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nanosoliton



Posts: 11
Joined: Jan. 2003

(Permalink) Posted: Jan. 07 2003,19:28   

I decided to join this group (among others) mostly because I suspect that there are a lot of misconceptions about intelligent design. For example, the very title of the group is called "Antievolution", and yet not only am I an IDer, but I also consider myself an evolutionist (for example, I agree with common descent as Michael
Behe does). What intelligent design does question is the Darwinian mechanism, that it cannot adequetely explain evolution. I have been reading several ID postings on the deamination of cytosine and I wanted to discuss it in several places.

When the DNA strand replicates, cytosine, and not thymine, pairs with the altered base. Similarly, deamination of cytosine produces uracil, which behaves like thymine. This has lead many to think that an
intelligent designer would not have used cytosine, especially with such a high rate of deaminiation. Since one of the driving principles of intelligent design might be error correction, why use cytosine when it can easily lead to errors? The half-life for deamination at 25 degrees C is approximately 340 yr. No reactions have
been described thus far that would produce cytosine, even in a specialized local setting, at a rate sufficient to compensate for its decomposition.

There are three considerations that make this actually support ID rather than argue against it that I will summarize.

One of the major points in this essay is that Hydrophobic interactions play a large role in protein folding and structure as well as alpha helix and beta sheet elongation/formation, further substantiation of this is shown from the fact that serine and not proline, which is a helix breaker, is formed after C-T transitions. So C-T transitions are used to evolve new proteins.

This hypothesis opens the door to a testable prediction from Intelligent Design theory:

"This hypothesis also makes a prediction that can be tested. For example, if the multicellular state was front-loaded with life's design, we would expect to find conserved, multicellular-specific proteins have crucial FLIYWVMCS residues that can explained by C-T
transitions relative to their ancestral state."
http://www.idthink.net/biot/deam/index.html


We may be seeing a direction on evolution forced by intelligent design principles.

--------------
Nelson Alonso

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Jan. 07 2003,21:20   

Hey Nelson, welcome to AE.

Unfortunately I don't have a week to really wrap my head around the cytosine deamination issue.  However I guess I was the "provoker" of the Mike Gene article you cite in that I posted the article "Confounded cytosine" which he is reacting to.

So if debate of this topic begins (by people other than me), let's start by accumulating the relevant links etc. on this thread and then go from there.

Here is an ARN post with some discussion, including some quotations from the article, with the hopes of laying out what Poole et al. were arguing.  Unfortunately this argument is embedded in a more complex discussion of various topics related to RNAworld and the origin of the genetic code which makes simple quoting difficult and I think confused subsequent discussion as it is not at all clear that the IDists involved accept or reject either RNAworld or a gradual origin of the genetic code and DNA.

ARN thread

Begin re-post of summary of Poole et al.:

===========
I do believe I provoked this particular MG essay when I posted this reference on ISCID:

Quote

Nat Rev Mol Cell Biol 2001 Feb;2(2):147-51
 
Confounded cytosine! Tinkering and the evolution of DNA.

Poole A, Penny D, Sjoberg BM.

Institute of Molecular BioSciences, PO Box 11222, Massey University, Palmerston North, New Zealand. a.m.poole@massey.ac.nz

Early in the history of DNA, thymine replaced uracil, thus solving a short-term problem for storing genetic information--mutation of cytosine to uracil through deamination. Any engineer would have replaced cytosine, but evolution is a tinkerer not an engineer. By keeping cytosine and replacing uracil the problem was never eliminated, returning once again with the advent of DNA methylation.
Here is the direct link although you may need subscription access.

There argument is complex but here is the gist:

Quote

The origin of DNA is a fundamental question in evolution. Early on, DNA replaced RNA, reflecting the superior information-storage capacity of DNA1, 2. Modern biochemical pathways provide an insight into this transition, as do RNA and uracil-DNA (U-DNA) viruses2, 3, suggesting that the replacement took place in two steps (Figs 1, 2a): replacement of ribose with deoxyribose, then replacement of uracil (U) with thymine (T)4. The first step was probably very complex, and has recently been reviewed elsewhere2, 5. Here we look at the second (UT) replacement, which is emerging as another example of why evolution is best viewed as a tinkerer, not as an engineer with an eye for 'good' design (Box 1).

[...]

Central to the story is cytosine ©, which readily deaminates to form U. This turns CG pairs into UG mispairs, and is an ongoing process in DNA6, 7 (Fig. 2b). Without repair, replication of a UG mispair would give one UA pair (which is read as a TA pair) and one CG pair. All organisms carry the machinery for repair of C deaminations — uracil-N-glycosylase (UNG), which recognizes and removes any U that it detects, leaving an abasic site. This is patched up by base-excision repair8, 9 (Fig. 3), which creates a gap in the DNA opposite G. DNA polymerase then fills the gap with dC, thus repairing the mutation. Occasionally, U (from dUTP) is incorporated opposite A, so both UG and UA pairs turn up in DNA. The UNG recognizes and removes U arising from either C deamination or misincorporation, allowing DNA to be faithfully repaired10-12.

[...]

Before T was a constituent of DNA, it would have been harder to detect C deaminations, because U was a bona fide constituent of early DNA at UA pairs. It is widely accepted that U--&gt;T replacement solved this problem because it allowed any U arising by C deamination to be detected unambiguously.

[...]

François Jacob14 has likened evolution to "tinkering". In contrast to an engineer, who works by design, obtaining all the necessary materials needed for construction of a prototype and finally testing it before putting it to work, a tinkerer makes use of whatever is at hand. This means that the result, although functional, is often far from perfect. A consequence of this modus operandi is that if something works in the short term it will be used, even if a better alternative is conceivable. New innovations cannot arise only to become useful when a subsequent function evolves, because there is no selection to maintain such innovations before they become useful.

Recent progress on the biochemistry of U removal reveals an unexpected diversity of reactions catalysed by members of the uracil-DNA glycosylase family (even though they all share a common origin), and allows the U--&gt;T conundrum to be resolved. New data15 on a closely related phenomenon — the repair of deaminated 5-methylcytosine (5-meC, which deaminates to T, resulting in a TG mismatch; Fig. 2b) — highlights the usefulness of the tinkering analogy for evolution. The problems solved by replacing U with T resurfaced once again when C methylation became a feature of the genome, with a member of the U-DNA glycosylase family being recruited to repair 5-meCT deaminations.

[...]

The trouble with T

As eukaryotic genomes became more complex, additional mechanisms of gene regulation developed. One such mechanism is DNA methylation, where a methyl group is added to position 5 on the cytosine ring, forming 5-meC (Ref. 15). The ability to regulate genes by C methylation would have been beneficial, but it came with a catch: 5-meC deaminates to T at a rate 2–4-fold higher than C deaminates to U (Fig. 2)21, meaning that a new form of mismatch became a problem. In eukaryotes, thymine-DNA glycosylase (TDG), which is evolutionarily related to UNG and MUG, repairs TG mismatches arising from deamination of 5-meC (Refs 17,25).

