Beckwith a former ID advocate or never an ID advocate? Please pick one.

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Francis Beckwith and his defender Denyse O’Leary seem to not be able to agree on what is wrong with Forrest’s critique of Beckwith in Synthese. Beckwith (2011) in Synthese:

This is why it strikes me as odd that Forrest claims that I am an ID advocate because I present “ID exactly as ID leaders do–their arguments are his arguments, restated without hedge or criticism” (Forrest 2011, p. 346). Not only does such a statement ignore my recent writings, explicitly critical of ID, that were available to Forrest many months before her article was to appear in print (Beckwith 2009c, 2009-2010, Beckwith 2010c), but it also ignores the academic responsibility I had in writing a graduate thesis in law on a matter of fundamental freedoms. In such writing, one is obligated to present the view under analysis with fairness and charity, especially when the nature, and not the veracity, of that view is the only thing relevant to the question one is trying to answer.

So, Beckwith ain’t no ID advocate and never was, I guess. But wait, what does O’Leary say over on UD today?

Frank Beckwith contacted me January 31, and we later spoke by phone. His problem was this: Barbara Forrest, a philosophy prof at Southeastern Louisiana University (and author of anti-ID screed The Trojan Horse) , had published a hostile account of his life and work in Synthese which implied that he was an ID advocate.

That was astonishing because we are led to expect that profs do their homework. Thus, Forrest should have known what everyone else does, that Beckwith is no such thing. I wrote about Beckwith’s rift with the ID theorists years ago here. I took the view that he had made his point far more loudly than was necessary, under the circumstances.

Wait, O’Leary is saying that Beckwith once was an ID advocate, and later had a break with the movement! That’s rather different than never having been an ID advocate. Why can’t Beckwith just say that he was snookered in the early 2000s by the sweet talk and alleged non-creationism-ness of the ID movement, he thought before 2005 that it had intellectual and scientific credibility and a serious legal chance, he painted an entirely rosy legal and intellectual picture of ID in his publications on the issue, and that he later realized he was horribly wrong about all this, and realized it rather later than most people? I hate to tell someone We Told You So…but, Mr. Beckwith, we did.

(As an aside, it’s clear that it’s not only O’Leary that thought Beckwith was on the ID side, and surprised when the turnabout came. Dembski posted wounded remarks himself at various points. I suspect that Beckwith’s position switches on the ID issue are part of larger trends in his life, i.e. (a) entering the academic mainstream with a faculty position at Baylor, and (b) converting from evangelicalism to Catholism (at the time, while head of the Evangelical Theological Society – you’ve got to give the man credit, when he changes positions, he does it in an big way!).)

A few minor points:

First, Beckwith’s statement about his legal writings on ID that “In such writing, one is obligated to present the view under analysis with fairness and charity, especially when the nature, and not the veracity, of that view is the only thing relevant to the question one is trying to answer” is just silly six ways at once. First, when writing in law review journals and the like, you are not a paid and contracted advocate for some legal party, you are, at least allegedly, supposed to be doing scholarship. This imposes certain obligations, such as exercising critical thinking and conducting a fair review of the evidence. After all, readers are likely to read your law review articles when they are thinking about what governmental actions are constitutional, whether or not some policy they are thinking about is Constitutional, and whether or not they are likely to win a lawsuit over the policy if such occurs. Beckwith’s work pre-2005 was a part – a large part – of the ID movement’s campaign to convince people that ID was not creationism and was good science, and therefore was totally fine in the public schools, and that Constitutional problems wouldn’t arise. We saw how that turned out. Beckwith’s work has only the tiniest whisper of mildly critical remarks about ID – the overwhelming, dominant message that any reader would have gotten from reading his work was that it was a revolutionary scientific movement with no tendency towards crankishness, pseudoscience, or creationism – even though, and this is the most incredible part of his writing – this was the mainstream and widespread scientific and academic view of ID even back then. Beckwith should have warned his readers that “most scholars think ID is worthless crap, a disguise for creationism, and ID advocates will have to overcome the obstacles this presents in political contexts and in the legal arena of expert witnesses, if they want to have any hope of getting into the science classroom and surviving the inevitable legal challenge.”

Heck, he should say that now, instead of endless rambling about Catholic philosophy and the like. Catholic philosophy might indeed cause problems for ID, but those aren’t the main problems. The main problems are that it is scientifically worthless, even though its allegedly scientific nature is the key selling point to the public and the schools – and that politically and historically it is just a dishonest, disguised version of creationism, literally and obviously devised to get around previous court decisions against creation science. Until Beckwith deals with these issues in detail, especially the cdesign proponentsists and connected evidence, he isn’t a serious commentator on ID, and is just throwing up a smokescreen around the key problems with the movement.

Second, Beckwith writes,

“Not only does such a statement ignore my recent writings, explicitly critical of ID, that were available to Forrest many months before her article was to appear in print (Beckwith 2009c, 2009-2010, Beckwith 2010c).”

Well, this ignores the completely obvious point that Forrest’s article, similar to most/all of the articles in this special issue, was “Received: 23 March 2009 / Accepted: 25 March 2009 / Published online: 15 April 2009”. So the 2010 references are irrelevant. It appears that Beckwith’s 2009c article was noted in February 2009, so was available (added in edit: Beckwith cited his critical remarks about ID, marginal as they are, online in November 2008 – judge for yourselves). However, the article is full of dismissive remarks about and critiques of the Kitzmiller decision, and Beckwith’s primary point is to argue for theology as a legally relevant form of knowledge! There is a lot more ID-defending than ID-criticism (if there is any at all, I’m not re-reading it at the moment, but a skim shows none – update: see the cited tidbit, linked above) in that article.

A less obvious point – I don’t blame Beckwith et al. for not knowing this, but it has led widespread misconceptions amongst ID advocates – is that the Synthese special issue was in the works long before 2009. I read at least one draft (Pennock’s article) in 2007 for sure, and perhaps others. Forrest’s article mostly reviews work up to 2006 and 2007, with a few later references that might have been late revisions during the final submission/review stage in 2009. Other articles in the issue are similar. It’s too bad that the publication process was slow, but as anyone in academia knows, this sort of delay is common. In my opinion, the Synthese articles should be read as if they are mostly products of work in 2007, unless there is substantial evidence to the contrary.

