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“We shouldn’t dismiss questions, even if some are ill-intentioned.”

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Okay, it’s finally becoming clear why all the backlash against ID. No, it’s not that ID is raising the wrong questions. No, it’s not that ID has been shown to be false (certainly Kirschner & Gerhart haven’t shown that). It’s that IDs proponents are, in the words of Marc Kirschner, “ill-intentioned.” Ah, yes, the old “argument from wickedness,” a favorite tool of scientific refutation.

Missing links
Proponents of Intelligent Design have exploited a vexing question at the heart of Darwin’s theory. Now, say two leading biologists, scientists can – and must – answer back.
By Peter Dizikes | October 23, 2005

IN A FEDERAL courtroom last week in Harrisburg, Pa., site of the ongoing trial to decide whether ninth-grade biology students in Dover should be required to hear about Intelligent Design, Michael Behe, a professor of biochemistry at Lehigh University, took the stand. Behe is the originator and main proponent of the term ”irreducible complexity,” a pillar of Intelligent Design, which refers to the notion that certain organic structures are too intricate to have evolved on their own.

Outlining his ideas for the court, Behe asserted that the flagellum of bacteria-the tail they use to swim, which Behe compares to an outboard motor-are just such inexplicable structures. ”The parts are ordered for a purpose and therefore speak to design,” said Behe.

Virtually all biologists dismiss Behe’s claims-indeed, most see Intelligent Design as a claim that research on complex structures is not possible, a position they reject. This is one reason biologists, to the dismay of some of evolution’s most vocal supporters, have often ignored the Intelligent Design movement altogether.

There are clear signs, however, that the looming presence of Intelligent Design has started having a discernible impact on evolutionary scientists. While it may not be driving their research, or dampening their sometimes boisterous internal debates, the public controversy may be forcing biologists of all kinds-and not just evolutionary biologists-to take a wide-angled view of their field, to examine how their current research contributes to evolutionary theory, and to consider how best to present evolution in the public sphere.

”We shouldn’t dismiss questions, even if some are ill-intentioned,” says Marc Kirschner, founding chair of the Department of Systems Biology at Harvard Medical School. ”But at the same time, we need to realize that science has real answers to these questions.”

Far from being restricted to the fossil record, as creationists often imply, research in the last 25 years from molecular biology, genetics, cell biology, and embryology has added greatly to the existing evidence for evolution. ”There are all sorts of demonstrations of evolution going on all the time,” notes John Gerhart, a biologist at the University of California, Berkeley.

Even so, Kirschner and Gerhart believe, some biologists and many science-literate general readers-not to mention a larger slice of the public-are unaware of the advances in the field. If Behe, for one, can question evolution, Kirschner and Gerhart contend, biologists have an increasing responsibility not only to explain evolution to the public, but to be fully aware of the evolutionary implications of their own work.

As it happens, Kirschner and Gerhart give several of these advances in evolutionary biology a broad public airing as coauthors of a new book, ”The Plausibility of Life,” published this week by Yale University Press. In it, they discuss the origins of complicated biological features-from the bat’s wing to the human eye-and present their theory of ”facilitated variation,” which they believe addresses a major question in evolution: How can small genetic changes develop into complex, useful body parts? In a sign of the times, they also rebut claims of irreducible complexity made by Intelligent Design advocates.

In so doing, Kirschner and Gerhart say, they are tackling an issue evolutionists have often left unexamined. ”The question of how variation could be produced has been there from the beginning,” says Gerhart, referring to the publication of Charles Darwin’s ”On the Origin of Species” in 1859. By the 1940s, the so-called ”Modern Synthesis” of evolutionary theory powerfully buttressed Darwin’s insights on natural selection with the post-Darwinian discoveries about the mechanisms of heredity. But, the authors write, the Modern Synthesis was ”silent” about the way organisms generated variation. It is not coincidental, they add, that because ”variation is the least understood of the theoretical underpinnings of evolutionary theory,” it thus ”is currently the favorite target” of creationists.

Kirschner and Gerhart say this situation has now changed. Organisms, they assert, have a far greater capacity to generate rapid and complex variations than even biologists had previously supposed. Moreover, from the genetic level up to our visible features, organisms have a modular structure. In this sense, complex features are less like singularly intricate structures than a collection of building blocks.

