EVOLUTION: what about this

[rossum]

There are, then 5,000 times more in a pound of soil. The evolution of an IC system should then be demonstrated in a pound of soil over a period of 4 years.

You need to read more about what research is going on. A paper from Blount, Borland and Lenski was published in March last year from the long-term E. coli experiment about the evolution of an IC system to digest citrate. See ." Proceedings of the National Academy of Sciences, USA 105:7899-7906Escherichia coli.

If one of the parts is not present and the system is still working, then it’s not IC.

That is the knockout definition and it is the type of IC that has repeatedly been shown to be evolvable by Lenski, Behe, Matzke and others. I will agree that this form of IC cannot evolve by direct means, but it is possible for it to evolve by indirect means such as scaffolding or co-option. There is coverage of this point in the article: The Müllerian Two-Step.

rossum

 

[reggieM]

Michael Behe’s response to the paper is informative. You made it sound like he agreed with your assessment, but on the contrary, he cites the findings as being supportive of the work he did in The Edge of Evolution.

From his Amazon.com blog

I discuss Lenski’s fascinating work in Chapter 7 of The Edge of Evolution, pointing out that all of the beneficial mutations identified from the studies so far seem to have been degradative ones, where functioning genes are knocked out or rendered less active. So random mutation much more easily breaks genes than builds them, even when it helps an organism to survive. That’s a very important point. A process which breaks genes so easily is not one that is going to build up complex coherent molecular systems of many proteins, which fill the cell.

… From this he deduced that a previous, lucky mutation had arisen in the one line, a mutation which was needed before a second mutation could give rise to the new ability.

I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. “If two mutations have to occur before there is a net beneficial effect — if an intermediate state is harmful, or less fit than the starting state — then there is already a big evolutionary problem.” (4) And what if more than two are needed? The task quickly gets out of reach of random mutation.

Even though the evolutionary literature contains discussions of multiple mutations (5), Darwinian reviewers drew back in horror, acted as if I had blasphemed, and argued desperately that a series of single beneficial mutations certainly could do the trick. Now here we have Richard Lenski affirming that the evolution of some pretty simple cellular features likely requires multiple mutations.

 

[rossum]

Michael Behe’s response to the paper is informative. You made it sound like he agreed with your assessment, but on the contrary, he cites the findings as being supportive of the work he did in The Edge of Evolution.

Behe’s 2004 paper was published before Lenski’s 2008 paper. Behe was cross-examined on his 2004 paper under oath during the Kitzmiller trial (Day 12 IIRC). In that testimony he agreed with the figure of 20,000 years that I quoted earlier.

From his Amazon.com blog

I discuss Lenski’s fascinating work in Chapter 7 of The Edge of Evolution, pointing out that all of the beneficial mutations identified from the studies so far seem to have been degradative ones, where functioning genes are knocked out or rendered less active. So random mutation much more easily breaks genes than builds them, even when it helps an organism to survive. That’s a very important point. A process which breaks genes so easily is not one that is going to build up complex coherent molecular systems of many proteins, which fill the cell.

I agree that more mutations break genes than improve them. Behe seems to forget that the majority of mutations are neutral and so if a neutral mutation is the required precursor then Behe’s argument fails.

… From this he deduced that a previous, lucky mutation had arisen in the one line, a mutation which was needed before a second mutation could give rise to the new ability

.
Behe provides no evidence that the first mutation was deleterious; on purely statictical grounds it was most likely to have been neutral. We shall have to wait for further results from Lenski’s team to be sure. Note that Behe agrees that Lenski hs indeed observed an instance of an IC system evolving - the first mutation was “needed” before the second mutation gave rise to the IC system. Behe again agrees, correctly, that an IC system can evolve. The only argument now is how likely it is to happen.

I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. “If two mutations have to occur before there is a net beneficial effect — if an intermediate state is harmful, or less fit than the starting state — then there is already a big evolutionary problem.” (4) And what if more than two are needed? The task quickly gets out of reach of random mutation

.
Notice that Behe says “if an intermediate state is harmful …” What if the intermediate state is neutral rather than harmful? Behe also leaves out the possibility of co-option which does not seem to have happened in this case, but is an element in other examples of the evolution of IC systems.

Even though the evolutionary literature contains discussions of multiple mutations (5), Darwinian reviewers drew back in horror, acted as if I had blasphemed, and argued desperately that a series of single beneficial mutations certainly could do the trick. Now here we have Richard Lenski affirming that the evolution of some pretty simple cellular features likely requires multiple mutations.

Multiple mutations were precisely what Behe and Snoke looked at and came up with the figure of 20,000 years. That is a very short time as far as evolution is concerned.

