Flagella, minimal complexity, and evolutionary noise

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Julie Thomas

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Apr 17, 1999, 3:00:00 AM4/17/99
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Flagellar Variations, Minimal Complexity, and Evolutionary Noise.


This article will seek to accomplish two things. First, it will
re-emphasize the IC state of eubacterial flagella despite the
variation that is seen in such structures. Secondly, it will
outline ways in which a design perspective can guide
research and even make predictions *about* evolution.
This article does not intend to convince anyone that
design has occurred or that the flagellum is the product
of design. This article is written for those who are open
to both design and evolution, who suspect there is some
kind of truth to the design inference, and who are thus
curious as how design concepts can be used to guide
research.


The Varying Flagella and Sloppy Simplicity

The bacterial flagellum remains a strong candidate for a design
event. Not only does a comparative analysis demonstrate Ur-IC
without any evidence of an evolutionary history (a pattern that is
predicted from a de novo design event), but the structure so strongly
resembles a designed artifact (a propellar driven by a rotary motor)
that several biologists have commented on this. In my previous
article on the design of the flagellum, I outlined the specific components
that are part of the E.coli flagella and demonstrated their irreducible
complex nature not only in terms of structure/function, but also in
terms of synthesis.

Although the E.coli flagellum, with about 40 flagella proteins,
shows irreducible complexity and the basic architecture of the E.
coli flagellum is widely distributed among eubacteria, the sequencing
of recent genomes have shown that flagellar function can occur with
a smaller number of components than seen in E. coli. For example,
biochemist David Ussery criticizes Behe's example of the flagellum
by pointing out the following on his web site:

"However, in the bacterium that causes syphilis (Treponema pallidum),
there are a total of 38 flagellar proteins; in the bacterium that causes lyme
disease (Borrelia burgdorferi), there are only 35 flagellar proteins; finally,
in a bacteria associated with ulcers (Helicobacter pylori) there are only
33 proteins necessary to form complete, fully functional flagella. It is
likely that as new bacterial genomes continue to be sequenced (at the
rate of about one a month!), organisms will be found which require
even fewer genes to make a completely functional flagella."

I only counted 36 flagellar genes for T. pallidum. And Aquifex
aeolicus (a bacterium not mentioned by Ussery) only has 27. This
would seem to supports Ussery's contention. But does it?

Ussery's point is interesting not as any type of refutation of IC,
but as a launching point for further inquiry employing the dual
concepts of systematic and thematic IC (see my earlier postings
"DNA replication and IC" and "Design and the F-ATPase" for
explanations of these concepts). In the examples cited by Ussery
the number of systematically IC components ranges from 33-40
players. This, of course, is not a terribly impressive variation when
we consider that spirocheates and proteobacteria are distantly
related. In fact, one might have expected a larger variation with
reference to spirocheates given that they employ their flagella
in a novel means of locomotion.

Nevertheless, it is apparent how the notion of sloppy simplicity
is guiding Ussery. The response to IC is to identify simpler and
simpler systems with the hopr that the IC essence will disappear.
This same logic is used elsewhere in the same article by Ussery:

"If you look at bacterial flagella, you find that some are indeed quite
complicated, but others are more simple. For example, the basal body
can vary with species - in E. coli there are four rings, in Bacillus subtilis
two rings, and in Caulobacter crescentus five rings. I can easily imagine
a scenario where a "primitive bacterium" might have one ring, and then
you have a flagellum with two rings, then three, and so on. This is a
"gradual, step-by-step" evolution, which is the antithesis of Behe's
argument."

While there is variation among flagella we need to inquire as to the
nature of this variation (Ussery's imagination is irrelevant). This
variation could be "large-scale" where significant thematic components are lost
and replaced by novel components. Or as Ussery implies, does this
variation reflect simpler and simpler states? Such large-scale change
would indeed pose a challenge to the IC essence of the flagellum. On
the other hand, the variation may be "small-scale" where peripheral parts have
been modified, lost, and added by evolution. This would constitute
"evolutionary noise" layered on top of a design event as evidenced by an
IC core. This change is consistent with my hypothesis
of *design followed by a history of evolution* (my critics continually
err in thinking that evolution has no place in my hypotheses). To determine
what type of change is evidenced by this variation, we need to determine first
if the eubacterial flagellum possesses an IC core, and if so, what it is.


The Flagellar IC Core

To determine if the eubacterial flagellum has an IC core, the
flagellar genes from four species of bacteria were compared. These
included the gm+ soil bacterium, B. subtilis; the spirochete, T. pallidum;
a gm- proteobacterium, H. pylori; and the thermophilic, gm- bacterium,
A. aeolicus (this genus represents the deepest branching lineage in the
eubacterial tree). These four were chosen because their
genomes have been sequenced and because they are all distantly related
from each other, so much so that it is possible to infer the flagellar
state in the last common ancestor of all eubacteria.

All structural flagellar genes were tabulated for each species (B.
subtilis has recently duplicated many of its flagellar genes and these
paralogs were not included in this analysis). From my scoring, there are
18 genes shared by all four species. They are listed below:

fliS, flgE, flhA, flhB, fliR, fliQ, fliP, fliI, motB, motA, fliD,
fliG, flgB, flgC, fliF, flgK, fliC, and flhF.

These genes apparently represent an IC core. To determine how
well this IC core maps to a designed artifact, the functions of each
gene were determined to see if they would fall nicely into thematic IC
(where components and sets of components would fall into
several functional themes). The demonstration of thematic IC can be
viewed as the "design blueprint" for making the bacterial flagellum.

As it turns out, most of these core IC genes fit into several thematic
themes as shown in Table I.


Table I. Flagellar Components Appear to Demonstrate Thematic IC.

Theme Genes/components
--------------------------------------------------------

Capped filament fliD, fliC/flaA/flaB*

Hook and adaptors for flgE, flgK
attachment to filament

Drive shaft flgB, flgC

Motor complex motA,motB, fliF
(MS ring complex)

Switch fliG

Export machinery flhA,flhB, fliR, fliQ, fliP,, fliI

Unknown fliS - essential, but function unknown
flhF - GTP-binding protein

*C,A,and B are different variants of flagellin filament proteins and
are thus grouped.
________________________________________________________

Many interesting insights emerge from Table I. First, flagellar stucture
and function in eubacteria appears to depend on 6 different functional
themes. However, much more research is needed. On one hand, the switch
and motor complex may be viewed as one functional theme. Yet on the
other hand, the motor complex may be viewed as involving a stator
and rotary motor theme. Furthermore, do fliS and flhF constitute new
functional themes or do they fit into pre-existing themes? A design theorist
would be interested in a better understanding of these functional components
to more clearly outline the individual functional themes that are part of
thematic IC. Clearly this is another area where design could guide
scientific research.

Secondly, as with the F-ATPase, the functional themes appear to be
comprised of more than one systematic component. Thus, once again,
we see how systematic IC can be used to infer thematic IC which can,
in turn, be used to explore systematic IC in a more focused manner.
The exception appears to involve the switching function (components
employed to switch flagellar rotation from clockwise to counterclockwise
and back) which involves in one gene product. This will be discussed below.

Finally, when we consider the manner in which the IC core reflects
thematic IC, the variation noted by Ussery is not that impressive.
That is, each theme appears to be essential for flagellar function
and in no case do we find the variation any of them to be omitted.
Thus, the variation we see does not demonstrate variation in
the actual components that represent the themes (in other words,
there is no other motor complex other than the MS ring complex),
but instead represents tinkering around the functional themes.


Minimal Complexity of the Bacterial Flagellum

Thematic IC suggests that six independent functional themes are needed
for flagellar function in eubacteria. These six themes are represented by
18 indvidual components. Thus, these 18 components reflect
thematic-systematic IC(t-s-IC). But does t-s-IC represent the minimal
complexity needed for flagellar function? This seems unlikely as
no flagella have been found with these few components. H. pylori
has 33 components, T. pallidum has 36, B. subtlis has 31, and A. aoelicus has
27. That the simplest flagellum (A.aeolicus) contains nine more components
than s-t-IC suggests that s-t-IC represents only the minimal *shared*
complexity that arose from the common ancestral state (ur-IC). Thus, the Ur-IC
state would include these 18 gene products, however, this Ur-IC
state may not reflect the minimal complexity needed for flagellar
function. Put simply, to make a functioning flagellum, we need not
only these 18 gene products, but some other undetermined products
whose identification has been blurred by evolution.

To estimate the minimal complexity of the Ur-flagellum, further
scoring was done with the four model species (redundant gene
duplications were not common and also not counted).


Table II. Genes found in 3/4 lineages.

Gene Species missing from Function

fliL H. pylori flagella assembly
fliH A. aeolicus flagella assembly
fliY A. aeolicus switch
fliM A. aeolicus switch
flgL H. pylori hook assembly
fliE A. aeolicus hook adaptor prot
flgG B. subtilis rod protein


Table III. Flagellar genes found in 2/4 species

Gene Species with Gene

flgD T. pallidum/H. pylori
flgH A. aeolicus/H. pylori
flgI A. aeolicus/H. pylori
fliN A. aeolicus/H. pylori


Table IV. Species-specific flagellar genes

Species Genes

T. pallidum flbD, cpfA
A. aeolicus flgA
B. subtilis fliZ, flhD, flhP, fliJ, fliK, fliT
H. pylori flaG

To estimate the minimal complexity, individual flagellar
components were weighted by their relative incidence
and summed (species-specific genes were averaged
(2.5 species-specific genes per lineage)).

18 (1.0) + 7 (0.75) + 4 (0.5) + 2.5 (0.25) = 25.87

This figure suggests that a minimum of 26 genes
products are needed to form a functional eubacterial
flagellum. That this number maps closely to
the number of components to A. aeolicus suggests
this species cannot simplify its flagellum much further
(furthermore, the 27 genes of A. aeolicus should
not be thought to represent all the 26 gene products
that would be part of the Ur-IC state).

But what if we made the same calculations with only
three of the genomes? If we remove A. aeolicus from
the comparison, I get a minimal complexity value
of 25.97. If we remove B. subtilis, the minimal
complexity becomes 26.10. If H. pylori is removed,
the minimal complexity is 24.77. If T. palladium is
removed, the minimal complexity is 25.66. Thus,
by looking at all four permutations of three of the
four genomes, the minimal complexity ranges
from 24.77-26.10 with an average value of 25.62.