[...]

Replacing U with T provided a means by which to fine-tune repair of C--&gt;U deaminations, but the problem of C deamination was never eliminated — it re-emerged in the form of 5-meC deamination. Tinkering also makes sense of the evolution of the 5-meC apparatus, which subsequently drove the recruitment of the U-excision apparatus into T excision because of the 'unforeseen' side effect of 5-meCT deamination. All this could have been avoided simply by eliminating C early in the evolution of the genetic material — but how boring life would be if evolution worked by engineering.

  
Wesley R. Elsberry



Posts: 4807
Joined: May 2002

(Permalink) Posted: Jan. 08 2003,00:51   

Hello, Nelson.

The ID movement's antievolutionism is well established.

The buzz-phrase "evidence against evolution" is often deployed by ID advocates. That ID advocates may not reject every observation, hypothesis, or theory found in evolutionary biology doesn't mean that the ID movement is not antievolutionary. Even the Institute for Creation Research accepts some instances of the action of natural selection occurring, which hardly means that the ICR is not antievolutionary.

Some places where ID and "evidence against evolution" coincide:

Ohioans Don't Want Evolution Only

Evidence Against Evolution

Can Neo-Darwinism Survive?

Columbus Dispatch is Blind to the Arguments and Evidence Against Evolutionism

Results of analysis of the public comments on the proposed Ohio Science Standards ...

Polls are meaningful

Notes on lecture by Phillip Johnson at KU, April 7, 2000

Critics: No science in intelligent design

Remarks to the Kansas State Board of Education

Skepticism's Prospects for Unseating Intelligent Design

Evolution FAQ

"So What Evidence IS There Against Evolution?"

No Admittance

College student challenges evolutionary theory

Evolution Rerun to Backfire; New Poll from Ohio

Transcript-NPR Talk of the Nation / Science Friday

Some DI Fellows discussing "evidence against" various bits of evolutionary biology:

Report from Hillsdale College Symposium on ID

Intelligent Design vs. Darwinism: Theories in Collision

Cobb County (Georgia) School Board Promotes Academic Freedom, Not Religion

Teach All the Evidence

Will “Santorum Language” Save Us From Scientific Fundamentalism?

This thread would be a suitable place to collect more instances of ID advocate use of the concept of "evidence against evolution".

Many of the instances here are not careful to delimit "evolution" to 'Darwinism', 'Neo-Darwinism', or similar bugbears of ID advocates.  Some explicitly reference particular things as evidence against common descent.  As "theyeti"'s IDism in One Lesson, or "No Free Hunch" says with tongue in cheek, "ID is whatever we say it is, and we don't agree."

Wesley

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
JxD



Posts: 16
Joined: Dec. 2002

(Permalink) Posted: Jan. 08 2003,01:41   

Quote
I decided to join this group (among others) mostly because I suspect that there are a lot of misconceptions about intelligent design.
 An inference to the best explanation here is that the IDers do a dismal job of explaining themselves.  When so many intelligent and educated individuals have so many similar "misconceptions" about a position that has been around since the time of Aristotle, it seems to me that the IDers ought to do some introspection and blame themselves.
Quote
One of the major points in this essay is that Hydrophobic interactions play a large role in protein folding and structure as well as alpha helix and beta sheet elongation/formation [...]
 I was not aware that hydrophobic interactions played any more of a significant role in alpha helix and beta sheet formation and elongation(!?), than, say, polar interactions between side chains, or hydrogen bonding between the amino and carbonyl groups of the peptide backbone.  Perhaps you have misquoted some source.
Quote
[...] further substantiation of this is shown from the fact that serine and not proline, which is a helix breaker, is formed after C-T transitions.
 Yet this is an odd observation, especially after mentioning the importance of hydrophobic interactions in the same breath, since serine is after all a polar amino acid (hydroxy side chain).  
Quote
So C-T transitions are used to evolve new proteins.
 OK.  But so are all other types of mutations.  A major assumption made in your argument is that, of the changing properties in amino acids resulting from C-T transitions, the differences in hydrophobicity dominate over, say, steric effects and other structural characteristics with regards to overall protein structure.  Otherwise, it does not seem to me that you can say C-T transitions affect evolutionary pathways through a particular mechanism (i.e. changes in hydrophobicity), especially in a manner that suggests intelligent foresight.  However, consider for instance Arg (CG_) -> Cys (UG_) changes.  Is the potential of the new Cys in forming new disulfide bonds with other Cys residues necessarily a negligible effect when compared to the changes in hydrophobicity?  The problem here is that you have greatly oversimplified the mechanisms underlying the propensities for alpha and beta chain formation.  A single residue and its specific properties do not by themselves determine peptide folding.
Quote
"This hypothesis also makes a prediction that can be tested. For example, if the multicellular state was front-loaded with life's design, we would expect to find conserved, multicellular-specific proteins have crucial FLIYWVMCS residues that can [be] explained by C-T transitions relative to their ancestral state"
I do not follow this train of logic. It appears to be a weak argument that comes in the form of ad hoc reasoning.  If A then B, and B is true... but that says nothing logically about the premise A (i.e. that some state was "front-loaded").  Furthermore, if we posit some initial state C0, from which life evolves, who is to say that there does not exist an earlier state B0 which gives rise to C0?  At the very least, the argument presented thus far does not rule that possibility out.  Going in the other direction, let us suppose that C0 gives rise to C1, which in turn gives rise to C2, etc. ... all the way up to Cn, which we currently observe.  While we are positing the intentions of the designer, wouldn't it make more sense for the designer to put desirable qualities of the later states directly into C0?  Why bank on stochastic processes that perhaps might not evolve an intended later stage?  It may very well be that C-T transitions coincide with certain evolutionary mutations.  So what?  This observation alone says nothing about ID, it seems, without doing some additional guesswork about the Designer's thinking.  But, ID has yet to offer us any evidence what the Designer cannot do or constraints on his designs.
Quote
http://www.idthink.net/biot/deam/index.html
I understand that Mike Gene is the IDer du jour, and so typically many IDers would naturally begin to parrot the latest ID scientist.  But in this case, I don't even think you took the time to read his essay carefully.
--------------------------------------------
edited to add citations for some articles (that are more recent than 1979) on helix-forming propensities from a quick Pubmed search:
Quote
Proteins 1999 Mar 1;34(4):497-507
 
Hydrogen bonds between short polar side chains and peptide backbone: prevalence in proteins and effects on helix-forming propensities.

Vijayakumar M, Qian H, Zhou HX.

Department of Physics and Atmospheric Science, Drexel University, Philadelphia, Pennsylvania 19104, USA.