Finally, returning to this:

In such writing, one is obligated to present the view under analysis with fairness and charity, especially when the nature, and not the veracity, of that view is the only thing relevant to the question one is trying to answer.

Even if one were supposed to be an advocate rather than a scholar in the law review context, it still isn’t true that “the nature, and not the veracity, of that view is the only thing relevant” to the question of the Constitutionality of ID. The legal argument about ID went like this:

1. Plaintiffs sue, alleging ID is creationism and therefore unconstitutional.

2. ID defenders reply and say, no, ID isn’t creationism, it’s science, and teaching science in science class is constitutional.

It is this argument, from the ID side, that makes the science questions politically and legally relevant, and crucial to the debate. This is precisely why ID advocates spend so much time and effort trying to argue, unconvincing as it is, that they are for real scientists, that they do research for reals, that they are supported by growing numbers of scientists, etc. I’ll agree that it’s not the primary issue – the primary issue is #1, and actually Beckwith has never seriously dealt with the immense historical evidence on this question – but ID advocates raise #2 as a rebuttal to #1, and thus anyone involving themselves in a legal or political (or intellectual) dispute about ID has to address it.

82 Comments

This is Beckwith’s “criticism” of ID from the 2009 article, publicized November 2008:

http://www.whatswrongwiththeworld.n[…]telli_1.html

I have Beckwith’s Law, Darwinism, and Public Education, subtitled “The Establishment Clause and the Challenge of Intelligent Design” sitting right here next to me. In 2003, Beckwith was uncritically citing ID materials and overlooking ID criticisms throughout that work: [“peer-reviewed” Behe’s “ground-breaking and best selling” book.…What the ID movement has accomplished in fewer than two decades is nothing short of astounding” ID exercises “its considerable intellectual muscle and sophisticated level of argument…shaping the direction and nature of public debate on evolution”]

He asserts that it is “legal to permit (or require) ID in public school science classes” in part because “its proponents make a reasonable and intellectually respectable case.”

Most egregiously he glosses over the obvious “ID is a sham argument” calling it ad hominem. He quotes liberally and approvingly from Behe, Paul Nelson, Steven Meyer and Phillip E. Johnson throughout the book. Clearly an ID-friendly book and glowingly cited by the Discovery Institute for years without objection by Discovery Fellow Beckwith.

If he’s not an ID supporter now, he certainly was.

But I understand the need to minimize the former enthusiasm and I applaud anybody who’s capable of reversing field.

What is clear is that Beckwith does not understand nor comprehend science.

At least, Beckwith does not demonstrate any understanding or comprehension of science. His comprehension is amateur at best at less than a 5th-grade level.

Thus, it’s not surprising that he projects a childish analysis, although I’d expect more from a university professor. However, in retrospect, I would not expect more from a Baylor professor.

Why can’t Beckwith just say that he was snookered in the early 2000s by the sweet talk and alleged non-creationism-ness of the ID movement, he thought before 2005 that it had intellectual and scientific credibility and a serious legal chance, he painted an entirely rosy legal and intellectual picture of ID in his publications on the issue, and that he later realized he was horribly wrong about all this, and realized it rather later than most people? I hate to tell someone We Told You So…but, Mr. Beckwith, we did.

But that’s not what happened.

From Beckwith’s piece here: http://www.whatswrongwiththeworld.n[…]telli_1.html

Despite my interest in this subject and my sympathy for the ID movement’s goal to dismantle materialism and its deleterious implications on our understanding of what is real and what counts as knowledge, I am not, and have never been, a proponent of ID. My reasons have to do with my philosophical opposition to the ID movement’s acquiescence to the modern idea that an Enlightenment view of science is the paradigm of knowledge. By seeming to agree with their materialist foes that the mind or intellect cannot have direct knowledge of real immaterial universals, such as natures, essences, and moral properties, many in the ID movement seem to commit the same mistake as the one committed by the late medieval nominalists such as William of Ockham, who gave us what is often called “Ockham’s razor,”

Beckwith doesn’t like ID because it gives too much to the Enlightenment and science. He wants to reject the entire Enlightenment and ID wants to pretend to be part of the Englightenment and not reject it all. Beckwith is too reactionary to be happy with ID.

Doc Bill said:

What is clear is that Beckwith does not understand nor comprehend science.

At least, Beckwith does not demonstrate any understanding or comprehension of science. His comprehension is amateur at best at less than a 5th-grade level.

Thus, it’s not surprising that he projects a childish analysis, although I’d expect more from a university professor. However, in retrospect, I would not expect more from a Baylor professor.

What is more amazing is that Beckwith has a Ph. D. in philosophy from Princeton University, which is ranked among the top five philosophy departments in the country. While completing his Ph. D., he apparently befriended a fellow student, one William Dembski, whom he met - I am surmising this since I haven’t checked, but I think I’m right - while Dembski was working on his Master’s in Divinity from Princeton Theological Seminary.

As for Nick’s rhetorical question, I think the correct answer is this: Once an IDiot means that you’re always an IDiot, especially when you have friends like Dembski and O’Leary.

Well, you know John, lots of people go to Princeton and it doesn’t mean they’re smart, it just means that they got through.

I find Beckwith’s arguments infantile and moronic. It’s not so much a matter of my University of London degree versus his Princeton degree as his argument is unsupported whereas mine is.

I’m surprised when Beckwith complains about people being “mean” to him when, in fact, he puts forth a weak, unsubstantiated argument and apparently expects everybody to exclaim, as in Jack Horner’s case, what a good boy he is, when, in effect, he’s a moron.

Sorry, Beckers, you should have taken up another vocation.

Doc Bill said:

Well, you know John, lots of people go to Princeton and it doesn’t mean they’re smart, it just means that they got through.

I find Beckwith’s arguments infantile and moronic. It’s not so much a matter of my University of London degree versus his Princeton degree as his argument is unsupported whereas mine is.

I’m surprised when Beckwith complains about people being “mean” to him when, in fact, he puts forth a weak, unsubstantiated argument and apparently expects everybody to exclaim, as in Jack Horner’s case, what a good boy he is, when, in effect, he’s a moron.

Sorry, Beckers, you should have taken up another vocation.

No Jack Horner is a lot brighter than Beckwith ever will be, and, unlike Beckwith, he never earned a Ph. D. Horner’s a maverick to be sure, but he’s produced more solid scientific research (on dinosaurs) than Beckwith has done with respect to philosophy.

