limits. Originally DNA replication was the function of an enzyme. Then it was a function of enzymes. Then molecular machines. Now factories of anchored machines. The MCM wheels now add a conveyer belt analog to the picture! As teleologist, I like to brainstorm about life as technology. And that would seem to fit well into the purpose of this forum, eh?
[ 21. June 2003, 12:30: Message edited by: Mike Gene ]
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charlie d.
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posted 21. June 2003 13:52
quote:
This vision is behind my prediction: “I will now make a prediction: If the cell is designed, we will find that they look more and more like Paley's watch.”
This would be a valid prediction, if it acknowedged every times cells do not behave like watches as failures of the prediction. Every time stochastic models dominate over binary, every time transient and labile associations are found, rather then stable ones, every time molecular engines are rather inefficient, every time awkward arrangements appear, every time things do not conform to neat flow charts, etc.
For instance, many ID advocates are fond to describe gene expression pretty much as a binary process, on or off, like electrical switches. This was indeed the model that dominated the gene expression field in the early years (up to the late '70s or so). Nice little charts could be drawn with inducers turning genes on, repressors off, feedback loops, etc. However, over the course of the past couple of decades it has become evident that stochastic models much better describe gene expression patterns both at the molecular and the cellular levels (see here for instance). Similar patterns are found for signal transduction systems, cell organization, cell responsiveness, proliferation and senescence, etc. These systems are so unlike human engineering, that engineers are in fact striving to replicate biology in engineered systems (just like they are striving to replicate evolutionary processes where true generation of unexpected inventive features is required), rather than using existing engineering knowledge to help interpret biology (as they might with a molecular machine).
So, a fair prediction is: "We will find that more features in living cells will conform to conventional engineering principles, rather than finding unexpected, unconventional, not engineering-like features." Of course, one could always claim, as some ID advocates here do, that when biological features don't conform to conventional technological engineering principles, it's just because they must be super-technologically engineered. But you agree that'd just be cheating, wouldn't it? ![[Wink]](wink.gif)
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Pim van Meurs
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posted 21. June 2003 16:49
Mike: As teleologist, I like to brainstorm about life as technology. And that would seem to fit well into the purpose of this forum, eh?
Sure, I also like to use analogous thinking to help us understand how nature "designed" these features. Of course its applicability to intelligent design becomes somewhat tenuous nevertheless your attempts are the closest I have seen to applying "Intelligent Design".
Considering something wheel-like, propellor like, motor like may help us understand its function. Will it help us anything beyond this? Nice thought for speculation perhaps? I love 'just so stories' :-)
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Mike Gene
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posted 21. June 2003 17:52
Charlie: quote:
This would be a valid prediction, if it acknowedged every times cells do not behave like watches as failures of the prediction. Every time stochastic models dominate over binary, every time transient and labile associations are found, rather then stable ones, every time molecular engines are rather inefficient, every time awkward arrangements appear, every time things do not conform to neat flow charts, etc.
I agree. In fact, if we consider the extreme of your “every time” list, it leads us to what cells were originally envisioned to be – a membrane bag filled with soup. The point is that cell biology has moved us away from this state and this is one of the big reasons I seriously infer design. Again, I spelled this out on my web page essay:
quote:
But be encouraged. The data are indeed gradually moving to a Paleyian perspective. The raw data are forcing more and more scientists away from the "bag of solution" mentality, to be replaced by a highly organized infrastructure entailing numerous, carefully linked molecular machines. In fact, I will now make a prediction:
If the cell is designed, we will find that they look more and more like Paley's watch. Agutter et al.'s claim that "Cells are highly ordered structures... So far as their internal dynamics is concerned, this means that most physicochemical processes are channeled or "directed" rather than random and suggests that little occurs in the cell on the basis of chance or as a simple consequence of the law of mass action." will ring more and more true with new discoveries.
On the other hand, ID will be falsified if this "highly ordered state" is really an illusion. That is, if further examination actually returns us more closely to the "bag of solution" view of the cell, the design inference behind the origin of the cell will be discredited.
It's very straightforward - the cell as "factory" = design; the cell as "soup" = non-design.
