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Date: 2003/01/09 21:29:28, Link
Author: Art
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.

Date: 2003/01/11 22:38:01, Link
Author: Art
Noel seems to be jumping the gun, IMO.  If we assume that "information" in this case is what Dembski would call Complex Specified Information (CSI), then I think we all must wait for that first piece of evidence showing that any facet of life (or nature, for that matter) actually possesses, or is described by, CSI.  As things stand at the present, there is no evidence that CSI exists, and plenty of data that shows that life is devoid of CSI.

If there is no CSI, then there is nothing for RM&NS to "create".



Date: 2003/01/13 22:56:59, Link
Author: Art
In the never-ending quest for "icons", I submit the following for everyone's consideration.  Comments, additional references, and more examples that combine molecular and morphological perspectives would be most appreciated.  (This is a slightly-modified version of a recent ARN post - suggestions to make it more suited for this board are invited as well.)

First, another accursed pubmed abstract (that need not be read in detail - instead, just note that some of the genes mentioned are known to be developmentally important ones Arabidopsis and other plants):

Quote
Proc Natl Acad Sci U S A 2001 Aug 28;98(18):10208-13

Accelerated regulatory gene evolution in an adaptive radiation.

Barrier M, Robichaux RH, Purugganan MD.

Department of Genetics, Box 7614, North Carolina State University, Raleigh, NC 27695, USA.

The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3/TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A/B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in the ASAP3/TM6 and ASAP1 regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. An increase in nonsynonymous relative to synonymous nucleotide substitution rate is also evident in the ASCAB9 structural gene in the Hawaiian species, but not to the extent displayed in the regulatory loci. The significantly accelerated rates of regulatory gene evolution in the Hawaiian species may reflect the influence of allopolyploidy or of selection and adaptive divergence. The analyses suggest that accelerated rates of regulatory gene evolution may accompany rapid morphological diversification in adaptive radiations.


Now, consider three plants from the group (pardon my taxonomical crudeness here) mentioned in this abstract:  ,
,
and
.  

It doesn’t take much of an eye to see stupendous morphological differences, easily dramatic enough to qualify as possibly macroevolutionary in nature.  Of course, this could only be if it could be shown that these plants share a common ancestry.

And indeed it can be so shown.  By a standard that even the staunchest YECer accepts, it can be strongly concluded that each of these (as well as other members of the Silversword alliance) share a common ancestry.  This is because, the vast morphological differences aside, they are interfertile.  As interestingly, for a number of other reasons (biological, geographic, historical, and molecular), it can be safely concluded that these vastly-different plants diverged from a common ancestor that looked something like

.

Reflect, now, on the abstract.  In this study, evidence for positive selection of alleles (that must have arisen via mutation - this follows from the natural history of the different genera) of developmentally-important genes - genes involved in flower structure and evolution - was described.  While it’s not a videotape, it stands as evidence of the sort that Wells claims does not exist - namely, that changes in developmentally-important genes are important in macroevolutionary progressions.

(Keep in mind that among the dramatic morphological differences that are seen in these examples are ones that involve floral structures.  Also, while others might argue with me, I would claim here that the range of morphologies shown in this post exceeds the range seen in placental mammals - just to give readers an idea of the scope of the differences.)

Date: 2003/03/09 09:44:49, Link
Author: Art
The discussion on ARN about chromosome evolution, and the supposed difficulties that karyotype differences pose for the evolution of, say, humans from a common ancetsor with other primates, brings to mind several similar discussions on AOL that have dealt with the same subject.  I won't begin to pretend that the following are an exhaustive list, or that they are the first or last word on the subject, but they are among the abstracts that address some specific issues.

The first one describes a great deal of karyotpic variability in populations of rats on Mauritius, all of which most likely arose from a small ancestral population.  The ramifications vis-a-vis the possibilities of chromosome evolution are obvious.

Quote
Chromosoma 1979 Oct 2;75(1):51-62

Mauritius type black rats with peculiar karyotypes derived from Robertsonian fission of small metacentrics.

Yosida TH, Kato H, Tsuchiya K, Moriwaki K, Ochiai Y, Monty J

All seventeen black rats collected from Mauritius Island were characterized by having many extra small acrocentric autosomes. Their basic karyotype was of Oceanian type, because of the presence of the large metacentric M1 and M2 pairs, but chromosome numbers in 13 specimens among them were 42, those of 3 specimens 43, and those of the remaining one specimen 44. Although the Oceanian type rat had 2 small acrocentric autosomes (pair no. 13), 16 Mauritius rats had 10 small acrocentrics, and the remaining one had 8 small acrocentrics. Comparative karyotype analysis between Oceanian and Mauritius type rats showed that the extra small acrocentrics found in Mauritius rats were due to Robertsonian fission of small metacentric pairs no. 14 and 18 of the original Oceanian type rat. Only one rat with 8 small acrocentrics showed the heteromorphic pair no. 18 consisting of one metacentric and two acrocentrics. The large metacentric M1 chromosome in 13 of 17 rats examined showed homologous pair, but two of them were heteromorphic by involving one metacentric M1 and two acrocentrics. In the remaining two rats M1 chromosome was not observed, but acrocentric pairs no. 4 and 7 were included. These acrocentrics were also suggested to be originated from Robertsonian fission of the large metacentric M1 chromosome. Robertsonian fission seemed to be one of the important mechanism found in karyotype evolution.


The second abstract describes variations in the karyotypes of a primate.  Of particular note is the occurrence of heterozygotes that from matings of parents with different karyotypes - this demonstrates conclusively that, in primates, changes in chromosome morphology are not always, invariably detrimental with respect to fertility or health.

Quote
Am J Phys Anthropol 1999 Oct;110(2):129-42

Complex, compound inversion/translocation polymorphism in an ape: presumptive intermediate stage in the karyotypic evolution of the agile gibbon Hylobates agilis.

Van Tuinen P, Mootnick AR, Kingswood SC, Hale DW, Kumamoto AT

Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
vantuine@post.its.mcw.edu

Karyotypic variation in five gibbon species of the subgenus Hylobates (2n = 44) was assessed in 63 animals, 23 of them wild born. Acquisition of key specimens of Hylobates agilis (agile gibbon), whose karyotype had been problematic due to unresolved structural polymorphisms, led to disclosure of a compound inversion/translocation polymorphism. A polymorphic region of chromosome 8 harboring two pericentric inversions, one nested within the other, was in turn bissected by one breakpoint of a reciprocal translocation. In double-inversion + translocation heterozygotes, the theoretical meiotic pairing configuration is a double inversion loop, with four arms of a translocation quadrivalent radiating from the loop. Electron-microscopic analysis of synaptonemal complex configurations consistently revealed translocation quadrivalents but no inversion loops. Rather, nonhomologous pairing was evident in the inverted region, a condition that should preclude crossing over and the subsequent production of duplication-deficiency gametes. This is corroborated by the existence of normal offspring of compound heterozygotes, indicating that fertility may not be reduced despite the topological complexity of this polymorphic system. The distribution of inversion and translocation morphs in these taxa suggests application of cytogenetics in identifying gibbon specimens and avoiding undesirable hybridization in captive breeding efforts.


The last abstract makes mention of a variant chromosomal race in  Australian aphids.  As I read the abstract, it seems as if this race arose while the aphids were "cultured" - e.g., there is not much question as to the ancestry of the race, nor of the fact that such a chromosomal variation was, in this instance, not an insurmountable barrier to overall karyotpic evolution.  If others see this differently or are more familiar with these things, please feel free to comment.

Quote
Genetics (1996) 144, 747-756

Microsatellite and chromosome evolution of parthenogenetic sitobion aphids in Australia.

Sunnucks P, England PR, Taylor AC, Hales DF

School of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia.

Abstract: Single-locus microsatellite variation correlated perfectly with chromosome number in Sitobion  miscanthi aphids. The microsatellites were highly heterozygous, with up to 10 alleles per locus in this species. Despite this considerable allelic variation, only seven different S. miscanthi genotypes were discovered in 555 individuals collected from a wide range of locations, hosts and sampling periods.  Relatedness between genotypes suggests only two successful colonizations of Australia. There was no evidence for genetic recombination in 555 S. miscanthi so the occurrence of recent sexual reproduction must be near zero. Thus diversification is by mutation and chromosomal rearrangement alone. Since the aphids showed no sexual recombination, microsatellites can mutate without meiosis. Five of seven microsatellite differences were a single repeat unit, and one larger jump is likely. The minimum numbers of changes between karyotypes corresponded roughly one-to-one with microsatellite allele changes, which suggests very rapid chromosomal evolution. A chromosomal fission occurred in a cultured line, and a previously unknown chromosomal race was detected. All 121 diverse S. near fragariae were heterozygous but revealed only one genotype. This species too must have a low rate of sexual reproduction and few colonizations of Australia.




Date: 2004/09/17 11:22:07, Link
Author: Art
Sal, this may be "piling on", but I have a recommendation for you.  You need to review Dembski's "parable" about the archer and the bulleyes.  Most, if not all, of the things you are arguing (here and on other boards) as possessing CSI are actually items that, using this parable, are rightly called fabrications.

Date: 2005/04/20 23:25:35, Link
Author: Art
Sorry for the intrusion, and for pushing my own favorite "icon", but what the hey...

Quote
Cite one piece, just one piece, of empirical data that links the changes in allele frequency that occurs under selection and the appearance of new structures, processes or adaptations.


They're not microglial cells (which, IMO, would not pass muster as a new structure, process, or adaptation in cewagner's eyes... but that's another discussion), but this icon fits the bill pretty nicely.  The thread is a bit dated, as there is more recent research dealing with the interesting genes, but it still suffices to lay to rest this particular canard.

Again, admittedly not microglial cells, and thus probably out of place.  But posted for the record nonetheless.



Date: 2006/02/10 05:46:55, Link
Author: Artist in trainig
Darn, I misspelled my name in the sign up. Now i'm in trainig.  :angry:

Thank you avocationist. Not many people call me sweet and you are right, I am a grandPA rather than a GrandMA.

This whole subject is a little new to me. When I went to college (UCBerkeley 1960) This whole darn thing wasn't a problem. I easily reconciled my christian faith with science because I never felt like they really crossed. I used to just explain away the problem with, God started the whole thing (which seems pretty obvious to me) and we are figuring out how it works with science. I wouldn't have cared much but my granddaughter, who is majoring in biology, has become all political over the ID in schools issue and she said some things to me which got me concerned. Go ahead, I say, teach all the science you want, it's a good thing, but don't make a point of saying God did NOT start the ball rolling.