Thus, it appears that a minimum of 26 protein products
are needed to construct a functioning bacterial flagellum.
We can propose therefore that the designed flagellum
was constructed with at least 26 proteins, although
it may have had more, as auxiliary proteins may have
been part of the original design. If these 26 proteins
constituted an IC system, then to evolve this system,
26 proteins with similar activities, yet part of
an undefined number of different systems, had to exist
and then all disappear without a trace, leaving behind
only the bacterial flagellum.

Thus far, we can predict that the originally designed
flagellum was composed of approximately 26 gene
products and that this minimal complexity is needed
to form a functional flagellum. Of those 26, 18 are still
identifiable as part of the Ur-IC state. A simple prediction
thus follows that is easily testable. While Ussery
predicted more genomes will contain fewer and fewer
flagellar genes, I predict that one will not find a functioning
flagellum with much less than 26 genes. I further predict
that that the Ur-IC state (or most of it) will be seen in
future genomes of flagellated bacteria.


Evolutionary Noise

Both Ur-IC and the minimal complexity also allows the
design theorist to identify the degree of evolutionary
noise (EN) that has occurred since the design event. To
determine EN, one first determines the number of
proteins that have been lost, replaced, or added since
the design event by subtracting the identifiable Ur-IC state
from the min-complexity, 26 - 18 = 8.

The evolutionary noise coefficient (ENC) is thus determined
as follows:

ENC = # genes lost, replaced, added by evolution
______________________________________
Ur-IC + # genes lost, replaced, added by evolution


ENC = 8/ 18+8 = 0.308


The ENC allows the design theorist to estimate the degree of
plasticity inherent in the designed system. For example, a novel
system that evolved in a specific species would not have any
shared components in other species. This system would not
demonstrate systematic-thematic IC and thus an Ur-IC state
would not be identified (Ur-IC = 0). In this case:


ENC = # genes lost, replaced, added by evolution
______________________________________
# genes lost, replaced, added by evolution

ENC = 1


If, however, no evolutionary change has occurred in the
system, the # genes lost, replaced, and added by evolution
would equal 0. The ENC = 0. Thus, the closer the ENC
is to 0 the more the system has resisted change and the closer
we are to the original designed state. Further analyses with
other IC systems are needed to determine how significant
the change is that is represented by an ENC of 0.308.


Reassessing the Scoring in Light of Thematic IC.

That six flagellar genes are found in 3/4 distantly
related bacteria raises the possibility that thematic
IC might help us identify further specific components
of the Ur-IC state. There are two noteworthy examples.

The Bushings

The first thing to note as the something obvious is missing from the
thematic list, namely, the L and P rings that form bushings in E. coli.
This lack is due to the inclusion of B. subtilis in the comparative analysis.
B. subtilis is a gm+ bacterium and thus has no need for P and L rings.
Should the P and L rings be included as part of the Ur-IC state?
Peter Nykios has proposed on talk.origins that the gm- state is more
ancient than the gm+ state. If this is the case, the original designed
bacterium would be gm- and require L and P rings. As support of for
this hypothesis, A. aeolicus, which not only has the simplest flagellum
but also branches deepest in the eubacterial phylogenetic tree, has both
L and P rings (from the genes flgH and flgI, respectively) as it is a true
gm- bacterium. In addition, A. aeolicus also expresses flgG (as do
T.pallidum and H. pylori, but not B. subtilis). One could thus propose,
as Peter did, that the gm+ state evolved from the gm- state early in
evolution.

It is important to understand that a design perspective is not an
anti-evolutionary perspective. That is, both Peter and I propose
design events that are followed by evolution. What this means
is that the design perspective Peter and I share allows us to
view *evolution* in a manner that can be quite different from the
manner it is commonly viewed. In this case, a design perspective
allowed Peter to predict that the gm+ state evolved from the gm-
state. His critics, lacking his design perspective, were unable to
make any type of prediction about this. Thus, design can lead to
predictions about evolution (and in some cases, these
predictions depend on the design perspective).

To support his prediction, Peter proposes that is far easier for
evolution to lose flagella than acquire flagella. There is good
support for this view, namely, we can track the loss of flagella.
For example, Shigella boydii and Shigella sonnei are two
species of bacteria without flagella. However, flagellar genes
were found in both strains containing several deletions and
disruptions (Al Mamun, et al., 1997, Cloning and characterization
of the region III flagellar operons of the four Shigella subgroups:
genetic defects that cause loss of flagella of Shigella boydii
and Shigella sonnei. J. Bacteriol. 179, 4493-500). It is thus
likely that flagella have been lost independently on multiple
occasions when bacteria occupy a niche where flagella are
not longer needed.

But what we don't see are any bacteria in the process of
acquiring flagella. This is odd as species which have
lost flagella long ago might find themselves in environments
where flagella would again be favored. But this is not
surprising given the IC nature of flagella. Unless all genes
are present to form a flagellum, they would have no function
and decay like pseudogenes (as in Shigella).

In fact, once we realize that flagella have been lost in many
lineages and that some of these non-flagellated
bacteria may have later found themselves in environments
where a flagellum would be advantageous, we can see more
clearly why the non-design explanations are weak. Put simply,
where are the different flagella themes within eubacteria?
Consider that Howard Hershey is arguing that the flagella of eubacteria
and archeabacteria show the independent evolution of such
structures (I look at Howard's hypothesis in another
posting). Well, why don't we see the independent acquisition of flagella
*within* the eubacterial tree? If flagella can be independently
acquired by evolution, why have they not been independently re-acquired
in eubacteria? Why haven't any eubacteria that have lost their
flagella given rise to a lineage that has re-evolved a *different*
type of flagellum?

To summarize, the loss of flagella are easier to evolve than the
acquisition of flagella. This view is not only supported by empirical
evidence (where we see flagella in the state of being lost but not in
the state of being acquired), but also by the multiple loss-events
giving rise to not a single re-acquisition of an independently
evolved flagellum. With these points in mind, I would have
to agree with Peter and tentatively propose the gm- flagellum, with both
P and L rings, is closer to the originally designed flagellum
in the first bacteria (this proposition assumes, however, that only
one form of flagellum was designed in eubacteria).

Support for this hypothesis not only stems from the fact the
A. aeolicus has a flagellum with both P and L rings, but it looks
as if the rings are in the process of being lost in spriochetes.
Sprirochetes are considered to be analogous to gm- bacteria in
terms of their cell membrane structure, yet their flagella are
uniquely arranged to form axial filaments. The genome of
T. pallidum indicates that it possesses neither the P or
the L ring (flgI and H, respectively). But the drive shaft
still incorporates the flgG protein which is where the
L and P ring are attached in gm- bacteria. The presence
of flgG may be vestigial in spirochetes reflecting that
they once had L and P rings. To test this hypothesis,
I surveyed the genome of another closely related spirochete,
B. burgdorferi. Like T. pallidum, it still has the flgG
protein. However, B. burgdorferi also has the P ring
(flgI), but not the L ring. T. pallidum and B. burgdorferi
thus look like bacteria in the process of changing a gm-
flagellum to something that looks more like a gm+
flagellum.


The Switch

Another interesting aspect of Table I is that the
switch is represented by only fliG. This is
significant as there is extentive data to indicate
the fliG works as part of a complex with fliN and
fliM. Comparing the four genomes, it becomes
clear that in addition to fliG, *either* fliN *or*
fliM is present. For example, while fliM is
lacking in A. aeolicus, it possesses fliN. And
while fliN is lacking in B. subtlis and T. pallidum,
both contain fliM. Thus, a thematic perspective
may group fliM and fliN together where at least
one of these two components is needed as part
of the switch complex with fliG.

What is interesting about this evolutionary loss
is that it actually highlights how an IC complex
may be composed of IC subsystems. FliM is lacking
only in A. aeolicus. Plenty of data exist that suggest
FliM's role in the switch complex is to act as
a mediary between the esential FliG component and
the chemotaxis protein, CheY (for example, see
Toker and Mcnab, 1997. JMB 273; 623-634).
If the coupling of chemotaxis to flagellar rotation
is through a mini-IC system, one would expect
that without FliM, CheY could not function. And
indeed, in A. aeolicus, not only is FliM lacking,
but so to is the entire chemotaxis system including
CheY. All of this suggests that A. aeolicus lost the
need for chemotaxis and thus lost all the genes that
are part of this potential mini-IC system.

If this analysis is valid, we can modify Table I to
include one new functional theme with three components
and add an additional component to the switch.

Table V. Modified Thematic IC Scoring

Theme Genes/components
--------------------------------------------------------

Capped filament fliD, fliC

Hook and adaptors for flgE, flgK
attachment to filament

Drive shaft flgB, flgC

Bushings/bearings flgG, flgH, flgI

Motor complex motA,motB, fliF
(MS ring complex)

Switch fliG, fliM/N

Export machinery flhA. flhB, fliR, fliQ, fliP,, fliI

Unknown fliS - essential, but function unknown
flhF - GTP-binding protein


Thus, we can raised our Ur-IC scoring from 18 to 22 suggesting
that these 22 gene products were present in the LCA of
eubacteria. But what does this do to our scoring of minimal
complexity?


Min complexity = 22 (1.0) + 5 (0.75) + 1 (0.5) + 2.5 (0.25) = 26.87

By using evolution and thematic IC to shift 5 gene products into the Ur-IC
state,the minimal complexity has increased from 26 to 27 genes. This maps
perfectly to the number of genes seen in A. aeolicus and again suggests
that this ancient lineage of bacteria expresses a flagellar state that
is close to the minimal functional state.

This shift also causes the evolutionary noise coefficient to drop:

ENC = 5/22 + 5 = 0.185

But how does the evolutionary noise coefficient drop by incorporating
evolutionary events? The key is that the ENC represents unidentified
evolutionary noise that could be used to dislodge the design inference.
The evolutionary events identified above do not in anyway cause
us to reconsider the scoring of the design inference. Less noise means there
is less likelihood that future understanding about the evolution in these
systems will cause us to reassess the design scoring.


Homologous genes?