Beckwith doesn’t like ID because it gives too much to the Enlightenment and science. He wants to reject the entire Enlightenment and ID wants to pretend to be part of the Englightenment and not reject it all. Beckwith is too reactionary to be happy with ID.

Well, that does give an explanation of how someone can protest that they are not an ID advocate, while never admitting error about all of the ridiculously favorable things they said about the “science” and “scientists” of the ID movement… however, IMHO if you still think ID is “ground-breaking” and has “considerable intellectual muscle and sophisticated level of argument”, then you’re still an ID advocate on the issues that are most important to the actual debate.

Here is the message that DI employee Robert Crowther got from Beckwith’s book:

Essential Reading: Law, Darwinism, and Public Education

Robert Crowther

Law, Darwinism, and Public Education: The Establishment Clause and the Challenge of Intelligent Design

By Francis J. Beckwith Rowman & Littlefield, 2004, 185 pages. ISBN 0-7425-1430-7

[…]

After recounting the history of cases which involved the “Creator in the courtroom,’ Beckwith turns to analyzing intelligent design. Under various legal definitions of religion, Beckwith contends that design is not religion as conventionally understood because it derives its support from empirical data and philosophical arguments. Intelligent design, Beckwith explains, is distinct from creationism, for it derives its support from the scientific argument rather than religious texts such as the book of Genesis.

Let me know when Beckwith starts harassing the DI for their “misrepresentations”…

But I understand the need to minimize the former enthusiasm and I applaud anybody who’s capable of reversing field.

bah.

what should be applauded is INTELLECTUAL HONESTY. Beckwith has always been in short supply of this, and changing his relative position hasn’t changed his poor reasoning skills one bit.

He doesn’t deserve your respect.

Wrong Jack Horner, the ref. was to the old nursery rhyme:

“Little Jack Horner Sat in the corner, Eating a Christmas pie; He put in his thumb, And pulled out a plum, And said ‘What a good boy am I!’ “

Doc Bill said:

Well, you know John, lots of people go to Princeton and it doesn’t mean they’re smart, it just means that they got through.

I find Beckwith’s arguments infantile and moronic. It’s not so much a matter of my University of London degree versus his Princeton degree as his argument is unsupported whereas mine is.

I’m surprised when Beckwith complains about people being “mean” to him when, in fact, he puts forth a weak, unsubstantiated argument and apparently expects everybody to exclaim, as in Jack Horner’s case, what a good boy he is, when, in effect, he’s a moron.

Sorry, Beckers, you should have taken up another vocation.

I am confusing Beckwith with Bradley Monton - I think that’s his name - who is a philosopher of science at University of Colorado, Boulder. It was he who befriended Dembski. Monton thinks he’s the new, improved, version of Steve Fuller.

Joe McFaul said:

…I understand the need to minimize the former enthusiasm and I applaud anybody who’s capable of reversing field.

I’m with Ichthyic here. Reversing field is only admirable if it’s done honestly. If Beckwith were to admit that he was wrong and acknowledge the critics whose views he dismissed in the past, then I would be the first to agree with you. But instead he’s trying to distance himself from the failing ID project while pretending he was right all along. I read plenty of Beckwith’s articles. When he says he never supported ID, that is nothing short of…well, I won’t use the obvious word, but academically unacceptable would be the polite way of putting it.

Chris Lawson said:

Joe McFaul said:

…I understand the need to minimize the former enthusiasm and I applaud anybody who’s capable of reversing field.

I’m with Ichthyic here. Reversing field is only admirable if it’s done honestly. If Beckwith were to admit that he was wrong and acknowledge the critics whose views he dismissed in the past, then I would be the first to agree with you. But instead he’s trying to distance himself from the failing ID project while pretending he was right all along. I read plenty of Beckwith’s articles. When he says he never supported ID, that is nothing short of…well, I won’t use the obvious word, but academically unacceptable would be the polite way of putting it.

I’m with you and Ichthyic too. Beckwith wants it both ways, but he’ll have credibility IF AND ONLY IF he acknowledges that he was wrong to endorse Intelligent Design cretinism in the first place. Since he’s refused to do this, he is not worthy of our respect, simply for failing to demonstrate some intellectual honesty on this very issue.

It astounds me that most of you PT folks are only capable of are ad-hominems and other logical fallacies. Insults aren’t arguments. In fact, in a refereed debate, you’d lose points.

By seeming to agree with their materialist foes that the mind or intellect cannot have direct knowledge of real immaterial universals, such as natures, essences, and moral properties, many in the ID movement seem to commit the same mistake as the one committed by the late medieval nominalists such as William of Ockham, who gave us what is often called “Ockham’s razor,”

Ah, a mistake. So I presume Mr. Beckwith has some supporting evidence other than mere fluffied-up words and pretend voices he hears? He is a scholar so I would guess that if he says something is a mistake then he has some scholarly type stuff to back it up with besides pretend la-la land stuff.

Despite my interest in this subject and my sympathy for the ID movement’s goal to dismantle materialism and its deleterious implications on our understanding of what is real and what counts as knowledge, I am not, and have never been, a proponent of ID. My reasons have to do with my philosophical opposition to the ID movement’s acquiescence to the modern idea that an Enlightenment view of science is the paradigm of knowledge. By seeming to agree with their materialist foes that the mind or intellect cannot have direct knowledge of real immaterial universals, such as natures, essences, and moral properties, many in the ID movement seem to commit the same mistake as the one committed by the late medieval nominalists such as William of Ockham, who gave us what is often called “Ockham’s razor,”

He doesn’t like ID, not because they don’t have enough evidence, but because they have way too much evidence. What could be more hilarious…

Superb, isn’t it?

Not only is Beckwith’s beef with ID that it takes science too seriously, but he thinks Ockham’s Razor is a “mistake”.

It astounds me that most of you PT folks are only capable of are ad-hominems and other logical fallacies. Insults aren’t arguments. In fact, in a refereed debate, you’d lose points.

what astounds me is that not only do you not understand what an ad hom is, but your comment is actually the ONLY one here that actually IS an ad hom, and contains no argument whatsoever.

what a wanker*.

*wanker, btw, is an insult, not an ad hom.

DaveW the clueless whined and moaned:

It astounds me that most of you PT folks are only capable of are ad-hominems and other logical fallacies. Insults aren’t arguments. In fact, in a refereed debate, you’d lose points.