A survey of 322 proteins showed that the short polar (SP) side chains of four residues, Thr, Ser, Asp, and Asn, have a very strong tendency to form hydrogen bonds with neighboring backbone amides. Specifically, 32% of Thr, 29% of Ser, 26% of Asp, and 19% of Asn engage in such hydrogen bonds. When an SP residue caps the N terminal of a helix, the contribution to helix stability by a hydrogen bond with the amide of the N3 or N2 residue is well established. When an SP residue is in the middle of a helix, the side chain is unlikely to form hydrogen bonds with neighboring backbone amides for steric and geometric reasons. In essence the SP side chain competes with the backbone carbonyl for the same hydrogen-bonding partner (i.e., the backbone amide) and thus SP residues tend to break backbone carbonyl-amide hydrogen bonds. The proposition that this is the origin for the low propensities of SP residues in the middle of alpha helices (relative to those of nonpolar residues) was tested. The combined effects of restricting side-chain rotamer conformations (documented by Creamer and Rose, Proc Acad Sci USA, 1992;89:5937-5941; Proteins, 1994;19:85-97) and excluding side- chain to backbone hydrogen bonds by the helix were quantitatively analyzed. These were found to correlate strongly with four experimentally determined scales of helix-forming propensities. The correlation coefficients ranged from 0.72 to 0.87, which are comparable to those found for nonpolar residues (for which only the loss of side-chain conformational entropy needs to be considered).

Quote
Proteins: Structure, Function, and Genetics
Volume 39, Issue 2, 2000. Pages: 132-141


The relative order of helical propensity of amino acids changes with solvent environment
Chartchai Krittanai, W. Curtis Johnson Jr

A model peptide of sequence Ac-Y-VAXAK-VAXAK-VAXAK-NH2, where X is substituted with one of nineteen amino acids (P excluded), was synthesized and titrated with methanol to study helical propensity as a function of solvent environment. The CD spectra of these peptides are largely random coil in 2 mM sodium phosphate buffer (pH 5.5) and show a conformational change to -helix with increasing methanol content. Singular value decomposition was used to correct the CD spectra for the absorbing side chains of W, Y, F, C, and M, and this correction can be substantial. With correction both W and F become good helix formers. The free energy for helix propagation was calculated using the Lifson-Roig statistical model for each of the nineteen amino acids at each point in their titration. The results show that the rank order of helical propensity for the nineteen amino acids changes with solvent environment. This result will be particularly important if proteins undergo hydrophobic collapse before secondary structures are formed, because amino acids can then see different solvent environments as the secondary structures are formed. Related amino acids are found to have interesting correlations in the shape of their titration curves. This finding provides one explanation for the limiting 70% accuracy in predicting secondary structure from sequence, since the helical propensities used are calculated for an average solvent environment.
[...]
Our absolute values of G0 for the propagation of a helix by a particular amino acid were calculated from the measurements by using the Lifson-Roig statistical model, which is two-state in residues. They can be compared with the results of Rohl et al.[33] and Yang et al. ,[37] which were calculated in the same way. The buffer systems were different among the three laboratories, as were the temperatures for the experimental measurements. Rohl et al. made their measurements at 0°C, Yang et al. at 4°C, while we made our measurements at 25°C. In aqueous solution, Rohl et al. find only one residue, A, that favors -helix formation (G0 less than -0.05). Yang et al. find two, A and E. We find seven: W, L, A, F, E, M, and D, with W and L better than A. Part of this difference is undoubtedly due to our correction for the CD of the aromatic side chains that reveals F and W as helix formers. It is possible that ion-ion interactions make D and E better helix formers for our host peptide but our analysis of the titration profiles above argues against this explanation. Rohl et al. find eight amino acids that are helix formers in 40% TFE: A, E, I, K, L, M, Q, and R, although they did not include the aromatic amino acids in these measurements. In 88% methanol we find only four amino acids that are not helix formers: C, D, G, and Y. Clearly solvent environment is important in determining the helical propensity of the amino acids. In 40% TFE Rohl et al. still find A to be the best helix former, but in 88% methanol we find ten amino acids that exceed A in their helix forming ability: W, F, I, Q. R, E, L, K, M and V. Rohl et al. find five amino acids that are significant helix breakers (G0 greater than 0.20) in 40% TFE: S, H, C, D, and G. We find only one in 88% methanol, G.

Quote
J Mol Biol 1998 Apr 24;278(1):279-89
Position dependence of non-polar amino acid intrinsic helical propensities.

Petukhov M, Munoz V, Yumoto N, Yoshikawa S, Serrano L.

European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, D-69012, Germany.

Until now and based on the success of the helix/coil transition theory it has been assumed that the alpha-helical propensities of the amino acids are position independent. This has been critical to derive the set of theoretical parameters for the 20 natural amino acids. Here, we have analyzed the behavior of several non-polar residues, Val, Ile, Leu, Met and Gly at the N-cap, at each position of the first helical turn and at a central helical position of a 16-residue peptide model system that starts with eight consecutive alanine residues. We have interpreted the results from these experiments with the model of the helix/coil transition (AGADIR), that indicates that the intrinsic helical propensity is position dependent. Gly, Val and Ile are more favorable at the first turn than in the middle of the alpha-helix, while for Leu and Met we observe the opposite behavior. The differences between the observed helical propensities are as large as 1.0 kcal/mol in some cases. Molecular modeling calculations using the ECEPP/2 force-field equipped with a hydration potential show that this effect can be explained by the combination of three factors: (a) the side-chains in the first helix turn are more solvent-exposed; (b) they have fewer intramolecular van der Waals' contacts; and ( c) they posses higher configurational entropy than that in the central position of an alpha-helix. The position-dependent results of the calculations are in reasonable agreement with the experimental estimates and with the intrinsic propensities of the amino acids derived from the statistical analysis of the protein structure database.
Quote
Fold Des 1998;3(2):119-26
Tolerance of a protein helix to multiple alanine and valine substitutions.

Gregoret LM, Sauer RT.

BACKGROUND: Protein stability is influenced by the intrinsic secondary structure propensities of the amino acids and by tertiary interactions, but which of these factors dominates is not known in most cases. We have used combinatorial mutagenesis to examine the effects of substituting a good helix-forming residue (alanine) and a poor helix-forming residue (valine) at many positions in an alpha helix of a native protein. This has allowed us to average over many molecular environments and assess to what extent the results reflect intrinsic helical propensities or are masked by tertiary effects. RESULTS: Alanine or valine residues were combinatorially substituted at 12 positions in alpha-helix lambda repressor. Functional proteins were selected and sequenced to determine the degree to which each residue type was tolerated. On average, valine substitutions were accommodated slightly less well than alanine substitutions. On a positional basis, however, valine was tolerated as well as alanine at the majority of sites. In fact, alanine was preferred over valine statistically significantly only at four sites. Studies of mutant protein and peptide stabilities suggest that tertiary interactions mask the intrinsic secondary structure propensity differences at most of the remaining residue positions in this alpha helix. CONCLUSIONS: At the majority of positions in alpha-helix lambda repressor, tertiary interactions with other parts of the protein can be viewed as an environmental "buffer" that help to diminish the helix destabilizing effects of valine mutations and allow these mutations to be tolerated at frequencies similar to alanine mutations.