As seen in Table V, the flagellar protein export machinery is
composed of a sub-IC system with 5 genes, flhA. flhB, fliR, fliQ, fliP,,
fliI. Most of these genes have homologs in other systems. FlhB, fliR,
Q, and P have homologs in the type III secretory system. FliI has
a homolog with the beta-subunit of the F-ATPases. None of
these homologs, however, provide good evidence for the step-by-step
evolution of the flagellum.

The sequence similarity between FliI and the beta subunit of the
F-ATPase is limited and may reflect only the shared ATP-binding
domains of both proteins. No other component of the F-ATPase and
flagellum share any sequence similarity.

As proposed earlier, the type III secretory homologs probably exist
as a consequence of the type III system evolving *from* this
export machinery of the flagella after gene duplication (and
possibly horizontal transfer). As noted above, design allows
one to propose specific hypothesis *about evolution.* In this
case, if the flagellum was designed, it is predicted that the
type III system evolved *from* flagellar components. This
prediction is clearly supported by the fact that not only are
these export components part of the Ur-IC state, none of
the four species analyzed have the type III secretory pathway.

Summary

I have attempted to show how variation within in an IC system
does not weaken the design inference that follows from the IC
system. On the contrary, it has always been granted that
a history of evolution would follow a design event. Thus,
the perspective that employs design also brings perspective
on how evolution has occurred since the design (showing that
design is NOT "anti-evolution"). In this case, an IC core of 18-22
components have been identified that probably reflects a significant
fraction of the Ur-state (the designed state in the last common ancestor of
eubacteria). The variation that is seen since this design
event does not remove any of the six functional themes or significantly
change the components involved in any functional theme.. The minimal
complexity of a functioning eubacterial flagellum is predicted to be
approximately 26-27 proteins, where 18-22 have remained to reflect the
designed state. This translates as an evolutionary noise
coefficient of 0.185 - 0.308. The evolutionary noise coefficient does
not represent any form of argument against evolution or for design,
it only serves as a tool for the design theorist to estimate the
degree to which the system she studies today reflects the
originally designed system. In the end, we are still left with the
flagellum as an IC system and a way to explore its design.

Finally, this form of analysis depends on the existence of
genomes that have been entirely sequenced and genetic
and biochemical data to assign functions to gene products.
Thus, a design perspective would clearly guide research
in terms of traditional science. A design perspective
would encourage that more genomes be sequenced and
more genetic and biochemical studies be conducted.
That the design perspective may not be needed is an
irrelevant point.

Appendix - Identifying Minimal Complexity and ENC in other
IC Systems.


To further test the notion of minimal complexity and evolutionary noise,
the same analyses done with the flagella above were done on all three of the
other IC systems I have scored as design products.


*F-ATPase

The F-ATPase has been previously analyzed in detail to find
four functional themes, each with two systematic components.

H. pylori, A. aeolicus, and B. subtilis were compared as spirochetes have
replaced their F-ATPases with the V-ATPases (possibly
through horizontal transfer).

All 3 species have the alpha, beta, gamma, delta, episilon, a, b, and c
subunits.

In both H. pylori and A. aeolicus, there is a duplicate for the b subunit, but
redundant duplicates are not counted. B. subtilis has a species-specific
factor coding for an I subunit as part of the F0 complex.

Thus, minimal complexity is:

8 (1.0) + 1(0.33) = 8.33.

The minimal complexity is slightly higher than the number of components
discussed in my article, "Design and the F-ATPases." It is predicted that
further comparative analyses among other eubacterial lineages will
decrease this value. The genome of Mycoplasma has been sequenced and
represents the smallest cellular genome known. Mycoplasma encodes
for the F-ATPase and has 8 subunits.


Evolutionary noise = 8.33 - 8 = 0.33

ENC = 0.33/ 8+0.33 = 0.04.

The ENC among the F-ATPases is close to 0 and thus suggests that this
modern complex closely resembles the originally designed state.


*DNA Replication

The components of DNA replication were scored in the same four
species in which flagellar components were determined. However,
at this point, the systematic IC components were not collapsed into
thematic IC through a more detailed functional analysis. Also,
genes involved in DNA modification and recombination were not
included in this analysis.

Four of the species contained 11 of the same gene products, three
shared 4 gene products, two shared six gene products, and there
was an average of 2 species-specific gene products.

Min comp = 11 (1.0) + 4 (0.75) + 6 (0.5) + 2 (0.25) = 17.5

To test this score, the number of gene products employed in
Mycoplasma DNA replication was conducted afterwards. When this value is
compared to the number of DNA replication proteins in Mycoplasma
(which represents the simplest cellular genome known), the
discrepancy is small (min comp = 17.5 and Mycoplasma = 16).
Furthermore, Mycoplasma contains all of the 11 gene products
that are scored as part of the Ur-IC system. Further analysis of the
functional roles of non-universal gene products may serve to lower
the min comp score.

The ENC was calculated:

ENC = 6.5/11+6.5 = 0.371

This value suggests that more evolutionary noise has obscured the
originally designed state of the DNA replication machinery than
either the F-ATPase or flagellum. However, future analyses in
light of thematic IC may also reduce this value.

To test this idea, I surveyed the genomes of H. influenzae and
the cyanobacterium, Synechocystis. In this case, the
minimal complexity was calculated to be:

11 (1.0) + 2 (0.833) + 1 (0.666) + 2 (0.5) + 4 (0.333) + 2.16 (0.133)
= 16.01.

Since the Ur-IC score remained unchanged (11), the ENC
dropped to 0. 313.

Thus, by comparing more genomes, not only does the minimal
complexity value map precisely to the number of gene products
used in M. genitalium, but the ENC value drops 15%. A
major caveat in this analysis is that replication genes are
usually grouped with repair, recombination, and modification
genes and I excluded these from this analysis. Thus, it
is possible that some of these genes play roles in replication
and the scoring may be off significantly. In the future,
I hope to revisit this whole analysis in a more rigorous
fashion.

*The Peptidoglycan Cell Wall

An earlier analysis of the bacterial cell wall demonstrated
the IC nature of peptidoglycan synthesis. The same four species
were again compared, but like DNA replication, no effort was
made to collapse the systematic components into thematic
IC.

All species shared 12 gene products, three of the four shared one
gene product, two of the four shared 4 gene products, and an
average of 4.75 gene products were species-specific.

The min complexity involved in peptidoglycan synthesis is
as follows:

Min comp = 12 (1.0) + 1 (0.75) + 4 (0.5) + 4.75 (.25) = 15.94.

Thus, 16 gene products are apparently required to synthesize
the cell wall, twelve of which can be assigned to the original
state. In this case, it was not possible to check this number
against the genome of Mycoplasma as this genus is unique among
eubacteria in having no cell wall.

The evolutionary noise coefficient was determined to be
0.24 showing that all four systems I have discussed have
similar ENCs (see Table VI).

Table VI. The Evolutionary Noise Coefficients of Four IC Systems
in Distantly Related Eubacteria

System ENC ENC after further thematic analysis
------------------------------------------------------------------------------
Flagellum 0.308 0.185
F-ATPase 0.04 0.04
DNA rep 0.314 ND
Cell wall syn 0.241 ND


These data clearly suggest that the F-ATPases may represent
the system that is closest to its originally designed state.
This further suggests that this system may be the best system
for study by a design theorist and supports my attempt to
decipher design motifs (ie, NAIGS) within this particular
system (see "Design and the F-ATPases").

Other suggestions for future research and analyses include:

--Sequencing of more genomes and re-scoring the Ur-IC
state, minimal complexity, and ENC in light of this
new information.

--Discovery of more functional information to determine
if non-universal components can be placed in the Ur-IC
state in light of thematic IC.

--Exploration of systems that are tied (but need not be tied) to
the IC systems in question. This would include DNA replication,
recombination and modification; flagella and chemotaxis;
and the F-ATPases and the electron transport chain.

--Determination if there is a hierarchy of IC. That is, do some
Ur-IC systems demonstrate an IC relationship with each other?
--


Evan Thompson

unread,
Apr 19, 1999, 3:00:00 AM4/19/99
to
In article <7faih8$eio$1...@alexander.INS.CWRU.Edu>,
iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:

This looks like an excessively long-winded and techical rehash of the old,
flawed "Eye argument" for design.

Many modern things look "irreducibly complex". What you're not
considering is that we don't know how many different stages things like
flagella went through. It may be that *none* of the genes which you
consider the "irreducibly complex core" were present in the first
flagella. Ignore the fancy parts you see in all modern flagella- what is
the simplest way to make a bacteria move? All we see is the end product-
it's like looking at an origami model of a grand piano- without the
step-by step sheet, you have no idea how the hell they folded a piece of
paper into that thing.
Or look at one of the machine guns they have on the nose of an Apache
helicopter. That's an irreducibly complex machine. It's got geared motors
to drive the belt, intricate mechanisms to eject the shell casings, pumps
and tubes of coolant to keep it from overheating- take out any of those
parts, and it will stop working. Yet the "evolution of the gun" did not
happen by humans inventing one of the component parts to a helicopter
minigun every few years for a millenium until they finally had one that
worked. The first gun was a short hollow tube you dump gunpowder in, drop
in a rock and then hold a burning splint to until it goes off. You move up
from that to medeival cannons, to flintlocks, muskets, rifles, gatling
guns, automatic machine guns, and the helicopter's minigun. Some of the
stages it went through have been lost, such as the flintlock striking
mechanism, the rod to tap down the musket ball, and the hand crank to
operate the first machine gun. These parts were necessary for the gun to
move to the next stage in its evolution, but they disappeared once they
were no longer necessary; like the scaffolding structures around a
building in progress. In natural evolution, there is no final building
plan, but the preexisting still-functional parts act as scaffolding for
the new and better parts.


Peter Nyikos

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Apr 21, 1999, 3:00:00 AM4/21/99
to
CC: Julie

evanPOTTEDMEATFO...@earthlink.net (Evan Thompson) writes:

>In article <7faih8$eio$1...@alexander.INS.CWRU.Edu>,
>iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:

>This looks like an excessively long-winded and techical rehash of the old,
>flawed "Eye argument" for design.

Really? I'd love to see any calculations in any published Eye Argument
that resemble those in Juile's article. I'd love to see any
predictions by design theorists as to what a minimal eye might
look like. I'd love to see any predictions by design theorists
as to what the ancestral eye of mollusks or cephalopods might
look like. I'd love to see anything resembling an evolutionary
noise coefficient.

