New Contributors

One should also not overlook Prof. Gross (et al.)'s excellent The Flight From Science And Reason which is a collection of papers from a conference inspired by Higher Superstition.

Wow, Paul Gross! Certainly a hero.

Indeed one should not overlook The Flight From Science and Reason. We're slowly but surely working our way through it, in an attempt to publish articles by every contributor to that wonderful book at Butterflies and Wheels.

We also just recently linked to Paul Gross' article 'Politicizing Science Education' in our Flashback section.

Exciting that we'll be able to read him at Panda's Thumb now!

Ms. Benson-

As I just wrote on my own blog, I am stunned that I've managed to be as involved as I've been with this issue for as long as I have without previously coming across Butterflies and Wheels. What a wonderful site, thank you for bringing it to my attention (I didn't say "our attention" because I presume my fellow contributors already knew of it and have been hiding it from me all this time). I will no doubt be a regular visitor.

We, too, are excited to have Paul Gross on board as a contributor. With the recent publication of Creationism's Trojan Horse, I don't know that he'll have the time to post often, but we will surely benefit from any contribution he chooses to make. I am hoping to obtain permission from Oxford Press at some point in the not-too-distant future to post a reasonably lengthy excerpt from this book, and perhaps even to coax Barbara Forrest to contribute an essay or two when she can.

Mr Brayton, Thanks! And I'm glad I mentioned it then. I know at least two of your contributors have been hiding B&W from you, since they've emailed me or posted comments there. But I won't name them - I'm no stoolie.

Anyway, this is a great site too, you guys do terrific work.

Science, Vol 304, Issue 5673, 983-987, 14 May 2004 Oscillating Global Regulators Control the Genetic Circuit Driving a Bacterial Cell Cycle Julia Holtzendorff, Dean Hung, Peter Brende, Ann Reisenauer, Patrick H. Viollier, Harley H. McAdams, Lucy Shapiro Department of Developmental Biology, School of Medicine, Beckman Center, Stanford University, Stanford, CA 94305, USA. Department of Electrical Engineering, School of Engineering, Stanford University, Stanford, CA 94305, USA. ABSTRACT: A newly identified cell-cycle master regulator protein, GcrA, together with the CtrA master regulator, are key components of a genetic circuit that drives cell-cycle progression and asymmetric polar morphogenesis in Caulobacter crescentus. The circuit drives out-of-phase temporal and spatial oscillation of GcrA and CtrA concentrations, producing time- and space-dependent transcriptional regulation of modular functions that implement cell-cycle processes. The CtrA/GcrA regulatory circuit controls expression of polar differentiation factors and the timing of DNA replication. CtrA functions as a silencer of the replication origin and GcrA as an activator of components of the replisome and the segregation machinery.

"Every organism contains, within its regulatory system, self-sustaining pacemaker circuitry that coordinates progression of the cell cycle. At a high level, all these cell-cycle control circuits exhibit parallels in mechanism and function. For example, phosphorylation pathways are interconnected with transcriptional regulatory networks, critical positive and negative feedback pathways, and targeted proteolysis. These mechanisms lead to the cyclical presence and/or activation state of key regulatory proteins that in turn control the modular functions that implement the cell cycle. The specific cell-cycle regulatory proteins in bacteria and eukaryotic cells are not homologous; rather, the homologies are at the level of system design."

This is such an article that, IMHO is prima facie evidence that there is more to what we see than can be explained by random processes and accidental mutations such as are described by neo-darwinian theory.

I propose that you explain to her precisely what is the "prima facie" evidence in her paper for your conclusion that "there is more to what we see than can be explained by random processes and accidental mutations such as are described by neo-darwinian theory."

Apparently (although I haven't taken a poll) I'm the only non-theist in the world who advocates for intelligent design.

Well, perhaps there's a reasonable explanation for that phenomenon.