ID seems like a good thing to me because it seems to me like it is allowing for the obvious design in the universe. Now, I don't have a science background it's true. I try to avoid making assumptions about what is and isn't science but if ID is simply allowing for the appearance of design in our universe, I don't see how it could be evil. I also don't see how it is "Crackpot" stuff if they really just want us to allow that God isn't "dead" as Nietche said. I have a hard time believing outside of my religious training I know, but I also know that I have experienced God's love or the Holy Spirit or whatever you want to call it. This experience is real and repeatable. Many people share the experience. Doesn't that qualify as science? Repeatable in different laboritories? Maybe I have to put my fingers in my ears sometimes to move forward just a little but there are some things that are really just too emotionally difficult to confront all at once. At first I thought all the posters here were simply mean spirited people trying to push God out of their lives because they were afraid of the implications but I am beginning to get the feeling that most of you are sincere and probably right in a limited kind of a way. No one here has been as mean sprited as Dave Scott or John Davidson seems to be over at Uncommon Descent. Still, they are the ones defending the idea that God shouldn't be worked out of our lives completely through science and so, in the end, I still have to side with them for the most part.

I know they are saying that it's not about God but it is. It is dangerous for people to live their lives without respect for the world we live in and therefore, respect for God. Science has begun to take a stand against respecting the grand mystery that is God and I think it is difficult to respond intelligently to that challenge because it is so far out in left field if you do have religious training. One good that may come of it is it will strip religion of some of its political baggage (maybe) but the bad is that our children will have nothing to cling to when their lives get truly difficult.

Date: 2006/02/10 08:59:17, Link
Author: Artist in trainig
"People have the right to live dangerously, I have been doing it for decades now and having lived on both sides of the fence I can say I much prefer the danger to the slavery of faith...,

Grown ups can get along fine in life without the need for a magic sky pixie.  People deal with the normal ups and downs in life all the time without imaginary big brothers or invisible daddies.  

It's a shame you view human beings as incompetant to face the world standing on their own two feet and thus need something or someone to cling to."

Mr. Christopher,

People do have the right to live dangerously. But we also live in a society of which there are rules of conduct and natural support mechanisms (George Bush aside). Faith is one of those support mechanisms and if you take it away, that may be all well and good for you and those who can live without it, but for me and many others who may not be as strong as you when it comes to coping with a harsh reality of meaninglessness and loss, faith is one of the things that helps us be strong in the face of adversity. If you take that part of ourselves away, don't you take away a respect for the very fact of our existence and a source of strength for people who might need it? What was it that allowed Martin Luther King Jr. to stand firm in the face of such daunting obsticles? Ghandi too, relied on faith for strength. Mother Theresa?

For those who choose to stand without God, maybe they have trancended a basic need that I and countless others seem to have. But when I look out at the night sky, I feel good imagining God. I would like to have understanding of God but it isn't necessary. I still feel good imagining God. And what is more important in life than feeling good, truth? What is truth? Something that can be replicated in a lab? Maybe. But truth is also quite slippery and I think it is a bit presumptuous to assume that you hold the truth in your test tube. If the ID sciences search for truth they will get no farther and perhaps not even as far but the scale is vast and we do not have the capacity to move very far.

Einstein was right when he realized the beauty in his equations but they aren't simple. And they aren't descriptive of the whole thing that is existence.

I have been reading Pandas Thumb for a few weeks now and I'm beginning to get an idea of what the problem is with the ID camp. God too is slippery and trying to pin him/her/it down into a high-school textbook is also dangerous. You get what we have in the middle east at the far end of that scale. But to claim that God isn't important is equally dangerous. I think.

Thank you for your comments.

Date: 2006/02/10 13:57:47, Link
Author: Artist in trainig
I'm sorry, I don't remember what thread I was in and I don't remember my user name, Maybe frank or Picasso.

Stevestory:
Quote
[QUOTE]
but for me and many others who may not be as strong as you when it comes to coping with a harsh reality of meaninglessness and loss

Why do I only ever hear this from the religious camp? I never hear fellow atheists talk about how grim and wretched life is. Where do religious people get this idea that life without god is meaningless and worthless? This erroneous idea goes quite against the evidence that we atheists are not depressed and nihilistic. Perhaps the religious people just don't appreciate the value of evidence.[/QUOTE]
You know, I think you are entirely missing the point.  I said that perhaps some people may be able to trancend that need but that I and many others, perhaps even some secular humanists, seek meaning. Maybe not like a quest for a Holy Grail but we can dedicate our lives or parts of our lives and even risk death for a cause. We seek and find meaning in our world and in at least some of our actions. If you allow faith into your world then you are also allowing meaning in. It's possible that you already have meaning or that you are happy with simply fulfilling your duty to our species' DNA. Good. That's not me.

Maybe faith is misguided. Maybe it is a way that our physiology has devised to get little dopamine boosts Pascal's wager always seemed a little stupid or small-minded to me.

Date: 2006/02/13 07:19:58, Link
Author: Artist in trainig
Ok. A week of reading books (finished Pandas, read the God Gene, visiting my biologist-in-training relative and reading every post and comment at UD. I appear here now to offer my humble apologies to those I might have slighted, no matter how drunk.

I am and remain a christian, whether that suits you or not. My faith in God has never, to my knowledge, done me harm, and it has done me so much good.

That said, ID is a hoax perpetrated on those of us who look to experts for information by those who see Christians as marks for scams. I don't know where they are doing it but somewhere there has to be money being bilked out of believers.

I give to my church because I know what we do with the money. We pay the guy who marries and buries us and who helps us when we need comfort. We provide a great deal of help to our city's homeless. We help members of our Church who fall on hard times. We, as far as I can remember, only promote Christianity through our public deeds.

This ID nonsense has to be promoted through our government. No one else is that corrupt with as many resources. If this is a nod to the uneducated Christians who follow the "Fundementalist" paths, it is sickening. I am signing off at this point, probably for good (this is not my lifes work) but for God's sake, follow reason, logic and truth and you will not lose God if you already have him.

THere is a value in God that is hard for an atheist (I don't know a better word but I suspect that one is inadequate) to understand. You may feel that it is our way to lie to ourselves but I assure you it is not that simple and for the most part, that is not the case. Truth and evidence must trump dogma and superstition or else we hand the reigns over to those who would use our fear to control us. Sounds a little preachy, I know but, hey, I'm a Christian.

Thought I'd throw this little nugget to you from
http://www.uncommondescent.com/index.php/archives/809

Quote
There is, in evolutionary psychology, no account of the emotions beyond the trivial, or of the sentiments,no account of action or intention, no account of the human ability to acquire mathematical or scientific knowledge, no very direct exploration of the mind’s power to act at a distance by investing things with meaning—no account, that is, of any of the features of the mind whose existence prompts a question about its origins. In its great hope as in so many other respects, evolutionary psychology has reposed its confidence on the bet that in time these things will be explained. If that is so, all that we on the outside can say is that time will tell.

And to that last statement, I would have to concur.

Date: 2006/05/20 20:38:10, Link
Author: Artist in trainig
Scale free network.

Date: 2006/10/18 05:29:01, Link
Author: Artist in trainig
Quote (Occam's Aftershave @ Oct. 18 2006,09:56)
IMPORTANT BREAKING NEWS!

Sun rises in the East!

Ocean found to be wet and salty!

AFDave caught lying, quote-mining, and plagiarizing again!

...no film at 11.

M*A*S*H reference?

As an occasional lurker, might I point out that perhaps Dave meant that the 1st quote was telling because it was taken out of context? His point (although dishonest at first because he did not go on to say that the author did not agree with the position) might have been that even a geologist realized that it was circular reasoning, and that after admitting circular reasoning, the author went on to deny his claim?

I think, in the interest of hearing him out you might want to hold him to lower standards than you might hold an educated person because he clearly doesn't understand his errors.

Dave, you can still be with God without denying reality. In fact, if you step back and simply walk with God, you might find that there is no need to construct an alternate reality to support him.

Bye.

Date: 2006/10/25 17:23:24, Link
Author: Artist in trainig
Quote (ScaryFacts @ Oct. 25 2006,18:17)
Quote (ericmurphy @ Oct. 25 2006,18:58)
Why does Dave do this?

Could it be Dave is the incarnation of "The Straw Man"?  He appears real, but is easily dismissed.

This might be the most perceptive comment on the entire double thread. How interesting.

Date: 2006/10/25 17:29:28, Link
Author: Artist in trainig
Quote (afdave @ Oct. 25 2006,22:24)
And please tell me how in the world are we to have a meaningful discussion of biological information.  Am I to take my entire lexicon and scratch everything out and write in new definitions?

That's what we call "learning".

Date: 2006/10/25 17:35:05, Link
Author: Artist in trainig
How about God?

Date: 2006/10/25 19:31:02, Link
Author: Artist in trainig
xyz:
A) The strength we draw on when it seems there is no hope.
B) The idea that we are small compared to the cosmos.
C) The force that gives us life and breath.

k.e., it's nice to be able to define God how ever you might wish. It might even be considered a luxury. I enjoy that luxury and I don't need your approval. I hope that is ok with you.

Date: 2006/10/25 20:51:56, Link
Author: Artist in trainig
Why? Are you starting a homeless shelter or building a recreation center or something?

Date: 2006/10/25 21:26:17, Link
Author: Artist in trainig
That would be for you to figure out now, wouldn't it?

Date: 2006/12/21 21:39:48, Link
Author: Art
Illinois. Maine. Morocco. Germany. The Upper Peninsula. Texas. EMass.  NYC.  Kentucky.

"Where are you from?"  A question that stumps me every time.

Date: 2007/07/22 14:35:16, Link
Author: Art
I'll add my agreement with the comments regarding quotations and their use.  One can leaf through whole volumes of, say, Annual Review of Biochemistry and find fewer quotes than are seen in even the excerpts on the "EE" web site.  

I'm wondering - how much of an editing project would it be to revise "EE" so that quotations are replaced with accurate representations of the opinions and/or results of the scientist(s) being cited?  How dramatically would the tone of "EE" change if this were done?  Is this a project that the authors of "EE" would undertake?

Date: 2007/08/01 18:38:57, Link
Author: Art
Quote (Reed A. Cartwright @ July 31 2007,09:24)
Now that it is set, someone PM me a mailing address and I'll make sure Prof. Steve Steve shows up at your place in time for the trip.

Whoever replied to Reed send me a PM to let me know that Prof. Steve Steve arrived safely.  Or let the board know.

Art

Date: 2007/09/23 17:09:21, Link
Author: Art
Telic Thoughts is as averse to facts and exposés that reveal their inconsistencies as any other creationist or ID forum.

Date: 2007/09/23 22:12:10, Link
Author: Art
Quote (silverspoon @ Sep. 23 2007,21:44)
....All in all, your exaggerations, and lack of knowledge of basic nuclear plant systems leaves me somewhat skeptical of your honesty and sanity.

Seriously, now.  Long-time ARN and TT participants understand that joy's ramblings are pretty far detached from reality.  But there's no reason to question her honesty - she really believes the stories she tells.

joy's, um, creative fiction gives TT much of its distinctive flavor.  Who's to argue with the wishes of the TT crew, and the face they choose to put forth to the world?  Read and enjoy, and remember who is doing the writing.

Date: 2007/10/11 17:46:04, Link
Author: Art
I haven't been keeping close tabs, so maybe someone can tell me - what has Marks hisself had to say about his essays, the errors, and of the spat between Dembski and Baylor?