It astounds me that you’re more concerned about the style rather than the substance of our critiques. Ichthyic has you pegged right; I endorse completely his observation regarding you.

DaveW said:

It astounds me that most of you PT folks are only capable of are ad-hominems and other logical fallacies. Insults aren’t arguments. In fact, in a refereed debate, you’d lose points.

I wasn’t aware that analyzing his books and other writings and quoting from the texts was ad hominem. Did you read “Law Darwinism and Public Education?” Did you read the links at WWWTW? Did you red the Discovery Institute’s glowing review of Beckwith’s work? Can you offer any explanation for these facts other than concluding that Beckwith was a ID advocate at one time and now finds that inconvenient?

DaveW said:

It astounds me that most of you PT folks are only capable of are ad-hominems and other logical fallacies.

As has already been observed, you don’t know what ad hominem means, and have confused it with “insult”.

Feel free to prove me wrong by explaining in your own words, without link to or cut and paste from a dictionary site, what ad hominem means, showing even one example of it here by anyone other than you, and showing how the example you choose can be differentiated from an “insult”.

Insults aren’t arguments.

Straw man construction. Did anyone say that they were arguments?

In fact, in a refereed debate, you’d lose points.

A highly telling remark. Refereed debating is a game. By definition, reality is suspended, and neither team can be convinced by the arguments of the other. Indeed, it is considered a great accomplishment to successfully defend an obviously wrong position.

Unfortunately, brainwashed people do indeed try to play the game of refereed debate in the real world. This, of course, renders them incapable of rational dialog. No evidence or logic can move them from their pre-determined position.

Incidentally, one would, of course, lose points, in a game of refereed debate, for misusing the term ad hominem.

Incidentally, one would, of course, lose points, in a game of refereed debate, for misusing the term ad hominem.

Or, to borrow that line from a movie:

“You keep using that word. I don’t think it means what you think it means.”

15 April 2011

Richard Lenski, “evolvability”, and tortuous Darwinian pathways Michael J. Behe

Several papers on the topic of “evolvability” have been published relatively recently by the laboratory of Richard Lenski. (1, 2) Most readers of this site will quickly recognize Lenski as the Michigan State microbiologist who has been growing cultures of E. coli for over twenty years in order to see how they would evolve, patiently transferring a portion of each culture to new media every day, until the aggregate experiment has now passed 50,000 generations. I’m a huge fan of Lenski et al’s work because, rather than telling Just-So stories, they have been doing the hard laboratory work that shows us what Darwinian evolution can and likely cannot do.

The term “evolvability” has been used widely and rather loosely in the literature for the past few decades. It usually means something like the following: a species possesses some biological feature which lends itself to evolving more easily than other species that don’t possess the feature, so that the lucky species will tend to adapt and survive better than its rivals over time. The kind of feature that is most often invoked in this context is “modularity.” That word itself is often used in a vague manner. As I wrote in The Edge of Evolution, “Roughly, a module is a more-or-less self-contained biological feature that can be plugged into a variety of contexts without losing its distinctive properties. A biological module can range from something very small (such as a fragment of a protein), to an entire protein chain (such as one of the subunits of hemoglobin), to a set of genes (such as Hox genes), to a cell, to an organ (such as the eyes or limbs of Drosophila).” (3)

Well, Lenski and co-workers don’t use “evolvability” in that sense. They use the term in a much broader sense: “Evolutionary potential, or evolvability, can be operationally defined as the expected degree to which a lineage beginning from a particular genotype will increase in fitness after evolving for a certain time in a particular environment.” (1) To put it another way, in their usage “evolvability” means how much an organism will increase in fitness over a defined time starting from genotype A versus starting from genotype B, no matter whether genotypes A and B have any particular identifiable feature such as modularity or not.

Lenski’s group published a very interesting paper last year showing that the more defective a starting mutant was in a particular gene (rpoB, which encodes a subunit of RNA polymerase), the more “evolvable” it was. (2) That is, more-crippled cells could gain more in fitness than less-crippled cells. But none of the evolved crippled cells gained enough fitness to match the uncrippled parent strain. Thus it seemed that more-crippled cells could gain more fitness simply because they started from further back than less-crippled ones. Compensatory mutations would pop up somewhere in the genome until the evolving cell was near to its progenitor’s starting point. This matches the results of some viral evolution studies where some defective viruses could accumulate compensatory mutations until they were similar in fitness to the starting strain, whether they began with one-tenth or one-ten-billionth of the original fitness. (4)

In a paper published a few weeks ago the Michigan State group took a somewhat different experimental tack. (1) They isolated a number of cells from relatively early in their long-term evolution experiment. (Every 500th generation during the 50,000-generation experiment Lenski’s group would freeze away the portion of the culture which was left over after they used a part of it to seed a flask to continue the growth. Thus they have a very complete evolutionary record of the whole lineage, and can go back and conduct experiments on any part of it whenever they wish. Neat!) They saw that different mutations had cropped up in different early cells. Interestingly, the mutations which gave the greatest advantage early on had become extinct after another 1,000 generations. So Lenski’s group decided to investigate why the early very-beneficial mutations were nonetheless not as “evolvable” (because they were eventually outcompeted by other lineages) as cells with early less-beneficial mutations.

The workers examined the system thoroughly, performing many careful experiments and controls. (I encourage everyone to read the whole paper.) The bottom line, however, is that they found that changing one particular amino acid residue in one particular protein (called a “topoisomerase”, which helps control the “twistiness” of DNA in the cell), instead of a different amino acid residue in the same protein, interfered with the ability of a subsequent mutation in a gene (called spoT) for a second protein to help the bacterium increase in fitness. In other words, getting the “wrong” mutation in topoisomerase — even though that mutation by itself did help the bacterium — prevented a mutation in spoT from helping. Getting the “right” mutation in topoisomerase allowed a mutation in spoT to substantially increase the fitness of the bacterium.

The authors briefly discuss the results (the paper was published in Science, which doesn’t allow much room for discussion) in terms of “evolvability”, understood in their own sense. (1) They point out that the strain with the right topoisomerase mutation was more “evolvable” than the one with the wrong topoisomerase mutation, because it outcompeted the other strain. That is plainly correct, but does not say anything about “evolvability” in the more common and potentially-much-more-important sense of an organism possessing modular features that help it evolve new systems. “Evolvability” in the more common sense has not been tested experimentally in a Lenski-like fashion.