In fact, I'd like a reference that even REMOTELY resembles
what Julie posted.


>Many modern things look "irreducibly complex". What you're not
>considering is that we don't know how many different stages things like
>flagella went through.

She considered that and more. Didn't you see what she wrote
about spirochetes, archae, gm+ and gm- bacteria?

Did you even READ what she wrote?


It may be that *none* of the genes which you
>consider the "irreducibly complex core" were present in the first
>flagella.

Anybody can list possibilities. The trick is to argue for them.
You might as well have written, "It may be that *none* of the
genes in our bodies were present in the first chordate." Would
you like to try and defend that statement any more or less
than you would like to try and defend the one you gave just now?

Ignore the fancy parts you see in all modern flagella- what is
>the simplest way to make a bacteria move?

By pushing and shoving them? ;-)

All we see is the end product-
>it's like looking at an origami model of a grand piano- without the
>step-by step sheet, you have no idea how the hell they folded a piece of
>paper into that thing.

So far, your post looks like a reworking of some anti-creationist
tract. Are you making ANY attempt in your mind to relate what you say
to what Julie wrote?

Just for starters, you don't REALLY think that origami model
arose from other origami art works thru natural selection,
do you? People copied ideas from each other, modified
older designs, experimented with one fold after another
until they got what they wanted.


>Or look at one of the machine guns they have on the nose of an Apache
>helicopter. That's an irreducibly complex machine.

What's wrong with Behe's mousetrap?


It's got geared motors
>to drive the belt, intricate mechanisms to eject the shell casings, pumps
>and tubes of coolant to keep it from overheating- take out any of those
>parts, and it will stop working. Yet the "evolution of the gun" did not
>happen by humans inventing one of the component parts to a helicopter
>minigun every few years for a millenium

What you say below seems to contradict that, allowing for
gradual evolution of the component parts.


until they finally had one that
>worked. The first gun was a short hollow tube you dump gunpowder in, drop
>in a rock and then hold a burning splint to until it goes off.

Sure. The hollow tube was invented first.

You move up
>from that to medeival cannons, to flintlocks, muskets,

Sure. Other component parts were invented. Rifling was added,
etc. etc. Older parts were modified to accommodate new ones.

All due to design ideas in the minds of designers. Since
weapons can't reproduce, natural selection doesn't enter
into the picture at all.

rifles, gatling
>guns, automatic machine guns, and the helicopter's minigun. Some of the
>stages it went through have been lost, such as the flintlock striking
>mechanism, the rod to tap down the musket ball, and the hand crank to
>operate the first machine gun. These parts were necessary for the gun to
>move to the next stage in its evolution, but they disappeared once they
>were no longer necessary; like the scaffolding structures around a
>building in progress. In natural evolution, there is no final building
>plan, but the preexisting still-functional parts

You mean like the sear in the trigger mechanism of some
rifles? Any idea what it was functioning for before it
was incorporated into the trigger mechanism? Methinks
it was expressly DESIGNED *for* the trigger mechanism and
had no use prior to that.

act as scaffolding for
>the new and better parts.

You know, for about two years now, Howard Hershey has
evaded the question of just what those pre-existing still-functional
parts were doing before they were incorporated. Or what
they looked like. Or how they were incorporated.

Two years ago, he did have a weird scenario.
He had this just-so story of bacteria expelling long waste proteins
thru pre-existing pores. Somehow one of the waste proteins
evolved into the dynamic flagellar filament in his scenario; and
one day, the scenario went, a "hook" got attached which prevented it
being expelled, and the filaments have been stuck in the pores ever since,
gradually developing into the modern flagellum.

Trouble is, his "hook", the stator, is not actually the real
hook, which connects the filament to something separate known
as the drive shaft. The stator is connected to the drive
shaft and not to the filament.

I suspect Howard at one point discovered to his chagrin that he had
been looking at the cartoons of the flagellum all wrong,
realized that he'd mistakenly assumed the flagellin filament and
drive shaft were one and the same, and swore off trying
to come up with just-so stories for how the flagellum
evolved.

Think you can do any better?

Peter Nyikos -- standard disclaimer --
Professor, Dept. of Mathematics
University of South Carolina
Columbia, SC 29208


Evan Thompson

unread,
Apr 21, 1999, 3:00:00 AM4/21/99
to

Peter Nyikos wrote:

> CC: Evan and Julie


>
> evanPOTTEDMEATFO...@earthlink.net (Evan Thompson) writes:
>
> >In article <7faih8$eio$1...@alexander.INS.CWRU.Edu>,
> >iz...@cleveland.Freenet.Edu (Julie Thomas) wrote:
>
> >This looks like an excessively long-winded and techical rehash of the old,
> >flawed "Eye argument" for design.
>
> Really? I'd love to see any calculations in any published Eye Argument
> that resemble those in Juile's article. I'd love to see any
> predictions by design theorists as to what a minimal eye might
> look like. I'd love to see any predictions by design theorists
> as to what the ancestral eye of mollusks or cephalopods might
> look like. I'd love to see anything resembling an evolutionary
> noise coefficient.

I mean it is, at its core, saying that all the complex parts of the
flagellum would have had to appear at once for it to work, just like the
eye argument. Did the lens come first, or the cornea- either way it
wouldn't focus. It makes the mistake of assuming that the intermediate
stages were incomplete parts of a modern human eye, when really they were
fully functional (though
inferior) simpler eyes.


A "minimal eye" would most likely be a spot of photo-sensitive nerve cells
on an animal's skin.

A minimal flagellum would not have a "motor" or even rotate, it would
simply flex back and forth in about the same method a bimetal strip would.

>
> In fact, I'd like a reference that even REMOTELY resembles
> what Julie posted.

I don't know of any published "eye argument", unless you cound creationist
pamphlets as "published". No one else is using the eye argument any more,
so I'd probably have to dig back to Descartes or the like. But it's still
talking about the idea of "irreducible complexity".


> Did you even READ what she wrote?

I didn't read all of it. Whatever she had to say probably could have been
said in a way that the newsreader didn't have to break it up into three
different posts.


> may be that *none* of the genes which you
> >consider the "irreducibly complex core" were present in the first
> >flagella.
>
> Anybody can list possibilities. The trick is to argue for them.

If you think it is even a possibility that none of the genes that make up
what is currently considered to be the minimal flagella information were
present in the first flagellum, then that casts doubt on them being
"irreducible".


> Just for starters, you don't REALLY think that origami model
> arose from other origami art works thru natural selection,
> do you? People copied ideas from each other, modified
> older designs, experimented with one fold after another
> until they got what they wanted.

I didn't mean it like that. I meant that the end result is tidy and
sharp, but to get there the artist had to crease, unfold, and refold the
paper a great number of times. It probably would not look, to the
observer, like a steady progress from a big square of paper to a grand
piano, but it might have to go through stages in which it looked more like
a kite, a bear, etc, in the process.
And we didn't see them folding it and don't have the step-by-step
instructions they used, so that makes it even more difficult to tell what
happed. Especially if someone is claiming that they didn't even fold it,
because it looks impossibly complex, they must have just cheated by
cutting up the paper and gluing it together on the inside where we can't
see the difference. If we had the step-by-step plans, there would be no
suspicion of cheating, but we don't have them and probably never will.


> It's got geared motors
> >to drive the belt, intricate mechanisms to eject the shell casings, pumps
> >and tubes of coolant to keep it from overheating- take out any of those
> >parts, and it will stop working. Yet the "evolution of the gun" did not
> >happen by humans inventing one of the component parts to a helicopter
> >minigun every few years for a millenium
>
> What you say below seems to contradict that, allowing for
> gradual evolution of the component parts.

Yes, a but each step there is a functioning gun. Each newer gun is better,
but the point is a gun doesn't need to be self-cooling and fire 300 rounds
per minute, as long as it can kill someone more effectively that throwing
a spear, it's an advantage.

Like any eye, even a crude light-and-and dark sensing spot, still serves a
purpose and is better than total blindness. Or any crude means of
locomotion, while not nearly as efficient as a flagellum, is better than
just sitting there.

> until they finally had one that
> >worked. The first gun was a short hollow tube you dump gunpowder in, drop
> >in a rock and then hold a burning splint to until it goes off.
>
> Sure. The hollow tube was invented first.
>
> You move up
> >from that to medeival cannons, to flintlocks, muskets,
>
> Sure. Other component parts were invented. Rifling was added,
> etc. etc. Older parts were modified to accommodate new ones.
>
> All due to design ideas in the minds of designers. Since
> weapons can't reproduce, natural selection doesn't enter
> into the picture at all.

I suspose I can't use a designed example to argue against design, but
since we only have one example of natural selection, and that is what I am
trying to make a comparison to, it is dificult.

With technology, though intelligent innovation plays a part, it is still
very much an "evolutionary" process. (the whole "standing on the shoulders
of giants" effect. )

I know weapons can't reproduce. But what would happen if they could?


> You mean like the sear in the trigger mechanism of some
> rifles? Any idea what it was functioning for before it
> was incorporated into the trigger mechanism? Methinks
> it was expressly DESIGNED *for* the trigger mechanism and
> had no use prior to that.

But it doesn't need to be there for the trigger to work, it's just a
refinement to make it a bit smoother and more comfortable. The trigger
mecanism used to be stuck ungracefully onto the side of gun.

Also, I said that that was a way biological systems differ from man-made
ones. There's no reason a gun should be made by modification of old parts
when we can build it to order any way we want- life doesn't have that
luxury.


> I suspect Howard at one point discovered to his chagrin that he had
> been looking at the cartoons of the flagellum all wrong,
> realized that he'd mistakenly assumed the flagellin filament and
> drive shaft were one and the same, and swore off trying
> to come up with just-so stories for how the flagellum
> evolved.

I find your repeated use of the phrase "just-so stories" interesting. Do
you have any explanation that is *not* a "just-so story"? I think that's
all anyone has at this point.


>
> Think you can do any better?

I'm not a molecular biologist (and neither are you, according to your sig.)
Where are these cartoons? I'd like to see them.
But I don't want to argue about flagella any more either, I have better things
to do and, from what I've heard so far, I doubt anything productive will
come of it.