Date: 2007/10/23 20:19:37, Link
Author: Art
Here's my own experience with Kirk:

http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000145;p=1

He makes lots of arguments here, and is refuted at every turn.  My own contribution was forcing Durston to confront experimental data that indicated that "information" (aka improbability), when it comes to polypeptide and polynucleotide functionality, was not a function of length of the polymer.  This contradicts every (I repeat - every!) calculation ever done by an IDist.

When confronted with experimental data that refuted a core tenet of ID, he sort of faded into the background.

Date: 2007/11/02 22:05:01, Link
Author: Art
Behe passes off ubiquitin-mediated degradation as gumming things up.  Apparently, he is not impressed with, um, sex determination, photomorphogenesis, neurogenesis, eye development, meiosis, root development, etc., etc., etc.  (These and more all involve Ub-mediated protein turnover.) I wonder if he has written Stockholm, demanding that the 2004 Nobel Prize in Chemistry be revoked.

I'm amazed at how much biology he has to shove under the rug, just to save his book.

Date: 2007/12/03 22:42:17, Link
Author: Art
Quote (Ftk @ Dec. 03 2007,16:17)
Blipes, they were in my post above:

1.  Precisely which pilum and which type-three secretory system [did Klebba] he have in mind?

2.  How exactly did a pilum shed its hair-like filament in becoming a type-three secretory system (last I looked, type-three secretory systems are microsyringes that do not have hair-like filaments)?

3.  What new genes need to be added to form a type-three secretory system from a pilum?

4.  What old genes need to be lost to form a type-three secretory system from a pilum?

5.  In the evolution from the pilum to the type-three secretory system, how many intermediate systems whose functions were neither that of a pilum nor that of a type-three secretory system were there?

Quote
2.  How exactly did a pilum shed its hair-like filament in becoming a type-three secretory system (last I looked, type-three secretory systems are microsyringes that do not have hair-like filaments)?


Look again.  The pilus and the "microsyringe" and but different manifestations of the same thing.  Both are protrusions extending out from the cell.  One is capped, one contacts and penetrates a neighboring cell.

This particular comment of Dembski's makes him look tres ignorant.

Quote
What new genes need to be added to form a type-three secretory system from a pilum?


Um, none.

Classical molecular microevolution.  (Which, when it refutes IC, is NOT accepted by IDists.  Apparently.)

Date: 2007/12/10 17:09:08, Link
Author: Art
Quote (Tracy P. Hamilton @ Dec. 10 2007,13:43)
Quote (Erasmus @ FCD,Dec. 10 2007,09:17)
Poachy, as last man standing, should probably press the issue regarding the failure to calculate the amount of CSI in a crunchy* peanut butter sandwich.  What a shame to ban an inquisitive bright young lady over a culinary debate.

*it can be smooth.  We never got the downlow which had more CSI, smooth or crunchy.

At least we know who the Intelligent Designer is:


Booker T. Washington

http://www.youtube.com/watch?v=8ceAPtJkbvs

Date: 2007/12/23 10:03:35, Link
Author: Art
Quote (afarensis @ Dec. 23 2007,00:48)
Holy crap! No wonder DaveScot gave DOL such a good review, here is footnote 45 in Chapter Five:


 
Quote
45 How is it possible for different DNA sequences that map onto the same amino acid sequence to induce
different proteins? Computer engineer David Springer conjectures that "ribosomes process codons at different
rates when the codons differ only by a redundant nucleotide replacement." He offers the following
analogy for the effect this has on protein folding: "Think of the ribosome like a caulk gun producing a
bead consisting of amino acid polymers that fold as they come out of the gun. If the rate at which the
bead comes out changes, then the shape it folds into changes as well." He also considers the possibility
that "RNA molecules dependent on specific gene sequences alter the way the protein is processed after
the ribosome finishes producing it." See David Springer, "The Sound of the Neutral Theory Exploding,"
Uncommon Descent (December 23, 2006): published online at http://www.uncommondescent.com
/archives/1901 (last accessed January 11, 2007).
:O

Wouldn't it be neat if DaveScot and Telic Thinker joy got together and whipped up a quantum caulk theory of everything?

Date: 2008/01/04 23:06:38, Link
Author: Art
Quote (Thought Provoker @ Jan. 04 2008,22:07)
Let me start by asking for forgiveness for the length of this post.  It will take a lot to show the difference between smoke and mirrors BS and what I think it an honest attempt.
...

"The Design Matrix is a method by which you can score a particular feature according to four different criteria to assess and quantify the strength of a design inference."

The four criteria are…

1. Analogy - How similar is the phenomenon to something known to be designed?

2. Discontinuity - How irreducibly complex is the phenomenon?

3. Rationality - How purposeful (i.e. functional) is the phenomenon?

4. Foresight - How much front loading is involved in the phenomenon? ...


In other words, the Design Matrix is ("It looks that way to Mike Gene")^4.

That isn't all that different from, say, Dembski's approach in NFL of calling the same probability three different things and multiplying them together to get some measure of improbability.

So, which is the smoke and mirrors?

Date: 2008/01/05 08:22:03, Link
Author: Art
It's ironic that you link to a discussion of Dembski's essay on specification.  One the one hand, you try to illustrate differences between Dembski and Mike Gene, with the claim that Dembski is the weaker of the two.  But, so far, you give us as many similarities as differences.  I've shown you one similarity.  The link to the essay on specifications brings up another.  

Mike Gene's laundry list is quite akin to a "method" for deriving a specification.  How does this set him apart from Dembski?  Why is Dembski so wrong and Mike Gene less so?

Also, what the heck does randomness have to do with ID?

Date: 2008/01/05 11:05:54, Link
Author: Art
TP, I'm very aware of the antipathy that ID proponents have for the concept of randomness. IMO, this stance reflects a distinct lack of critical and careful thinking, as randomness really is beside the point when it comes to ID.  ID proponents who think otherwise simply haven't thought things through.

Just trying to provoke some thought here   :p



Date: 2008/01/05 11:12:34, Link
Author: Art
A postscript for Thought Provoker - my comments aren't about TDM, but rather your claims that Mike Gene is making a better argument than Dembski.  If you cannot stand serious criticism of an assertion you apparently take to be gospel, you should stick to places like Telic Thoughts.  The participants here are not going to roll over and wonder in amazement at your contradictory claims.  TT participants more likely will.

Date: 2008/01/06 11:47:57, Link
Author: Art
Instead of just "studying" Mt. Rushmore, why not perform a parallel Design Matrix analysis of Rushmore and New Hampshire's Old Man of the Mountain.  Limit the analysis to information you can obtain from no closer than one mile away, and with the naked eye.  (This approximates the level of analysis of biological systems that Telic Thinkers are happy with.)



Date: 2008/01/07 08:32:19, Link
Author: Art
Here is the paper that goes with the abstract.

Date: 2008/01/16 07:03:06, Link
Author: Art
Quote (EoRaptor013 @ Jan. 15 2008,23:24)
Quote (Art @ Jan. 06 2008,12:47)
Instead of just "studying" Mt. Rushmore, why not perform a parallel Design Matrix analysis of Rushmore and New Hampshire's Old Man of the Mountain...

You do know the Old Man died? He fell off the mountain and all the king's horses, etc.
Just sayin'.

Sounds like planned obsolescence to me.

That settles it - The Old Man was designed.

Date: 2008/02/05 11:59:37, Link
Author: Art
Quote (Richardthughes @ Feb. 05 2008,10:22)
Get ready for quantum woo:

http://www.physorg.com/news120735315.html

 
Quote
Genetic 'telepathy'? A bizarre new property of DNA
Scientists are reporting evidence that intact, double-stranded DNA has the “amazing” ability to recognize similarities in other DNA strands from a distance. And then like friends with similar interests, the bits of genetic material hangout or congregate together. The recognition — of similar sequences in DNA’s chemical subunits — occurs in a way once regarded as impossible, the researchers suggest in a study scheduled for the Jan. 31 issue of ACS’ Journal of Physical Chemistry B.

As I have explained on other boards:

Actually, IMO this article just shows that DNA molecules can aggregate much as do proteins.

Things like ammonium sulfate and polyethylene glycol (PEG) are often used in protein purification, and they work by excluding the protein from the bulk solvent phase. This works well for proteins, that have very different chemical properties even though their basic compositions are similar. In principle, different sequences of DNA should have different physico-chemical properties, even if they are very subtly so. The quoted study shows that, when DNA molecules are "squeezed" out of solution by PEG, they have a very slight tendency to associate with pieces of DNA with the same sequence. The tendency is very subtle (the two-fold tendency to "associate" with each other means just that the sub-phases in the PEG-excluded phase have a slight bias for one or the other of the two DNA molecules being studied) and not likely to have any relevance to real-life biological systems.

Date: 2008/03/04 07:53:34, Link
Author: Art
Quote (olegt @ Mar. 03 2008,20:37)
The thread “No process can result in a net gain of information” underlies 2LoT is silly, and doubly so.  First DLH picks up a paper from a third-rate physics teacher at a third-rate university (who publishes his stuff in the aforementioned silly journal Entropy), then the church choir sings variations of “Entropy is disorder."  

Entropy does not equate disorder.  This common misunderstanding has been discussed many times by physicists, but it isn't going away anytime soon.  Consider this excerpt from an  article published in the Journal of Chemical Education:
   
Quote
To aid students in visualizing an increase in entropy many elementary chemistry texts use artists' before-and-after drawings of groups of "orderly" molecules that become "disorderly".  This has been an anachronism ever since the ideas of quantized energy levels were introduced in elementary chemistry.  "Orderly-disorderly" seems to be an easy visual support but it can be so grievously misleading as to be characterized as a failure-prone crutch rather than a truly reliable, sturdy aid.

Oil and water.  

Anyone can violate the SLOT on their kitchen countertop.

Date: 2008/03/07 23:07:01, Link
Author: Art
Quote (Paul Nelson @ Mar. 07 2008,14:45)
Alb asked,

       
Quote
What about the problem with the statement in EE about Haeckel's embryos, for example?


We’re juggling relative terms -– “many” versus “some” versus “a few” textbooks have used Haeckel's drawings, or derivatives of them.  I don’t know what textbooks you have in your office.  Are any of them in this brief survey?

http://www.discovery.org/a/3935

Donald Prothero just re-published the Romanes 1910 figure, based on Haeckel, although he attributes the material to von Baer; he also supports the validity of ontogeny recapitulating phylogeny.  So use of the drawings persists.

What needs to be done -– and we’ve haven’t done it -– is a thorough (exhaustive) survey of high school and college textbooks, so that actual frequency of usage of Haeckel-derived drawings, and their context, can be determined.  The document I linked to provides a start, but it’s not exhaustive.

I could see changing “many” (on p. 69) to “some,” but I’d have to persuade my co-authors.

Patrick Frank's analysis beats the DI's effort all to heck.  I wonder if he could stand being cited in EE.