In my own view, the most interesting aspect of the recent Lenski paper is its highlighting of the pitfalls that Darwinian evolution must dance around, even as it is making an organism somewhat more fit. (1) If the “wrong” advantageous mutation in topoisomerase had become fixed in the population (by perhaps being slightly more advantageous or more common), then the “better” selective pathway would have been shut off completely. And since this phenomenon occurred in the first instance where anyone had looked for it, it is likely to be commonplace. That should not be surprising to anyone who thinks about the topic dispassionately. As the authors note, “Similar cases are expected in any population of asexual organisms that evolve on a rugged fitness landscape with substantial epistasis, as long as the population is large enough that multiple beneficial mutations accumulate in contending lineages before any one mutation can sweep to fixation.” If the population is not large enough, or other factors interfere, then the population will be stuck on a small peak of the rugged landscape.

This fits well with recent work by Lenski’s and others’ laboratories, showing that most beneficial mutations actually break or degrade genes (4), and also with work by Thornton’s group showing that random mutation and natural selection likely could not transform a steroid hormone receptor back into its homologous ancestor, even though both have very similar structures and functions, because the tortuous evolutionary pathway would be nearly impossible to traverse. (5, 6) The more that is learned about Darwin’s mechanism at the molecular level, the more ineffectual it is seen to be.

1. Woods, R. J., J. E. Barrick, T. F. Cooper, U. Shrestha, M. R. Kauth, and R. E. Lenski. 2011 Second-order selection for evolvability in a large Escherichia coli population. Science 331: 1433-1436.

2. Barrick, J. E., M. R. Kauth, C. C. Strelioff, and R. E. Lenski, 2010 Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Molecular Biology and Evolution 27: 1338-1347.

3. Behe M. J., 2007 The Edge of Evolution: the search for the limits of Darwinism. Free Press, New York.

4. Behe, M. J., 2010 Experimental Evolution, Loss-of-function Mutations, and “The First Rule of Adaptive Evolution”. Quarterly Review of Biology 85: 1-27.

5. Bridgham, J. T., E. A. Ortlund, and J. W. Thornton, 2009 An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461: 515-519.

6. See my comments on Thornton’s work at the middle of http://behe.uncommon descent.com/page/2/ and the bottom of http://behe.uncommondescent.com/.

babs gerber said:

In my own view, the most interesting aspect of the recent Lenski paper is its highlighting of the pitfalls that Darwinian evolution must dance around, even as it is making an organism somewhat more fit. (1) If the “wrong” advantageous mutation in topoisomerase had become fixed in the population (by perhaps being slightly more advantageous or more common), then the “better” selective pathway would have been shut off completely. And since this phenomenon occurred in the first instance where anyone had looked for it, it is likely to be commonplace. That should not be surprising to anyone who thinks about the topic dispassionately. As the authors note, “Similar cases are expected in any population of asexual organisms that evolve on a rugged fitness landscape with substantial epistasis, as long as the population is large enough that multiple beneficial mutations accumulate in contending lineages before any one mutation can sweep to fixation.” If the population is not large enough, or other factors interfere, then the population will be stuck on a small peak of the rugged landscape.

This fits well with recent work by Lenski’s and others’ laboratories, showing that most beneficial mutations actually break or degrade genes (4), and also with work by Thornton’s group showing that random mutation and natural selection likely could not transform a steroid hormone receptor back into its homologous ancestor, even though both have very similar structures and functions, because the tortuous evolutionary pathway would be nearly impossible to traverse. (5, 6) The more that is learned about Darwin’s mechanism at the molecular level, the more ineffectual it is seen to be.

I’m not sure how this supports any of the ID/creationist claims.

There is nothing particularly surprising going on given the fact that the evolutionary process has no particular goal.

Even in far simpler systems one sees that the directions further evolution takes depends on what happened in previous generations.

Even in crystal or dendritic growth, inclusions of other atoms, dislocations caused by increasing stresses as the system grows, and any “imperfection” that emerges in the evolutionary process, simply redirects the path of subsequent evolution. And it is not likely the process could ever be repeated by rerunning the experiment.

So what exactly is your point? It seems that you are implying that evolution has a goal.

I don’t think BG had any particular point, it was just a copy-paste of a Behe article from UD. I didn’t pay it much mind, to the extent I bothered to look it over it seemed to be the usual content-free obfuscation.

mrg said:

I don’t think BG had any particular point, it was just a copy-paste of a Behe article from UD. I didn’t pay it much mind, to the extent I bothered to look it over it seemed to be the usual content-free obfuscation.

Agreed, mrg. BG demonstrated his/her worthiness as a DI IDiot Borg drone by this cut and paste.

What is more amazing is that Beckwith has a Ph. D. in philosophy from Princeton University, which is ranked among the top five philosophy departments in the country.

I believer his PhD in philosophy is from Fordham, which is not so highly ranked.

Mike Elzinga said:

babs gerber said:

In my own view, the most interesting aspect of the recent Lenski paper is its highlighting of the pitfalls that Darwinian evolution must dance around, even as it is making an organism somewhat more fit. (1) If the “wrong” advantageous mutation in topoisomerase had become fixed in the population (by perhaps being slightly more advantageous or more common), then the “better” selective pathway would have been shut off completely. And since this phenomenon occurred in the first instance where anyone had looked for it, it is likely to be commonplace. That should not be surprising to anyone who thinks about the topic dispassionately. As the authors note, “Similar cases are expected in any population of asexual organisms that evolve on a rugged fitness landscape with substantial epistasis, as long as the population is large enough that multiple beneficial mutations accumulate in contending lineages before any one mutation can sweep to fixation.” If the population is not large enough, or other factors interfere, then the population will be stuck on a small peak of the rugged landscape.

This fits well with recent work by Lenski’s and others’ laboratories, showing that most beneficial mutations actually break or degrade genes (4), and also with work by Thornton’s group showing that random mutation and natural selection likely could not transform a steroid hormone receptor back into its homologous ancestor, even though both have very similar structures and functions, because the tortuous evolutionary pathway would be nearly impossible to traverse. (5, 6) The more that is learned about Darwin’s mechanism at the molecular level, the more ineffectual it is seen to be.

I’m not sure how this supports any of the ID/creationist claims.

There is nothing particularly surprising going on given the fact that the evolutionary process has no particular goal.