Julie Thomas

unread,
Apr 21, 1999, 3:00:00 AM4/21/99
to

In a previous article, evanPOTTEDMEATFO...@earthlink.net (Evan Thompson) says:


Evan writes:

>This looks like an excessively long-winded and techical rehash
>of the old, flawed "Eye argument" for design.

Except that the flawed eye argument doesn't translate into a
flawed flagellum argument. As far as the eye goes, we can find
all kinds of eyes and arrange them in a simple-to-complex
fashion. In other words, we do indeed find "half-an-eye" in
Nature in the form of a gradient of simpler eyes. Not so with
the flagellum. The gradient of simpler-to-complex is not much
a gradient at all. They is no flagellar analog of the "eye spot" or
"optic cup." In fact, what I proposed in this article as that there
exists a minimal level of complexity needed for a eubacterial
flagellum that includes ca. 26 gene products, where 18 of them
can be identified. Furthermore, apparently these gene products
need to fulfill about six different functional themes. Thus far,
we can't get much simpler, even though the bacterial species I
used are probably every bit as diverse as the animals Darwin and
Dawkins used to trace the evolution of the eye.

So, until you find eubacterial flagella built with 5, 9, 13, 18, and 22
gene products, you have no basis for likening my case to the "flawed
eye argument."

>Many modern things look "irreducibly complex". What you're not
>considering is that we don't know how many different stages things like

>flagella went through. It may be that *none* of the genes which you


>consider the "irreducibly complex core" were present in the first
>flagella.

Anything is possible. But I am not engaged in apologetics. If these
states existed apart from your imagination, feel free to outline the data
that indicates this.

>Ignore the fancy parts you see in all modern flagella- what is
>the simplest way to make a bacteria move?

Twitching motility and gliding are the two other ways, but neither
involve homologous components and are unrelated to flagella.

>All we see is the end product- it's like looking at an origami model of
>a grand piano- without the step-by step sheet, you have no idea how
>the hell they folded a piece of paper into that thing.

True. And this is a good rationalization to explain the total lack of
evidence for the evolution of something when you think that something
has indeed evolved. However, another interpretation might be that the
total lack of evidence exists because that thing didn't evolve. It's all
a matter of different perspectives.

--


Julie Thomas

unread,
Apr 21, 1999, 3:00:00 AM4/21/99
to

In a previous article, evanPOTTEDMEATFO...@earthlink.net (Evan Thompson) says:

>> predictions by design theorists as to what a minimal eye might
>> look like. I'd love to see any predictions by design theorists
>> as to what the ancestral eye of mollusks or cephalopods might
>> look like. I'd love to see anything resembling an evolutionary
>> noise coefficient.
>
>I mean it is, at its core, saying that all the complex parts of the
>flagellum would have had to appear at once for it to work, just like the
>eye argument. Did the lens come first, or the cornea- either way it
>wouldn't focus. It makes the mistake of assuming that the intermediate
>stages were incomplete parts of a modern human eye, when really they were
>fully functional (though
>inferior) simpler eyes.

And the fully functional, though inferior, simpler bacterial
flagella are found in what species?

>A "minimal eye" would most likely be a spot of photo-sensitive nerve cells
>on an animal's skin.
>
>A minimal flagellum would not have a "motor" or even rotate, it would
>simply flex back and forth in about the same method a bimetal strip would.

While my notion of a minimum flagellum is constrained by
the data, yours appears to exist entirely in your imagination.
--


Matt Silberstein

unread,
Apr 21, 1999, 3:00:00 AM4/21/99
to
In talk.origins I read this message from Peter Nyikos
<nyi...@math.sc.edu>:

[snip]


>
>Just for starters, you don't REALLY think that origami model
>arose from other origami art works thru natural selection,
>do you? People copied ideas from each other, modified
>older designs, experimented with one fold after another
> until they got what they wanted.
>

Sounds like evolution to me.

[snip]

Matt Silberstein
-------------------------------------------------------
You are the humanitarian.
You want to save the world.
Take the gun.

From "The President's Analyst"


John Wilkins

unread,
Apr 21, 1999, 3:00:00 AM4/21/99
to
In article <371f916f...@nntp.ix.netcom.com>, mat...@ix.netcom.com
(Matt Silberstein) wrote:

|In talk.origins I read this message from Peter Nyikos
|<nyi...@math.sc.edu>:
|
|[snip]
|>

|>Just for starters, you don't REALLY think that origami model
|>arose from other origami art works thru natural selection,
|>do you? People copied ideas from each other, modified
|>older designs, experimented with one fold after another
|> until they got what they wanted.
|>

|Sounds like evolution to me.
|

What's more it sounds like evolution through undirected variation and
natural selection - only the mechanism and fidelity of heredity is
different (imitation rather than nucleotide duplication).

But then I'm entirely biassed
<http://wehiz.wehi.edu.au/~wilkins/papers/theories/evoltheory.html>

--
John Wilkins
Head, Graphic Production
The Walter and Eliza Hall Institute of Medical Research
Melbourne, Australia
<mailto:wil...@WEHI.EDU.AU><http://www.wehi.edu.au/~wilkins>


howard hershey

unread,
Apr 22, 1999, 3:00:00 AM4/22/99
to
Julie Thomas wrote:
>
> In a previous article, evanPOTTEDMEATFO...@earthlink.net (Evan Thompson) says:
>
> >> predictions by design theorists as to what a minimal eye might
> >> look like. I'd love to see any predictions by design theorists
> >> as to what the ancestral eye of mollusks or cephalopods might
> >> look like. I'd love to see anything resembling an evolutionary
> >> noise coefficient.
> >
> >I mean it is, at its core, saying that all the complex parts of the
> >flagellum would have had to appear at once for it to work, just like the
> >eye argument. Did the lens come first, or the cornea- either way it
> >wouldn't focus. It makes the mistake of assuming that the intermediate
> >stages were incomplete parts of a modern human eye, when really they were
> >fully functional (though
> >inferior) simpler eyes.
>
> And the fully functional, though inferior, simpler bacterial
> flagella are found in what species?
>
> >A "minimal eye" would most likely be a spot of photo-sensitive nerve cells
> >on an animal's skin.
> >
> >A minimal flagellum would not have a "motor" or even rotate, it would
> >simply flex back and forth in about the same method a bimetal strip would.
>
> While my notion of a minimum flagellum is constrained by
> the data, yours appears to exist entirely in your imagination.
> --
Well, actually the bimetal strip type of 'flagella' does exist in
eucaryotes. Which again brings up the test I proposed to present
evidence for whether or not the eubacterial flagella is a product of
design. Motility is a function which some cells need. Evolutionary
design, of course, meets these needs by historical accident rather than
by intelligent teleological foresight; appropriating proteins used for
different purposes and modifying them to new functionality.
*Intelligent* design, OTOH, produces functional elements intelligently,
for purposeful reasons. Thus the existence of more than one different
solution to the problem of motility (for unicellular organisms we have
eubacterial flagellin, archaeal flagellin, eucaryotic flagella,
tubulin-based motility, gliding motility in eubacteria, the interesting
modification of flagella seen in the spirochaetes) presents the
opportunity for testing (*comparing* directly the assumptions that go
into the two mechanisms rather than, as Julie does, pretending that the
absence of evidence for one provides support for the other). [No,
Julie, I do not think that the current absence of evidence for design
absolutely rules out the possibility of design; my preference for
evolutionary mechanisms in the absence of any complete or clear-cut
evidence for *either* design or evolution is because the necessary
conditions for evolutionary mechanisms are known to exist and there is
evidence that these mechanisms can produce similarly complex results.
In contrast, the necessary conditions for intelligent design of these
systems is unevidenced and no biochemical system (prior to humans) has
ever been shown to be produced by intelligent design. If you come up
with evidence for design that doesn't amount to your personal disbelief
that some IC systems evolved, I will be happy to hear it.]

Which gets us back to the proposed test of *intelligent* design versus
historical accident by *comparing* the assumptions behind the two
mechanisms *with* evidence rather than pointing out the absence of
evidence. Among the different (and I would say historically
independent) solutions to motility in unicellular organisms, the two
procaryotic flagella provide the most useful direct test because they
have such similar modes of action and overall morphology, yet are
constructed of such different materials. Your job is to demonstrate
that there are good *intelligent* design reasons why these two similar
sturctures use such different materials. My position is that, like the
marsupial lions and wolves compared to their eutherian counterparts,
historical accident produces similar overall morphology because of the
constraints of selection (there are only so many ways to produce a large
carnivore), but, because of historical independence, often does it using
distinctly different materials (using incisors rather than canines)
because of the independence of the invention. It is not the case that
incisors are better or worse than canines (there is no design reason to
use one over the other). The marsupial lion would almost certainly be
just as effective a predator if someone did a dental transplant.
Similarly, ichthyosaurs, dolphins, and some teleostean fish show some
overall morphological similarity (because of selection limited by the
physical properties of hydrodynamic efficiency), but use quite different
components (and, in one case, a 90 degree rotation). Obviously, I would
regard the obvious reply, which Peter has used in the past - "there were
two teams of designers" - as decidedly silly and omphalic. That would
be like saying, "The same. Different. Doesn't matter. The designer can
do it and once I call a system 'designed' everything I see in the system
can be attributed to design." And I "know" that you would never use
such an argument.

Since "looks like intelligent design to me" seems to be the key factor
in deciding whether or not a system is designed, I would argue that a
pair of biochemical systems that produce the same functionality by use
of completely different materials "look like independent historical
accident" to me rather than being products of the same "intelligent
design" process. But perhaps you can yet demonstrate the reasons why an
*intelligent* designer would produce such similar yet different systems
that doesn't amount to omphalistic explanation.

While you are at it, perhaps you could provide three *short* lists: 1) A
list of the systems that you have, by your reasoning, concluded were
designed and *unlikely* to have evolved. A short description of the
criteria that led to this conclusion would be nice. 2) Another list of
the systems you have, by your reasoning, concluded were evolved and
*unlikely* to have been designed. A short description of the criteria
that led to this conclusion would be nice. 3) A third list of systems
you have, by your reasoning, decided not to currently include in list 1)
but that you do not want to include in list 2) because you think it
quite possible that your HYPE designer might have designed them too
(even though they do not meet all the criteria of list 1). A *short*
description of your reasoning would be nice.

