New Contributors

| 23 Comments

I would like to welcome two new contributors to the Panda’s Thumb crew.

Mike Dunford has been a contributor to talk.origins for so long that he almost doesn’t feel like the new kid on the block any more. Currently, Mike is an Nth year senior at the University of Hawaii at Manoa, where he is (finally) completing his B.S. in Zoology. Following completion of his undergraduate work, he plans to continue to study evolution in island environments (especially ones with good beaches). Current interests include speciation processes in sympatric populations, and the evolution of introduced species. In the past, he has worked as a paleontological lab technician. Other interests include the history of geology, especially in 19th century England.

Paul R. Gross is University Professor of Life Sciences, emeritus, at the University of Virginia. His baccalaureate and doctoral degrees are from the University of Pennsylvania. He holds honorary degrees from Brown University and the Medical College of Ohio. He is a developmental and molecular biologist who has taught at Brown, Rochester, MIT, and the University of Virginia. A Fellow of the American Academy of Arts and Sciences, he served from 1978 to 1988 as President and Director of the Marine Biological Laboratory in Woods Hole, MA, and was Vice President and Provost of the University of Virginia, where he helped to found and served as Director of the Molecular Biology Institute. He is co-author with Norman Levitt of Higher Superstition (Johns Hopkins, 1994, 98) and with Barbara Forrest of Creationism’s Trojan Horse: The Wedge of Intelligent Design (Oxford, 2004).

A hearty Panda’s Thumb welcome to Mike and Paul. Protostome Pilsners are on the house for the next hour. Cheers!

23 Comments

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.

Congratulations to all of the contributors for their excellent articles and opinions.

I know I said I was gone, but something came up that I just can’t help mentioning.

Since I’m not a “contributor” and probably never will be, the only way for me to express myself here is to comment in an already existing thread.

I just got the latest issue of Science and I thought this was an extremely interesting piece of work. Evolutionists continually disparage intelligent design, saying that it’s not science and chiding ID theorists for not publishing their work in “peer-reviewed” scientific journals. This is not true. There are hundreds, if not thousands of peer-reviewed articles that appear each year in highly regarded scientific journals that support intelligent design. The support is not in the interpretation or the ‘spin” but in the data itself. 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. Do me a favor, don’t waste our time by responding to me with smart-alecky comments, personal attacks or insults. Just read the article in it’s entirety and think about it. As scientists, that’s the least I can expect from you.

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.

And a quote from the report:

“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.

Charlie, that is an interesting article although I disagree with your conclusion. I do believe that the article is prima facia evidence that testable hypotheses and trained scientists can generate interesting results.

Unfortunately, as we’ve discussed before, ID adherents aren’t interested in proposing testable hypotheses.

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.”

Here is her website

http://devbio1.stanford.edu/usr/ls/

Don’t be intimidated! If you aren’t intimidated by us, you have no reason to be intimidated by her. She hasn’t read your website yet.

As you’ve undoubtedly been told, the scientist who proves that an intelligent “being” or “force” is necessary to explain the diversity of life on earth is going to HIT THE BIG TIME very quickly. I have NO DOUBT that such a discovery would be the greatest scientific advancement since Einstein’s contributions to physics and it’s impact on the course of human history would probably be at least as great as the life of Jesus Christ.

.R. Ewing wrote:

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.”

While I don’t know Dr. Shapiro and I can’t predict her response, my track record is dismal wrt communicating my views to other scientists. Over the past several years I have sent similar communications to people like Sean Carroll, Andy Knoll, Susan Rosenberg and a slew of others addressing their work and asking them similar questions. As soon as they think you’re a creationist, that’s the end of it. From that point on you get nothing. Apparently they are afraid that their words will be used against them by religious creationists and they don’t want to be put in that position. The affect of this is to have a chilling affect on legitimate scientific inquiry and mitagates against the free exchange of ideas. It’s almost impossible to convince people that I’m not a creationist and that my motives are purely scientific. Apparently (although I haven’t taken a poll) I’m the only non-theist in the world who advocates for intelligent design.

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.