Even in far simpler systems one sees that the directions further evolution takes depends on what happened in previous generations.

Even in crystal or dendritic growth, inclusions of other atoms, dislocations caused by increasing stresses as the system grows, and any “imperfection” that emerges in the evolutionary process, simply redirects the path of subsequent evolution. And it is not likely the process could ever be repeated by rerunning the experiment.

So what exactly is your point? It seems that you are implying that evolution has a goal.

Mike Elzinga said:

babs gerber said:

In my own view, the most interesting aspect of the recent Lenski paper is its highlighting of the pitfalls that Darwinian evolution must dance around, even as it is making an organism somewhat more fit. (1) If the “wrong” advantageous mutation in topoisomerase had become fixed in the population (by perhaps being slightly more advantageous or more common), then the “better” selective pathway would have been shut off completely. And since this phenomenon occurred in the first instance where anyone had looked for it, it is likely to be commonplace. That should not be surprising to anyone who thinks about the topic dispassionately. As the authors note, “Similar cases are expected in any population of asexual organisms that evolve on a rugged fitness landscape with substantial epistasis, as long as the population is large enough that multiple beneficial mutations accumulate in contending lineages before any one mutation can sweep to fixation.” If the population is not large enough, or other factors interfere, then the population will be stuck on a small peak of the rugged landscape.

This fits well with recent work by Lenski’s and others’ laboratories, showing that most beneficial mutations actually break or degrade genes (4), and also with work by Thornton’s group showing that random mutation and natural selection likely could not transform a steroid hormone receptor back into its homologous ancestor, even though both have very similar structures and functions, because the tortuous evolutionary pathway would be nearly impossible to traverse. (5, 6) The more that is learned about Darwin’s mechanism at the molecular level, the more ineffectual it is seen to be.

I’m not sure how this supports any of the ID/creationist claims.

There is nothing particularly surprising going on given the fact that the evolutionary process has no particular goal.

Even in far simpler systems one sees that the directions further evolution takes depends on what happened in previous generations.

Even in crystal or dendritic growth, inclusions of other atoms, dislocations caused by increasing stresses as the system grows, and any “imperfection” that emerges in the evolutionary process, simply redirects the path of subsequent evolution. And it is not likely the process could ever be repeated by rerunning the experiment.

So what exactly is your point? It seems that you are implying that evolution has a goal.

You appear to be assuming evolution is real at a systems level and the molecular level points the opposite direction. People use to believe all swans were white too.

babs gerber said:

You appear to be assuming evolution is real at a systems level and the molecular level points the opposite direction.

To reiterate Mike, what exactly is your point?

Evolution at “system” level is indisputable. If it was demonstrably seen to be driven by non-random directed processes at molecular level then the only possible conclusion would be Divine or Intelligent meddling in the process.

DS said:

ben aditare said:

Are you saying that if evolution isn’t real that ID must be true? The fact is that Lenski has falsified evolution since he has placed a time stamp on the process. Too little is happening over a massive amount of DNA - Lenski’s experiment is “Time in a Bottle”. We know how fast mutation arise in human DNA and the rate is in the ball park with Lenski’s results. There are vastly fewer humans since the common ancestor compared to the numbers Lenski wors with and we know the total mutations required for the human condition so we know the engine driving is totally insufficient by many orders of magnitude to see what we see about us (we have to consider all the blind alleys that were negative or neutral).

Right. Lenski has falsified evolution. Maybe you better ask him about that. I think he would disagree with you. You know, the guy who actually performed the experiments and published the results. Was that his conclusion? Why do you think that you are better qualified to interpret his results than he is?

Why is it that every creobot, when faced with an absolutely solid confirmation of the predictions of evolutionary theory, is psychologically incapable of drawing any conclusion other than, “this falsifies evolution”?

Just to recap, in case you missed it, here are the main conclusions of the Lenski experiment:

1) Random mutations occur

2) Over time these variants undergo selection in the environment

3) Eventually new functions can arise through random mutations

4) The importance of historical contingency in the above process is well documented

5) There is absolutely no evidence of any directed mutations, intelligence or purpose in the mutations

And from this you conclude that evolution is falsified! Man, I’m glad the results weren’t any more ambiguous or you would have concluded that this was proof of big foot. Hand waving arguments about mutation rates in other species (without even providing any real numbers) aren’t going to cut it. Face the facts, evolution is confirmed and ID is falsifed. Deal with it.

you didn’t take into account how fast mutations happen. The rate at which a mutation moves through the human population has been established in a Chinese test reported in New Scientist a couple of years ago. Same ballpark as seen in the Lenski experiment. We roughly know the total population size of humans since the common ancestor. Vastly lower than the number of e Coli in the Lenski experiment. Thus we know for absolute certainty when we run the numbers based on how fast mutations make changes that humans have not evolved. You can’t argue with the numbers. Does that prove ID. Not in my book. All we know for sure is all the people advocating evolution here on this forum have been proven to be 100% wrong. No one really knows how life got started or how it gets to be what we see about us.

gerald welt said: All we know for sure is all the people advocating evolution here on this forum have been proven to be 100% wrong. No one really knows how life got started or how it gets to be what we see about us.

Oh, how tiresome.

I speak under correction, and ask the indulgence of the biologists present, but isn’t it the case that a sexually reproducing organism would exhibit a much higher mutation rate than a bacterium?

Dave Luckett said:

I speak under correction, and ask the indulgence of the biologists present, but isn’t it the case that a sexually reproducing organism would exhibit a much higher mutation rate than a bacterium?

I’m not a biologist either, but sexual reproduction tends to predominate in large, relatively long-lived oranisms like us, with one popular theory of “why” being the “Red Queen’s Race”. Pathogens evolve very rapidly and so they would kill us off if we didn’t adapt. Sexual recombination reshuffles genomes, increasing genetic diversity and in effect providing more “options” for evolutionary change.

There’s some questions about the Red Queen’s Race, but it has a lot going for it.

gerald welt said:

you didn’t take into account how fast mutations happen. The rate at which a mutation moves through the human population has been established in a Chinese test reported in New Scientist a couple of years ago. Same ballpark as seen in the Lenski experiment. We roughly know the total population size of humans since the common ancestor. Vastly lower than the number of e Coli in the Lenski experiment. Thus we know for absolute certainty when we run the numbers based on how fast mutations make changes that humans have not evolved. You can’t argue with the numbers. Does that prove ID. Not in my book. All we know for sure is all the people advocating evolution here on this forum have been proven to be 100% wrong. No one really knows how life got started or how it gets to be what we see about us.