Date: 2008/03/23 13:43:15, Link
Author: Art
Quote (TAG @ Mar. 23 2008,13:39)
 
Quote (stevestory @ Mar. 23 2008,02:49)

Hmm....Cordova, Behe, Dembski, Berlinski...

Should we be suspicious of people whose names end in vowels?

:D

And look, 3 of the 4 atheist "horsemen" have surnames ending in 's': Dawkins, Hitchens, Harris.

I never know how to make their names possessive.

No need.  Atheists are all commies, so they don't actually own anything.

Date: 2008/03/29 07:28:33, Link
Author: Art
Um, David Barton is an acceptable source at UD???

I know, I know.  Dog bites man.

Date: 2008/04/05 11:58:07, Link
Author: Art
Quote (Bob O'H @ April 05 2008,08:33)
At the start of his post on Fisher's Fundamental Theorem, Sal quotemines four people: Walter ReMine, Mae Wan Ho, Stan Salthe and Mike Lynch.  ReMine is a creationist, Salthe is an oddball philosopher who dislikes evolutionary biology because of its moral implications.  Mike Lynch is a proper biologist, one of the big names in evolutionary biology (I really should buy his book!).  But who is Mae Wan Ho?

Well, Wiki helps.  Apparently she is a "noted and controversial holistic scientist" who believes that living creatures do not obey the second law of thermodynamics. She also signed the Disco Institute's Dissent From Darwin list.  So, not looking good as far as main-stream science.

Then I googled a bit, and found this little snippet in an interview:
       
Quote
ACRES U.S.A. So, what actually happens when we eat these foods?

HO. As I already mentioned, these modified genetic materials were designed to overcome the natural barriers between species. What happens when we eat ordinary vegetables and animal protein is that the DNA is broken down by our enzymes. Then, our cells also have enzymes for breaking them down further, and ultimately they will be nutrition for the cell. Unfortunately, if you design genetically modified DNA to jump into genomes and to overcome species barriers, then there is a chance that this DNA can avoid enzymatic breakdown and get into other unrelated species. For example, one of the dangers of these organisms is that, as I said previously, they are mainly made up of genetic material belonging to viruses and bacteria. So if these genetic materials meet other viruses and bacteria, they can join up to make new combinations — new viruses and bacteria that cause diseases and resist medical treatment.

Apparently she used to be a lecturer in genetics.  But she still believes in magic.  I'm rather more sceptical that sticking a strand of DNA to a gold particle, and then  shooting it at a plant will give the sequence the ability to avoid degredation later.

Where I shred one of Ho's more ludicrous claims:
------------------
On the cauliflower mosaic virus 35S promoter

Much has been made by anti-GMO zealots about alleged potential risks involved in using the CaMV 35S promoter in transgenic crops. These supposed risks are three-fold: it has been claimed that the 35S promoter might activate silent viruses in crops and humans, that this promoter could possibly activate potential oncogenes in humans cells, and that recombination in the 35S promoter (resident in human cells) could lead to chromosome breaks, cancer, etc. All of these claims are not only hypothetical to the point of absurdity (no anti-GMO zealot has ever documented any such adverse event associated with the 35S promoter), they are contrary to the actual science that underlies the activity of this promoter and its use in transgenic crops. The following is an attempt to explain the truth of the matter.

The first claim is often associated with assertions that the 35S promoter, as used in trangenes, is a “super-promoter”, a virulent, virus-specific agent that is capable of wreaking all manner of havoc, including massive activation of silent autonomous genetic elements in plants and humans. The fact of the matter is that the 35S promoter, while more active than many, is non-descript in both its overall activity and the tissue distribution of this activity. A list of references at the end of this post should be consulted for more information; for now, it suffices to point out that this promoter is relatively simple (two elements, or small DNA sequences that mediate interactions with transcription factors, with as many as perhaps five subelements amongst these) and is recognized by two or three host transcription factors. There are no viral factors involved, nor is the 35S promoter even close to the most active one that can be found in eukaryotic cells. Thus, it is no more likely to disrupt molecular homeostasis in plants than any of a large number of other promoters, or, when introduced into human cells (via, for example, consumption of plants), any of a number of “natural” plant promoters. (This latter possibility is, as we will see later, absurd.)

[As an aside, Ho claims that naked CaMV DNA is much more likely to be taken up by cells than packaged DNA. From the response to the criticisms raised by Futterer et al:

     
Quote
The intact, encapsidated CaMV, consisting of the CaMV genome wrapped in its protein coat, is not infectious for human beings nor for other non-susceptible animals and plants, as is well-known, for it is the coat that determines host specificity in the first instance. However, the naked or free viral genomes may be more
infectious and have a wider host-range than the intact virus.
This assertion is grounded in a comparison with studies showing that, with animal viruses, DNA is able to establish infections in non-hosts. This is but one of many shameless deceptions that can be found in Ho’s writings. Beyond the fact that the comparison is scientifically wrong, Ho’s implication vis-à-vis the relative infectivities of CaMV particles and DNA is also incorrect. Plant viruses do not enter cells via receptor-mediated processes, but rather are introduced mechanically. Because of this, intact virus particles are invariably more infectious than naked nucleic acid, owing to the greater stability of nucleoproteins. Ho claims that the 35S promoter has been converted to a form that is better at moving from cell to cell that an intact virus, but the fact is that just the opposite is true.

While we’re on the subject of Ho’s shameless deceptiveness, the next sentence in the passage is:

     
Quote
Human T-cell leukemia viral genomes formed complete viruses when injected into the bloodstream of rabbits (1).
The abstract from reference 1 shows us that the cited study involves , not HTLV-1 itself, but clones that had previously been adapted for rabbit cells. This abstract is at the end of the post.

I haven’t checked all of Ho’s references, but with each of the ones I did track down, I found that Ho had completely misrepresented the claims and findings of the cited studies. I am not impressed by her scholarship.]

The second claim arises, at least in part, from a claim by Ho that, because caulimoviruses share genomic features with retroviruses, the 35S promoter will, like retroelements, inadvertently activate genes by insertion into them. This claim is, IMO, a piece of willfull deception. Retroviruses act in the described manner owing to a unique feature of their genomes: they are terminally redundant, and the redundancy includes the promoter used to make RNA copies of the genome. In ascii art format, they are like:

>------>

with > denoting the promoter and its orientation. If the element inserts in the proper orientation, the terminal > will activate expression of otherwise silent genes.

The CaMV 35S promoter, as used in transgenic crops, does not have this property. Rather (and Ho herself illustrates this in her literature), it is used in the form:

>------- T

where T is a terminator of transcription. This means that any transcription starting from > will never get into adjacent host DNA, thus eliminating the chances of inadvertent activation of plant, or human, DNA at the insertion site. (There is a possibility that an enhancer element in the 35S promoter might act at some distance to disrupt normal gene expression, but this possibility can be estimated by empiral examination of transgenic collections to be small, and unrelated to the wild and inaccurate claim made by Ho.)

The third claim, that the recombination hotspot in the 35S promoter can cause wide-spread genetic havoc in those who eat GMO crops, can be seen to be absurd by doing nothing more than some simple math. First, recall that, in order for this to occur, the 35S promoter has to find its way, stably, into the genome of a human cell. Such an occurrence, through ingestion of GMO crops, has never been demonstrated (nor, as the numbers that follow indicate, will it). Consider, for example, the uptake of DNA by human cells. In the lab, if given optimal (very large) quantities of DNA, human cells must be specially treated in order to take up DNA. Typically, 10-100% of a sample of 1 million cells will take up a purified plasmid if treated with co-precipitating agents or powerful electrical impulses. However, leave out these agents, and none of the cells take up the DNA. Conservatively, it is safe to say that less than 1 cell in 10^4, when given very large quantities of DNA, will take any up. Translated to a human scale, if a typical human body has 10^12 cells, and if each and every one of them is bathed in large quantities of DNA, at the very most 10^8 will take any up (and likely many orders of magnitude less than this - but we’ll be generous for now).

But that’s just uptake. In order for the imagined adverse events to occur, this DNA must integrate into the human genome. This will have to be via non-homologous recombination, and will occur in 1 in 10^4 to 1 in 10^6 cells (typically - I’m probably overstating this as well, but we’re being generous). Using the higher number, this means that, in a typical human body, at most 10^4 cells, if bathed in very large concentrations of DNA, would ever end up with a copy in their genome.

But we’re not done yet. Remember, we’re talking about transgenic crops as the source of DNA. That proportion of a typical plant genome that could be 35S promoter is vanishingly tiny - 350/5,000,000,000 (350 being Ho’s size of the 35S promoter, and 5x10^9 a typical haploid genome size of a crop plant). Rounding things to make the typing easy, this is about 10^-7. Adding this consideration to the above, we now find that, if 1000 people had all of their cells bathed in very high concentrations of crop plant DNA, only 1 cell in all of these people might end up with the 35S promoter in its genome. That’s 1 cell in 1000 people.

But there’s more. In most of the body, very small quantities (if any) of crop plant DNA will be seen. Since DNA uptake is directly affected by DNA quantity, this means that the actual frequency would be much less than described above. It’s hard to say just how much, since it’s hard to know what fraction of plant DNA survives intact into the bloodstream, but it’s safe to say that the actual rates of uptake would be, very generously, 1% of those seen in optimized lab experiments. 1% of the cells in a body might see more DNA than this, but the uptake in even these cells would be less than seen in lab settings. But we’ll say, for now, that these cells (I am thinking of the cells in the digestive tract) are for some reason spectacularly efficient. (This helps in the math, so I’ll be generous here.) All of these considerations mean that 1 cell in 100,000 people might actually end up with the 35S promoter in its genome. (This is an incredibly generous estimate, but, as we will see, even this generosity cannot save the zealots.)

Now we can turn to the frequency of occurrence of adverse events involving the 35S promoter. Not every promoter recombined or causes chromosome breaks - if this were true, it could not be used as a tool. A lot of empirical observation tells us that such events are not common - while I don’t have a number at hand, it’s safe to say that fewer than 1 in 1000 such elements would ever undergo such an event once resident in a eukaryotic genome. (This number is too generous, as well. But I’m lazy.) This means that, if 100 million people were to be eating GMO crops, 1 cell in this population (at the very most) might undergo some sort of damage or breakage as a result of the presence of the 35S promoter. That’s far, far lower than the natural rate of chromosome alteration - which makes Ho’s objections completely irrelevant.

But it’s even worse for Ho and her cohort. DNA damage and chromosome breakage in and of itself will not cause cancer (which is Ho’s assertion in much of this). Many different events need to occur for cancer to develop. For one thing, the breakage must be in a “strategic” location in the genome. I don’t know how many there are - common sense says they are few, otherwise cancer would be rampant in all people. But let’s say that there are 3 million such places. That’s 0.1% of the genome. This means that, in a population of 100 billion people (20 earths, roughly), 1 cancer might be attributable to the 35S promoter. (The impact on overall cancer rates would, I daresay, be infinitesimally small.)