Significantly, Kirschner and Gerhart write, while random genetic mutations in our DNA code cause variations, these mutations do not create random effects (a traditional working assumption of many evolutionists). Instead, all organisms have maintained an essentially intact set of vital mechanisms-metabolism, reproduction of DNA, growth mechanisms, and more-for at least 2 billion years. These elements, along with a long-conserved body plan common to many animals, serve as the platform for subsequent, often more visible variations.

Consider the elephant’s trunk, the elk’s antlers, and the narwhal’s tusk, which all appear to be distinct, complex innovations. But as Kirschner and Gerhart point out, the same type of cell guided their growth in each animal. Moreover, the modular structure of life means these body parts could develop without affecting the rest of the organism. (A corollary is that it only takes limited genetic changes to bring about large bodily changes.) So the trunk, antlers, and tusk are really just different expressions of the same type of genetic activity-funneled through the process of natural selection, in which variations useful to a particular environment tend to survive over time.

Kirschner and Gerhart also suggest Behe does not consider modularity in his claim that only ”staggeringly complex biochemical processes” lie behind the composition of, say, an eye. As they note, the eyes of insects and mammals, each of which appear to be singularly complex, share important biochemical building blocks and connections among their components.

”People should be asking about the nature of complexity, not just how complex it is,” amplifies Kirschner, in conversation. ”You look at a clock, and you see that every part is purposely made. That’s what you would do if you were an Intelligent Designer. But instead, when you look at biology, you find that there are very few types of parts, and they are being co-opted from one place to another. We have a Lego-like capacity to very easily generate new structures.”

So far, ”The Plausibility of Life” is receiving a warm welcome from biologists. ”This is a great contribution for scientists, and I hope the general public can get a lot out of it,” says Bruce Alberts, a biochemist at the University of California, San Francisco, and a former president of the National Academy of Sciences. But the authors are realistic about its immediate impact on the evolution-creation battles. ”I’m not so vain as to think this book will stem the tide of the whole culture war that’s going on,” says Kirschner.

Some observers are even more blunt about whether progress in biology deters evolution’s opponents. ”It makes virtually no difference,” says Ronald Numbers, a historian of science at the University of Wisconsin, and author of ”The Creationists,” a history of the subject. ”Creationist arguments have changed a lot, but rarely as science has gone forward.”

Nevertheless, scientists themselves insist that the kinds of insights Kirschner and Gerhart present need to be more effectively communicated. ”We have failed to prepare our public to deal with challenges to the nature of science, from people who don’t like our findings,” says Alberts. As president of the National Academy of Sciences-his term ended in July-Alberts says he ”has tried to use this, with the [Intelligent Design] movement now outraging scientists, as a teaching moment for faculty to re-think their courses….We want people to understand what science is and why [Intelligent Design] isn’t science.”

Among other things, that means tackling the creationists’ mantra that evolution is ”only a theory,” and explaining that it is based on natural principles, which can be studied and tested in labs like any other science. Granted, evolutionists must toe a fine line between emphasizing the certainties of the discipline and acknowledging areas that need more work. ”Science has got to be an open process,” argues Alberts, adding that if events like the Dover trial limited biologists’ impulse to debate one another, it would ”harm science more than the [Intelligent Design] movement itself.”

If anything, Kirschner and Gerhart hope their book will have an impact at least as substantial on their colleagues in biology. For too long, they say, researchers in its different domains-from evolutionists in the field to cell biologists in the lab-have remained isolated. ”I wouldn’t call it an antagonism as much as one not knowing anything about the other,” Gerhart offers.

Kirschner likes to invoke the much-quoted declaration of famed 20th-century biologist Theodesius Dobzhansky that ”nothing in biology makes sense except in the light of evolution” (the title of a 1973 essay). ”In fact, over the last 100 years, almost all of biology has proceeded independent of evolution, except evolutionary biology itself,” Kirschner declares. ”Molecular biology, biochemistry, physiology, have not taken evolution into account at all.”