And here is one on beta sheet propensities:
Quote
Proc Natl Acad Sci U S A 1999 Aug 3;96(16):9074-6
 
Intrinsic beta-sheet propensities result from van der Waals interactions between side chains and the local backbone.

Street AG, Mayo SL.

Division of Physics, Mathematics, and Astronomy, California Institute of Technology, MC 147-75, Pasadena, CA 91125, USA.

The intrinsic secondary structure-forming propensities of the naturally occurring amino acids have been measured both experimentally in host-guest studies and statistically by examination of the protein structure databank. There has been significant progress in understanding the origins of intrinsic alpha-helical propensities, but a unifying theme for understanding intrinsic beta-sheet propensities has remained elusive. To this end, we modeled dipeptides by using a van der Waals energy function and derived Ramachandran plots for each of the amino acids. These data were used to determine the entropy and Helmholtz free energy of placing each amino acid in the beta-sheet region of phi-psi space. We quantitatively establish that the dominant cause of intrinsic beta-sheet propensity is the avoidance of steric clashes between an amino acid side chain and its local backbone. Standard implementations of coulombic and solvation effects are seen to be less important.
 I will add more recent research if the discussion deems it necessary.

  
Art



Posts: 69
Joined: Dec. 2002

(Permalink) Posted: Jan. 09 2003,21:29   

Hi Nelson (and everyone else, for that matter),

Regarding the IHE, here are a few more quotes and abstracts to help maintain perspective.  The first two are from the ISCID thread (thanks, JxD, for mentioning my later post), and the latter are abstracts of papers that Mike Gene cites as supportive of his thesis.

Quote
Another quote that may be relevant: (from Maki, Ann.l Rev. Genet. 36, 279-303, 2002):

“The nature of native replication errors caused solely by action of the replicative apparatus has been extensively characterized, whereas less is known about spontaneous DNA lesion that potentially induces spontaneous mutations (24). Active oxygen species are produced in aerobically growing cells and attack DNA to produce a wide range of lesions. An estimated 3000–5000 oxidative DNA lesions/cell/generation are produced in cells of E. coli under normal aerobic growth conditions (78). Free nucleotides are attacked more efficiently by oxygen radicals than DNA, and in a number of different species, oxidized nucleotides are produced in the cellular nucleotide pool. Among them, 8-oxodGTP (58) and 2-OHdATP (37) possess extraordinarily strong mutagenicity. Considering their high production rate, these mutagenic compounds are potentially the most powerful source of spontaneous mutations. Methylation and hydrolytic decomposition of DNA such as depurination and cytosine deamination cause a variety of endogenous DNA lesions (24). However, the spontaneous frequency of these events is estimated to be much lower than that for the oxidation of DNA.”


Quote
Perhaps another relevant study:

J Bacteriol 2002 Dec;184(24):6866-72
Transcription-dependent increase in multiple classes of base substitution mutations in Escherichia coli.
Klapacz J, Bhagwat AS.
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
We showed previously that transcription in Escherichia coli promotes C. G-to-T. A transitions due to increased deamination of cytosines to uracils in the nontranscribed but not the transcribed strand (A. Beletskii and A. S. Bhagwat, Proc. Natl. Acad. Sci. USA 93:13919-13924, 1996). To study mutations other than that of C to T, we developed a new genetic assay that selects only base substitution mutations and additionally excludes C. G to T. A transitions. This novel genetic reversion system is based on mutations in a termination codon and involves positive selection for resistance to bleomycin or kanamycin. Using this genetic system, we show here that transcription from a strong promoter increases the level of non-C-to-T as well as C-to-T mutations. We find that high-level transcription increases the level of non-C-to-T mutations in DNA repair-proficient cells in three different sequence contexts in two genes and that the rate of mutation is higher by a factor of 2 to 4 under these conditions. These increases are not caused by a growth advantage for the revertants and are restricted to genes that are induced for transcription. In particular, high levels of transcription do not create a general mutator phenotype in E. coli. Sequence analysis of the revertants revealed that the frequency of several different base substitutions increased upon transcription of the bleomycin resistance gene and that G. C-to-T. A transversions dominated the spectrum in cells transcribing the gene. These results suggest that high levels of transcription promote many different spontaneous base substitutions in E. coli.


The abstract from reference 6 of Mike Gene's paper (the bolded statements highlight results that indicate that the support for IHE is not so strong as suggested by Mike Gene):

Quote
Proc Natl Acad Sci U S A 1988 May;85(10):3499-503

Spectrum of spontaneous mutation at the APRT locus of Chinese hamster ovary cells: an analysis at the DNA sequence level.

de Jong PJ, Grosovsky AJ, Glickman BW.

York University, Department of Biology, North York, ON, Canada.

The spectrum of spontaneous mutation of an endogenous mammalian cell gene has been determined at the DNA sequence level. Thirty independent spontaneous APRT- mutations were cloned and subsequently completely sequenced. Twenty-seven contained single base substitutions. Of these, 22 were G.C to A.T transitions, suggesting a major role for the deamination of cytosine in spontaneous mutagenesis of Chinese hamster ovary cells. The remaining mutants included a tandem double substitution, a -1 frameshift, and a 17-base-pair deletion flanked by a 2-base-pair direct repeat. Many of the independently recovered mutants were clustered at sites of multiple occurrence (hot spots). One site accounted for greater than 25% of all independently recovered events. Mutations were generally located within the coding sequence, although two mutations occurred within the consensus sequence for a 3' splice site.


Finally, the abstract for reference 7.  IMO, the support that one may see for IHE in this study is questionable.

Quote

Mutat Res 1990 Jan;243(1):21-8

Specificity of spontaneous mutation in the lacI gene cloned into bacteriophage M13.

Yatagai F, Glickman BW.

Radiation Biology Laboratory, Institute of Physical and Chemical Research, Saitama, Japan.

We have studied the specificity of spontaneous mutation in the lacI gene of Escherichia coli cloned into bacteriophage M13. The comparison of the spectrum of 85 spontaneous mutations with that of the lacI gene carried on an E. coli F' episone revealed the following characteristics: (i) base substitution was predominant, accounting for 80% of spontaneous events compared with only 11% on the F' episome; (ii) among the base substitutions, the majority were G:C----A:T transitions (86%); (iii) not one mutation recovered on M13 corresponded to a mutation at the spontaneous hotspots seen in the F' spectrum (i.e., neither the addition or deletion of the tetramer 5'-CTGG-3' at position 620-631 nor the A:T----G:C transition at position +6 of lacO were recovered). The enhanced rate of cytosine deamination in single-stranded DNA, the unique replication mechanism and the refractory nature of single-stranded DNA to excision-repair processes present likely explanations for the observed mutational spectrum.

   
nanosoliton



Posts: 11
Joined: Jan. 2003

(Permalink) Posted: Jan. 12 2003,20:44   

Hi everyone, thanks for the welcome. Forgive me for the delay in responding, I have been having trouble getting online lately. I hope the moderator doesn't mind me making seperate posts for each reply, it does look a little spammy, so I'll try to reply to a couple of people in a post at a time. My first post here has little to do with the cytosine deamination issue and the evidence pertaining to it. However, this is only because I want to respond chronologically, with a full response to Wesley's post, and this may take me some time. Art's post is last chronologically, so my last post will pertain directly to the evidence for Mike's hypothesis.