Then there’s the matter of coupling - just because a strategic site has been “hit” doesn’t mean that cancer will ensue. Many other events must also occur - such that, very “optimistically”, only 1 in a thousand or so of such events would actually contribute directly to the development of cancer.

Which brings us the bottom line, for now - in Ho’s worse-case scenario, if 100 trillion people consumed GMO crops that included 35S promoter-containing constructs, 1 person might develop cancer as a direct result of activities associated with this promoter. IMO, that’s not much of a risk - certainly, much, much, much lower than the risk that consumers of organically-grown foods face from, say, contamination by E. coli.

A bibliography pertaining to the transcriptional properties of the 35S promoter:

EMBO J 1989 Dec 20;8(13):4197-204, The ocs-element is a component of the promoters of several T-DNA and plant viral genes. Bouchez D, Tokuhisa JG, Llewellyn DJ, Dennis ES, Ellis JG.

Plant Cell 1989 Dec;1(12):1147-56, ASF-2: a factor that binds to the cauliflower mosaic virus 35S promoter and a conserved GATA motif in Cab promoters. Lam E, Chua NH.

Plant Mol Biol 1994 May;25(2):323-8, The plant transcription factor TGA1 stimulates expression of the CaMV 35S promoter in Saccharomyces cerevisiae. Ruth J, Schweyen RJ, Hirt H.

Proc Natl Acad Sci U S A 1989 Oct;86(20):7890-4, Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants. Lam E, Benfey PN, Gilmartin PM, Fang RX, Chua NH.

EMBO J 1990 Jun;9(6):1685-96, Combinatorial and synergistic properties of CaMV 35S enhancer subdomains. Benfey PN, Ren L, Chua NH.

EMBO J 1990 Jun;9(6):1677-84, Tissue-specific expression from CaMV 35S enhancer subdomains in early stages of plant development., Benfey PN, Ren L, Chua NH.

Finally, the abstract I promised:

     
Quote
Proc Natl Acad Sci U S A 1996 Jun 25;93(13):6653-8

Infectivity of chimeric human T-cell leukemia virus type I molecular clones
assessed by naked DNA inoculation.

Zhao TM, Robinson MA, Bowers FS, Kindt TJ.

Laboratory of Immunogenetics, National Institute of Allergy and Infectious
Diseases, National Institutes of Health, Rockville, MD 20852, USA.

Two human T-cell leukemia virus type I (HTLV-I) molecular clones, K30p and K34p were derived from HTLV-I-infected rabbit cell lines. K30p and K34p differ by 18 bp with changes in the long terminal repeats (LTRs) as well as in the gag, pol, and rex but not tax or env gene products. Cells transfected with clone K30p were infectious in vitro and injection of the K30p transfectants or naked K30p DNA into rabbits leads to chronic infection. In contrast, K34p did not mediate infection in vitro or in vivo, although the cell line from which it was derived is fully infectious and K34p transfectants produce intact virus particles. To localize differences involved in the ability of the clones to cause infection, six chimeric HTLV-I clones were constructed by shuffling corresponding fragments containing the substitutions in the LTRs, the gag/pol region and the rex region between K30p and K34p. Cells transfected with any of the six chimeras produced virus, but higher levels of virus were produced by cells transfected with those constructs containing the K30p rex region. Virus production was transient except in cells transfected with K30p or with a chimera consisting of the entire protein coding region of K30p flanked by K34p LTRs; only the transfectants showing persistent virus production mediated in vitro infection. In vivo infection in rabbits following intramuscular DNA injection was mediated by K30p as well as by a chimera of K30p containing the K34p rex gene. Comparisons revealed that virus production was greater and appeared earlier in rabbits injected with K30p. These data suggest that several defects in the K34p clone preclude infectivity and furthermore, provide systems to explore functions of HTLV-I genes.




Date: 2008/04/21 22:57:10, Link
Author: Art
Simply unbelievable:
 
Quote
Before writing this off, something like that has already been developed - the patent is jointly held by Monsanto and the USDA - it's called "Terminator Technology." It wasn't deployed because it makes plants sterile and transgenes are highly promiscuous. Just a little tweaking could have such a gene-packet targeted to human sterility, and it could be put into the whole world's staple food crops. Humanity could be sterile in less than 5 years.

Telic thinking at its finest.

Date: 2008/04/27 13:29:55, Link
Author: Art
LOL

Commenter Jean asks about another commenter's publication record, responding to a quip about Berlinski. A quick check of Berlinski's h-factor on SCI yields a value of 1, and an average citation rate for his papers of 0.1 (probably rounded - he has three citations total for all 27 articles/notes/comments/reviews).

Yup, that's a real powerhouse of scholarly output.  Berlinski has been cited THREE times in scholarly works over the years.



Date: 2008/04/27 14:25:44, Link
Author: Art
More amusement, courtesy of Bradford:
 
Quote
This ad hom response illustrates the value of Expelled: No Intelligence Allowed. I never see an evolutionary biologist slimed like this and it is not because they are all stellar performers.

Um, yeah.  Nothing like this.

Typical TT fare.  Heaping lies on top of hypocrisy.

Date: 2008/05/09 23:55:43, Link
Author: Art
Quote (Hermagoras @ May 09 2008,20:23)
Gotta say, as a rhetoric of science person myself, I'm embarrassed for my field by Ms. Venkatesan.

Myself, I'm amused by the parallels between Venkatesan and Sternberg.

Start with their decidedly postmodern views (ID is every bit as postmodern when it comes to science as what is described in the WSJ piece) and end with the similar reflexive responses to criticism (sue the SOBs).  

Don't the UD people ever think before they post?

Date: 2008/05/20 21:17:10, Link
Author: Art
Lexington, KY.

That's where the real UK is.

Date: 2008/05/23 22:37:39, Link
Author: Art
Quote (fusilier @ May 23 2008,08:27)
Indianapolis, Indiana

....

Home of the latest Rape of The Taxpayer NFL stadium.

I thought they built that for DCI Championships.

Date: 2008/06/23 23:15:13, Link
Author: Art
MikeGene:  
Quote
Since he did try to stir up a witch hunt against you, I suppose the ethical and fair thing to do is to allow you to question your accuser. I'll leave the thread open a little longer.

The concept of a telic thinker behaving ethically boggles the mind.  (And ruins keyboards...)

Date: 2008/06/26 07:23:24, Link
Author: Art
Langan's CTMU in a nutshell - "Chris thinks, therefore the universe is".

Those were amusing times on ARN.



Date: 2008/06/26 07:46:31, Link
Author: Art
CTMU/Langan threads:

Does anyone really understand CTMU?

Logical theology

More fun.

Still more.

Enough for now.

Date: 2008/07/05 20:04:38, Link
Author: Art
Quote (Zachriel @ July 05 2008,17:35)
Very interesting. Guts blogged  on "Your Inner Fish", by Neil Shubin. I posted some clearly pertinent information about the author, the codiscoverer of Tiktaalik roseae, an intermediate organism between fish and tetrapods. I provided a link to the official Tiktaalik website for those who might be interested in finding out more. The website has pictures of the expedition team, including Neil. Apparently, my comment was so controversial it was deleted, and I can no longer post on the thread.

By the way, for the benefit of Telic Thoughters, this is what scientists look like:



(Neil Shubin is in front.)

Why am I not surprised?  (That's my last comment on TT - the crew there are so on edge that they cannot stand any probing questions.)

Date: 2008/07/05 20:04:38, Link
Author: Art
Quote (Zachriel @ July 05 2008,17:35)
Very interesting. Guts blogged  on "Your Inner Fish", by Neil Shubin. I posted some clearly pertinent information about the author, the codiscoverer of Tiktaalik roseae, an intermediate organism between fish and tetrapods. I provided a link to the official Tiktaalik website for those who might be interested in finding out more. The website has pictures of the expedition team, including Neil. Apparently, my comment was so controversial it was deleted, and I can no longer post on the thread.

By the way, for the benefit of Telic Thoughters, this is what scientists look like:



(Neil Shubin is in front.)

Why am I not surprised?  (That's my last comment on TT - the crew there are so on edge that they cannot stand any probing questions.)

Date: 2008/07/06 17:59:03, Link
Author: Art
Geepers, Guts.  Try as you might, you cannot be stupider than joy.  She's had decades of practice, and I suspect you're still in the rookie leagues.

Heck, you haven't yet approached Bradford's pathetic level of argumentation.  You'll need to continue this vacuous evasion for a few years to catch up to him.

And as melt-downs go, yours cannot touch the quality of MikeGene's screen-smokers.

Bottom line - you're still peon fourth class in MikeGene's coterie.  Try to accept your lot in life and get on with things.

Date: 2008/07/06 17:59:03, Link
Author: Art
Geepers, Guts.  Try as you might, you cannot be stupider than joy.  She's had decades of practice, and I suspect you're still in the rookie leagues.

Heck, you haven't yet approached Bradford's pathetic level of argumentation.  You'll need to continue this vacuous evasion for a few years to catch up to him.

And as melt-downs go, yours cannot touch the quality of MikeGene's screen-smokers.

Bottom line - you're still peon fourth class in MikeGene's coterie.  Try to accept your lot in life and get on with things.

Date: 2008/07/09 07:50:05, Link
Author: Art
Quote (Ftk @ July 09 2008,07:40)
We keep asking the same questions because your answers are horrifically lame.  I assure you that I've scanned through talkorigins with a fine tooth comb...I even mentioned Theobald's 29+ evidences in my above post.  Those responses don't amount to diddly squat.  It amazing those simple responses is all it takes to convince you folks that the ToE is not a controversial theory.

Here are some more questions for you, and of course Erasmus, since you both seem to also be under the impression that there are no controversial issues surrounding the ToE that should be addressed by students.  Let's test our students on these questions, since they should be easy to answer considering that the ToE is such as solid, unquestionable theory...

   
Quote
Students can explain in detail how evolutionary theory explains the Cambrian Explosion.

Students can describe the changes in genes and embryological development by which complex biological structures such as the human eye evolved.

Students can delineate the lines of evidence by which evolutionary theory has decisively refuted intelligent design. etc.

Students can explain how inanimate matter spontaneously self-organized into the first living cell with its complex machinery and information-rich DNA molecule, without the need for design.

Students can explain how evolutionary theory solves the problem that DNA cannot exist without protein and protein cannot exist without DNA.

Students can describe how co-option explains the evolution of the bacterial flagellum. They will identify the naturally selectable functions of all the independent parts prior to co-option, show that they were capable of interfacing with each other, and identify the specific mutations or other random genetic changes that produced the assembly machinery and assembly instructions necessary for the co-option process.

Students can explain how a land-dwelling mammal such as a cow or hippopotamus evolved by random genetic errors and natural selection into a whale. Students will show how the breathing, digestive, vision, hearing, lactation and other critical systems evolved in a step-by-step fashion such that each generation was viable during the transition from a land-dwelling mammal into a mammal that spends its entire life in the open ocean.

Students should be able to explain how random mutation created the symbols used in the universal genetic code.