As a result, scientists working on genetics, cells, and molecules-a background Kirschner and Gerhart share-have not always considered how components of an organism reveal both its physiological properties and evolutionary properties and provide a window into the history of the organism. Evolutionary science, argue Kirschner and Gerhart, will advance as more biologists place their lab research within this evolutionary framework.

Nonetheless, many scientists think a convergence of biology’s disciplines is now at hand. Whereas evolutionary biologists have famously debated whether the gene, organism, or even species is the proper unit of natural selection, current research increasingly integrates these things. ”This is where it’s happening,” says Daniel Hartl, an evolutionary geneticist at Harvard. ”Evolutionists and others in the field are not arguing about reductionism any more. What’s exciting is putting it all together, from the genetic level to the organism.”

. . .

Kirschner’s present domain, systems biology, is one such burgeoning research area. In it, scientists do not intensively study one part of the body at its lowest level of complexity, as in molecular biology, but rather look at the interactions of parts or functions. Even for science enthusiasts, this can seem arcane. But Kirschner is hopeful the current interdisciplinarity of biology will help the long-term public understanding of evolution.

”I think it will affect the teaching of biology,” suggests Kirschner. Comprehending the genetic basis of evolution, he thinks, will reduce the number of ”just-so” stories often used in the classroom to explain adaptations, and can provide a broad set of organizing principles by which we understand animals even more diverse than the elephant, elk, and narwhal.

”If you take all the genes of a human and look at them, most of them look just like genes in other organisms, and many of them look like genes in bacteria,” explains Gerhart. Closely related species have closely matching genetic codes. But even bacteria and humans, distant relatives, share identical stretches of DNA relating to the metabolism. Such data provides powerful evidence for evolution by common descent.

None of which, Kirschner reminds us, is to suggest that biologists have finished their work. ”Scientists are in a bit of a dilemma here,” Kirschner acknowledges, when it comes to making their case in the public sphere. ”How do you argue that we should still study evolution if the subject is complete? I think we need to portray evolution as a tremendous and active area of investigation, where the basic principles can be well-supported. But nothing in science is ever totally complete.”

One question science cannot currently answer, Kirschner agrees, concerns the origins of life-although, unlike the Intelligent Design supporters, he considers it within the realm of scientific inquiry. This summer, Harvard announced it would fund a large-scale project on the subject, linking an interdisciplinary roster of researchers in an investigation of questions situated at the very beginning of evolution-like the development of the first cells.

”From the single-cell bacterium to the human being, we understand evolution extraordinarily well, in many parts of it,” Kirschner says. ”But there are still specific issues where we have fragments of information. That’s OK. We don’t know everything.”

Peter Dizikes is a journalist living in Arlington. He frequently writes about science and technology.

[Article originally posted at http://www.boston.com/news/globe/ideas/articles/2005/10/23/missing_links?mode=PF.]