Nic and Wesley,

Frances has been arguing at the ISCID board for some time now that Mike's conclusion is essentially the same as Poole's. Now, it is my opinion that the majority in this thread disagree with this notion. If so, why hasn't anyone corrected him? For example, Nic quotes:

Quote

The first step was probably very complex, and has recently been reviewed elsewhere2, 5. Here we look at the second (UT) replacement, which is emerging as another example of why evolution is best viewed as a tinkerer, not as an engineer with an eye for 'good' design


However, Mike's observation is that this is not an example of evolution "best viewed as a tinkerer", rather, Mike's observation is that this consitutes good evidence for  efficient intelligent engineering. If this is the same as a non-teleological perspective I cannot fathom why. However, this is not "anti-evolutionist" as it does propose a mechanism of evolution. Which brings me to Wesley's point:

Quote

The buzz-phrase "evidence against evolution" is often deployed by ID advocates. That ID advocates may not reject every observation, hypothesis, or theory found in evolutionary biology doesn't mean that the ID movement is not antievolutionary. Even the Institute for Creation Research accepts some instances of the action of natural selection occurring, which hardly means that the ICR is not antievolutionary.


If teleology can be employed in evolutionary thinking this makes the inner workings of evolution and evolutionary mechanisms quite different. I agree that the blind watchmaker mechanism for evolution is clearly argued against in most ID literature, however, it is my contention that BWM thinking has largley hijacked the evidence for evolution and that pointing this out is not necessarily "anti-evolution", in fact, it can be argued that this is very pro-evolution. Your links don't really contradict this merging of evolutionary thinking and intelligent design:

Ohioans Don't Want Evolution Only:

This link talks about the controversy surrounding the Ohio school board decision. I cannot fathom why critics of this move do not want evidence for and against Darwinian evolution.


Evidence Against Evolution:

This is a link to an article by Absolute Truth Ministries. I do not see the relevance of it, and worse, it makes the mistake of making an argument from impossibility, something that the author of irreducible complexity himself, Michael Behe, does not argue.

Can Neo-Darwinism Survive?:

This is a link to apologetics article as well,  however, the title correctly points out that what IDist argue against is not evolution per se, but it's mechanism.

Columbus Dispatch is Blind to the Arguments and Evidence Against Evolutionism:

It is very misleading to link to this. This is clearly a creationist article which mentions evidence from Mt St. Helens, etc. ID theory as currently espoused does not entail a young earth or young earth evidence. The next couple of links also fall under the same category.

Philip Johnson is indeed very critical of evolution, however, but I think he also focuses on mechanism.  ID theory itself is not necessarily based on a rejection of common descent and can actually be quite comparable with it.

Critics: No science in intelligent design:

This article makes quite a few mistakes:

Quote

Supporters of intelligent design contend Earth's abundance of wildly differing flora and fauna is too complex to have evolved from a shared ancestor in the primordial ooze.


As I have stated, many ID advocates, like myself, accept common descent of said flora and fauna, however, they reject the mechanism by which this evolution could have occured.

Remarks to the Kansas State Board of Education:

The so called "icons of evolution" discussed here is a good discussion of where evolutionary theory has gone astray with outdated information in the textbooks. Isn't this good?

Skepticism's Prospects for Unseating Intelligent Design:

This is a good article about what intelligent design is and does, and why it rejects the Darwinian mechanism. I have no idea what relevance this has to your point.

Evolution FAQ:

This is a good FAQ about the sterility of the Darwinian mechanism to account for evolution.


"So What Evidence IS There Against Evolution?":

Many IDist don't have a problem with monophyletic origin of organisms.


No Admittance:

I have no idea why you linked me to this article.


The same criticism can account for the rest of the links, although I wouldn't mind discussing the rest if you guys disagree.

Wesley said:
This thread would be a suitable place to collect more instances of ID advocate use of the concept of "evidence against evolution".

Nelson:
I agree. Here is my contribution to the contrary point:

ID as a mechanism for evolution:

http://www.idthink.net

Here are articles that discuss:
A Teleological Hypothesis Regarding the Degradosome Machine

Reviewing Simon Conway Morris' Ideas in Relation to Front-Loaded Evolution

New Views on Evolution

The Universal Genetic Code

Designing Evolution Through Deamination Part 1 and 2

Also from the Discovery Institute:

Intelligent Design and Creationism just aren't the same:

http://www.discovery.org/viewDB....id=1329

Intelligent Design can offer Fresh Ideas on Evolution:

http://www.discovery.org/viewDB....id=1313

Intelligent Design is not Creationism:

http://www.discovery.org/viewDB....&id=286

Shapiro's thoughts on evolution:

http://bmb.bsd.uchicago.edu/jShapiro.html

Stanely Salthe:

http://www.nbi.dk/~natphil/salthe/

--------------
Nelson Alonso

  
Wesley R. Elsberry



Posts: 4807
Joined: May 2002

(Permalink) Posted: Jan. 12 2003,22:56   

Nelson,

You appear to be making an "argument from restricted connotation".  Your connotations of "intelligent design" and "antievolution" do not count as universally or even widely acceded.

I think that it is clear that ID advocates -- and this category is inclusive of many holding a young-earth creationist view -- often urge consideration of "evidence against evolution".  The plain import is that these people take an antievolutionist stance.

Having taken pains to urge ID as a "big tent" idea, ID advocates cannot simply dismiss those of their ranks who hold to a YEC stance, or repudiate their use of ID rhetoric and arguments.  Those YEC advocates of ID are just as much part of the movement as those who are OEC or partial accommodationist.

As for the link to the description of the Rodney LeVake case, Nelson may not recognize why the link is relevant, but others will easily see that LeVake is an ID advocate who espouses the "evidence against evolution" strategy of antievolutionary activism.

I have no idea why ID should be urged by Nelson as a "mechanism" of evolution, when we have a proclamation by no less an authority than William Dembski that ID is not that kind of theory.

As noted before, ID advocates seem to tell us, "ID is what we say it is, and we don't agree."

Wesley

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
nanosoliton



Posts: 11
Joined: Jan. 2003

(Permalink) Posted: Jan. 12 2003,23:15   

This is my last post for the night. See you all tomorrow.

Wesley:
You appear to be making an "argument from restricted connotation".  Your connotations of "intelligent design" and "antievolution" do not count as universally or even widely acceded.