2004 ANNUAL MEETING AAAS: Science, Vol 303, Issue 5661, 1122 , 20 February 2004 RNA Rules Metabolite Production Jennifer Couzin SEATTLE, WASHINGTON--Small RNA molecules have electrified scientists in recent years with their newly discovered roles in controlling gene expression. The surprises are apparently far from over: Another kind of RNA can detect levels of small molecules that help a cell run smoothly, and it can switch genes on or off depending on the cell's needs. Molecular biologist Ronald Breaker of Yale University and his colleagues unearthed these multitalented RNA molecules--a class called riboswitches--after wading through decades of scientific literature and puzzling over a handful of unsolved mysteries. Small molecules called metabolites mediate a cell's survival, and metabolite production is fine-tuned by genes that indirectly sense metabolite levels. It had long been assumed that specific proteins bind to a metabolite and trigger expression or repression of genes. But Breaker, as well as researchers at other universities, uncovered seven cases in bacteria, some as old as 30 years, in which frustrated scientists searched in vain for that key protein. There was a reason they couldn't find it, he says: The mystery protein was actually messenger RNA (mRNA). It normally carts the information from DNA to a cell's ribosome, where it's translated into a protein. Riboswitches--so named because they are composed of RNA --are portions of specific mRNAs that bind to a metabolite. That changes the shape of the mRNA and switches a gene off, or occasionally on. ...At the AAAS meeting, Breaker reported on his eighth bacterial riboswitch. The switch mediates levels of glucosamine, a key sugar that helps bacteria build their cell walls. Unlike the previous seven (those unsolved mysteries from the past), the new riboswitch is also a ribozyme, a scissorlike molecule that can cut up RNA. It uses this ability to control gene expression. When glucosamine reaches high levels in the cell, the metabolite binds to mRNA and induces the mRNA to cut itself. That prompts a plunge in gene expression, because DNA's message to churn out glucosamine can no longer be transcribed. Mysteriously, the mRNA gets sliced at a site that doesn't code for protein but that still manages to disrupt gene expression. "We don't know why" that happens, says Breaker. "It's a little eerie," notes Sean Eddy, a computational biologist at Washington University in St. Louis, Missouri. Still, it's clear that "bacteria are loaded" with riboswitches, says Breaker. He's confirmed two more that aren't yet published and has 10 other candidates. The switches have also been found in fungi and plants, and Breaker is planning to start hunting for them soon in animals.

Riboswitches are mRNA structures regulating gene expression via direct binding of small molecules. Remarkable features of these apparently very ancient regulatory elements are: i) conservation over large phylogenetic distances (eubacteria, archaea, eukaryota), and ii) involvement in a variety of regulatory interactions at the level of of transcription and translation. Computational analysis has played a major role in the discovery and mechanistic interpretation of riboswitches. At present several riboswitches regulating metabolism of vitamins, amino acids and purines are known. Analysis of these and other regulatory elements in combination with other techniques of comparative genomics allowed us to identify new enzymes and transporters related to riboflavin, thiamin, cobalamin, nickel, lysine and methionine metabolism. Several functional predictions have been experimentally confirmed. Examples illustrating evolution of regulatory networks involving riboswitches will be presented.

Perhaps the most intriguing form of RNA yet discovered is the riboswitch, isolated last year by Ronald R. Breaker's lab at Yale. He and others have long wondered how, billions of years ago, the very earliest chemical precursors to life got along in the RNA world before DNA and proteins existed. They speculated that such proto-organisms would need to use RNA as sensors and switches to respond to changes in the environment and in their metabolism. To test the idea, they tried to create RNAs with such capabilities. "Our laboratory successfully produced a number of synthetic RNA switches," Breaker recalls. Dubbed riboswitches, these long RNAs are both coding and noncoding at once. As the RNA folds up, the noncoding end becomes a sensitive receptor for a particular chemical target. A collision with the target flips the switch, causing the other end, which contains a standard blueprint for a protein, to change shape. The riboswitch thus gives rise to a protein, much like a normal gene does-but only when it senses its target.

While the argument from personal incredulity may be acceptable to some,...

I prefer to explore the issues in more detail.

Can Riboswitches be understood from an evolutionary perspective?

What I find fascinating and relevant to the origin of life and RNA is that "clay mixture called montmorillonite not only helps form little bags of fat and liquid but helps cells use genetic material called RNA.

"Our laboratory successfully produced a number of synthetic RNA switches," Breaker recalls. Dubbed riboswitches, these long RNAs are both coding and noncoding at once. As the RNA folds up, the noncoding end becomes a sensitive receptor for a particular chemical target. A collision with the target flips the switch, causing the other end, which contains a standard blueprint for a protein, to change shape. The riboswitch thus gives rise to a protein, much like a normal gene does-but only when it senses its target.

Charlie: There's no reason at all why I can't conclude that the liklihood of these systems emerging without intelligent input is very small, bordering on impossible, without being accused of personal incredulity.

THat is correct but that is NOT what has happened here Charlie. Thus your comment is a non sequitur.

Charlie: Evolutionists just dismiss ID as crackpottery without giving it it's scientific due.

Again, this seems to be more of a personal belief than a supportable argument. In fact I can refer you to such websites as Talkreasonor Antievolution.org or Talkorigins to show that not only scientists have shown why ID is fallacious but also that they have taken it seriously.

Charlie: I looked at the Breaker Lab page and I was surprised at the numerous references to selection and evolution. He might just get a mention in my forthcoming book "How Really Smart People Can Have Really Stupid Ideas"

When lost for arguments, lets use the ad hominem approach eh Charlie? That's another common fallacy seen.