Yet I am wrong – it’s not that straightforward. We can all agree that cells were not designed by humans thus we can’t really say that cells should be no different from something we design. In fact, there are at least three very significant differences between cells (assuming they were designed) and the products of human engineering:
1. Cells are an example of nanotechnology, while the products of our engineering are not. Design principles that may apply at one scale do not necessarily translate to another.
2. The cells we study are not the direct products of a designer, but the descendents of billions of years of evolution.
3. It is reasonable to assume that if cells were designed, a design science far more advanced than ours was used.
If we return to Paley’s watch, we can see why the analogy will not perfectly fit. Compared to a cell, the watch is a lumbering, clumsy design with severe limitations. In fact, I think it safe to say that if we built a living cell so that it perfectly mapped to a watch, such a cell would be too rigid to survive the onslaughts experienced by life and would thus fail to persist/evolve. Take your criteria of transient and labile associations rather then stable ones. It is the transient and labile associations that make life possible. Imagine the process of cell division without transient and labile associations. Imagine the ability to adapt quickly to a change in the environment, such that a new array of genes are expressed, all without transient and labile associations. Etc.
It is not cheating to recognize the implications of the three main differences between designed life and human artifacts.
[ 21. June 2003, 17:55: Message edited by: Mike Gene ]
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John Bracht
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posted 21. June 2003 20:47
Charlie d,
I think you're oversimplifying the issue by claiming that nobody really thinks of enhancers or repressors anymore, or that we can't draw "Nice little charts could be drawn with inducers turning genes on, repressors off, feedback loops, etc." I'm currently in a Ph.D program for biology, and I've certainly seen plenty of precisely these sorts of "nice little charts". Certainly, they simplify the real picture (all our models of biology do) but they capture the essence of what really goes on. Indeed, take a look here to see an example from one of my classes, replete with diagrams of inducers and repressors. Feedback loops are common in biology. So your blanket dismissal of these ideas is not accurate. Sure, there may be noise or stochastic effects in the system. But modern engineers have developed ways to deal with noise and mitigate its effects, as appears to be true in these biological systems. And as Mike pointed out, we're dealing here with nanotechnology, which imposes a set of constraints that we barely understand--contraints which would undoubtedly apply to human engineering at this scale also.
John
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Rex Kerr
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posted 22. June 2003 07:14
Mike, you've come up with an impressive list of citations where molecules that undergo rotational motion are called wheels. And I certainly do not dispute that rotational motion is found in many places in biological systems. (I'm not sure why it was ever thought to be impossible, given that linear motion isn't really any simpler than rotational motion; the topology of the support is just different. I suppose it's yet another case of silly humans deciding that things must be simple (as they perceive simple).)
However, you never really addressed my question, which was whether Holliday meant wheel in the same sense as is used in the references. Perhaps it doesn't matter; questions about rotational motion are interesting in their own right. To be fair to Holliday, though, I think he was trying to point out that certain large-scale systems are extraordinarily difficult to generate through numerous, slight, advantageous changes in morphology. A wheel, such as is found on a car or bicycle, is an example of such a device. It's basically a statement of irreducible complexity: one cannot remove part of a wheel and still have a functioning system.
The question, then, becomes why organisms seem to be missing large-scale structures such as car wheels, lasers, and RF antennas. Or to put it another way: why, from a design perspective, would organisms have nanoscale design but not macroscale design? (From an evolutionary perspective, the answer is obvious: chemistry is nanoscale; that's all there was to work with, and there was no mechanism to see the "big picture".)
(Note: I found insightful the list of distinctions between human design and our observation of functional systems at the molecular level in biology. I do think these points aid in comparing human design with biological systems.)
I'm afraid I'm not going to cede the complexity of life to design camp. Designs can be simple, too. Why, if a simple soup will work, not design a soup? I think the answer is hinted at by a quote from Einstein: "Make things as simple as possible but no simpler."
People simultaneously assumed that the cell was a bag of solution, and were baffled by how it could perform certain functions that were essential to life that couldn't take place in an unordered solution (such as cell divsion, motility, transport of nutrients, etc. etc.). I'm sure we'll find additional structure in other places that we too readily assume are simple, such as lipid bilayers, carbohydrate moities, and so on.
But I don't think this really gets at the distinction between design and evolution, unless there is needless structure and organization. There is selective pressure for increased organization and structure if that organization and structure is beneficial. 3 billion years is a long time to build up advantageous structures. What it can't do is generate neat and tidy structures simply for the sake of being neat and tidy (unless neat and tidy happens to also be simple to generate).
