Intelligent Design is NOT Creation[ism]

I'm sorry, you misunderstood. I asked you where I had said that the eukaryotic/prokaryotic "transformation" was specifically and soley due to RM and NS. Well, the observation of endosymbiosis, for one thing:

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GroEL and the maintenance of bacterial endosymbiosis.

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Fares MA, Moya A, Barrio E.

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Molecular Evolution and Bioinformatics Laboratory, Biology Department, National University of Ireland, Maynooth, Co. Kildare, Ireland.

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Many eukaryotic organisms have symbiotic associations with obligate intracellular bacteria. The clonal transmission of endosymbionts between host generations should lead to the irreversible fixation of slightly deleterious mutations in their non-recombinant genome by genetic drift. However, the stability of endosymbiosis indicates that some mechanism is involved in the amelioration of the effects of these mutations. We propose that the chaperone GroEL was involved in the acquisition of an endosymbiotic lifestyle not only by means of its over-production, as proposed by Moran, but also by its adaptive evolution mediated by positive selection to improve the interaction with the unstable endosymbiont proteome.

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Comparative gene expression in the symbiotic and aposymbiotic Aiptasia pulchella by expressed sequence tag analysis.

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Kuo J, Chen MC, Lin CH, Fang LS.

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Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung 944, Taiwan, ROC.

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Intracellular symbiotic relationships are prevalent between cnidarians, such as corals and sea anemones, and the photosynthetic dinoflagellate symbionts. However, there is little understanding about how the genes express when the symbiotic relationship is set up. To characterize genes involved in this association, the endosymbiosis between sea anemone, Aiptasia pulchella, and dinoflagellate zooxanthellae, Symbiodinium spp., was employed as a model. Two complementary DNA (cDNA) libraries were constructed from RNA isolated from symbiotic and aposymbiotic A. pulchella. Using single-pass sequencing of cDNA clones, a total of 870 expressed sequence tags (ESTs) clones were generated from the two libraries: 474 from symbiotic animal and 396 from aposymbiotic animal. The initial ESTs consisted of 143 clusters and 231 singletons. A BLASTX search revealed that 147 unique genes had similarities with protein sequences available from databases; 120 of these clones were categorized according to their putative function. However, many ESTs could not assign functionally. The putative roles of some of the identified genes relative to endosymbiosis were discussed. This is the first report of the use of EST analysis to examine the gene expression in symbiotic and aposymbiotic states of the cnidarians. The systematic analysis of EST from this study provides a useful database for future investigations of the molecular mechanisms involved in algal-cnidarian symbiosis.

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loning and Characterization of the First Cnidarian ADP-Ribosylation Factor, and Its Involvement in the Aiptasia-Symbiodinum Endosymbiosis.

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Chen MC, Cheng YM, Wang LH, Lin CH, Huang XY, Liu MC, Sung PJ, Fang LS.

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Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan 944, R.O.C.

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Marine cnidarian-microalgal endosymbiosis is a form of intracellular association that contributes greatly to the high primary productivity of reefs; however, little is known about its molecular mechanisms. Since the ADP-ribosylation factor (ARF) family proteins are key regulators of host intracellular vesicle transport systems, which are critical to many endosymbiotic interactions, we set out to clone and characterize ARF proteins in the symbiotic sea anemone Aiptasia pulchella. Experiments indicated that at least 3 ARF protein classes (class I, class II and class III) were present and expressed as a single messenger RNA species in Aiptasia, with highest mRNA expression levels for apARF1, medium for apARF5, and lowest for apARF6. Quantitative analysis revealed a great reduction at both the RNA and the protein levels in apARF1, but not apARF5 and apARF6, in the symbiotic animals. The apARF1 protein was highly homologous in sequence to other known ARF1 proteins and displayed a Golgi-like localization pattern. Overall, our study identified apARF1 as a potential negative regulator of Aiptaisia-microalgal endosymbiosis.

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And of course there's the genetic evidence:

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A molecular timeline for the origin of photosynthetic eukaryotes.

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Yoon HS, Hackett JD, Ciniglia C, Pinto G, Bhattacharya D.

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Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, Iowa, USA.

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The appearance of photosynthetic eukaryotes (algae and plants) dramatically altered the Earth's ecosystem, making possible all vertebrate life on land, including humans. Dating algal origin is, however, frustrated by a meager fossil record. We generated a plastid multi-gene phylogeny with Bayesian inference and then used maximum likelihood molecular clock methods to estimate algal divergence times. The plastid tree was used as a surrogate for algal host evolution because of recent phylogenetic evidence supporting the vertical ancestry of the plastid in the red, green, and glaucophyte algae. Nodes in the plastid tree were constrained with six reliable fossil dates and a maximum age of 3,500 MYA based on the earliest known eubacterial fossil. Our analyses support an ancient (late Paleoproterozoic) origin of photosynthetic eukaryotes with the primary endosymbiosis that gave rise to the first alga having occurred after the split of the Plantae (i.e., red, green, and glaucophyte algae plus land plants) from the opisthokonts sometime before 1,558 MYA. The split of the red and green algae is calculated to have occurred about 1,500 MYA, and the putative single red algal secondary endosymbiosis that gave rise to the plastid in the cryptophyte, haptophyte, and stramenopile algae (chromists) occurred about 1,300 MYA. These dates, which are consistent with fossil evidence for putative marine algae (i.e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution.