I am working (as is obvious from list 3) from a presumption that what
you are really positing is a designer to explain abiogenesis (a designer
to invent the *entirety* of a - or three types of - cell) rather than a
designer to merely modify or introduce only certain IC systems in some
sort of a cell that arose by natural law abiogenesis (especially given
your ridicule of the idea of cells with RNA genomes or *anything*
simpler than current forms of life). This differs from Peter's ideas,
which merely moves abiogensis back one iteration and posits non-IC
aliens (at least for the systems he considers the IC ones designed by
aliens) which modify naturally arisen cells from their world prior to
transhipment to ours. My presumption also arises from noting (and I m
sure it has not escaped your notice) that any designer 'intelligent'
enough to design complicated IC systems should have no problem at all
with simpler systems.


Matt Silberstein

unread,
Apr 22, 1999, 3:00:00 AM4/22/99
to
In talk.origins I read this message from howard hershey
<hers...@indiana.edu>:

[snip]

>While you are at it, perhaps you could provide three *short* lists: 1) A
>list of the systems that you have, by your reasoning, concluded were
>designed and *unlikely* to have evolved. A short description of the
>criteria that led to this conclusion would be nice. 2) Another list of
>the systems you have, by your reasoning, concluded were evolved and
>*unlikely* to have been designed. A short description of the criteria
>that led to this conclusion would be nice. 3) A third list of systems
>you have, by your reasoning, decided not to currently include in list 1)
>but that you do not want to include in list 2) because you think it
>quite possible that your HYPE designer might have designed them too
>(even though they do not meet all the criteria of list 1). A *short*
>description of your reasoning would be nice.
>

I would also like to see current best guess for when the designed
material arrived on Earth. I wonder if we can determine in some way
how many design events took place. (I understand that this means
design events from the Earth's POV. A batch of stuff from Xordax may
have been designed at a variety of times and simply arrived on Earth
at one time.)

Dr Pepper

unread,
Apr 30, 1999, 3:00:00 AM4/30/99
to

[ To reply via netmail, address the message to gri...@gci-net.com,
and put "To: Dr Pepper", without the quotes, as the first non blank
line in the text. That's in the text, not in the subject line. ]

Ok, here's an example of what i was referring to.

You claim that a design approach is a viable approach to scientific
inquiry because design researchers, having decided that this widespread
DNA sequence is IC, are then motivated to look for it in organisms that
are thought not to have it, and voila! they find it there too, just a
little further down the tracks.

Ok, but wouldn't a standard evolutionary researcher think "hmm, this is
a primative and well conserved feature, i should check out these other
organisms to see what they have instead" and thus end up doing the same
thing?

And if futuure improvements in DNA reading make it possible to
absolutely demonstrate the non existence of this sequence in even one
organism, will it suddenly become non-IC?


10 2 grixit
DR PEPPER @
4 gci-net.com


howard hershey

unread,
Apr 30, 1999, 3:00:00 AM4/30/99
to
Dr Pepper wrote:
>
> [ To reply via netmail, address the message to gri...@gci-net.com,
> and put "To: Dr Pepper", without the quotes, as the first non blank
> line in the text. That's in the text, not in the subject line. ]
>
> Ok, here's an example of what i was referring to.
>
> You claim that a design approach is a viable approach to scientific
> inquiry because design researchers, having decided that this widespread
> DNA sequence is IC, are then motivated to look for it in organisms that
> are thought not to have it, and voila! they find it there too, just a
> little further down the tracks.
>
> Ok, but wouldn't a standard evolutionary researcher think "hmm, this is
> a primitive and well conserved feature, i should check out these other

> organisms to see what they have instead" and thus end up doing the same
> thing?
>
> And if futuure improvements in DNA reading make it possible to
> absolutely demonstrate the non existence of this sequence in even one
> organism, will it suddenly become non-IC?

No. It will become IC minus 1 or ur-IC. Or perhaps we will find that
some other protein in this particular system was 'designed' to take up
the IC function of the missing protein. The only way that a system can
be shown to be non-IC is to show, with detailed and complete evidence
for every step, that the system could form stepwise *for this particular
function* from scratch with all intermediates being functional for the
teleological end result. But the only such IC systems one attributes to
a designer are those that occur at some vague early point.

Julie Thomas

unread,
May 1, 1999, 3:00:00 AM5/1/99
to

In a previous article, gri...@gci-net.com (Dr Pepper) says:

>
>[ To reply via netmail, address the message to gri...@gci-net.com,
> and put "To: Dr Pepper", without the quotes, as the first non blank
> line in the text. That's in the text, not in the subject line. ]
>
>Ok, here's an example of what i was referring to.
>
>You claim that a design approach is a viable approach to scientific
>inquiry because design researchers, having decided that this widespread
>DNA sequence is IC, are then motivated to look for it in organisms that
>are thought not to have it, and voila! they find it there too, just a
>little further down the tracks.
>
>Ok, but wouldn't a standard evolutionary researcher think "hmm, this is

>a primative and well conserved feature, i should check out these other


>organisms to see what they have instead" and thus end up doing the same
>thing?

Sure. But this is irrelevant as I have never claimed a design
approach is needed, now have I? What HAS been claimed is
that a design approach is useless and unable to generate
testable research. It is *this* claim that has been
shown false. That naysayers continue to deny this against
the backdrop of several practical demonstrations shows only
that this is a very threatening realization. And I suppose
it would be for some. It does not threaten me to know
that design is not needed to explore the biological world
for so many. But it does seem to threaten some that I
don't need evolution to explain and explore the origin of these
systems. Now, I wonder why that is.



>And if futuure improvements in DNA reading make it possible to
>absolutely demonstrate the non existence of this sequence in even one
>organism, will it suddenly become non-IC?

Ah, but what you need to show is that the sequence was
not an IC component in the last common ancestor. I am
engaged in an investigation, not apologetics.
--


Mark J. Koebbe

unread,
May 2, 1999, 3:00:00 AM5/2/99
to

Julie Thomas wrote:
>

[snip a few comments]

> >Ok, here's an example of what i was referring to.
> >
> >You claim that a design approach is a viable approach to scientific
> >inquiry because design researchers, having decided that this widespread
> >DNA sequence is IC, are then motivated to look for it in organisms that
> >are thought not to have it, and voila! they find it there too, just a
> >little further down the tracks.
> >
> >Ok, but wouldn't a standard evolutionary researcher think "hmm, this is
> >a primative and well conserved feature, i should check out these other
> >organisms to see what they have instead" and thus end up doing the same
> >thing?
>
> Sure. But this is irrelevant as I have never claimed a design
> approach is needed, now have I?

Then you are saying this is 'unnecessary'?

What HAS been claimed is
> that a design approach is useless and unable to generate
> testable research. It is *this* claim that has been
> shown false.

Where?

That naysayers continue to deny this against
> the backdrop of several practical demonstrations shows only
> that this is a very threatening realization.

No practical demonstrations have been offered.

And I suppose
> it would be for some. It does not threaten me to know
> that design is not needed to explore the biological world
> for so many.

But it seems to bother you that so many realize this and ignore it as
useless with regard to science. Why would you keep posting?

But it does seem to threaten some that I
> don't need evolution to explain and explore the origin of these
> systems.

No, what is 'threatening' is to abandon the critical reasoning behind
science, suggest that this type of thinking is related to 'science', and
assert that it is any more useful then explanations like 'god did it'.

> Now, I wonder why that is.

See above.

>
> >And if futuure improvements in DNA reading make it possible to
> >absolutely demonstrate the non existence of this sequence in even one
> >organism, will it suddenly become non-IC?
>
> Ah, but what you need to show is that the sequence was
> not an IC component in the last common ancestor.

First, what is needed is to show that there is something IC. This has
never been done except by the truth of assertion.

I am
> engaged in an investigation, not apologetics.

Without a demonstration of 'IC'....it is only apologetics.

Regards,

MJK

> --


howard hershey

unread,
May 2, 1999, 3:00:00 AM5/2/99
to
Julie Thomas wrote:
>
> In a previous article, gri...@gci-net.com (Dr Pepper) says:
>
> >
> >[ To reply via netmail, address the message to gri...@gci-net.com,
> > and put "To: Dr Pepper", without the quotes, as the first non blank
> > line in the text. That's in the text, not in the subject line. ]
> >
> >Ok, here's an example of what i was referring to.
> >
> >You claim that a design approach is a viable approach to scientific
> >inquiry because design researchers, having decided that this widespread
> >DNA sequence is IC, are then motivated to look for it in organisms that
> >are thought not to have it, and voila! they find it there too, just a
> >little further down the tracks.
> >
> >Ok, but wouldn't a standard evolutionary researcher think "hmm, this is
> >a primative and well conserved feature, i should check out these other
> >organisms to see what they have instead" and thus end up doing the same
> >thing?
>
> Sure. But this is irrelevant as I have never claimed a design
> approach is needed, now have I? What HAS been claimed is

> that a design approach is useless and unable to generate
> testable research.

The *assumption* that current biological features of organisms serve a
useful function and appear to be well suited to serve that function has
been known for a long, long time. That *is* Paley's argument after all,
and Paley's argument *usually* produces results that are
indistinguishable from the end results of blind evolution. Darwin
certainly understood that, as has every biologist before or since. The
features (molecular or morphological) of organisms do indeed typically
serve a useful function and are well-suited to function. In that sense,
saying that 'fairies did it' to explain the existence of a system that
functions well and making predictions based on the idea that systems
have useful functions will be right quite often. But none of that helps
to distinguish or decide whether, in fact, a fairy did it or whether,
instead, it evolved. You can explain most systems based on the
assumption that the fairy designed it well. You will indeed find much
*data* that the fairies did a good job; that is, you will find data that
can convincingly show that biological systems work well and are
integrated into the functioning of the organism (and the system) as a
whole quite well. But you will not find evidence that fairies are
*required* to do this by looking only at that kind of data. Fairies are
hypothetical and unevidenced. And data that cannot distinguish between
*intelligently* designed systems and systems that evolved is merely data
and not evidence to that relevant point. Paley's argument will still
work to explain the workings of most biological systems and can be used
to make predicitions on the assumption that this or that system was
designed and thus is likely to function well. I have EXPLICITLY and
OFTEN stated that the design approach can be used to generate testable
research. It does so from the same circular logic that Paley used, most
biological systems function well and are well integrated, so they appear
like a designed system, so, by assuming that the system is designed you
can then point out or predict that most systems function well.

