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| The Design Matrix: A Consilience of Clues by Mike Gene |
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| Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body |
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| Catalyzing Inquiry at the Interface of Computing and Biology |
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| System Modeling in Cellular Biology: From Concepts to Nuts and Bolts |
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| The Plausibility of Life By Marc W. Kirschner and John C. Gerhart |
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| Agents Under Fire by Angus Menuge |
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| Life's Solution by Simon Conway Morris |
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| Information Theory, Evolution and the Origin of Life by Hubert P. Yockey |
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| The Fifth Miracle by Paul Davies |
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| Nature, Design, and Science by Del Ratzsch |
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| Origination of Organismal Form by Muller & Newman |
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| Biased Embryos and Evolution by Wallace Arthur |
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| Rare Earth by Peter Ward and Donald Brownlee |
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| The Privileged Planet by Guillermo Gonzalez and Jay Richards |
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| The Way of the Cell by Franklin Harold |
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| The Volitional Brain by Benjamin Libet |
 |
| Evolution in Four Dimensions by Eva Jablonka & Marion Lamb |
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| The Evolution-Creation Struggle by Michael Ruse |
February 19th, 2007 at 10:59 am
Cool. I should find out if my lecture room has power point…then find out how to use power point.
Comment by Bilbo — February 19, 2007 @ 10:59 am
February 19th, 2007 at 7:08 pm
Awesome.
Comment by thesciphishow — February 19, 2007 @ 7:08 pm
February 19th, 2007 at 8:54 pm
Now ponder the fact that homologs of the hexameric ring (the big piece) and the b and delta subunits (the long stator on the outside) are found in the flagellum and type 3 secretion system.
Comment by Nick Matzke — February 19, 2007 @ 8:54 pm
February 20th, 2007 at 3:52 am
I do.
Comment by MikeGene — February 20, 2007 @ 3:52 am
February 20th, 2007 at 1:08 pm
Nick:
Yes. It seems we two choices: common descent or common design.
Comment by Bilbo — February 20, 2007 @ 1:08 pm
February 20th, 2007 at 1:53 pm
I'm pondering how these little suckers are assembled, and what possible benefit might an incomplete one might be.
Comment by chunkdz — February 20, 2007 @ 1:53 pm
February 20th, 2007 at 2:00 pm
Or both.
Comment by Deuce — February 20, 2007 @ 2:00 pm
February 20th, 2007 at 2:52 pm
Strange that you guys invoke common design now, when Mike Gene used ID to predict that this postulated homology would not pan out, whereas I used evolution to predict that it would.
Comment by nickmatzke — February 20, 2007 @ 2:52 pm
February 20th, 2007 at 2:58 pm
Nick:
Some references?
Comment by Bilbo — February 20, 2007 @ 2:58 pm
February 20th, 2007 at 3:32 pm
Mike Gene on common design:
http://www.idthink.net/biot/cr...
Comment by Bilbo — February 20, 2007 @ 3:32 pm
February 20th, 2007 at 6:07 pm
Bilbo,
Compare my update to the Big Flagellum Essay and Mike Gene's critique of ATPase/flagellum hypothesis in the original Big Flagellum Essay.
Comment by Nick Matzke — February 20, 2007 @ 6:07 pm
February 20th, 2007 at 6:09 pm
Quoth Mike Gene: "this explanation ["common design"] has history of being used in a purely ad hoc manner."
This is exactly what you guys are doing here.
Comment by Nick Matzke — February 20, 2007 @ 6:09 pm
February 20th, 2007 at 6:21 pm
Hi Nick,
Where did I "use ID to predict that this postulated homology would not pan out?"
Comment by MikeGene — February 20, 2007 @ 6:21 pm
February 20th, 2007 at 8:20 pm
Here, for instance:
You used IC to argue against the hypothesized homology between the two systems. But in fact, over the last few years two new homologies between the two systems have been published in the peer-reviewed literature (as have mechanistic and structural similarities between F1-alpha/beta and FliI).
Comment by Nick Matzke — February 20, 2007 @ 8:20 pm
February 20th, 2007 at 8:28 pm
Nick:
References? In that paragraph, Mike was talking about essential interactions in the FoF1-ATP synthase like that between DELSEED and M23 that are not found in the TTSS; not about similarity between sequences.
Comment by Guts — February 20, 2007 @ 8:28 pm
February 20th, 2007 at 9:01 pm
Guts, I would guess Nick is referring to this:
(from his updated paper)
Comment by Bilbo — February 20, 2007 @ 9:01 pm
February 20th, 2007 at 9:14 pm
Nick, most of what you and Mike are talking about is way over my head. If both of you continue to contribute to this discussion, though, I think it might become a rather interesting thread. My own — and no doubt — very simplistic view, is that since all three systems depend upon a wheel in order to work, it wouldn't surprise my if a designer decided to use similar parts for the wheel in all three systems. But I'm sure I'm just revealing my utter ignorance here.