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GP
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posted 22. June 2003 10:26
quote:
1. Cells are an example of nanotechnology, while the products of our engineering are not. Design principles that may apply at one scale do not necessarily translate to another.
2. The cells we study are not the direct products of a designer, but the descendents of billions of years of evolution.
3. It is reasonable to assume that if cells were designed, a design science far more advanced than ours was used.
Hi Mike,
It seem appropriate given this list for me to go back to a discussion topic that I started with you previously[+]. In particular, I am interested in point 3 -- a design science far more advanced than ours. In my opinion, this specific difference -- well, let's be fair, and call it what it really is, an assumption -- renders the previous two points moot. If we're assuming a design science "far more advanced" than ours, then what you and John are both talking about is properly called science fiction, not science. For instance, since there is absolutely no limit to how "far more advanced" that science is, nor is there any dependence on how advanced our own science may go, we may posit that the first cells on this earth were a result of beings (perhaps evolved from H. sapiens!) time-travelling from the future, playing with multiple dimensions and infinite-wavelength zero-energy quantum energy. This renders point 2 irrelevant, since we'd have no idea how long a "billions of years of evolution" actually took to design, nor do we have any reason to suspect that we'd be aware of any present design interventions if they're utilizing "design science far more advanced than ours." Why couldn't they zap or brains and make us forget? If point 2 doesn't matter, than point 1 is equally trivial. After all we can never be sure what "design principles" in this parallel universe would be gazillion years from now. Point 3 is the escape hatch that charlie d was talking about, and something Holliday also observed:
quote:
This example also illustrates another major flaw in the creationists position.What do they suppose the limits of design to be? Why not introduce electronics into animals? Why do all vertebrates have only four limbs? Why do mammals not have wings, like an angel, as well as these limbs? These questions, and many others, become absurd. The evolutionary argument can well explain the change of fishes, fins into the limbs of land-based animals. It can explain the evolution of these limbs to the flippers of whales, and the wings of birds and bats. It is well known that the evolution of quantitative changes is much more readily accomplished than that of qualitative ones. Thus, whales and other marine mammals still have lungs and breathe air millions of years after they took to the sea. There are no constraints on an imagined all-powerful creator, but there are many contraints on evolution by natural selection.
Now, to be fair to IDists, Holliday was talking about Creationists. But I frankly do not see the difference between "an imagined all-powerful creator" and an assumed "design science that is far more advanced than ours."
Once again, point 3 goes directly to the heart of a question I asked previously about a constraints on a minimal intelligence:
quote:
However, answers can always be generated depending on the model of the front-loaded system. For instance, you later write that it is up to theology to determine whether or not God is a micromanager. Suppose in fact that theology determines God to be a micromanager, intervening across deep time. Does the validity of your front-loading thesis actually depend on reconciliation with theology or vice-versa? In any case, I hope I have made more clear my initial question about your human-like intelligence. In particular, I wanted to know if you actually try to minimize your dependence on the model of the engineer to interpret the results. At present, I do not see this effort made.
At the time I asked this question, I got no response (or perhaps it was dismissed as "generic philosophical material" that you found less interesting). But yet it rears its head here again -- how does one go about minimizing hypotheticals about the designers?
We can all agree that cells were not designed by humans thus we can’t really say that cells should be no different from something we design.
No, I disagree. I have no reason to believe that human designs cannot develop in the future so as to design living organisms. Nor do I have any reason to suspect that the designers aren't time-travelling humans from the future or another parallel universe. Tell me how I could distinguish the possibility.
[+]http://www.iscid.org/boards/ubb-get_topic-f-6-t-000290-p-3.html
Hi John,
You wrote: quote:
And as Mike pointed out, we're dealing here with nanotechnology, which imposes a set of constraints that we barely understand--contraints which would undoubtedly apply to human engineering at this scale also.
Please share with us some examples of design constraints that human engineers have no understanding of but yet constrain our present nano-engineering efforts.
[ 22. June 2003, 10:28: Message edited by: GP ]
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Pim van Meurs
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posted 22. June 2003 12:23
John: And as Mike pointed out, we're dealing here with nanotechnology, which imposes a set of constraints that we barely understand--contraints which would undoubtedly apply to human engineering at this scale also.