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Cooperation of endo- and exoribonucleases in chloroplast mRNA turnover.

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Bollenbach TJ, Schuster G, Stern DB.

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Boyce Thompson Institute for Plant Research, Tower Rd, Ithaca, New York 14853, USA.

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Chloroplasts were acquired by eukaryotic cells through endosymbiosis and have retained their own gene expression machinery. One hallmark of chloroplast gene regulation is the predominance of posttranscriptional control, which is exerted both at the gene-specific and global levels. This review focuses on how chloroplast mRNA stability is regulated, through an examination of poly(A)-dependent and independent pathways. The poly(A)-dependent pathway is catalyzed by polynucleotide phosphorylase (PNPase), which both adds and degrades destabilizing poly(A) tails, whereas RNase II and PNPase may both participate in the poly(A)-independent pathway. Each system is initiated through endonucleolytic cleavages that remove 3' stem-loop structures, which are catalyzed by the related proteins CSP41a and CSP41b and possibly an RNase E-like enzyme. Overall, chloroplasts have retained the prokaryotic endonuclease-exonuclease RNA degradation system despite evolution in the number and character of the enzymes involved. This reflects the presence of the chloroplast within a eukaryotic host and the complex responses that occur to environmental and developmental cues.

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Now, why would chloroplasts have their own redundant gene expression systems?

It looks like you missed my reply to you in Message 70.--Percy

So, what you're saying is, ID has accomplished nothing. Well, that's what I thought.

This is a point that I've been making and you've been ignoring. The ultimate creator of ID is a divine being, but you prefer to ignore this obvious implication of ID because it reveals its religious foundation. As I said in Message 70, no scientific field puts limits on inquiry as ID does when it says that the active agent behind design is not an object of study. I, too, am a theist. But I don't believe a divine being directed the course of evolution, and I don't think Meert or Miller do, either, though now I'm not as sure as I once was.--Percy

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crashfrog:
Well, the observation of endosymbiosis, for one thing:

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LoL!!! You can't be serious. The first article you posted talks about symbiotic relationships between eucaryoyes & procaryotes: So that doesn't do anything for you.The second article is more of the same.The thrid article again assumes eucs. evolved from procs. and sets out to find evidence for that. That is subjective testing.

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crashfrog:
Now, why would chloroplasts have their own redundant gene expression systems?

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Because they were designed that way.

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"...the most habitable place in the solar system yields the best view of solar eclipses just when observers can best appreciate them." from "The Privileged Planet"

Wouldn't a prokaryote with an endosymbiont be a eukaryote, by definition? I don't see the assumption. They say "if this is true, this is what we would find. Do we find it?" How else would you test a theory? Designed by what mechanism? What's your positive evidence that these gene control mechanisms are the result of design?Moreover, why would these organelles be designed in such a way that genetic phylogenies can be accurately constructed?

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Phylogeny of plastids based on cladistic analysis of gene loss inferred from complete plastid genome sequences.

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Nozaki H, Ohta N, Matsuzaki M, Misumi O, Kuroiwa T.

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Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. nozaki@biol.s.u-tokyo.ac.jp

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Based on the recent hypothesis on the origin of eukaryotic phototrophs, red algae, green plants, and glaucophytes constitute the "primary photosynthetic eukaryotes" (whose plastids may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis), whereas the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary or tertiary endosymbiotic events (involving a phototrophic eukaryote and a host cell). Although phylogenetic analyses using multiple plastid genes from a wide range of eukaryotic lineages have been carried out, some of the major phylogenetic relationships of plastids remain ambiguous or conflict between different phylogenetic methods used for nucleotide or amino acid substitutions. Therefore, an alternative methodology to infer the plastid phylogeny is needed. Here, we carried out a cladistic analysis of the "loss of plastid genes" after primary endosymbiosis using complete plastid genome sequences from a wide range of eukaryotic phototrophs. Since it is extremely unlikely that plastid genes are regained during plastid evolution, we used the irreversible Camin-Sokal model for our cladistic analysis of the loss of plastid genes. The cladistic analysis of the 274 plastid protein-coding genes resolved the 20 operational taxonomic units representing a wide range of eukaryotic lineages (including three secondary plastid-containing groups) into two large monophyletic groups with high bootstrap values: one corresponded to the red lineage and the other consisted of a large clade composed of the green lineage (green plants and Euglena) and the basal glaucophyte plastid. Although the sister relationship between the green lineage and the Glaucophyta was not resolved in recent phylogenetic studies using amino acid substitutions from multiple plastid genes, it is consistent with the rbcL gene phylogeny and with a recent phylogenetic study using multiple nuclear genes. In addition, our analysis robustly resolved the conflicting/ambiguous phylogenetic positions of secondary plastids in previous phylogenetic studies: the Euglena plastid was sister to the chlorophycean (Chlamydomonas) lineage, and the secondary plastids from the diatom (Odontiella) and cryptophyte (Guillardia) were monophyletic within the red lineage.