Nelson:
Even if this is true, it is quite irrelevant. If I can function well, and even contribute to, Intelligent Design using these connotations, and even if I am the only one, then I have essentially refuted the idea that intelligent design is necessarily antievolutionist.

Wesley:
I think that it is clear that ID advocates -- and this category is inclusive of many holding a young-earth creationist view -- often urge consideration of "evidence against evolution".  The plain import is that these people take an antievolutionist stance.

Nelson:
Again, I think that ID, even if the IDer is a YEC, usually addresses the mechanism of evolution. Even Paul Nelson, a YEC, has stated this. Most YEC clothes are removed when they enter into a particular ID field. No evidence for a young earth, or for the inspiration of the Bible, can be found in any ID literature. If YECs can co-exist with evolutionists like Behe et. al. , then why call ID as a whole antievolutionist? Why not address specifically which antievolutionist within ID is urking you?


Wesley:
Having taken pains to urge ID as a "big tent" idea, ID advocates cannot simply dismiss those of their ranks who hold to a YEC stance, or repudiate their use of ID rhetoric and arguments.  Those YEC advocates of ID are just as much part of the movement as those who are OEC or partial accommodationist.

Nelson:
And the evolutionists and atheists within ID are just as much part of ID as the YECs and OECs are. So what?

Wesley:
As for the link to the description of the Rodney LeVake case, Nelson may not recognize why the link is relevant, but others will easily see that LeVake is an ID advocate who espouses the "evidence against evolution" strategy of antievolutionary activism.

Nelson:
The link to Mike Gene's "front-loading" evolution will see that Gene is an ID advocate who espouses ID as a mechanism for evolution and does not flat out reject evolution as YECs do.

Wesley:
I have no idea why ID should be urged by Nelson as a "mechanism" of evolution, when we have a proclamation by no less an authority than William Dembski that ID is not that kind of theory.

Nelson:

William Dembski has stated:

Quote

To be sure, mechanisms can be programmed by an intelligence. But any such intelligent programming of evolutionary mechanisms is not properly part of evolutionary biology.

Intelligent design, by contrast, teaches that biological complexity is not exclusively the result of material mechanisms but also requires intelligence, where the intelligence in question is not reducible to such mechanisms. The central issue, therefore, is not the relatedness of all organisms, or what typically is called common descent. Indeed, intelligent design is perfectly compatible with common descent. Rather, the central issue is how biological complexity emerged and whether intelligence played a pivotal role in its emergence.


In fact, this is exactly what I have in mind when I say ID is not necessarily anti-evolutionist.


Wesley:
As noted before, ID advocates seem to tell us, "ID is what we say it is, and we don't agree."

Nelson:
I think that ID is quite simply design detection within Biology. All IDers agree with this.  I think that even YECs realize, (or at least they should)  that philosophical baggage inherent in their, or anyone else's, pressuppositions must be abandoned for the sake of finding the empirical truth of intelligent design, even if this means "re-taking" evolution from BWM advocates.

--------------
Nelson Alonso

  
nanosoliton



Posts: 11
Joined: Jan. 2003

(Permalink) Posted: Jan. 14 2003,22:58   

The:
*sigh*  IDists argue both against the mechanism of evolution and the *fact* of evolution.

Nelson:
What "fact" of evolution are you referring to? Common descent is not a "fact" by any means.

The:
The movement as a whole does NOT limit itself to the first.  Now you and a number of other IDists may not have a problem with evolution, but a large number of people who call themselves IDists, including members of the national political movement, argue strongly against the idea that evolution happened at all.  The point is that you can't claim that ID isn't antievolutionary.  For many people, including prominent leaders of the movment, this is precisely what it is.  

Nelson
Actually, prominent leaders of the movement, in fact, leaders of the ID movement, such as Dembski and Behe, state that ID and common descent are compatible. So I indeed can claim that ID is not necessarily antievolutionary.

The:
Wesley is pointing out something far more significant:  YECs are a prominent part of the ID movement.  

Nelson:
As I stated, most YEC clothing comes off when they enter into a particular ID field. Young earth arguments are simply not a  part of ID.

The:
The Raelians agree with intelligent design too, but they are not part of the movement, and hence one cannot gauge what ID is or isn't merely according to what they think.  

Nelson:
Sure you can. Show me an atheist that agrees with YEC tenets.

The:
(But the fact that people with an almost diametrically opposite view of morality can call themselves IDists just shows how utterly useless ID is for causing "cultural renewal".)  

Nelson:
The reason why is quite simple. ID is simply design detection and not a moral compass. A murderer who agrees with intelligent design doesn't show that ID is an utterly "useless" cultural device, the reason is that it is not a cultural device.




The:
Yes, but I pointed out that how one goes about "detecting" design has everything to do with the facts of nature one accepts.  Many prominent IDists, like Philip Johnson for example, argue that we detect ID because evolution could not have occured.  

Nelson:
Reference? Please quote Philip Johnson saying that we detect ID because evolution could not have occured.


The:
No he doesn't.  ID simply says nothing about the age of the Earth.  He can leave the hat on; there is nothing contradictory about a young earth and ID.

Nelson:
No, which is why a YEC can be an IDer. However, that being an IDer does not entail a young earth, this point seems moot.

The:
Rubish.  The ID movement does not recognize any ID hypotheses, instead preferring to take the route that doing so is not relevant to ID, since all they're doing is "detecting design".  

Nelson:
Where do you get this from? In fact, there are many testable ID hypothesis, such as the one I brought up in this very thread.

The:
And aside from a few rare exceptions, I have not seen any IDists put forth any hypothesis about anytyhing.  The closest thing is Mike Gene's frontloading, which aside from being excessively ad hoc, is also lacking in detail to the point of being useless scientifically.  

Nelson:
Mike's hypothesis is certainly not lacking in detail, in fact it is quite detailed. For example, that multicellular life was evolved through unicellular life. It even offers a testable prediction, that genes, for example, essential in higher organisms would be found in primitive organs functioning in a non essential role. Or the C-T transition were incorporated by the designer to faciliate protein evolution. Many IDers also hold to the hypothesis that intelligent design occured at the origin of life. That the first cell was intelligently designed , followed by evolution thereafter. Many IDers put forth hypothesis about a lot of things.


The:
You're right that it's not inconsisten in its attribute of design detecton.  But it is inconsistent in what the members of the movement cite as evidence for ID.  "Evidence against evolution" can't be evidence for ID as well as front-loaded evolution.  At least one of them has to be wrong.

Nelson:
The "evidence against evolution" you refer to is evidence against the mechanism of evolution, namely a blind watchmaker. All IDers argue that the blind watchmaker mechanism is insufficient.


The:
Why don't IDists do that for us?

Nelson:
You should be responsible for your own muddling of the facts.

The:
It's not my fault that these mutually exclusive ideas are all part of the same movment.

Nelson:
The ideas central to the movement is that design in biology is real and detectable.