J.R.R. Ewing wrote:

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

Yes, there is a reasonable explanation. The explanation, IMHO, is that I misspoke and there are indeed thousands of non-theists (and theists alike) who suspect, (although they don’t advocate) intelligent design. I’m a reasonably well educated and intelligent person and I can easily see that the emergence of these kinds of biological systems are well beyond the realm of chance. I’m not talking about the beaks of finches here, I’m talking about molecular biochemistry and biophysics.

I don’t see how you can do research like this and still hold to a darwinian paradigm.

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.

A “little eerie” indeed…

Charlie: I don’t see how you can do research like this and still hold to a darwinian paradigm

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? Or what are the alternatives, scientifically speaking?

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” (see Link).

So in other words, RNA and cells may have arisen under the same circumstances. Getting RNA to self replicate inside such a cell would be the first step to understand how evolutionary pathways may have shaped the cell from RNA through ribosomes, riboswitches to DNA and protein. Given the evidence I would say that evolutionary biology holds more answers than for instance ‘ID’.

Some relevant links

Breaker Lab

or

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.

and

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.

Link

Seems that riboswitches fit in well within the reigning paradigm of RNA world.

Pim wrote:

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

There’s no reason why it shouldn’t be acceptable to most people, most of the time. It has been demonized by some to denigrate legitimate conclusions. The business of science is not to “prove” things, as Richard Feynman so eloquently stated, but to say what is most likely. 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.

I prefer to explore the issues in more detail.

As do I. It’s much to early in to game to be making unequivocal statements one way or the other. Evolutionists just dismiss ID as crackpottery without giving it it’s scientific due.

Can Riboswitches be understood from an evolutionary perspective?

I hope by that you don’t mean “can we find a way to shoehorn this troubling data into a believable evolutionary paradigm”.

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.

This is a very interesting report and certainly bears further investigation. But I think you will agree, it’s a looooooong road from there to functional cells. 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”

Dr. Breaker states:

“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.

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

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.

Charlie: “can we find a way to shoehorn this troubling data into a believable evolutionary paradigm”.

As I have shown there is no need to consider these data either troubling nor at odds with evolutionary pathways. In fact, Charlie’s suggestion shows to me an unfamiliarity with the actual state of science as it applies to riboswitches, RNA world.

Riboswitches fit in exquisitely well with the RNA world. That riboswitches seem to go back to the dawn of life only strengthens the importance of these findings.

. 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.

J.R.R. Ewing wrote:

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.”

I sent the following e-mail to Dr. Shapiro:

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

And I got back exactly what I expected:

Nothing.

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!

Charlie Wrote:

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?

Unlikely iven the fact that 1) research in this area is still happening 2) your presumption may be fallacious which was

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?

As far as the lack of any reply, what relevance do you think this has? And if you expected no feedback or reply then what was the purpose of your email?

But I am always looking forward to you supporting your assertion quoted above. Certainly given the lack of supporting evidence, why should such assertions be considered relevant?

Pim wrote:

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

No.

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.

Pim wrote:

Too bad. But perhaps not really unexpected.

Not by those who know me. I’m not a research scientist and I never have been. All the research that needs to be done is currently being done by others, as I have pointed out many times. My role is to look at the research that is coming out of the labs and analyze and interpret it. I guess that makes me a “theorist” :-)

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 Wrote:

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.

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? It’s like having a system for playing the Lotto which “works” after the numbers have already been selected (according to the manufacturer), but is no better than chance otherwise (although the manufacturer promises to upgrade to a working model after you purchase). I would not buy such a system any more than I’d buy the Designer-of-the-Gaps approach you’re selling here.

DaveS wrote:

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?

I don’t know what you mean by “Design Inference”. That’s a term that I’ve never used so a defintion or explanation is required. I say that there are some systems which exhibit certain characteristics by which we can unequivocally state are the result of intelligent design*. I’ve laid out this argument at great length and I don’t really want to keep repeating the same stuff over and over. These systems to which I refer are called “machines”, which I have also painstakingly defined. Since living organisms qualify as “machines” under the definition I give, we can say with some degree of certainty (barring some yet to be discovered First Principle) that they are the product of intelligence.

(* 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)

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)

I get it! Kind of like a really nice beach or a swimming hole, neither of which could ever exist without an intelligent designer.

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This page contains a single entry by Ed Brayton published on April 29, 2004 9:42 AM.

Spontaneous origin of … something was the previous entry in this blog.

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