My added comments on blue.

Behe is correct in that deleterious mutations will greatly hamper the evolution of systems on the “other side” of such a mutation. However he is not taking into consideration the majority of mutations which are neutral rather than deleterious - in humans about 95% of mutations are neutral.

Behe agrees that IC systems can evolve and that Lenski has found an example of such an event. Behe disagrees with most biologists as to how probable such events are. The fact that Lenski found an example within a few decades implies that such events are not rare.

rossum

 

[reggieM]

The fact that Lenski found an example within a few decades implies that such events are not rare.

Behe disagrees with that also and pointed out that Lenski’s findings did more to support his thesis in The Edge of Evolution than to argue against it.

I draw a few conclusions from this.

1. The task looked at the simplest IC structures. A full refutation of Behe’s hypothesis needs to look at the most complex IC structures.
2. Whether there are IC systems existing in nature remains a question open to debate (if it were not, then none of the “further research” you mentioned would be necessary). Thus, the proposal that there is “nothing to debate” is refuted. (Or regarding the question of probablity – if neutral mutations cannot function as the precursor then the probability is far worse).
3. I’m confident that StAnastasia adopted the typical evolutionist’s attitude towards Michael Behe (dismissing everything he has done as “lacking even the slightest whiff of the truth”).

 

[rossum]

1. The task looked at the simplest IC structures. A full refutation of Behe’s hypothesis needs to look at the most complex IC structures.

Behe’s original hypothesis was that IC structures could not evolve. This has now been shown to be incorrect and Behe has accepted this. He modified his hypothesis and it now looks like:IC systems are unlikely to evolve.
Much work is going on to determine just how unlikely it is that IC systems can evolve. Behe’s own 2004 paper was one attempt to calculate probabilities for the evolution of a simple IC system. Lenski’s experiment provides some real world data for the evolution of another simple IC system. I agree that less work has been done on complex IC systems but that is because the probability calculations depend on what path is taken to get to the system. In a system with many parts, there are a large number of possible orders in which the parts can be assembled. Does a subset of the parts make up a separate subsystem with a different function - if so then that subsystem can evolve separately and then be co-opted into the final IC system. The final calculated probability is very dependent on the exact path taken to reach the goal and with a complex system there are many many posible paths. This makes the calculations far from simple.

1. Whether there are IC systems existing in nature remains a question open to debate (if it were not, then none of the “further research” you mentioned would be necessary). Thus, the proposal that there is “nothing to debate” is refuted. (Or regarding the question of probablity – if neutral mutations cannot function as the precursor then the probability is far worse).

You are incorrect, IC systems have evolved and are known to have evolved. Behe himself has published figures showing that IC systems can evolve. The current work in this area is looking at getting a more accurate measure of how probable or improbable it is that a given IC can evolve.

1. I’m confident that StAnastasia adopted the typical evolutionist’s attitude towards Michael Behe (dismissing everything he has done as “lacking even the slightest whiff of the truth”).

I will leave it to St Anastasia to speak for herself.

rossum

 

[StAnastasia]

Perhaps you’ll be impressed by this:
A SCIENTIFIC DISSENT FROM DARWINISM

Sorry, not impressed. Most of these people are not biologists, and don’t publish, and are not mainstream to the profession of biology. “Project Steve” http://ncseweb.org/taking-action/project-steveis closing in on evidence of 100,000 biologists alone who assume the truth of evolution.

"The project was named in honor of the paleontologist Stephen Jay Gould (1941-2002). It began in 2003, with an official press release on February 16, 2003.[7] The press release was issued at the American Association for the Advancement of Science’s 2003 convention in Denver, Colorado, after a lecture by Lawrence Krauss titled “Scientific Ignorance as a Way of Life: From Science Fiction in Washington to Intelligent Design in the Classroom.” Krauss made the actual announcement and directed the reporters to NCSE Director Eugenie Scott, who was sitting in the audience in the front row.[8]

The original goal was to collect the signatures of 100 Steves, but this goal was reached in about 10 days. Both Nobel Prize-winning Steves in science, Steven Chu (who has since been appointed Secretary of Energy in Barack Obama’s Cabinet) and Steven Weinberg, were among the first 100 Steves. Over 200 Steves responded in the first month.[8] As the news of Project Steve spread by word-of-mouth, ever-increasing numbers of Steves contacted the NCSE, and the list continued to grow.