> It is *this* claim that has been

> shown false. That naysayers continue to deny this against


> the backdrop of several practical demonstrations shows only
> that this is a very threatening realization.

Au contraire, I have EXPLICITLY stated *many* times that I think that a
HYPE can be invented to explain *anything* that evolution can. That is,
in fact, the main reason I object to HYPE hypotheses in general. You
keep claiming that I am misrepresenting your model for determining that
some system is designed and yet you never seem to have caught on that my
objection is not that the HYPE hypothesis cannot make predictions, but
that the HYPE hypothesis cannot, even under your tutelege, make
predictions that discriminate between intelligent design and evolution.
The normal fallback of science is inference from known mechanisms of
evolution that can be explicitly ruled out (and I agree that IC can be
used, in some cases, to rule out direct step-wise Darwinistic
mechanisms). You actually do have to weed through all known mechanisms
and present evidence that you have evidence that supports your
mechanism. That is rather hard to do when the 'mechanism' is something
as vague as a designer of some sort did it by thinking complexity into
specificity similar to humans designing automobiles but without the
evidence or some other such mumbo-jumbo.

You have not proposed a way that one can, in principle, show that
something was not intelligently designed, aside from asking for evidence
for evolutionary mechanisms. The real question is, if evolutionary
models were unknown, is there any way, in principle to exclude your HYPE
mechanism from explaining any feature of life? I cannot think of any.
If there were no HYPE hypothesis, there would still be ways to (at least
tentatively) rule out direct Darwinism for some features, duplication
and divergence for other features, acquisition of new functionalities
for other features, aggregation of subsystems (like mitochondria and
eucaryotes) into integrated systems, co-evolution, etc. That does not
mean that I would always have, or would be likely to be able to gather,
the evidence to be able to do this, and certainly I would be unlikely to
rule out a possibility if that is what happened (falsifiability does not
mean it must be falsified). But each of those evolutionary mechanisms
are potentially falsifiable. A vague, rather than specific, HYPE is
not. In that sense, Peter's aliens are much better than your vague
designer.

> And I suppose
> it would be for some. It does not threaten me to know
> that design is not needed to explore the biological world

> for so many. But it does seem to threaten some that I


> don't need evolution to explain and explore the origin of these

> systems. Now, I wonder why that is.

I am not threatened. I know you are proposing a useless (as far as
science is concerned) HYPE explanation of no real significance that only
pretends to explain the origins of systems (by using phrases like
designing by producing complexity with specificity). Until you start
presenting *evidence* directly to the point of origins rather than
*data* that you can interpret as showing the Glory of the HYPE in
producing a functioning system (See, ma, it *functions*!), I will regard
your argument as merely Paley in molecular drag. Paley's argument is
not, however, a stupid one. Most of the time systems do function well
so that predictions made on the basis of apparently 'intelligent'
functionality will often work. It is just not a scientific explanation.


>
> >And if futuure improvements in DNA reading make it possible to
> >absolutely demonstrate the non existence of this sequence in even one
> >organism, will it suddenly become non-IC?
>
> Ah, but what you need to show is that the sequence was

> not an IC component in the last common ancestor. I am


> engaged in an investigation, not apologetics.

One can only analyse the molecules of that fraction of life that reached
the present. You somehow seem to think that *all* intermediate stages
in the evolution of a system must exist in some present organism if
evolution is to be true, just like some of the YE creationists who think
that all the intermediates between rats and humans must exist in the
present or be visible in the fossil record for evolution to be true.
Nature is not so generous with real evidence. Where did you learn this
strawman idea?
> --


Mark Isaak

unread,
May 2, 1999, 3:00:00 AM5/2/99
to
Julie Thomas wrote:
>What HAS been claimed is that a design approach is useless and unable to
>generate testable research. It is *this* claim that has been shown
>false.

But of course. Since evolution produces design as well as any designer,
the design approach should produce many of the same results as the
evolutionary approach. But can it produce anything original?
--
Mark Isaak atta @ best.com http://www.best.com/~atta
"My determination is not to remain stubbornly with my ideas but
I'll leave them and go over to others as soon as I am shown
plausible reason which I can grasp." - Antony Leeuwenhoek


Michael Suttkus, II

unread,
May 2, 1999, 3:00:00 AM5/2/99
to
howard hershey wrote:
>
> Au contraire, I have EXPLICITLY stated *many* times that I think that a
> HYPE can be invented to explain *anything* that evolution can.

Kindly forgive the ignorant newbie, but what's HYPE?
Hypothetical Entity is my best guess.

--

Non est ad astra, mollis e terris via.
There is no easy way from the Earth to the stars.
- Seneca


howard hershey

unread,
May 2, 1999, 3:00:00 AM5/2/99
to
Michael Suttkus, II wrote:

>
> howard hershey wrote:
> >
> > Au contraire, I have EXPLICITLY stated *many* times that I think that a
> > HYPE can be invented to explain *anything* that evolution can.
>
> Kindly forgive the ignorant newbie, but what's HYPE?
> Hypothetical Entity is my best guess.

Sorry, I usually do give the definition at least once. HYPE is
HYpothetical Posited Entity. So your guess was on target. HYPE refers
to any evidenceless entity or agent posited to solve a problem. Some
HYPEs are more reasonable than others by the standard inferences of
scientific methodology. For example, positing the existence of
filiamentous proteins prior to the existence of direct or indirect or
inferential evidence for the same is one thing because one can certainly
make the case that the conditions to produce such proteins were present
at the time they are needed. Positing entire civilizations of
intelligent creatures in the complete absence of evidence for the same
is something else.

Jonathan Stone

unread,
May 2, 1999, 3:00:00 AM5/2/99
to
In article <372C4F...@indiana.edu>, howard hershey <hers...@indiana.edu> writes:
|> Julie Thomas wrote:
[snip]

|> > >And if futuure improvements in DNA reading make it possible to
|> > >absolutely demonstrate the non existence of this sequence in even one
|> > >organism, will it suddenly become non-IC?
|> >
|> > Ah, but what you need to show is that the sequence was
|> > not an IC component in the last common ancestor. I am
|> > engaged in an investigation, not apologetics.
|>
|> One can only analyse the molecules of that fraction of life that reached
|> the present. You somehow seem to think that *all* intermediate stages
|> in the evolution of a system must exist in some present organism if
|> evolution is to be true, just like some of the YE creationists who think
|> that all the intermediates between rats and humans must exist in the
|> present or be visible in the fossil record for evolution to be true.
|> Nature is not so generous with real evidence. Where did you learn this
|> strawman idea?

Howard,

I think you missed the *real* strawman lurking here, which is that
Julie is apparently saying her nonscientific viewpoint -- IC, as
determined by Julie, sans reproducible protocols -- is correct,
until proof to the contrary.


Julie Thomas

unread,
May 2, 1999, 3:00:00 AM5/2/99
to


In reply to Dr. Pepper, I wrote:

> Sure. But this is irrelevant as I have never claimed a design

> approach is needed, now have I? What HAS been claimed is


> that a design approach is useless and unable to generate
> testable research.

Howard replies:

>The *assumption* that current biological features of organisms serve a
>useful function and appear to be well suited to serve that function has
>been known for a long, long time.

Yes, and it is a research assumption that predates evolution, showing
that evolution is not necessary for making this working assumption.

>That *is* Paley's argument after all,
>and Paley's argument *usually* produces results that are
>indistinguishable from the end results of blind evolution. Darwin
>certainly understood that, as has every biologist before or since.

Indeed. Darwin's brilliance was in coming up with an alternative
view, not a refutation. Of course, since Darwin's explanation is
only an alternative explanation, we need not be obligated to use
it as the only explanation.

>The features (molecular or morphological) of organisms do indeed typically
>serve a useful function and are well-suited to function.

Function clearly follows from design. It is the at the heart of the
design mechanism. In contrast, it does not clearly stem from
evolution. In evolution, a feature may have no function, may be
of only partial use, or may be "well-suited." Thus, when we
explore an unknown feature, evolution provides no predictions
about its function. Consider a specific example from a recent
exchange I had with Paul.

Speaking of the central pair of microtubules in eukaryotic
flagella, Paul wrote:

>It's a piece of architecture; the central pair could be a historical
>reflection of the mechanism of assembly,

I thus replied:

"Showing us how evolution does not lead to the prediction that these
central pair have a function. However, if one proposes the 9+2 state
was designed, this leads to a prediction of function for the central
pair. This highlights yet one more way in which design and
evolution can lead to different approaches. In this example, evolution
makes no prediction and is thus unfalsifiable. Whether or not the
central pair have a function, they evolved. All bases are covered.
In contrast, the design explanation is falsifiable. If the central pair
have no function, they cannot be scored as design events."

Or consider the F-ATPase itself. Right now, no one knows
what the alpha subunit is doing, it could be, as Paul might argue,
"a historical reflection of the mechanism of assembly." Evolution
gives us no reason to think it has a function. After all, would you
argue that evolution predicts it will have a function? If so,
would evolution thus be falsified if it turns out not to have a function?
Of course not.

>In that sense,
>saying that 'fairies did it' to explain the existence of a system that
>functions well and making predictions based on the idea that systems
>have useful functions will be right quite often.

Fairies are not known to exist. Intelligent agents and designers are.
To invoke a fairy, one would have to invoke a pure HYPE. To invoke
an intelligent designer, one extrapolates (as you do when you invoke
simpler and sloppier beings).


>But none of that helps to distinguish or decide whether, in fact, a fairy
>did it or whether, instead, it evolved. You can explain most systems based
>on the assumption that the fairy designed it well. You will indeed find much
>*data* that the fairies did a good job; that is, you will find data that
>can convincingly show that biological systems work well and are
>integrated into the functioning of the organism (and the system) as a
>whole quite well.

If you attempt to identify the designers, you go beyond any empirical
and testable method. But yes, intelligent design does lead to testable
predictions about the existence of function. Evolution can explain
this information after the fact, but it is useless at making these
types of predictions (thus remains unfalsifiable at this level).

>But you will not find evidence that fairies are
>*required* to do this by looking only at that kind of data.

No one has proposed that fairies are required to do anything.
Thus, this lack of evidence is meaningless.

>Fairies are hypothetical and unevidenced.