The:
It would make more sense to me if these people would quit calling themselves IDists and instead call themselves something that actually describes their scientific beliefs.  For example, YEC, OEC, frontloader, alien seeder,etc.  The only thing that these viewpoints have in common is a metaphysical belief in "design".  They are not compatible scientifically.  

Nelson:
How is design a metaphysical belief? If Behe can work with a YECer on the irreducible complexity of the flagellum and put forward a picture of the first originally designed state, then ID as a "movement" turns into a scientific research program.

The:
Nelson, you're missing the point.  IDists do argue against the mechanism of evolution.  But they also argue against the fact of evolution.

Nelson:
There you go again with this fact. What fact of evolution are you talking about?

The:
What is a causual observer supposed to think about this?  

Nelson:
That ID has an empirical methodology that can detect design.

The:
That ID is or isn't antievolutionary?  The claim that ID isn't necessarily antievolutionary is only correct because it isn't necessarily anything.

Nelson:
Sure it is, it is an empirical design detector. You see? Everytime you say ID is nothing it is easily refuted by this simple fact. Check out "No Free Lunch" by William Dembski, you'll see what I mean.

The:
Absolutely any view of natural history conceivable is compatible with ID.  What makes someone an IDist is that they think that somewhere natural processes couldn't have been responsible for life.  For many people who call themselves IDists, this "somewhere" is the common descent of species.  


Nelson:
No, any view of natural history is not compatible with ID. All IDers disagree that life evolved through chance mutations and selection alone.


The:
It's not irrelevant to the fact that the ID movement does not take a stance on the age of the Earth.  You might take a stance on this, but the ID movement as a whole is too cowardly to state specifically how old the Earth is, as well as whether or not organisms have shared ancestry.  My point stands:  ID is not evolutionary or antievolutionary, it is not old Earth or young Earth, it is a hodge-podge of anti-naturalist rants that are frequenly in contradiction.

Nelson:
IDers do take a stance on the age of the earth. I think the earth is 4.6 billion years old, so does Behe, so does Dembski, so does Johnson. The reason why ID as a whole does not exclude those who say otherwise is that it is simply concerned with design detection, at least at this point.

I could see a day when ID becomes a unified theory of life on earth, but that day cannot come until it has gained some maturity, then maybe you'll see some exclusion.

theyeti:
I have read where both Philip Johnson and Jonathan Wells have stated that they're "skeptical" of the standard age of the Earth because they've become so cynical of the scientific community. This is clearly a rhetorical bone for the YECs -- the movement does everything it can to keep them hanging on.

Nelson:
This is false. In reply to Dawkins' question in this matter, Philip Johnson replied

The:
Nelson, that article by Johnson proves my point exactly.

Nelson:
No Theyeti, that article completely , and directly, contradicts your point exactly. You stated that you thought Philip Johnson was skeptical of the young earth, when in fact, Philip Johnson stated:

Quote

Do you think the age of our planet is closer to 4000 million years or closer to 100,000 years? The former, but with the caveat that I have made no effort to investigate the subject personally and am merely accepting the current scientific consensus.


So Philip Johnson accepts the current scientific consensus that the earth is closer to 4000 million years old.

The:
Here's the very next sentence that you left out for some reason:  

Nelson:
No actually I didn't leave anything out. In fact, I anticipated your reply by saying:

Quote

. He says he would "have more confidence" in geologists if not for their philosophical assumptions, but he certainly does not hold to a young earth.  


You then move the goal posts by saying:

"Notice how he leaves himself an obvious escape hatch?"

How in the heck is this an escape hatch? The man is obviously telling you how he feels about the issue.

The:
 He does not claim that the evidence shows that the Earth is old; rather he says that he hasn't investigated it and that it's irrelevant and furthermore that he's so cynical of the scientific community that he's reluctant to believe anything we say.  Which proves my point exactly.

Nelson:
No he says that he accepts the scientific consensus but would have more confidence in scientists if they wouldn't hold to philosophical assumptions. This is completely different from saying that he is skeptical of the age of the earth, which contradicts your point.


The:
Nonsense Nelson.  You can't tell what he adheres to from that statement, which is exactly how he wants it.

Nelson:
Sure you can, here is the quote again:

Quote

Do you think the age of our planet is closer to 4000 million years or closer to 100,000 years? The former,



The:
That's the whole point -- he highly circumspect about what he believes.  He won't defend a young Earth and Noah's flood and the like, but he won't repudiate it either.  If you can find where he does, I'll eat my hat.  Personally, I think Johnson is probably a YEC.

Nelson:
How many YECs would tell Dawkins that they accept the current scientific  consensus concerning the age of the earth?

The:
The fact that the movment won't take a stance on the age of the Earth is primary justification.

Nelson:
That YECs can be IDers is simply due to the fact that ID is an empirical methodology that detects design in Biology. The accusation that IDers somehow have a mental connection with YECs that keeps them "hanging on" is moronic.



The:
It means that the ID movement avoids criticizing even the most egregious claims of the YECs.  It means that it doesn't take a stance on the age of the Earth or Noah's flood in order to avoid alientating the YECs, who make up probably more than half of the movement.  

Nelson:
Why would they? The truth or falsehood of any Biblical narrative does not entail the truth of ID.


The:
What purpose do you think?  Do I really have to explain the political utility to you?

Nelson:
Yes, since it is obvious you have a pre-canned ad hominem argument barracading any kind of good point IDers try to make.

The:
Michael Behe is only one individual.  As far as I know, he is the only prominent IDist to take a stance on the common ancestry of organisms.  

Nelson:
There are only a hand-ful of prominent IDers, which is why I only named one. However, I am part of a large group of IDers that accepts common descent and takes a stance on it.

The:
Moreover, he's not even consistent about it.  He heaps all sorts of praise on antievolutionists like Jonathan Wells

Nelson:
Errors in textbooks that Wells points out doesn't say anything about why Behe believes in common descent.

The:
and Walter ReMine.  

Nelson:
Behe's praise for ReMine is this:

Quote

I myself was floored by his discussion showing that the sickle cell gene actively works through natural selection to exclude a more efficient mutant, HbC from gaining a foothold in malaria-prone populations


So, how is Michael Behe inconsistent?

The:
The point is that the movement, as a whole, does not claim that orgainisms have shared ancestry.  How else could Behe coexist with Johnson, who is an antievolutionist, and Paul Nelson, who's a YEC?

Nelson:
Because they all agree that there is intelligent design. What you don't understand, accentuated by the fact that you think common descent is a fact, is that science is tentative, and it is quite wise to be skeptical and cautious in our theories, even if it's the age of the earth.

The:
Nelson, this is getting old.  The ID movement does both.  They argue against common descent and they argue that it's an irrelevant issue.  Often times, it's different people arguing each, but this doesn't change the fact that they're all in the same Big Tent, all suggesting that they all follow the same "scientific theory".  Your complaints about people seeing the ID movement as antievolutionary are unfounded -- people see it that way because it often is that way.  Except for when its not.  It's inconsistent and ad hoc, simply redefining itself whenever it's advantageous.    