Project Steve captured the attention of the media. The first media coverage included articles in the Washington Times, Science, the Oakland Tribune and an interview of NCSE director Eugenie Scott by Australian science journalist and radio broadcaster Robyn Williams for the Australian Broadcasting Corporation’s radio show, “The Science Show”. “The Science Show” arranged for Geoff Sirmai and David Fisher of the Australian musical comedy team “Comic Roasts” to write the “Steve Song”, a parody of the Monty Python song about Spam, for Project Steve.[9][10] The song had its debut on “The Science Show” episode featuring the interview of Scott which aired on Australian Broadcasting Corporation Radio National on the 8th of March, 2003.[11]

Cambridge University Lucasian Professor of Mathematics Stephen Hawking was the 300th Steve to sign the list. By the time the announcement was made on April 21, 2003, another five had joined to bring the total number of Steves to 305.[12] By December 26, 2003, St. Stephen’s Day, Project Steve had grown to 400 scientists.[13]

As Project Steve reached the 400 scientist mark, the NCSE decided to offer a commemorative novelty Project Steve t-shirt. The t-shirt is emblazoned with the proclamation, “Over _00 Scientists named Steve Agree, Teach Evolution!” in large letters, where the blank contains the most recent hundreds mark. A list of the current signatories is included in a smaller typeface on the t-shirt as well.

Eugenie Scott, Glenn Branch and Nick Matzke published an article in the July/August 2004 issue of the Annals of Improbable Research (with all the Steves that had signed up to that point listed as co-authors) called The Morphology of Steve which contained “the first scientific analysis of the sex, geographic location, and body size of scientists named Steve”[14]. The data were obtained using NCSE’s “pioneering experimental steveometry apparatus”—the t-shirt.

Shortly after the second anniversary of Project Steve in February 2005, 543 Steves had signed the list. A front page story in the Ottawa Citizen marking this event was published on February 20, 2005.[15] On September 12, 2005, the 600th Steve signed the list.[16] By February 16, 2006, the third anniversary of Project Steve’s official launch, the Steve-o-meter stood at 700.[17] On April 24, 2007, the list had grown to 800 Steves.[18]

There have been articles about Project Steve in The Times, Scientific American, Yale Daily News, Focus on the Family’s Family News in Focus, The Guardian, MIT’s TechTalk, The Arizona Republic, among many others.[19]

 

[StAnastasia]

He is definitely biased.

As are we all. But Alec strikes me as balanced, direct, and courteous, even if not friendly to theism.

 

[buffalo]

Sorry, not impressed. Most of these people are not biologists, and don’t publish, and are not mainstream to the profession of biology. “Project Steve” http://ncseweb.org/taking-action/project-steveis closing in on evidence of 100,000 biologists alone who assume the truth of evolution.

"The project was named in honor of the paleontologist Stephen Jay Gould (1941-2002). It began in 2003, with an official press release on February 16, 2003.[7] The press release was issued at the American Association for the Advancement of Science’s 2003 convention in Denver, Colorado, after a lecture by Lawrence Krauss titled “Scientific Ignorance as a Way of Life: From Science Fiction in Washington to Intelligent Design in the Classroom.” Krauss made the actual announcement and directed the reporters to NCSE Director Eugenie Scott, who was sitting in the audience in the front row.[8]

The original goal was to collect the signatures of 100 Steves, but this goal was reached in about 10 days. Both Nobel Prize-winning Steves in science, Steven Chu (who has since been appointed Secretary of Energy in Barack Obama’s Cabinet) and Steven Weinberg, were among the first 100 Steves. Over 200 Steves responded in the first month.[8] As the news of Project Steve spread by word-of-mouth, ever-increasing numbers of Steves contacted the NCSE, and the list continued to grow.

Project Steve captured the attention of the media. The first media coverage included articles in the Washington Times, Science, the Oakland Tribune and an interview of NCSE director Eugenie Scott by Australian science journalist and radio broadcaster Robyn Williams for the Australian Broadcasting Corporation’s radio show, “The Science Show”. “The Science Show” arranged for Geoff Sirmai and David Fisher of the Australian musical comedy team “Comic Roasts” to write the “Steve Song”, a parody of the Monty Python song about Spam, for Project Steve.[9][10] The song had its debut on “The Science Show” episode featuring the interview of Scott which aired on Australian Broadcasting Corporation Radio National on the 8th of March, 2003.[11]

Cambridge University Lucasian Professor of Mathematics Stephen Hawking was the 300th Steve to sign the list. By the time the announcement was made on April 21, 2003, another five had joined to bring the total number of Steves to 305.[12] By December 26, 2003, St. Stephen’s Day, Project Steve had grown to 400 scientists.[13]

As Project Steve reached the 400 scientist mark, the NCSE decided to offer a commemorative novelty Project Steve t-shirt. The t-shirt is emblazoned with the proclamation, “Over _00 Scientists named Steve Agree, Teach Evolution!” in large letters, where the blank contains the most recent hundreds mark. A list of the current signatories is included in a smaller typeface on the t-shirt as well.