Yes, but intelligent agents are not. They exist and are evidenced.
SIBO merely extrapolates on the basis of analogy (which is
what archaeology does to detect design [although its basis
for extrapolation is much stronger] and what science does
to explain evolution [its basis for extrapolation is much the
same as SIBOs]).

>And data that cannot distinguish between
>*intelligently* designed systems and systems that evolved is merely data
>and not evidence to that relevant point.

Re-read that claim all by itself folks. In his rush to dismiss the design
inference, Howard has used such a broad brush that he paints himself
into a corner where there is no longer any evidence for evolution (as
he has failed to do the very thing he demands).

>Paley's argument will still
>work to explain the workings of most biological systems and can be used
>to make predicitions on the assumption that this or that system was
>designed and thus is likely to function well. I have EXPLICITLY and
>OFTEN stated that the design approach can be used to generate testable
>research.

Very well. I will cite you the next time someone claims design is incapable
of generating a testable research program.

>It does so from the same circular logic that Paley used, most
>biological systems function well and are well integrated, so they appear
>like a designed system, so, by assuming that the system is designed you
>can then point out or predict that most systems function well.

Yes, indeed, it works. But I have also broken out of the circular
logic and use objective criteria to identify data patterns that
get scored as design. With this focus, the design/function/purpose
equations bear their fruit.

It's an alternative way of viewing things. And it works.

>> It is *this* claim that has been

>> shown false. That naysayers continue to deny this against
>> the backdrop of several practical demonstrations shows only
>> that this is a very threatening realization.

>Au contraire, I have EXPLICITLY stated *many* times that I think that a


>HYPE can be invented to explain *anything* that evolution can. That is,
>in fact, the main reason I object to HYPE hypotheses in general.

Quit with the HYPE-ocrisy. Every time you attempt to explain the
origin of these systems, you employ all kinds of hypes.

>You keep claiming that I am misrepresenting your model for determining that
>some system is designed and yet you never seem to have caught on that my
>objection is not that the HYPE hypothesis cannot make predictions, but
>that the HYPE hypothesis cannot, even under your tutelege, make
>predictions that discriminate between intelligent design and evolution.

Oh, but it has. You have just never caught on that I am not looking
for razzle-dazzle predictions that work as magic bullets to settle the issue
once and for all and thus, demand consensus. Things are far too subtle.
But the discriminating predictions exist. Design allowed me to predict
the type III system evolved from the flagellum. Your evolutionary views
predicted otherwise. Design allowed me to make various predictions about
the OriC (including its mechanism), many of which were contrary to
your predictions and those of others. Design allowed me to go out on the limb
and make specific predictions about the mechanism of the F-ATPase, none
of which, AFAICT, have been made by evolution. What will utlimately
make the discrimination is not the "here and there" examples, but the sum
total of the coherency and fruitfulness of the different perspectives.
As I see it, the main problem is that evolution is not a very good
predictor (for how could it be?), but is very good at explaining, after
the fact, just about any form of data science provides.

>The normal fallback of science is inference from known mechanisms of
>evolution that can be explicitly ruled out

The normal fallbacks of science do not apply in SIBO.

>and I agree that IC can be
>used, in some cases, to rule out direct step-wise Darwinistic
>mechanisms).

This is good. Thus, IC is a good *start* and I build around it by
taking into consideration the following:

>You actually do have to weed through all known mechanisms
>and present evidence that you have evidence that supports your
>mechanism.

What SIBO does is find that there is no good evidence that all these
known mechanisms of evolution were behind the origin of these
systems. It can't rule out "could happen" claims or show that
something is impossible.

>That is rather hard to do when the 'mechanism' is something
>as vague as a designer of some sort did it by thinking complexity into
>specificity similar to humans designing automobiles but without the
>evidence or some other such mumbo-jumbo.

SIBO has successfully screened out features so that they are
not attributed to design.

>You have not proposed a way that one can, in principle, show that
>something was not intelligently designed, aside from asking for evidence
>for evolutionary mechanisms. The real question is, if evolutionary
>models were unknown, is there any way, in principle to exclude your HYPE
>mechanism from explaining any feature of life? I cannot think of any.

Since you cannot exclude it, your own logic means that you have
no evidence for evolution.

>If there were no HYPE hypothesis, there would still be ways to (at least
>tentatively) rule out direct Darwinism for some features, duplication
>and divergence for other features, acquisition of new functionalities
for other features, aggregation of subsystems (like mitochondria and
>eucaryotes) into integrated systems, co-evolution, etc.

But none of this is sufficient to rule out a "could-happen" world
which is the very basis of your position.

>That does not mean that I would always have, or would be likely to be
>able to gather, the evidence to be able to do this, and certainly I would
>be unlikely to rule out a possibility if that is what happened
(falsifiability
>does not mean it must be falsified). But each of those evolutionary
mechanisms
>are potentially falsifiable.

But not the belief that the system evolved. SIBO is about scoring,
remember.

>A vague, rather than specific, HYPE is not. In that sense, Peter's aliens
are
>much better than your vague designer.

Once again, SIBO has successfully filtered out features so that they
are not scored as design products. In stark contrast, note that
Howard's method scores everything as a product of evolution (even
if there is no evidence of its evolution) and cannot come up with
realisitc criteria to prevent such scoring.

>> And I suppose
>> it would be for some. It does not threaten me to know
>> that design is not needed to explore the biological world
>> for so many. But it does seem to threaten some that I
>> don't need evolution to explain and explore the origin of these
>> systems. Now, I wonder why that is.

>I am not threatened. I know you are proposing a useless (as far as
>science is concerned) HYPE explanation of no real significance that only
>pretends to explain the origins of systems (by using phrases like
>designing by producing complexity with specificity). Until you start
>presenting *evidence* directly to the point of origins rather than
>*data* that you can interpret as showing the Glory of the HYPE in
>producing a functioning system (See, ma, it *functions*!), I will regard
>your argument as merely Paley in molecular drag. Paley's argument is
>not, however, a stupid one. Most of the time systems do function well
>so that predictions made on the basis of apparently 'intelligent'
>functionality will often work. It is just not a scientific explanation.

Of course SIBO does not offer a "scientific explanation." It is not
science.

>> >And if futuure improvements in DNA reading make it possible to
>> >absolutely demonstrate the non existence of this sequence in even one
>> >organism, will it suddenly become non-IC?
>
>> Ah, but what you need to show is that the sequence was
>> not an IC component in the last common ancestor. I am
>> engaged in an investigation, not apologetics.

>One can only analyse the molecules of that fraction of life that reached
>the present. You somehow seem to think that *all* intermediate stages
>in the evolution of a system must exist in some present organism if
>evolution is to be true, just like some of the YE creationists who think
>that all the intermediates between rats and humans must exist in the
>present or be visible in the fossil record for evolution to be true.
>Nature is not so generous with real evidence. Where did you learn this
>strawman idea?

I don't ask for all possible intermediates. But the identification of
intermediates is highly relevant. Otherwise, what's the point of
Darwin's and Dawkins' demonstration of an eye-continuum?
If you propose simple and sloppy states, why not expect this
proposal to be supported by some evidence?

--


John Wilkins

unread,
May 2, 1999, 3:00:00 AM5/2/99
to
In article <372C848F...@nowhere.in.particular>, "Michael Suttkus,
II" <The...@nowhere.in.particular> wrote:

|howard hershey wrote:
|>
|> Au contraire, I have EXPLICITLY stated *many* times that I think that a
|> HYPE can be invented to explain *anything* that evolution can.
|

|Kindly forgive the ignorant newbie, but what's HYPE?
|Hypothetical Entity is my best guess.
|

Hypothetical Posited Entity - a term/acronym first introduced, I think, by
Ian Hacking.

--
John Wilkins
Head, Graphic Production, The Walter and Eliza Hall Institute
of Medical Research, Melbourne, Australia
<mailto:wil...@WEHI.EDU.AU><http://www.wehi.edu.au/~wilkins>


Wade Hines

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May 2, 1999, 3:00:00 AM5/2/99
to

Jonathan Stone wrote:
>
> In article <372C4F...@indiana.edu>, howard hershey <hers...@indiana.edu> writes:
> |> Julie Thomas wrote:
> [snip]
>

> |> > >And if futuure improvements in DNA reading make it possible to
> |> > >absolutely demonstrate the non existence of this sequence in even one
> |> > >organism, will it suddenly become non-IC?
> |> >
> |> > Ah, but what you need to show is that the sequence was
> |> > not an IC component in the last common ancestor. I am
> |> > engaged in an investigation, not apologetics.
> |>
> |> One can only analyse the molecules of that fraction of life that reached
> |> the present. You somehow seem to think that *all* intermediate stages
> |> in the evolution of a system must exist in some present organism if
> |> evolution is to be true, just like some of the YE creationists who think
> |> that all the intermediates between rats and humans must exist in the
> |> present or be visible in the fossil record for evolution to be true.
> |> Nature is not so generous with real evidence. Where did you learn this
> |> strawman idea?
>

> Howard,
>
> I think you missed the *real* strawman lurking here, which is that
> Julie is apparently saying her nonscientific viewpoint -- IC, as
> determined by Julie, sans reproducible protocols -- is correct,
> until proof to the contrary.

Jonathan,

I think you miss the intricacy of the web. When cornered, Julie isn't
claiming truth, just 'an interesting avenue to explore'.

To people who suggest that evolutionary explanations are better
evidenced, she asks for conclusive proof or whatever lesser level
of evidence is unobtainable. Sometimes for instance, "just-so" stories
are pooh-pooh'd as trivial and other times they are asked for.

Meanwhile, designology simply is an assertion which at varying times
gets Julie's vote of confidence in terms like "as I have previously
shown".

But I warn you, as smart as you think you are, be careful about playing
the game with Julie. She is so good at it, I think it might not even
be conscious.


Mark Isaak

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May 3, 1999, 3:00:00 AM5/3/99
to
In article <7gie1e$l0i$1...@pale-rider.INS.CWRU.Edu>,

Julie Thomas <iz...@cleveland.Freenet.Edu> wrote:
>Function clearly follows from design.

I thought your definition of design was the same as people's normal
understanding of the term. Function *can* follow from design, or it might
not, at least by the usual definition. Would you care to clarify exactly
what *your* definition of design is?

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