The contrast between pseudoscience (as Dembski gives us) and real science cannot be made more clear than this litany.

The correct approach, one that IDists abhor, is to ask students 1.  why is each of these a reasonable hypothesis (this asks students to examine what we know at the moment, AND what we do not know); and 2. how one would go about further testing the stated hypothesis.

This will never be seen in the ID class, because "the experiment has not been done" is the be all and end all of science.  And the IDist would always argue against such an approach in an authentic science class, because the idea that we may learn something sends IDists into fits.

An aside - Ftk, since you're tossing out interesting subjects, maybe you could detail for your readers here the reasons why the work of Yarus and coworkers does not adequately answer the last point Dembski raises.  Please be specific, explicit, and complete - don't leave out any observations and calculations.

Date: 2008/07/23 01:13:34, Link
Author: Art
Quote (keiths @ July 23 2008,00:09)
Quote (bystander @ July 22 2008,21:15)
1. Where the heck do you fit all this front loaded information?

This isn't necessarily an insurmountable problem, depending on the amount of information that actually needs to be front-loaded.  DNA is pretty compact.  There is a species of amoeba that contains 690 billion DNA base pairs, which is more than 200 times as many as in humans.

The problem may indeed be insurmountable, at least for ID proponents.  This is because they believe that new protein-coding genes cannot arise de novo, and they believe that genomes are fairly littered with ORFans.  If you grant people like Paul Nelson a few hundred ORFans per species, then we're talking about the need to "store" information for millions or billions of proteins.  All of this has to be in the ancestral front-loaded creature.  I believe an ancestral genome that could encode a few billion proteins is far larger than one might reasonably hypothesize or could probably exist, and that this is a serious problem for "front loaders".

Date: 2008/07/23 07:42:13, Link
Author: Art
Quote (keiths @ July 23 2008,01:40)
 
Quote (Art @ July 22 2008,23:13)
The problem may indeed be insurmountable, at least for ID proponents.  This is because they believe that new protein-coding genes cannot arise de novo, and they believe that genomes are fairly littered with ORFans.

That's why I specified that I was talking about Mike Gene's version of front-loading in particular.  As far as I can tell, he has no problem with the idea of protein-coding genes arising de novo.

He seems to think more along these lines:  the designer front-loads enough information to bias evolution in certain directions, but the guidance ends there.  Many of the particulars evolve in an unguided fashion (apart from the influence of the initial front-loaded bias).

I've been discussing things like this with Mike Gene since 2000.  The most one can say is that he is non-committal when it comes to the origination of new proteins.  Heck, he never really accepted that T-urf13 is a definitive example of de novo origination of a new protein-coding gene, and he never acknowledged that front-loading only works if one grants that life is a low or zero-CSI proposition.

No, I believe my criticism most definitely applies to Mike Gene's front-loading.  (I'd been hoping for, like, forever that Mike Gene and Paul Nelson would have a knock-down, drag-out on TT over this matter, but the illusion of a united front took precedent over critical thinking and "teach the controversy".)

Date: 2008/07/27 23:04:26, Link
Author: Art
Quote (dvunkannon @ July 27 2008,22:11)
Quote (Tracy P. Hamilton @ July 27 2008,22:24)
 
Quote
A Simpleton Gene Origination Calculation
PaV

In this month’s Nature Genetics, there is an article by Zhou, et. al., dealing with the generation of new genes in Drosophila melanogaster—the fruit fly. While only having access to the abstract, I nonetheless was struck by one of their findings: the rate of new functional gene generation. As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.”

Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.


That would be lovely, but the 1000 gene difference between man and chimpanzee is not new genes for the most part.

It would be even lovelier if the number was close to 1000. Instead, it seems to be closer to 154.

Additional bonus tard for free: PaV thinks the rate of uptake of new genes is constant at the fly's rate. That might work in baraminology, where a fly has always been a fly. So PaV has shown that according to baraminology, it has been 1.75 billion years since Noah's Ark and the Great Flood. Of course, if flies spent most of their developmental history as single celled creatures with faster changes to their genomes, then the rate isn't constant and PaV's calculation fails.

ID prediction: the first comments to this post will hail the calulation as a breakthrough, there will be a brief period of riducule by DS which will not be preserved by the fossil record, and subsequent comments will ignore it in favor of analogies to Expelled.

1.  As indicated above, PaV totally screws up the matter of differences between humans and chimps.

2.  The paper PaV cites is talking only about what Paul Nelson calls ORFans.  Most Drosophila genes arose via duplication and rearrangement of existing genes and exons, not by de novo creation of totally new genes.  Duplication etc. are frequent enough to easily account for the totality of the Drosophila proteome.  

3.  The paper PaV discusses is actually very damaging to the ID case.  I've explained it here and here.

Date: 2008/07/28 06:49:47, Link
Author: Art
PaV now says:
 
Quote
"PO: Current Darwinian thought suggests that so-called ‘gene conversion’ is the process/mechanism by which speciation can occur, and, presumably, up to macroevolutionary changes. However, this mechanism presupposes that duplicated genes have no function, and are therefore free to neutrally evolve–something which is now being questioned since psuedogenes have been found to be involved in gene regulation. Again, without having access to the entire paper, the critical phrase seems to be ‘new function’: that is, the authors are not just talking about the rate of gene duplication, but the rate at which these new genes develop a new function. My ’simple’ calculation based on this rate points out that the rate which they measure is entirely too slow to account for major taxonomic change—macroevolution."


Well, that explains things.  Don't bother to actually read the paper before making grand proclamations about the results and their significance.

Date: 2008/08/26 20:20:38, Link
Author: Art
Quote (CeilingCat @ Aug. 26 2008,01:03)
Nobel committee take note:          
Quote
I was being literal about the cytoplasm determining whether a cell is destined to become a fly or a horse (fly/horse taken from title of geneticist Sermonti’s book “Why a Fly is not a Horse”). In it he writes the only thing we know for certain about why a horse is a horse and not a fly is because its mother was a horse.

Um ...

 
Quote
Mol Gen Genet. 1991 Jan;225(1):11-6.

Protoplast fusion mediated transfer of oligomycin resistance from Nicotiana sylvestris to Solanum tuberosum by intergeneric cybridization.

Perl A, Aviv D, Galun E.

Department of Plant Genetics, Weizmann Institute of Science, Rehovot, Israel.

We have successfully bridged the intergeneric barriers between Nicotiana and Solanum with respect to chondriome transfer. To enable this transfer we utilized the donor-recipient protoplast-fusion procedure. Consequently protoplasts of a Nicotiana sylvestris line with putatively oligomycin-resistant mitochondria (line OliR38) were used as irradiated chondriome donors and iodoacetate-treated protoplasts of Solanum tuberosum cv. Desiree served as recipients. The plated fusion products as well as their derived colonies and calli were exposed to gradually increasing levels of oligomycin. The resulting plantlets had potato morphology and were analyzed with respect to their mitochondrial DNA and chloroplast DNA. Fifteen out of 50 regenerated plants were verified as true cybrids. Detailed analyses of one cybrid revealed chondriome components from the oligomycin-resistant donor line, OliR38, but retention of the plastome of potato. This cybrid was oligomycin-resistant as revealed by root-culture analysis. It was thus verified that due to selection, chondriome components could be transferred from a N. sylvestris donor into a cybrid having all the phenotypic features controlled by the nucleus of the recipient fusion partner (S. tuberosum).


That's right, UDers - the nucleus determines the phenotype of the organism.

Date: 2008/09/15 21:04:08, Link
Author: Art
Quote (Ftk @ Sep. 15 2008,20:50)
I'm not trying to be a jerk by posting this.  I know you guys are worried that Palin might stop science in it's tracks so you won't vote for the McCain ticket, but I wonder what if any of you guys worry about the stuff in this clip about Obama.  I've heard these issues mentioned in the past, and it seems a bit worrisome to me.  

Honestly, I don't have anything against Obama.  During the start of the campaigns I actually leaned his direction.  I even posted postive youtube stuff at my blog.  But, as time went on, I started hearing things that freaked me out just a bit.

I've no doubt that all the candidates have skeletons in there closet, but some of these things about Obama worry me a bit.

What do you guys think?

Yes, we need to get past the the stupid scare tactics in the clip (eerie music, etc.), but is there need to worry about this stuff?

In a word, no.

Ftk, you're so gullible.  You probably still think Harry Truman was a mob flunkie to the very end.

(Actually, odds are that you don't even get my allusion.)

Date: 2008/10/19 12:01:22, Link
Author: Art
Quote (Bob O'H @ Oct. 19 2008,11:26)
Busy goings on at UD today.  First Dr. Dr. D. plugs a new programme, reveals that he's finally got a paper accepted, and also complains that there's too much politics and not enough science ID.

In response, Dave decides to try and sound sciency, with inevitable results.  The biologists amongst you, in particular, will find this amusing.  As I'm back in moderation, I'll leave my comments here as well:

 
Quote
Dave - you're comparing apples and oranges.  Lenski and co. were looking at the evolution of a new function - at the start of the experiment the bacteria didn't have any genes for lactose digestion.

In the paper you cite here, Xie looks at induction of genes that are already present.  His <i>E. coli</i> strains already have the genes for lactose digestion, so there is no evolution.  What he is looking at is the details of how expression of the genes is triggered, not how these genes originate.

Um, wasn't Lenksi et al. all about citrate utilization?

Date: 2008/10/19 19:56:34, Link
Author: Art
NKU to host interactive mock trial on creation science and evolution in the classroom

News from NKU...

Thursday - October 16, 2008
For immediate release...

HIGHLAND HEIGHTS, Ky. - On Oct. 22, Northern Kentucky University will host a unique interactive mock trial that will turn local citizens into jurors on the hotly-contested issue of whether public school science teachers should be allowed to teach creation science, which attempts to use scientific means to prove the Genesis account of creation.

The trial, which will take place at 7 p.m. at NKU's University Center Otto M. Budig Theater, is free and open to the public. It is sponsored by the Northern Kentucky Forum, the NKU Scripps Howard Center for Civic Engagement and Nonprofit Development and the NKU Chase College of Law Center for Excellence in Advocacy.

The first 200 people in attendance will have an opportunity to serve as jurors, using small remote control clickers to register their opinions both before and after the trial. At the conclusion of the proceeding, they will decide the case.

"It is part of the mission of the Scripps Howard Center to conduct public forums," said Mark Neikirk, the Centers executive director. "I've heard President Votruba state many times that a college campus should be a safe place for difficult conversations." Neikirk said that while the evolution/creation science debate is a difficult conversation, he felt it could be more productive if held as a mock trial.

The Trial: Scott v. Chandler County School Board

The trial centers around the termination of fictitious biology teacher Susan Scott (a traditionally trained evolution adherent), who according to her complaint, encouraged students to "explore creation theories." Scott, who will be played by Simon Kenton High School teacher Heather Mastin, is suing the fictitious Chandler County School Board for wrongful termination and seeks reinstatement, compensatory damages and a judicial declaration that the school board violated her First Amendment rights.