No, you didn’t take into account how fast mutations happen. If you did, why didn’t you present any numbers? Why didn’t you present even one reference? Why do you reach a conclusion, completely unsupported by anything other than wishful thinking, completely contrary to the conclusion reached be every expert, and expect everyone to blindly accept your ignorant opinion as evidence?

Human last shared a common ancestor with chimps nearly seven million years ago. SInce that time the divergence in the two genomes is only about 1.5%. There was plenty of time and plenty of mutation. You do know that evolution actually occurs faster in small populations don’t you? You do know that the mutation rate isn’t usually the limiting factor don’t you? The only one who is 100% wrong is you.

As for the question Dave asked, not necessarily. Of course eukaryotes have a much higher rate of recombination than bacteria, but the per generation mutation rate may be about the same. Of course, given the shorter generation time, that would translate into a higher overall number of mutations, but not necessarily a faster rate of evolution.

Well the Gish gallop seems to be in full force here. gerald completely ignored each of the five points I made about the Lenski paper. Then he starting talking about human evolution, even though that was not what the paper was about. Then he tried to bring in abiogenesis, as if that had anything whatsoever to do with anything.

And no matter what the results of any experiment, once again, they disprove evolution! Lenski would be rolling over in his grave, if he were dead.

Well here is a question for you ben and gerry (on your rocky road to denial), if humans didn’t evolve, why do they share SINE insertions in a nested hierarchy with other primates? (I can provide references, but only if you promise to read them). How do you think that humans got here? Got a reference for that? Thought not.

DS said:

gerald welt said:

you didn’t take into account how fast mutations happen. The rate at which a mutation moves through the human population has been established in a Chinese test reported in New Scientist a couple of years ago. Same ballpark as seen in the Lenski experiment. We roughly know the total population size of humans since the common ancestor. Vastly lower than the number of e Coli in the Lenski experiment. Thus we know for absolute certainty when we run the numbers based on how fast mutations make changes that humans have not evolved. You can’t argue with the numbers. Does that prove ID. Not in my book. All we know for sure is all the people advocating evolution here on this forum have been proven to be 100% wrong. No one really knows how life got started or how it gets to be what we see about us.

No, you didn’t take into account how fast mutations happen. If you did, why didn’t you present any numbers? Why didn’t you present even one reference? Why do you reach a conclusion, completely unsupported by anything other than wishful thinking, completely contrary to the conclusion reached be every expert, and expect everyone to blindly accept your ignorant opinion as evidence?

Human last shared a common ancestor with chimps nearly seven million years ago. SInce that time the divergence in the two genomes is only about 1.5%. There was plenty of time and plenty of mutation. You do know that evolution actually occurs faster in small populations don’t you? You do know that the mutation rate isn’t usually the limiting factor don’t you? The only one who is 100% wrong is you.

As for the question Dave asked, not necessarily. Of course eukaryotes have a much higher rate of recombination than bacteria, but the per generation mutation rate may be about the same. Of course, given the shorter generation time, that would translate into a higher overall number of mutations, but not necessarily a faster rate of evolution.

you are the one asserting evolution is true, the burden of supplying numbers in on you. Qualitative arguments aren’t scientific. Tell us what % of mutations worked in the Lenski case to create positive results (even as he created zero new species with all these mutations). Then tell us how many successful mutations it takes to create present day human population from the common ancestor. Then tell us the quantity of that population (hint try 10^8).

What you will see if you run the numbers is that Lenski has falsified evolution. Good learning lesson for you. And Lenski’s mutations represent a loss of genetic information which bolsters the creationist’s entropy argument.

As to: “ why do they share SINE insertions in a nested hierarchy with other primates?” I don’t believe in ID, I am agnostic, but one can argue conservation of design.

As to: “How do you think that humans got here?”

No clue, as I said before I am agnostic. This is the only scientific POV. What I do know for sure is that you and no one else has a clue either. And the personal attacks on ID folks I see here shows you folks have an agenda that is not scientific and is evidence of a generalized hatred of religion so you just use evolution as a tool. A workman is know by his tool and the evolution tool has been falsified by Lenski.

gerald welt said: you are the one asserting evolution is true, the burden of supplying numbers in on you.

Nobody has any obligation to you whatsoever. If you want to challenge people to talk sense into you, anybody can see that would be Mission Impossible.

mrg said:

gerald welt said: you are the one asserting evolution is true, the burden of supplying numbers in on you.

Nobody has any obligation to you whatsoever. If you want to challenge people to talk sense into you, anybody can see that would be Mission Impossible.

Even a philosophical sophist recognizes that being deliberately and arbitrarily invincible to your opponents’ arguments is something not to boast about.

Creationists always demand that we show them the evidence, only for them to then arbitrarily handwave it away.

And then they get huffy and pouty because no one takes them seriously.

Stanton said: And then they get huffy and pouty because no one takes them seriously.

Well, I’m hoping he declares victory – he will do so inevitably anyway – and then flounce off in a huff to wherever it is creationists flounce off to.

Not that I particularly want him to go away mad. Just as long as he goes away.

gerald welt said:

you are the one asserting evolution is true, the burden of supplying numbers in on you. Qualitative arguments aren’t scientific. Tell us what % of mutations worked in the Lenski case to create positive results (even as he created zero new species with all these mutations). Then tell us how many successful mutations it takes to create present day human population from the common ancestor. Then tell us the quantity of that population (hint try 10^8).

What you will see if you run the numbers is that Lenski has falsified evolution. Good learning lesson for you. And Lenski’s mutations represent a loss of genetic information which bolsters the creationist’s entropy argument.

As to: “ why do they share SINE insertions in a nested hierarchy with other primates?” I don’t believe in ID, I am agnostic, but one can argue conservation of design.

As to: “How do you think that humans got here?”

No clue, as I said before I am agnostic. This is the only scientific POV. What I do know for sure is that you and no one else has a clue either. And the personal attacks on ID folks I see here shows you folks have an agenda that is not scientific and is evidence of a generalized hatred of religion so you just use evolution as a tool. A workman is know by his tool and the evolution tool has been falsified by Lenski.