Comment by Bilbo — February 20, 2007 @ 9:14 pm
February 20th, 2007 at 10:13 pm
Guts:
Hmm…Guts, did you add that part in later? Now I'll have to go back and try reading both their papers again….right.:roll:
Comment by Bilbo — February 20, 2007 @ 10:13 pm
February 21st, 2007 at 9:22 am
Bilbo wrote:
Hi Bilbo,
I'm not familiar with the specifics of ATP synthase or the TTSS, but in general there is a simple criterion for distinguishing common design from common descent. Common descent forms nested hierarchies. Common design does not , unless the designer deliberately chooses to make it appear as if common descent had happened.
Comment by keiths — February 21, 2007 @ 9:22 am
February 21st, 2007 at 10:33 am
Keiths:
I'm not sure how far I should pursue this, since — for all I know — it may have nothing to do with the current example of homologous proteins between the ATP synthase, the TTSS, and the bacterial flagellum. However, I don't think nested hierarchies by themselves should be the sole determinant of common descent. We would also want some plausible evolutionary pathway from one to the other. And if the functions of the proteins in the three systems are similar, it may be that they were chosen because they are optimal for those kinds of systems. But again, I'm speaking out of ignorance here. So if Nick or some other critic wants to slap me down, just be gentle.
Comment by Bilbo — February 21, 2007 @ 10:33 am
February 21st, 2007 at 1:11 pm
Hi Bilbo — this has misled many people, but while the flagellum and F1F0-ATPase are both rotary motors, the "rotating bits" are in different places and probably not directly related.
Essentially the flagellum/F1F0-ATPase homology idea is that *inside* the rotating base of the flagellum, the inner proteins that form the secretion machinery (aka "Type 3 Secretion") are homologous to the F1F0-ATPase. This might mean that the flagellum has two rotary motors, one inside the other.
(Although I wouldn't bet on it. For various reasons it looks to me like export/secretion might be the ancestral function, and the rotation and linkage of proton pumping to ATP are traits that were derived in the line leading to the F1F0-ATPase and its relatives. The duplication that produced the alpha/beta subunits is already known to be derived.)
(Note that the previous paragraph was not an idea present in the 2003 Big Flagellum Essay.)
Comment by nickmatzke — February 21, 2007 @ 1:11 pm
February 21st, 2007 at 4:01 pm
Thanks for trying, Nick. But this is still way too much for my small brain to handle. Perhaps if I find time to sit down and study all of this for a week or so, I might get it.
Comment by Bilbo — February 21, 2007 @ 4:01 pm
February 21st, 2007 at 5:28 pm
Hi Bilbo,
I have been planning on writing this up in simpler terminology, but I am waiting for what Mike Gene says in his book!
Nick
Comment by Nick Matzke — February 21, 2007 @ 5:28 pm
February 21st, 2007 at 9:35 pm
Bilbo wrote:
Bilbo,
Nobody is arguing that a nested hierarchy based on a single character is decisive evidence for common descent. But when you look at character after character, both molecular and morphological, and they all yield congruent hierarchies, then the odds that this is not due to common descent are infinitesimal — unless, as I said before, the designer chose to make life appear as if common descent had taken place.
Common design predicts that hierarchies based on different characters need not be congruent. Common descent predicts that they will be. Common descent is overwhelmingly confirmed.
See Douglas Theobald's excellent online summary of this here.
Comment by keiths — February 21, 2007 @ 9:35 pm
February 21st, 2007 at 9:39 pm
Hi Nick,
You may as well get started, as the flagellum does not appear until volume 2.
Comment by MikeGene — February 21, 2007 @ 9:39 pm
February 21st, 2007 at 10:11 pm
IC is not ID, Nick. I have yet to make an ID case. All in good time.
Comment by MikeGene — February 21, 2007 @ 10:11 pm
February 22nd, 2007 at 11:22 am
Hmmm…
ID=religion
IC=ID
therefore
IC=religion
Should mousetraps be considered sacred relics then?
Comment by chunkdz — February 22, 2007 @ 11:22 am
February 22nd, 2007 at 6:09 pm
Keiths, we may not be disagreeing, just miscommunicating. I assume that the chimpanzee and humans share many homologous features, which can be explained by common descent. And I think a plausible evolutionary scenario exists to explain that.
But in the issue of the ATP synthase, the TTSS, and the bacterial flagellum, the evolutionary scenario doesn't appear to be nearly as plausible. And if the similar proteins perform similar functions in all three systems, it could be common design is involved. But again, I'm talking about systems I don't fully understand, so I'm not trying to argue dogmatically for common design. Just wondering if it would explain things in this case.
Comment by Bilbo — February 22, 2007 @ 6:09 pm