Very nice, crandaddy. Speaking of wonders such as computers I have a third scenario which is that there are neural networks of arbitrary complexity built into all forms of life. The hardware is quantum computing elements by which a mere handful are hypothesized to have sufficient computation power to predict how proteins will fold. I give credit to Greg Bear's SF book "Darwin's Radio" for making me think about it. Interestingly the first working quantum computing elements made by IBM use the spin states of carbon atoms in amino acids for memory elements (qubits). Google it for details. I forget why they chose amino acids but something about them made them perfect for quantum computing. One might reasonably wonder if nature is using for the same purpose. It doesn't seem like anything humanity has devised wasn't anticipated by something in nature... DaveScot
Mr. Belding, I am also unaware of any detailed chains whereby one organism has evolved into something completely different; moreover, I don't think anybody has been able to construct a plausible model whereby such a macroevolutionary change is even hypothetically possible. In fact, this is what is necessary to refute each and every instance of proposed intelligent design. If unguided naturalistic processes are unable to account for the phenomenon in question, then intelligent causation is, at least for the time being, the most plausible explanation. "I am not sure what a scientific proponent of ID would propose for an explanation of how all the biological novelty arose. What are some options?" Intelligent Design theorists try to determine whether or not something is designed by an intelligent agent. How it was designed is not the direct subject of inquiry. However, this is not to say that the method of design is unworthy of consideration. As for the origin of biological complexity and novelty, it could be the case that the intelligent agent front loaded the biological blueprints into the universe from the big bang and programed the universe to unfold accordingly, or the intelligence could have intervened in the course of natural events to create it in the same way that humans create such technological wonders as computers. These are just two scenarios that come to mind. David crandaddy
taut seems to be saying that lab tests cannot show macroevolutionary change...that must mean macroevolution isnt truly science? all too many scientists claim that testability is required of all empirical science and that means ID isnt science. tho, design inference can surely be tested, so thats a fallacy from the start. the point is- if you can speed up mutation rates via complex equipment in the hands of intelligent agents (scientists), and do it for yrs and yrs and still not get any speciation, then how on earth is it possible that its going to happen without an intelligent agent guiding it in nature? no matter how long of a period were talking about. fruit flies surely didnt take millions of yrs to change into something else. that doesnt make sense, because we have millions of species in a few billion yrs. that means, every few thousand yrs, we should see some clear changes among life forms. theyve done nothing special with fruit flies. fruit flies that are damaged and dying...fruit flies that are slightly larger, fruit flies with wings in the wrong places, fruit flies with eyes in the wrong places. even intelligent agents (scientists) in complex lab experiments cant make any truly meaningful changes and thats after theyve drastically sped up mutation rates. even worse with e coli since the generations are even shorter, thus many more generations have been produced...but still- only e coli are left in the end. if intelligent agents cant break the barrier with sped up mutation rates that often times equal the same time span ur talking about...and theyre indeed using large populations- how can we, with a straight face, posit that fruit flies somehow changed into some new life form merely via NS and RM? if neodarwinian evolution were true- the prediction from these tests over many decades would be the arrival of new body forms...even small body form changes. something other than what they started out with, yet they can only get more fruit flies, more e coli and nothing else. if mutation rates have been sped up, as they have, with these tests...can we not confirm that the predictions have failed? which means the predictions have been falsified, which makes it not so much a science at all? the problem is, scientists in general wont do that- theyll continually claim- we need more time. we need different conditions to break the barrier of new body forms, new features, new novel info. additions. then, in a thousands yrs, theyll continue to claim they STILL havent had enough time. is there no limit to how many failed predictions a theory can make before its tossed aside? darwin was wrong on too many points to even count, yet we still call it neodarwinism. why? if large portions of his theory (maybe nearly all if it) were wrong, why do scientists even invoke his name? dogma, thats why. anyone, no matter how little science background they have, can see that this is a dogmatic fervor that is present in this camp, and theyll do anything to hold onto their views no matter how much evidence is mounted against it. to me, its become a farce. in everyday life, we see that randomness acting on ANY mechanism will not produce anything of value, nor will it create anything new, nor will it create something from something else. all of these types of actions require intelligent input- ALWAYS. yet, we continue to proclaim a trillion happy accidents. can anyone name any other field of study (just one) where a trillion accidents have done anything at all? let alone anything of immense value? jboze3131
tautologydna You sell short what can be accomplished in a lab. Mutation rates in the laboratory can be accelerated by any desired order of magnitude. Mutated organisms don't have to compete in order to have their genes fixed in the population. You're trying to obfuscate failed predictions with inability to carry out the experiment. The experiments didn't acheive the expected results. Get used to it. NeoDarwinian evolution is the most thoroughly tested and failed theory in the history of science. DaveScot