Interesting, so intelligent design has the same constraints as regularities/chance? I would say that would make an ID inference quite a bit trickier would you not agree?
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Pim,
You're being put on suspension for 2 days. Unless you have something more positive to contribute to our boards (more than the one sentence quips you've become accustomed to), then you're going to face being banned for a longer period of time. Either play by our rules, or we revoke your privilege.
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5. Start addressing the thoughts of your fellow discussion partners - don't rehash your 3 favorite criticisms over and over to the neglect of the main ideas
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7. For the sanity of our readers, write in whole sentences and string sentences together in a readable fashion.
[ 22. June 2003, 15:26: Message edited by: Moderator ]
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Jack
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posted 22. June 2003 14:32
Deleted.
[ 22. June 2003, 18:50: Message edited by: Jack ]
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Mike Gene
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Member # 149
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posted 22. June 2003 20:42
Rex,
It’s difficult to tell what Holliday meant given that he never defined the wheel for his article in BioEssays . Yet, as far as I can tell, Holliday has rotary motion in mind:
quote:
Let us consider the wheel, the invention of which was undoubtedly one of the most important milestones in the social evolution of man. Rotary motion was probably first used with wooden rollers to move heavy stones…….There are innumerable other examples of wheels and rotary motion in our everyday life.
In fact, I think he dismisses the flagellum as a wheel because he is focused on the filament (thinking of the flagellum as being built from a “single structural protein) rather then the basal body.
As for the issue of wheels in macro-scale design, my hypothesis is that life is an expression of nanotechnology. Macro-scale structures evolved from a designed state. And this is where my interest in front-loading fits.
However, even a creationist might have trouble swallowing macro-scale design. If the designer pieces together structures on a macro-scale, the designer would be required to do this work every time the large scale structure appeared. In other words, the designer would have to intervene every time an organism reproduced. Of course, we all know that structures on the macro-scale are not assembled – they are “grown” from developmental programs implemented at the nano-scale. This raises the question of whether a functional wheel could be grown through developmental processes. And what’s more, one could also argue that limbs are actually better designs than wheels. Who gets around better on a camping trip – the walking man or the man in the motorized wheel-chair?
I certainly don’t expect you to concede complexity to the design camp. These are squishy topics that can be explained from different points of view. You ask a good question about the soup: “Why, if a simple soup will work, not design a soup?” You provide part of the answer: “I think the answer is hinted at by a quote from Einstein: "Make things as simple as possible but no simpler."” Yet another part of the answer may speak to front-loading as original structures (and structural material) will impose a direction on evolvability.
As for evolution of structures over 3 billion years, I would point out that many of these structures did not have 3 billion years of evolution in their history. Much of this stuff maps to or very near the origin of cells on this planet.
Finally, you write:
quote:
But I don't think this really gets at the distinction between design and evolution, unless there is needless structure and organization. There is selective pressure for increased organization and structure if that organization and structure is beneficial. 3 billion years is a long time to build up advantageous structures. What it can't do is generate neat and tidy structures simply for the sake of being neat and tidy (unless neat and tidy happens to also be simple to generate).
I think it’s important to realize this discussion is more of a ‘teleology vs. non-teleology’ than a ‘design vs. evolution’ dispute, as evolution is not synonymous with non-teleology. As for needless structure and organization, from a design point of view, needless things are not going to be perpetuated by evolution. Thus, we’d have to posit a rather odd designer to get the distinction you want – a designer that continually intervenes in order to deposit needless things. That seems to be an odd expectation to have about any designer.
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charlie d.
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Member # 159
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posted 22. June 2003 21:00
quote:
Mike:
Yet I am wrong – it’s not that straightforward. We can all agree that cells were not designed by humans thus we can’t really say that cells should be no different from something we design. In fact, there are at least three very significant differences between cells (assuming they were designed) and the products of human engineering:
1. Cells are an example of nanotechnology, while the products of our engineering are not. Design principles that may apply at one scale do not necessarily translate to another.