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This message has been edited by crashfrog, 09-27-2004 11:33 AM

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Percy:
This is a point that I've been making and you've been ignoring.

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What point? That you can misrepresent ID? I knew that.

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Percy:
The ultimate creator of ID is a divine being, but you prefer to ignore this obvious implication of ID because it reveals its religious foundation.

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Not really. If the evidence points to a divine being then it is not religious in nature. Also ID doesn't say anything about the ultimate creator. Biological ID just cares about life on Earth.

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Percy:
As I said in Re: ID is not Creation (Message 70), no scientific field puts limits on inquiry as ID does when it says that the active agent behind design is not an object of study.

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Yeah right. As if the theory of evolution doesn't limit inquiry by saying we don't care how life first started on Earth. Double-standards Percy.

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Percy:
I, too, am a theist. But I don't believe a divine being directed the course of evolution, and I don't think Meert or Miller do, either, though now I'm not as sure as I once was.

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I haven't asked Joe or Ken but every other alleged christian evolutionist I have discussed this with tells me that humans were the intent of God. That would mean random had no part in bringing forth humans. IOW humans were a goal. According to the theory evolution doesn't have a goal (except for perhaps survival).As I said in Re: ID is not Creation (Message 70), no scientific field puts limits on inquiry as ID does when it says that the active agent behind design is not an object of study.

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"...the most habitable place in the solar system yields the best view of solar eclipses just when observers can best appreciate them." from "The Privileged Planet"

Since divinity cannot be substantiated by evidence, by definition, no conclusion of divinity can be anything but religious.

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crashfrog:
Wouldn't a prokaryote with an endosymbiont be a eukaryote, by definition?

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Nope. It would be a procaryote with an endosymbiont. Eucs require a nucleus.

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crashfrog:
I don't see the assumption. They say "if this is true, this is what we would find. Do we find it?" How else would you test a theory?

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They need to verify that. IOW there could be, and usually is, more than one way to get the same results.

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crashfrog:
What's your positive evidence that these gene control mechanisms are the result of design?

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And where is yours that these gene control mechanisms are the result of nature acting alone?The orgenelles in question are much shorter in sequence than the procs we now observe. What happened to truncate them? Please provide the evidence for this truncation event.This message has been edited by ID man, 09-27-2004 11:40 AM

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"...the most habitable place in the solar system yields the best view of solar eclipses just when observers can best appreciate them." from "The Privileged Planet"

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crashfrog:
Since divinity cannot be substantiated by evidence, by definition, no conclusion of divinity can be anything but religious.

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Another baseless assertion by crashfrog.Life exists and is evidence. What is the positive evidence that life came into existence by nature acting alone? If that can't be substantiated then what are the alternatives?

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"...the most habitable place in the solar system yields the best view of solar eclipses just when observers can best appreciate them." from "The Privileged Planet"

So, you have no evidence that these mechanisms are the result of design? Then why did you say that they were?

The basis is in reason, ID man. Why possible test could distinguish between a non-divine entity and a divine entity merely feigning non-divinity?If divinity cannot be falsified, it cannot be supported evidentially. That the laws of physics exist, and are sufficient to account.

Well here is one Christian Evolutionist that will tell you that there is no indication that humans were the intent of GOD. To believe that humans were a goal makes GOD out to be a very illogical and insecure critter.If humans were the goal, why would GOD have created a universe that took 14+ billion years to get to something that could have been there at day one. It assumes that all life that came before humans was simply wasted effort and non-productive nonsense.The idea that there is something unusal or even exceptional about humans is a very human centric idea. It is making GOD in our own image.Pretty silly.

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Aslan is not a Tame Lion

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crashfrog:
That the laws of physics exist, and are sufficient to account.

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Another baseless claim. Where did the laws of physics come from?

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"...the most habitable place in the solar system yields the best view of solar eclipses just when observers can best appreciate them." from "The Privileged Planet"

Irrelevant, point not under discussion. But I'm glad you've made it clear that your only response, when challenged for positive evidence of your position, is to change the subject.