Sorry gerald, but Lenski and his team did create new bacterial species from their laboratory E. coli strains. Again, as I noted a few days ago, theirs has been one of the most interesting, most insightful, experiments in microevolution, and one that is still in progress.

One of Lenski’s former students, Paul Turner, now at Yale is looking independently at E. coli evolution within lab strains:

http://www.yale.edu/turner/projects/ecoli.htm

As for Lenski himself, this is how he summarizes his ongoing experiment:

“Long-Term Evolution Experiment

In a long-term evolution experiment with E. coli, we founded 12 replicate populations from the same ancestor, and these populations have evolved for more than 30,000 generations in identical environments. We have performed competition experiments to quantify changes in organismal fitness, analyzed whole-genome expression arrays to find beneficial mutations in genes encoding global regulators, and measured spontaneous mutation rates to discover changes in DNA-repair functions - among many other approaches and findings. Even after more than a decade of study, we continue to find fascinating evolutionary changes in these evolving populations.”

You can read more about his research here:

http://myxo.css.msu.edu/ResearchInterests.html

So you were saying that Lenski’s work “falsifies” evolution? I don’t think so, and nor does his former student Turner or Lenski himself.

gerald the religious kook:

gerald welt said:

you are the one asserting evolution is true, the burden of supplying numbers in on you. Qualitative arguments aren’t scientific.

Fine display of ignorance and religious induced brain damage here.

The numbers were run in the early 20th century by the then new fangled science of population genetics. The work of Haldane, Fisher, Wright and others.

You sound ignorant because you have never heard of them and have no idea what population genetics even is.

Given the known mutation rates in humans and common selection coefficients in a sexually reproducing population, there is no problem whatsoever in humans evolving at the rate they have been and are.

To make Gerald sound even dumber, what is rate limiting most of the time in evolution isn’t mutation rates, it is selection pressure. The mutation rates are much higher than they need to be to account for observed rates of evolution.

You can see this most readily with adaptive radiations. Whenever ecospace opens up, new species arise quite rapidly. Cichlids in African lates, the Galapogos islands, and Hawaiian Drosophila are just a few common examples.

raven, I’ve had African coffee. If there are cichlids in it, they’d have to be very highly adapted, is all I can say.

This is really an old argument with Beckwith, though he tends to dress it in different costumes from time to time. Way back in 2003 he argued to the Texas State Board of Education that, according to the law, ID was fine to teach to kids – or something so close to that that the creationists on the Texas Board presumed he meant that it was legal to teach creationism and ID.

But I’ve been to law school, and I’ve worked in education, and I’ve worked in science, and I’ve worked in public policy. I chose to make the legal case – he claimed I misunderstood the science. I pointed out the science for ID doesn’t work, he said I was philosophically in error … you begin to see the trend.

It finally struck me that Beckwith was just badly naming and highlighting a hypothetical argument. He was claiming that, hypothetically, if there were science to back ID, it could be taught. But of course, when I confronted Beckwith, he claimed again I misunderstood the law, or the science, or the price of bananas in Brooklyn and the price of Brooklyn Dodger baseball cards in Costa Rica. Or something like that.

Still, I think he’s arguing a hypothetical, though he does not understand that. On this blog I’ve made the case before, and I expanded on the idea at my own.

My understanding of Beckwith’s claims is that he is arguing, for example, that the Federal Aviation Administration would have the power to regulate pig farms, if pigs flew. It’s a perfectly logical case: FAA may regulate aviation, and regulate against aviation hazards (think of birds that fly into airplane engines). Therefore, if pigs flew, FAA could regulate pig farms.

I think Beckwith doesn’t understand that, in his mind, he’s turned the unturnable corner. He is, in effect, arguing that FAA should regulate pig farms now, and that such regulation is critical to prevent pigs and pig excrement from fouling general and commercial aviation.

He’s just failed to understand that pigs don’t fly, at least not in the real world. His hypothetical is valid, if only pigs flew.

In the real world, Beckwith’s version of the legalities of teaching creationism including ID would be valid, if only there were science to back ID. It’s a big if only.

In the real world, there is no science to back ID, just as in the real world, pigs don’t fly.

It’s a bit of a crude analogy. But I think it flies better than Beckwith’s claims that he is not an IDist.

Great comment Ed!

Creationists always demand that we show them the evidence, only for them to then arbitrarily handwave it away.

I know. And it makes me crazy.

It’s not so serious, but it reminds me of Willis Carto’s groups offering a reward for anyone who could prove the Holocaust happened. No matter what was presented to them, they’d wave it away as being incomplete, or off the mark, or not enough.

Then they ran into Mel Mermelstein. Mermelstein took it to court. The courts agreed that Mermelstein’s evidence was sufficient to the proof (and more – the court took judicial note of the Holocaust).

I think of Mel Mermelstein whenever the creationists try to wave evidence away.

You know, that’s why science keeps winning in courts. In the real world, with real evidence rules, with people trained in logic and making good judgments, evolution seems always to win.

I take solace and encouragement from that.

Dave Luckett said:

raven, I’ve had African coffee. If there are cichlids in it, they’d have to be very highly adapted, is all I can say.

After that comment, alas, I have African coffee all over my screen. No cichlids, though.

In the real world, with real evidence rules, with people trained in logic and making good judgments, evolution seems always to win.

I take solace and encouragement from that.

It’s been noted that Scalia wrote a vigorous dissent in Aguillard, and that his position seems to have persuaded Thomas, Roberts, and Alito. Depending on how a case is constructed and argued, it is entirely possible that Kennedy will join those four, and “find” that the law permits preaching creationism in science class, for whatever legal rationalizations the Scalia contingent decide suits their preferences. And three of those four are young, so a solid majority of religious right wingers on the Court is a very real possibility within the next 10 years.

I’d take more solace and encouragement if you could show me I’m wrong about that.

Ed Darrell said:

Dave Luckett said:

raven, I’ve had African coffee. If there are cichlids in it, they’d have to be very highly adapted, is all I can say.

After that comment, alas, I have African coffee all over my screen. No cichlids, though.

You’re too late

Another adaptive radiation has already begun.

Flint, Scalia’s defense was historically in error – that is, it was wrong on the history. I suspect one of the clerks did the lifting, and relied on David Barton for the history.

Consequently, I don’t fear that the three Musketeers you name will be unduly influenced by the decision, so long as there is a real hearing before hand.

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