2. The cells we study are not the direct products of a designer, but the descendents of billions of years of evolution.
3. It is reasonable to assume that if cells were designed, a design science far more advanced than ours was used.
If we return to Paley’s watch, we can see why the analogy will not perfectly fit. Compared to a cell, the watch is a lumbering, clumsy design with severe limitations. In fact, I think it safe to say that if we built a living cell so that it perfectly mapped to a watch, such a cell would be too rigid to survive the onslaughts experienced by life and would thus fail to persist/evolve. Take your criteria of transient and labile associations rather then stable ones. It is the transient and labile associations that make life possible. Imagine the process of cell division without transient and labile associations. Imagine the ability to adapt quickly to a change in the environment, such that a new array of genes are expressed, all without transient and labile associations. Etc.
So you expect cells to look like Paley's watch, but not really like Paley's watch. Cellular mechanisms are going to become obviously technological, but not really the "technology" we are used to. In fact, it seems that anything would qualify as technology as long as it is "a complex-looking thing that does something reasonably well". That ain't much of a stretch for a prediction, then.
John:
I didn't say that nobody uses diagrams (I know I do), but that we now realize that stochastic models are better descriptors, in most instances. Activators and repressors are still valid terms, because factors do repress and activate; similarly, flow charts do represent the general, direct functional relationships between proteins and/or genes (depending on the context). They are still useful. We are just not under the illusion any more that they represent a faithful depiction of the system. Lots of aspects in cell regulation do not work like anything an engineer would make: not only cellular processes try to minimize noise, as you say, but in fact they often exploit it to achieve buffering and subtle qualitative and quantitative control. We don't do that, because we build from the top down (and eliminate noise when we find it - it's much easier to engineer that way).
Of course, John and Mike, one can argue that cellular processes are precisely the way a super-bioengineer would design them, and just the way we would if we had to and could. But that's reasoning backwards: that's why Paley took a watch as his example (the pinnacle of known technology of his time). If he had used a protonic snorfblatt as his example, neither his contemporaries nor ourselves would have taken him very seriously.
[ 22. June 2003, 21:04: Message edited by: charlie d. ]
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Mike Gene
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Member # 149
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posted 22. June 2003 23:07
I list three ways in which designed cells (assuming they existed) would differ from the designs we humans currently construct. Rather than worry where such things lead or how they may complicate matters, the first step is to consider whether they are valid distinctions.
These points illustrate that while we might expect many similarities between human designs and the designed cells, we should also expect to see some differences. Point 1 notes that cells are an expression of nanotechnology, while the designed artifacts we use as models as not expressions of nanotechnology. This is a significant difference. For example, the aspect of assembly takes on a different flavor. In our large scale world, designers can directly assemble things and thus usually favor stable assemblages. On the nano-scale, we would depend more on self-assembly properties and thus suddenly, those transient and labile associations might come in handy. Does anyone really expect us to build a microscopic Ford Mustang that looks and functions exactly like a Mustang driving down the road?
Point 2 notes that the cells we study today are the evolutionary descendents of the designed cells originally deposited on the planet. Are we to believe that 3 billion years of evolution would not add some element of noise to the original designs?
I don’t really see how anyone can dismiss these two points of difference and their implications. Clearly, it is a simple fact that a Ford Mustang is not an expression of nanotechnology nor the 3 billion year evolutionary descendent of an originally designed machine.
Point 3 seems to be the main point of contention for GP. Okay, let’s begin by assuming it is true that the original cells on this planet were the product of design at the hands of some intelligent agency. Now, there are only three possibilities concerning the design science of this agency:
1. Their design science was inferior to ours.
2. Their design science was equivalent to ours.
3. There design science was superior to ours.
Given that our design science struggles with designing proteins, it seems safe to assume that any intelligent agent capable of designing those cells possessed a science that was superior to ours.
Thus, the question that matters is whether the three points of distinction would be valid consideration if the original cells were designed . If someone wants to make the following arguments, I’m all ears:
1. We should expect nanotechnology to be no different from our large scale designs.
2. Evolution would not add any noise to the original designs.
3. The designers of life would be expected to have the same knowledge base and design science as we currently possess (or worse).
Now, from here, one can acknowledge the points of difference are real and significant, but worry that they mess things up too much.