Scott will be represented by local attorney Phil Taliaferro, who will argue that teaching creation theory is not only permitted in Kentucky, but legally protected. The defendant, Chandler County School Board, will be represented by local attorney Margo Grubbs, who will argue that Scott's termination was justified under existing law.

Scott's chief witness will be the real-life Dr. Ben Scripture, who received his Ph.D. in biochemistry from the University of Notre Dame in1998. Dr Scripture has earned degrees from the University of California at Berkeley (a A.B. in zoology) and Grace Theological Seminary (M.Div.). Dr. Scripture has published articles in the Journal of Biological Chemistry and the Journal of Molecular Biology. He hosts weekly radio programs, "Scripture on Creation" and "That's What Scripture Says" on radio stations in Fort Wayne, Ind., and Indianapolis, and on the Good News Network stations covering the southeastern region of the U.S.

The school board will be represented in court by fictional superintendent Bryan Boone, who will be played by retired Boone County Superintendent Bryan Blavatt. Its key witness will be real-life evolution advocate Ed Kagin, a Union, Ky., attorney. Kagin is a founder of the Free Inquiry Group and co-authored The Fundamentals of Extremism: The Christian Right in America. He is the originator of Camp Quest, the nation's first residential secular summer camp. He has run unsuccessfully as "the candidate without a prayer" for the Kentucky Supreme Court and Senate. Kagin is the national legal director for American Atheists and was awarded "Atheist of the Year" by that group in 2005 and 2008.

As is so often the case, the legalities of the issue aren't black and white. Kentucky has fairly strict guidelines that suggest evolution-only instruction, but also has a pro-Genesis statute. And, of course, the question isn't confined to the Commonwealth. It is playing out again in the national political debate - as it so often does - and is heating up in a number of states.

The trial judge will be played by retired Kenton County Circuit Court Judge Doug Stephens.

Northern Kentucky Forum

The mock trial is the first of what Northern Kentucky Forum, a partnership between the Scripps Howard Center, Legacy and Vision 2015, hopes will become monthly events that attract diverse audiences, advocate for public dialogue but not any one position, provide for audience input and allow all sides of a given issue to be represented. "We'll always be looking for a way to bend the format," Neikirk said, "to look at issues in a different way."

The next forum will be held Nov. 12 and will focus on the results of the presidential election and what impact it will have upon the region. Other upcoming forum topics tentatively planned include Northern Kentuckys role in Frankfort; public education; energy policy; and diversity in the region.

Date: 2008/11/03 06:07:44, Link
Author: Art
Quote (stevestory @ Nov. 02 2008,18:03)
I am utterly disappointed. Utterly. Here we are 2 days before the election and McCain's got nothing? No last minute surprise? No shocking new allegations? They're putting out robocalls about Barack having a half-aunt who's here illegally? Jeremiah Wright? That's it?

Um, perhaps you've noticed that the USA seems to be carpet bombing parts of Pakistan, in what would seem to be a desperate attempt to bag Bin Laden before Tuesday.

Date: 2008/12/29 14:48:29, Link
Author: Art
Quote (J-Dog @ Dec. 29 2008,12:35)
The Design Of Life Update - Because it is all about Teh Science::

....

His research makes Dr. Seelke an ideally qualified scientist to carefully review the way DoL's authors handled the Ambrose "minimal gene mutations" question. Here, then, are a few of Prof. Seelke's comments: "I got a chance to read Dembski's discussion of Ambrose's work, and it's a good analysis of the problems with forming a new structure."

Hmmm...  that wouldn't be the same Dembski who, in NFL, implied that females are evolutionary dead-ends, would it?

Dembski would almost certainly consider  the transition in plants from annual to perennial to be irrelevant as well.

Date: 2009/02/01 23:40:24, Link
Author: Art
Quote (sledgehammer @ Feb. 01 2009,20:07)
 
Quote (stevestory @ Jan. 31 2009,22:19)
Durston doesn't seem to understand the math he's parading around.

...A google on "Durston 70 bits" yielded only 9 hits, one of which was this ISCID discussion  from 2002, where he introduces the same equations as he displayed in that you-tube.  ...

...Now that was in 2002.
The man is not stupid. He knows very well what this means for his theory.

Perhaps not stupid, but in 2002 Durston was incredibly unaware of a rather simple mathematical fact, one that ruins his entire thesis.

As I stated in my last response on that 2002 ISCID thread:

 
Quote
Hi Kirk,

No need for you to respond to this, but I thought I'd add something to help (maybe) you find some fruitful directions for analysis.

You said:

     
Quote
3. Even if it turns out in the end that all proteins have an Nf/N somewhere around 1 in 10^11, all that would indicate is that they are within the reach of natural processes, according to my hypothesis, which puts a lower limit for Nf/N of 8 x 10^-22. So ID would not be required to generate functional proteins. However, for the barebones life form, we need a minimum of 150 specific genes. Not just any genes, but 150 highly specified genes. Given that the specificity of the average gene is assumed to be about 10^-11, the genomic specificity for 150 specified genes would be about 10^-1650.


I think it's important to keep one simple thing in mind (simple, yet often overlooked). Say that we are speaking of a collection of 150 functional specifications, each of which can be satisfied by families of polypeptides that each have an Nf/N of about, say, 10^-13. It turns out that, in a single collection of 10^16 polypeptides of random sequence, each and every one of these different functional specifications will be represented at least once. This means that, in this hypothetical collection, the probability of "obtaining" this collection of 150 enzymes will be 1 - not the impossibly small number suggested in your statement.


Six+ years later, Kirk still does not acknowledge this simple reality.

Date: 2009/02/10 07:14:43, Link
Author: Art
Quote (KenGee @ Feb. 09 2009,23:53)
Dave Tard has been reading creationist mags in the joh again. He has posted some crap from creationist Alex Williams. Alex has written a great deal about the evilution, even a few books, but why did Dave mention his greatest work Alex Williams: The great sex positions everA link Now that is something I'd read.

Someone needs to ask DS what the STOP sign for transcription is.

Date: 2009/02/28 18:37:02, Link
Author: Art
LOL.  In responding to a recent Panda's Thumb essay, DaveScot says (among other things) by way of summarizing the views Philip Skell holds when the latter disses evolution as a productive field of research:
     
Quote
“ID disputes the notion that chance and necessity alone produced all the living things and the differences between them.”

Of course, Skell himself says rather different things:
     
Quote
“Contrary to the beliefs of Professor Coyne and some other defenders of Darwin, these advances are not due to studies of an organism's ancestors that are recovered from fossil deposits. Those rare artifacts--which have been preserved as fossils--are impressions in stones which, even when examined with the heroic efforts of paleontologists, cannot reveal the details that made these amazing living organisms function.”

(“these advances” are other aspects of biology)
     
Quote
“To conflate contemporary scientific studies of existing organisms with those of the paleontologists serves mainly to misguide the public and teachers of the young.”

     
Quote
“Examining the major advances in biological knowledge, one fails to find any real connection between biological history and the experimental designs that have produced today's cornucopia of knowledge of how the great variety of living organisms perform their functions.”

     
Quote
“Yet many popularizers of Darwin's theory now claim that without the study of ancient biological history,…”

     
Quote
“But fossils fail to inform us of the nature of our ancient antecedents--because they have been transformed into stones that give us only a minuscule, often misleading impression of their former essences and thus are largely irrelevant to modern biology's experimentations with living organisms.”

     
Quote
“For instance, we cannot rely upon ruminations about the fossil record

     
Quote
The essence of the theory of evolution is the hypothesis that historical diversity is the consequence of natural selection acting on variations.

Things are pretty bad in ID land when the denizen at UD are putting words in the mouths of the vanguard.

Date: 2009/03/18 22:29:03, Link
Author: Art
A comprehensive list isn't worth compiling - this paper teems with stupidity.  But some items just scream out:

 
Quote
Copying (transcription) of the gene began at a specially
marked START position, and ended at a special STOP
sign.


Mr. Williams confuses transcription with translation, thereby reducing his credibility to the level of, say, Ken Ham.  (For any fans of Williams who are reading this, please post the STOP sign for transcription in eukaryotes.  Lots of people are interested.)

 
Quote
Genes were scattered throughout the chromosomes,
somewhat like beads on a string, although some areas
were gene-rich and others gene-poor.


Beads on a string describes the appearance of nucleosomes, not genes.

 
Quote
About 93% of the genome is transcribed (not 3%, as expected). Further study with more wide-ranging
methods may raise this figure to 100%. Because much
energy and coordination is required for transcription
this means that probably the whole genome is used by
the cell and there is no such thing as ‘junk DNA’.


Utter garbage.  (Pun intended - I have posted some essays that put this particular ID delusion to rest.)

 
Quote
Transcription proceeds not just one way but both
backwards and forwards.


Um, transcription proceeds in one and only one direction - 5' -> 3'.  The "backwards" direction (3' -> 5') doesn't happen.

 
Quote
The non-protein-coding regions (previously thought
to be junk) are now called untranslated regions (UTRs)
because while they are transcribed into RNA, they are
not translated into protein. Not only has the ENCODE
project elevated UTRs out of the ‘junk’ category, but it now
appears that they are far more active than the translated
regions (the genes), as measured by the number of DNA
bases appearing in RNA transcripts. Genic regions are
transcribed on average in five different overlapping and
interleaved ways, while UTRs are transcribed on average
in seven different overlapping and interleaved ways. Since
there are about 33 times as many bases in UTRs than in
genic regions, that makes the ‘junk’ about 50 times more
active than the genes.


UTRs are parts of protein-coding genes, not the non-coding RNA genes that so fascinate ID antievolutionists.  The business about interleaving is incomprehensible garbling of the two studies Williams is misrepresenting.

One final note - Williams should consider that a better term than code for the various properties he is so taken with is language.  And then he might reflect on the implications of the existence of multiple languages in the cell (in a manner of speaking).  Specifically, multiple languages -> multiple designers -> polytheism, etc., etc....  

Don't Christian IDists ever stop and think about what they write?

Date: 2009/10/11 14:00:00, Link
Author: Art
Sal says:
       
Quote
Are pseudogenes transcribed?

See:

How the Junk DNA Hypothesis has Changed by Richard Sternberg.

If pseudogenes are transcribed, then this is yet another gaffe by Ken Miller and Richard Dawkins.

Actually, the gaffe is Sternberg's.  As explained here.  The brief bottom line - there is a lot of background transcription of junk DNA, and the products of this transcription are broken down almost immediately.  Sternberg is wrong to claim, as he does
   
Quote
...if one considers functional DNA to be equivalent to transcription units ..

that all transcribed DNA is functional.  

I'd post this on TT, but I was silently disinvited long ago.



Date: 2009/11/05 10:58:16, Link
Author: Arts Myth
Quote (sledgehammer @ Nov. 05 2009,10:15)
   
Quote (Freddie @ Nov. 05 2009,07:36)
Yet one more string to add to that talented bow.  Author, consitutional consultant, and now ... textbook editor.  Can anyone say "Jack of all trades ... "
       
Quote

3
O'Leary
11/05/2009
8:59 am

As a sometime textbook editor with an excellent reputation, I would say that we must be clear, who are the final users? The students.