Eugenie Scott, Glenn Branch and Nick Matzke published an article in the July/August 2004 issue of the Annals of Improbable Research (with all the Steves that had signed up to that point listed as co-authors) called The Morphology of Steve which contained “the first scientific analysis of the sex, geographic location, and body size of scientists named Steve”[14]. The data were obtained using NCSE’s “pioneering experimental steveometry apparatus”—the t-shirt.

Shortly after the second anniversary of Project Steve in February 2005, 543 Steves had signed the list. A front page story in the Ottawa Citizen marking this event was published on February 20, 2005.[15] On September 12, 2005, the 600th Steve signed the list.[16] By February 16, 2006, the third anniversary of Project Steve’s official launch, the Steve-o-meter stood at 700.[17] On April 24, 2007, the list had grown to 800 Steves.[18]

There have been articles about Project Steve in The Times, Scientific American, Yale Daily News, Focus on the Family’s Family News in Focus, The Guardian, MIT’s TechTalk, The Arizona Republic, among many others.[19]

Project Steve - Establishing the Obvious:
A Response to the NCSE

 

[reggieM]

ReggieM: “Whether there are IC systems existing in nature remains a question open to debate”

Rossum:

You are incorrect,

Wikipedia: “Accordingly, the debate on irreducible complexity concerns two questions: whether irreducible complexity can be found in nature, and what significance it would have if it did exist in nature.”

 

[reggieM]

Sorry, not impressed. Most of these people are not biologists …

Ok, but I’m still waiting to be impressed by the actual number of the “loads” of priests you know. Apparently, it’s longer than the list I posted, right?

 

[StAnastasia]

Ok, but I’m still waiting to be impressed by the actual number of the “loads” of priests you know. Apparently, it’s longer than the list I posted, right?

Fewer than 100.

 

[ricmat]

Originally Posted by reggieM forums.catholic-questions.org/images/buttons_cad/viewpost.gif
Ok, but I’m still waiting to be impressed by the actual number of the “loads” of priests you know. Apparently, it’s longer than the list I posted, right?

Fewer than 100.

Actually, I personally know fewer than 1,000,000 priests. Are you impressed?

 

[wildleafblower]

Word gets around. There are plenty of people in the Vatican that know me.

 

[ricmat]

Note: my post #447 above should have ended with

rather than

 

[rossum]

ReggieM: “Whether there are IC systems existing in nature remains a question open to debate”

Rossum: You are incorrect,

We agreed previously to use the ‘knockout’ definition of IC:A single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning. (Darwin’s Black Box, 39)
On that definition there are many many IC systems in nature. The human body is an IC system. Remove its brain and it ceases to function. Remove its heart and it ceases to function. The vertebrate eye is and IC system. Remove the retina or the optic nerve and it ceases to function. There are many more IC systems to be found that meet the above definition, including Behe’s usual examples - the vertebrate blood clotting system, the vertebrate immune system and the bacterial flagellum. All of them are ‘knockout’ IC and all of them have evolved.

rossum

 

[ricmat]

We agreed previously to use the ‘knockout’ definition of IC:A single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning. (Darwin’s Black Box, 39)On that definition there are many many IC systems in nature. The human body is an IC system. Remove its brain and it ceases to function. Remove its heart and it ceases to function. The vertebrate eye is and IC system. Remove the retina or the optic nerve and it ceases to function. There are many more IC systems to be found that meet the above definition, including Behe’s usual examples - the vertebrate blood clotting system, the vertebrate immune system and the bacterial flagellum. All of them are ‘knockout’ IC and all of them have evolved.

You had some numbers above for bacteria evolution. Vertebrates have much smaller population sizes than bacteria, and much longer gestational cycles.

How long should it take to evolve a vertebrate eye? Using what population sizes? How many generations? Don’t forget the optic nerve, the “programming” in the brain to actually use the incoming data, and the downstream (feedback) control (both hardware and software) of the iris and lens focus.

 

[StAnastasia]

1. I’m confident that StAnastasia adopted the typical evolutionist’s attitude towards Michael Behe (dismissing everything he has done as “lacking even the slightest whiff of the truth”).

Now that’s confidence. Of course I don’t dismiss Michael Behe’s service to the Church, to his wife and children, to his academic institution, etc. I’m sure it’s been exemplary service.