Charlie: Of course, these synthetic RNA switches did not bootstrap themselves intom existence, they are the product of human intelligence

That is correct but that is not going to help Charlie much now is it? Unless Charlie wants to argue that thus this is evidence of intelligent design, a common fallacy seen in ID circles that since science requires intelligence, any findings must be seen as relevant to ID. In fact what science is working towards is combining the fascinating data on clay, RNA and cells with self replicating RNA leading to RNA switches.

I see also that Charlie is not proposing any relevant scientific alternatives to Riboswitches. In contrast, science is proposing and exploring the relevant pathways and finding more and more evidence to support their hypotheses.

No wonder that ID proponents can be observed using common logical fallacies when confronted with such facts.

. He and others have long wondered how, billions of years ago, the very earliest chemical precursors to life got along in the RNA world before DNA and proteins existed. They speculated that such proto-organisms would need to use RNA as sensors and switches to respond to changes in the environment and in their metabolism. To test the idea, they tried to create RNAs with such capabilities.

Ms. Shapiro is a very nice person whom I've had the pleasure of meeting when I was in graduate school. She is interested in ANY useful ideas which might help us to understand how the cell cycles in bacteria and eukaryotic cells evolved. I propose that you explain to her precisely what is the "prima facie" evidence in her paper for your conclusion that "there is more to what we see than can be explained by random processes and accidental mutations such as are described by neo-darwinian theory."

Dear Dr. Shapiro, I just finished your article in Science as indicated above and I wish to congratulate you on a fine piece of work. I was then drawn to your web site where I spent some time going over your research work and reading some of your other papers. Again I was quite impressed and excited about the work you're doing. Only one thing bothered me, however. I read the following on your site: "The results obtained by studying these regulatory events have led to the conclusion that the bacterial cell cycle is regulated by a complex genetic network . We have to understand the "engineering" (by evolutionary selection) of these biochemical logic networks. The coordination of DNA replication and the cell cycle is a fundamental problem whose study has yielded remarkable insights into the behavior of eukaryotic cells." The words "(by evolutionary selection)" troubled me because it is my opinion that evolutionary selection is incapable of "engineering" these kinds of complex regulatory networks in which multiple processes and multiple functions are integrated in such a way that they not only support each other, but also support the overall function of the system. It is my opinion that such systems require insight to build and are beyond the capability of random chance. After all, selection can only act on what is already there. It has no power on it's own to "engineer" (design and assemble) anything at all. On the other hand, I also read this in your paper: "These mechanisms lead to the cyclical presence and/or activation state of key regulatory proteins that in turn control the modular functions that implement the cell cycle. The specific cell-cycle regulatory proteins in bacteria and eukaryotic cells are not homologous; rather, the homologies are at the level of system design." I hope that your use of the word "design" was carefully considered and not at all accidental! My question to you is this: At what point does the organization and adaptation of process and structure to function observed in the interactions of genes with one another and with their associated RNA's when they are expressed preclude a darwinian machanism of chance mutation and natural selection in their etiology? In your mind, has that point been reached? Charles Wagner

Charlie, that was a pretty good letter! When did you send it? If it's been a week, try sending it again and say that you are worried about it not getting to her the first time.

Also, you might want to cc one or all of the grad students or post-docs who are on the letter. They may have more time to draft a response than Dr. Shapiro does.

Thanks for sharing the info, in any event. Let's keep our fingers crossed!

My question to you is this: At what point does the organization and adaptation of process and structure to function observed in the interactions of genes with one another and with their associated RNA's when they are expressed preclude a darwinian machanism of chance mutation and natural selection in their etiology? In your mind, has that point been reached?

— Charlie

The words "(by evolutionary selection)" troubled me because it is my opinion that evolutionary selection is incapable of "engineering" these kinds of complex regulatory networks in which multiple processes and multiple functions are integrated in such a way that they not only support each other, but also support the overall function of the system. It is my opinion that such systems require insight to build and are beyond the capability of random chance. After all, selection can only act on what is already there. It has no power on it's own to "engineer" (design and assemble) anything at all.

Can we expect research on your part to show support for your claims?

Too bad. But perhaps not really unexpected. If one presumes the requirement of intelligent design then it may be often to look beyond such possibility and do the actual science. What would ID propose in this context which would expand our understanding of how the system arose?

In the past an appearance of complexity has more than once been abused as a 'God of the gap' argument. Our inability to understand how something may have happened led to an inference of design, only to be rejected once science caught up.

Too bad. But perhaps not really unexpected.

Our inability to understand how something may have happened led to an inference of design, only to be rejected once science caught up.

True enough, but we shouldn't conclude that since there have been some cases where our inability to understand led to a false inference of design that design should be rejected in *all* such cases. Especially when other explanations fail.

— Charlie

Since the Design Inference sometimes gives us false negetives and now you're saying here that it sometimes gives false positives, what good is it at all?

they are made up of multiple structures and/or multiple processes each of which supports a function and also supports the functions of other structures and processes and all of these structures and processes are integrated in such a way that they support the overall function of the system)