"Jack-off. Halt raids"

"Masturbate nuns."

Date: 2009/12/08 16:55:21, Link
Author: Art
Quote (Kattarina98 @ Dec. 08 2009,06:58)
Clive Hayden answers to a request that is lost in the limbo of moderation:  
Quote
Arthur Hunt,

   Quite completely wrong.

I don’t allow links to that site Arthur, and I have to admit I’m disappointed to see that you post there.

http://tinyurl.com/yzmbgzc

What Clive thought was too dangerous for UD.

Date: 2009/12/30 07:47:19, Link
Author: Art
Quote (CeilingCat @ Dec. 30 2009,00:26)
[URL=http://www.uncommondescent.com/uncommon-descent-contest/uncommon-descent-contest-19-spot-the-mistakes-in-the-following-baffflegab-explanation-of-i




%3Cbr%3Entelligent-design-theory/#comment-343867]Mung thinks hard.[/URL]    
Quote
24
Mustela Nivalis

12/28/2009  1:25 pm
jerry at 23,

Every time I pick something up, I am violating a law of physics, namely gravity.

That’s not the case at all. When you pick something up, you apply a force that is greater than that exerted by gravity. That force comes from your muscles, supported by your skeleton and fueled by the food you’ve eaten. All elements of the action obey the laws of physics.

Next message:    
Quote
25
Mung

12/28/2009 1:35 pm
When you pick something up, you apply a force that is greater than that exerted by gravity. That force comes from your muscles, supported by your skeleton and fueled by the food you’ve eaten. All elements of the action obey the laws of physics.

So that force in the muscles just “poofs” out of nowhere? What physical law generates that force, keeping in mind that f=ma?
Unfortunately, I don't think he's joking.

Classic Mung (scroll down to post 7640117):

 
Quote
I posted some material that explained where at least some of the water in the cell comes from. Did you read it?

Hint: It doesn't come from sea water.

While I appreciate your efforts, you seem to be missing the point on a number of issues.

The water in cells does not, afaik, come from water in the surrounding environment. Nor does it come from stars. (What was the purpose of that post?) It is produced as the result of certain specific biochemical reactions.


(I've bolded the incredible part.)  This statement came from his/her reading of something about intermediary metabolism, electron transport, and respiration.

Date: 2010/02/24 14:52:11, Link
Author: Art
Quote (Tom Ames @ Feb. 24 2010,11:59)
Does anyone remember DNAUnion from the ARN days?

I'm starting to miss that guy...


http://www.meetup.com/SoutheastAlabamaFreethought/members/8628491/

Date: 2010/02/24 14:53:15, Link
Author: Art
Quote (Dr.GH @ Feb. 24 2010,12:26)
Quote (Tom Ames @ Feb. 24 2010,09:59)
Does anyone remember DNAUnion from the ARN days?

I'm starting to miss that guy...

Ah yes.

Who was PLA?


Paul Nelson.

Date: 2010/11/29 13:51:23, Link
Author: Art
Quote (Thought Provoker @ Nov. 27 2010,13:18)
Congratulations, Zachriel.

It looks like you have made such an impression at Telic Thoughts, you are no longer just Banned, you are now a person-who-shall-not-be-named.

In a comment concerning the WWII bombing of Dresden, I said something similar to "It's too bad Zachriel is banned because he probably would have something interesting to say on this".

After which my comment got stuck in the spam queue.

When ask for help, Bradford explained...

   
Quote
TP, the comment was stuck in the spam queue. Reason being the last part of the comment directed at the banning policy. I'd advise you to repost the otherwise productive comment without the last part.

link

So I checked by sending a comment asking if
the name Zachiel was added to the spam filter.

It got stuck in the spam filter too.

ETA - changed "problem" to "probably"

I'd hate to think that I am the reason no one can comment on art at TT.

Date: 2011/03/30 23:36:00, Link
Author: Art
Quote (paragwinn @ Mar. 30 2011,22:47)
Quote (Lou FCD @ Mar. 30 2011,20:30)
   
Quote (Richardthughes @ Mar. 30 2011,12:08)
MathGrrl:

http://www.uncommondescent.com/intelli....-375666

     
Quote
421

MathGrrl

03/30/2011

9:54 am
[SNIP]

my post now numbered 201, namely:

[SNIP]

That's an interesting turn of phrase I've bolded in Mathgrrl's quote.

As much as I would like to report some memory hole occurrence, it seems it's the opposite (shocking, I know). Comments are being inserted between existing entries, causing numerical reference discrepancies.
To start, M. Holcumbrink @ 67 and markf @ 74 refer to Upright Biped @ 31, which is correct. But when O'Leary @ 54 and Spiny Norman @ 69 refer to Niwrad @ 37, Niwrad is actually at 40. By comment 192, niwrad refers to Noesis @ 176 but Noesis is now at 184. I did notice adjoining  comments with the same time stamps, so maybe a database/display update timing problem, causing a delay in displaying time-conflicted entries?

A "moderated" comment may not appear in the thread for hours (or longer), but when it does, it gets inserted in the place where it would have been if it had not gone into the moderation queue.  Any comments made after the moderated comment get re-numbered.

Date: 2011/09/18 14:31:28, Link
Author: Art
Quote (sparc @ Sep. 17 2011,00:21)
IMO this thread needed an update.
Since the announcement at UD on May 1st, 2010 Bio-Complexity published the six articles listed below:  
Quote
Vol 2010

Research Articles

The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations
Douglas Axe

A Vivisection of the ev Computer Organism: Identifying Sources of Active Information
George Montañez, Winston Ewert, William Dembski, Robert Marks

Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness
Ann K Gauger, Stephanie Ebnet, Pamela F Fahey, Ralph Seelke

Critical Reviews

The Case Against a Darwinian Origin of Protein Folds
Douglas Axe
         
Quote
Vol 2011

Research Articles

The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway
Ann K Gauger, Douglas D Axe

Critical Reviews
Can the Origin of the Genetic Code Be Explained by Direct RNA Templating?
Stephen C Meyer, Paul Nelson
Underlined are authors who happen to be members of the editorial board of Bio-Complexity which is quite impressive number-wise:      
Quote
Editor in Chief

Matti Leisola, Enzymology and Enzyme Engineering; Aalto University School of Chemical Technology, Finland

Managing Editor

Douglas Axe, Protein Structure–Function; Biologic Institute, United States

Editorial Board

David Abel, Origin of Life; The Origin-of-Life Science Foundation, United States

William Basener, Statistics and Population Modeling; Rochester Institute of Technology, United States

Michael Behe, Biochemistry and Biological Complexity; Lehigh University, United States

Walter Bradley, Origin of Life; Baylor University, United States

Stuart Burgess, Biomimetics and Biomechanics; University of Bristol, United Kingdom

Russell Carlson, Biochemistry; University of Georgia, United States

William Dembski, Mathematics and Information Theory; Discovery Institute, United States

Marcos Eberlin, Chemistry; State University of Campinas, Brazil

Charles Garner, Prebiotic Chemistry; Baylor University, United States

Loren Haarsma, Biophysics; Calvin College, United States

Peter Imming, Organic Chemistry; Martin Luther University, Germany

James Keener, Bioengineering and Mathematics; University of Utah, United States

David Keller, Biophysical Chemistry and Molecular Machines; University of New Mexico, United States

Branko Kozulic, Biochemistry; Gentius Ltd, Croatia

Wolf-Ekkehard Lönnig, Plant Genetics; Max Plank Institute for Plant Breeding Research (retired), Germany

Jed Macosko, Biophysics and Molecular Machines; Wake Forest University, United States

Robert Marks, Evolutionary Computing and Information Theory; Baylor University, United States

Scott Minnich, Bacterial Pathogenicity; University of Idaho, United States

Norman Nevin, Medical Genetics; Queen's University of Belfast (emeritus), Ireland

Edward Peltzer, Ocean Chemistry, United States

Colin Reeves, Genetic Algorithms and Information Theory; Coventry University, United Kingdom

Siegfried Scherer, Microbial Ecology; Technische Universität München, Germany

Ralph Seelke, Microbiology; University of Wisconsin-Superior, United States

David Snoke, Physics and Modeling; University of Pittsburgh, United States

Richard Sternberg, Genomics, Cladistics and Theoretical Biology; Biologic Institute, United States

Scott Turner, Physiology, Ecology and Evolution; State University of New York-Syracuse, United States

Ji?í Vácha, Pathological Physiology and Evolutionary Theory; Masaryk University (emeritus), Czech Republic

John Walton, Chemistry; University of St Andrews, United Kingdom

Jonathan Wells, Cell and Developmental Biology; Biologic Institute, United States

Copyeditor

Ann Gauger, Molecular Genetics and Molecular Biology; Biologic Institute, United States

32 editors for six articles by a total of 11 authors of which five belong to the editorial team. At the same time five members of the editorial team (underlined) and three authors (Dembski, Meyer, Nelson) are fellows of the Discovery Institute. Quite an endeavor for six articles.

It would seem as if the DI has something against Asians.

Date: 2012/05/18 20:22:39, Link
Author: arthuriandaily
Quote (Assassinator @ Dec. 27 2008,16:32)
@ Daniel:

I would like to add to the following quote from Bill:
 
Quote
Recall that the problem with supernatural causation is that any observation can be reconciled with it. Because any observation can be reconciled with it, it is incapable of making testable predictions.

This is the case because we know zero about the designer. This problem can only be solved when we have actual candidates for being the designer, candidates from wich we know the capabilities and limitations. This is exactly how real world design detection (in archeology) works.


Really, it is like the evolutionary predecessors to a flat earth: javascript:emoticon(':O')

http://arthuriandaily.wordpress.com/2012.......t-earth :O

Date: 2012/05/18 20:24:14, Link
Author: arthuriandaily
Quote (Assassinator @ Dec. 27 2008,16:32)
@ Daniel:

I would like to add to the following quote from Bill:
 
Quote
Recall that the problem with supernatural causation is that any observation can be reconciled with it. Because any observation can be reconciled with it, it is incapable of making testable predictions.

This is the case because we know zero about the designer. This problem can only be solved when we have actual candidates for being the designer, candidates from wich we know the capabilities and limitations. This is exactly how real world design detection (in archeology) works.


Really, it is like the evolutionary predecessors to a flat earth:

http://arthuriandaily.wordpress.com/2012.......t-earth :O

Date: 2013/09/08 19:33:02, Link
Author: Art
Quote
Nick is off to a postdoc in Kentucky where he will be doing actual biological research, another characteristic that will distinguish him from almost all of his antievolutionist detractors.

I thought Dr. Matzke (has a nice ring to it) was going to be in Knoxville TN, probably decked out in that awful shade of orange.

Not that he'd not be welcome in Kentucky - heck, that would be one more cause for sleepless nights for Ken Ham.  But ....

 

 

 

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