I was referring to his biology work. I’m sure the biologists on this forum would know better than I the extent to which Behe’s work is cited by his scientific peers. As Barbour notes in Religion in and Age of Science, one way of testing the cogency of a theory is to look at its fruitfulness. If Behe’s ID theory is widely accepted, cited, and imitated by colleagues and graduate students who are building on his ID theory as they construct their own research programs, that is telling. If his work is largely ignored as irrelevant, that too is telling.

StAnastasia

 

[StAnastasia]

If Behe’s ID theory is widely accepted, cited, and imitated by colleagues and graduate students who are building on his ID theory as they construct their own research programs, that is telling. If his work is largely ignored as irrelevant, that too is telling. StAnastasia

Caveat: as an addendum, let me say that if next week or next year or a century from now some stunning piece of evidence is unearthed that provides powerful proof for ID, Michael Behe will no doubt be hailed as a prophetic voice. After all, both Gregor Mendel and Alfred Wegener do not seem to have enjoyed success or adulation in their lifetimes, and yet now genetics and place tectonic theory are seemingly indispensable to biology and geology.

StAnastasia

 

[rossum]

How long should it take to evolve a vertebrate eye?

Again, you need to keep up with the literature. See: Nilsson DE, Pelger S. “A pessimistic estimate of the time required for an eye to evolve”. Proc R Soc Lond B Biol Sci. 1994;256:53–8.

That paper came up with an estimate of 364,000 generations - and note that they used “pessimistic” assumptions. Given the quick generation times of simple vertebrates that probably equates to something less than 250,000 years.

rossum

 

[reggieM]

Again, you need to keep up with the literature. See: Nilsson DE, Pelger S. “A pessimistic estimate of the time required for an eye to evolve”. Proc R Soc Lond B Biol Sci. 1994;256:53–8.

It’s a very good thing to keep up with “the literature”. The great thing about evolutionary theory is that “evidence” is only limited by the constraints of one’s own imagination.

A Pessimistic Estimate of the Time Required for an Eye to Evolve
Nilsson, Dan-E.; Pelger, Susanne
Proceedings: Biological Sciences, Volume 256, Issue 1345, pp. 53-58
adsabs.harvard.edu/abs/1994RSPSB.256…53N
Theoretical considerations of eye design allow us to find routes along which the optical structures of eyes** may have evolved**. If selection constantly favours an increase in the amount of detectable spatial information, a light-sensitive patch will gradually turn into a focused lens eye through continuous small improvements of design. An upper limit for the number of generations required for the complete transformation can be calculated with a minimum of assumptions. Even with a consistently pessimistic approach the time required becomes amazingly short: only a few hundred thousand years.

---

**A Science Myth from the New York Times **

On June 26 the New York Times ran an article by Douglas H. Erwin, senior scientist at the Smithsonian’s National Museum of Natural History, in which he stated as demonstrated fact the power of natural selection to create the eye. We now can see (forgive the pun) that natural selection “is the primary agent in shaping new adaptations.”

His example? “Computer simulations,” he declares, “have shown how selection can produce a complex eye from a simple eyespot in just a few hundred thousand years.”

Really, Dr. Erwin? Where is your proof of this important fact? What computer simulations, published where and when and by whom? Just a citation or two will do.

One also might scoff at the exaggerated faith shown computer simulations in general, since they frequently cannot even predict next week’s weather accurately. But leave that topic alone for now. Let’s just have the evidence of published computer simulations referred to by Dr. Erwin.

One suspects that the Erwin claim is based on Dan Nilsson & Susan Pelger’s study, “A Pessimistic Estimate of the Time Required for an Eye to Evolve,” Proceedings of the Royal Society, London B (1994) 256, 53-58. However, as Dr. David Berlinski pointed out a few years ago in Commentary, that paper contains no computer simulation whatsoever, a point obvious to anyone reading it and confirmed in writing by its senior author. It was Richard Dawkins who conveyed the widespread impression to the contrary, both in River out of Eden (1995) and The New Statesman of July 16, 1995. The thesis that there exists a computer simulation for the development of the eye is an urban myth that has built upon Dawkins’ uncorrected error.

Details may be found in Volume 115, Number 4 of Commentary, April 2003, under the title “A Scientific Scandal.”

The New York Times should retract Dr. Erwin’s claim or substantiate it. So should Dr. Erwin. This isn’t hard to research and the reply should not be fudged with the name-calling and hand waving that has become standard Darwinist dialogue. Either there are actual computer simulations that back the Dawkins/Erwin/New York Times assertion about evolution of the eye by natural selection, or there are not.