For example, GP seems to be arguing that if we are to assume a superior design science, what keeps us from going to the far extremes, where “the first cells on this earth were a result of beings (perhaps evolved from H. sapiens!) time-travelling from the future, playing with multiple dimensions and infinite-wavelength zero-energy quantum energy?” This is a good question for which there is no solid answer.
We can note that we do have a built-in epistemic check. Namely, that if the design science generated designs that were completely lacking in human-like features, we would never recognize them as designs. Thus, we would only catch something that at least overlaps with our design science.
We can also note that the problem posed is inherent in any attempt for one intelligent being to identify design in the products of another being with a superior design science. Thus, to simply throw in the towel is to write off such a potential reality. Others are of course free to dismiss ID because of such methodological concerns, but my own curiosity remains.
What I can do is to take this methodological problem and exploit it in a predictive sense. If life was designed, using a design science superior to ours, this allows me to make two further predictions.
1. Our own design science will be informed by the fundamentals of cell and molecular biology. Thus, when Charlie notes that engineers are in fact striving to replicate biology in engineered systems, this supports the original hypothesis. One might expect Ben Franklin to get many insights if we could send back a jet airplane.
2. As explained elsewhere, advances in our own design science will illuminate the workings of the cell.
GP cites Holliday about there being no constraints on an imagined all-powerful creator. He also wants minimal hypotheticals about the designers. Yet it’s the hypotheticals that create the methodological constraints. For example, I assume that the designers are not trying to intentionally communicate with human beings through their designs. Nothing was designed to get us to laugh or instill a sense of awe. One expression of communication would be deception. Thus, because of this assumption, I am constrained from using the existence of pseudogenes as evidence of a deceptive designer. Another assumption is that the designers were bioengineers and not artists. This assumption puts massive constraints on my views. Because pseudogenes are non-functional, I cannot attribute them directly to design. I cannot explain some biological feature as the artistic whim of a designer. I also seek to
It would seem to me the issue is not about either complaint in isolation (minimizing hypotheticals vs. imposing methodological constraints), but about trying to find an optimal balance, where one makes enough assumptions to yield enough constraints and then takes this investigative creation for test drives. This is the impetus behind my investigation from a front-loading perspective. Assume a designer that creates life to exploit evolution and see if there is a pay-off. Whether the investigative formula is the Right One is not important – it’s whether it’s on the right track.
We need to keep in mind that this approach is not a free-for-all. I am quite sensitive to the data and not simply out to force a design perspective on things. The very fact that I do not seek to attribute design to everything clearly shows this. What’s more, it’s not as if I am trying to credit a sloppy bag full of soup and a clumsy way of making proteins to some “advanced science” that we cannot ponder.
Let me address the excerpt that GP wants me to address:
However, answers can always be generated depending on the model of the front-loaded system. For instance, you later write that it is up to theology to determine whether or not God is a micromanager. Suppose in fact that theology determines God to be a micromanager, intervening across deep time. Does the validity of your front-loading thesis actually depend on reconciliation with theology or vice-versa?
I’m suspicious of any theological claim that presumes to have figured out God. But if God is indeed the designer, and God is indeed a micromanager, of course the validity of my front-loading hypotheses would hinge on such realities. The objective behind my front-loading hypotheses is not to Find The Answer, but to develop a research approach with testable hypotheses to see how well it illuminates biotic reality.
In any case, I hope I have made more clear my initial question about your human-like intelligence. In particular, I wanted to know if you actually try to minimize your dependence on the model of the engineer to interpret the results. At present, I do not see this effort made.
If I were to minimize my dependence on the model of the engineer, I could attribute biological features to artistic design. I could likewise attribute non-functional or hodgepode, jury-rigged, sloppy conglomerations to a intelligent designer. Are you suggesting this is a better approach?
Finally, I wrote: We can all agree that cells were not designed by humans thus we can’t really say that cells should be no different from something we design.
GP: No, I disagree. I have no reason to believe that human designs cannot develop in the future so as to design living organisms. Nor do I have any reason to suspect that the designers aren't time-travelling humans from the future or another parallel universe. Tell me how I could distinguish the possibility.
I’m simply pointing out that we should not expect designed cells to look exactly like something that was designed by humans in 2003. If you are to assume human designs in the distant future (distant enough to entail time travel), then yes, I expect there will be significant differences in design, such that an automobile from 2003 fails to capture properties of designed artifacts from 2700.
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