Nelson:
Again, ID is simply design detection. Some do argue against CD, some don't. However, the fact that CD is compatible with ID, shows that it is not necessarily antievolution.

Quote  
So which is it? Do IDers argue against common descent or do they shrug it off?  


THEY ARGUE BOTH!  THEY ARE INCONSISTENT!  Why can you not understand this simple point?

Nelson:
Your problem is that you can't get your creationist arguments out of your head. So you see ID as simply antievolution, you cannot fathom it any other way. So when I show you someone who believs in common descent, you try desperately try to pooh pooh it, like you tried above with Behe and failed. You see, even if one IDer agrees with common descent, then antievolutionist is simply not an accurate phrase for ID. And again, ID is not inconsistent about it's central tenet, namely , that intelligent design exists and can be detected.


The:
But the issue remains, how does one detect design?  The way that IDists go about claiming evidence for design is not consistent.

Nelson:
Actually it is, they detect it through the use of specified complexity criteria.

Quote  
theyeti:

[i]Again, I'm not sure who has stated that ID as a whole is specifically antievolutionist. The correct answer IMO is that it's neither evolutionist nor antievolutionist. It's also neither old-Earth or young-Earth. It simply doesn't take a positive stance on any issue, other than the metaphysical notion that life exhibits design, and that there is somehow empirical evidence of this. But many IDists utilize antievolutionary arguments and call this evidence for ID, so if many people are under the impression that ID is indeed antievolutionary, you have only other IDists to blame.

No, ID takes a positive stance in a non-metaphysical notion, that if intelligent design exists in Biology, it can be detected.


It's hard to find how your statement was relevant to mine.  The idea that life or the universe is designed is a metaphysical notion, but evidence per se is not.  Metaphysics comes into it when one has to define exactly what one means by design.  Given a good non-question-begging defintion, I could say, without metaphysical assumptions, whether the evidence says, "yes", "no", or "we can't tell".  Here's the kicker, something that I've had to repeat numerous times now:  The ID movment will not define what it means by design.  

Nelson:
You must not be familiar with intelligent design literature, which explains why you are making so many mistakes with it as a whole. Intelligent Design in biological systems can be labeled as such when it exhibits specified complexity. It is quite simple actually.

Nelson:
All IDers agree with this. This is a positive, empirical stance. What data would you accept as evidence for intelligent design?

The:
Which of the billions of mutually exclusive ideas of "intelligent design" are you referring to?  The one that says that living organisms don't share common ancestry, or the one that claims front-loading?  Which kind of front-loading?  Unless you are specific about what happened when and how and by whom, then all you're asking for is evidence for a metaphysical notion, and physical evidence cannot be applied to such things.

Nelson:
My question is quite simple, and if you cannot answer it then you are unqualified to say whether there is evidence of ID, or if ID is a valid scientific hypothesis. In fact, you cannot even speak of evolution if you cannot distinguish design from apparent design.

So again, what would you cause you to infer design behind some biological system?

--------------
Nelson Alonso

  
ExYECer



Posts: 36
Joined: May 2002

(Permalink) Posted: Jan. 15 2003,11:34   

Hi Nelson

I notice you seem to have abandoned our front loading discussions?

Oh well, lets see what else we can talk about

Nelson:
What "fact" of evolution are you referring to? Common descent is not a "fact" by any means.

Please explain because given the available data common descent is quite strongly supported by the data. The root of the tree may be quite difficult to determine but there are hundreds of millions of years of evidence of common descent out there. Perhaps you can explain to us, perhaps even in your own words, why you object to common descent as a fact?

Nelson in response to: Many prominent IDists, like Philip Johnson for example, argue that we detect ID because evolution could not have occured.  

Nelson:
Reference? Please quote Philip Johnson saying that we detect ID because evolution could not have occured.

ID is simply detected through elimination of chance and regularity. Hence ID has no positive approach to detection but merely relies on elimination.


Nelson:
Mike's hypothesis is certainly not lacking in detail, in fact it is quite detailed. For example, that multicellular life was evolved through unicellular life. It even offers a testable prediction, that genes, for example, essential in higher organisms would be found in primitive organs functioning in a non essential role. Or the C-T transition were incorporated by the designer to faciliate protein evolution. Many IDers also hold to the hypothesis that intelligent design occured at the origin of life. That the first cell was intelligently designed , followed by evolution thereafter. Many IDers put forth hypothesis about a lot of things.


That's also known as painting the bulls eye around the arrow. That many IDers put forth hypotheses has nothing to do with the lack of predictive power of ID. We have been discussing front loading with you, although you seemed to have become a bit shy on that topic.
Mike's 'predictions' are meaningless if he cannot explain the motives of a designer, the limitations of a designer, the moment of the design and when natural forces can explain the observations much better and in much less ad hoc fashion than ID. Front loading as I have shown has nothing to add to science by presuming without evidence that there was ID involved.

Nelson:
That ID has an empirical methodology that can detect design.

Interesting and can it detect intelligent design from non intelligent design? Of course not. ID's methodology is inherently flawed as has been shown now by a large number of scientists. ID's methodology is even flawed from the perspective of philosophy since it cannot separate front loading from intervention and thus can not claim to be a replacement for methodological naturalism.

Nelson:
Sure it is, it is an empirical design detector. You see? Everytime you say ID is nothing it is easily refuted by this simple fact. Check out "No Free Lunch" by William Dembski, you'll see what I mean.

Enlighten us since I have checked it out, and read it btw, and I fail to see that ID is something. Any particular items you would like to discuss in detail rather than glancing over them?

Nelson:
My question is quite simple, and if you cannot answer it then you are unqualified to say whether there is evidence of ID, or if ID is a valid scientific hypothesis. In fact, you cannot even speak of evolution if you cannot distinguish design from apparent design. So again, what would you cause you to infer design behind some biological system?

Are you qualified to speak about the eyes of a lobster since you seem to be unfamiliar with the primary research Nelson? But lets address your question.

First of all whether or not ID can ever become able to distinguish itself from purely natural methods does not mean that we cannot show that life on earth evolved. We are now talking about the observations and trying to explain the mechanisms. But ID has no mechanisms while science does provide mechanisms to explain the observations in a non ad hoc manner.

What would you cause to infer design behind some biological system?

I addressed a similar question by Mike Gene

Quote

Mike wants to know what data would cause me to suspect that evolution was front loaded. This would require the following 1. Mike needs to define what the purpose or goal(s) are of the intelligent agent 2. Mike has to show that given the chaotic and unpredictable nature of the world around us, this goal can be reliably reached 3. it can be shown that natural processes without intelligent design could not have achieved the state at t=t_0 4. it can be shown that there was indeed an intelligent agent present at t=t_0.


What would Nelson lead to infer design ?

  
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