"Uh, oh, are they on the slippery slope toward saltationism?" They are on a slippery slope towards the truth. Ignore the screams of terror coming from the big babies as they accelerate... DaveScot
The article "Missing links - Proponents of Intelligent Design have exploited a vexing question at the heart of Darwin's theory. Now, say two leading biologists, scientists can - and must - answer back." is quite a piece of propaganda. An good conversation allows each participant to speak for themselves. Dizikes does not report on any ID theme in a way I recognize as core ID. Missing links is not the problem I have in accepting extensive evolution and common descent. It is missing long chains of life forms between species thought to be related by descent. Certainly species are related by common components and common features integrated by similar bio-networks. "Modularity", mentioned in the article, is of course a design idea and holding to natural selection as a design achiever probably requires neo-Darwinists to coopt notions of modularity. If neo-Darwinism, all biological novelty results from random mutations and natural selection, is accepted then one expects between species related by common descent chains of life forms with two adjacent forms differing by at least a randomly mutated genetic part. Since the related species survived a sure conclusion is the species in the chain survived to breed once. A reasonable expectation is that some chains persist. As far as I am aware no such chains of life forms exist anywhere with significantly different life forms at the end of the a chain. neo-Darwinism asserts the chains were there once. I am not sure what a scientific proponent of ID would propose for an explanation of how all the biological novelty arose. What are some options? RussellBelding
Aquila When someone points out that only evolutionary biologists are qualified to make judgements about evolution I like to counter with "only engineers are qualifed to make judgements about design". :-) DaveScot
"Ah, yes, the old “argument from wickedness,” a favorite tool of scientific refutation." It's the second oldest trick in the book. --Maxwell Smart DaveScot
The thing I find most puzzling about ID opponents is that they seem to be so vehemently opposed to the mere suggestion that mankind may not be an accident - that he might actually have some meaning and value to his life. Which side *really* has the evil intentions? crandaddy
"'variation is the least understood of the theoretical underpinnings of evolutionary theory,' it thus 'is currently the favorite target' of creationists." Is that so? I fail to see how "variation" alone has any substantial import with regards to either irreducible or specified complexity. I find it funny, and actually a little pathetic, how Darwinian apologists like to throw out such a blatant fallacy and then gloat with a false sense of victory over their "ill-intentioned" dissenters. Kirschner: "‘You look at a clock, and you see that every part is purposely made. That’s what you would do if you were an Intelligent Designer. But instead, when you look at biology, you find that there are very few types of parts, and they are being co-opted from one place to another. We have a Lego-like capacity to very easily generate new structures.'" Forgive me, Dr. Kirschner, if I fail to see how a chunck of plastic is similar to this: http://www.expasy.ch/cgi-bin/show_thumbnails.pl . David crandaddy
Tautologydna said... "Perhaps not satisfying to you, but that is the nature of this kind of science. It has a historical nature in the way physics doesn’t. That’s just the way it is. How you going to prove that JFK was shot by Lee Harvey Oswald ? You can’t repeat that experiment either." Tauty, don't be so silly. The last time I checked, Physics is not only historical in nature, but it is the only science that is today capable of directly observing the distant past. How else could the finest minds in our little world come to the conclusion that our universe started with a BANG? And are you saying JFK's murder was the result of random, purposeless processes? That would be a silly analogy with suposedly evolutionary processes, wouldn't it? dougmoran
jboze3131- ... but still fruit flies. Fruit flies evolved over millions of years, in a complex environment, with large populations. Those kinds of experiments can't be performed in a lab. However, at the scale that can be reproduced in a lab, many interesting evolutionary changes have been observed. Perhaps not satisfying to you, but that is the nature of this kind of science. It has a historical nature in the way physics doesn't. That's just the way it is. How you going to prove that JFK was shot by Lee Harvey Oswald ? You can't repeat that experiment either. tautologydna
TomG -- yes and no (it depends on how you define "complex"). The question, though, is irrelevant. The question is if they can do so without some form of teleology. The nylonase gene was generated in 9 days by an organism that did not have it before. However, this is clearly impossible from a Darwinian standpoint (at that mutation rate, the organism would have achieved error catastrophe if the mutations were not specifically directed). I discuss it here: http://crevo.blogspot.com/2005/06/evolution-chance-and-design-to-cb940.html johnnyb
"Organisms, they assert, have a far greater capacity to generate rapid and complex variations than even biologists had previously supposed." Uh, oh, are they on the slippery slope toward saltationism? avocationist
btw. they also claim that evolution has been tested in the lab and the support is there for it. did i miss the tests that transformed one life form into another different form? as i mentioned...theyve done yrs of study with mutations and not ONCE have they changed anything into anything else. fruit flies with extra wings...e coli that are slightly bigger. but still fruit flies and still e coli. sorry, that claim of lab testing is a false one. jboze3131
a few items. first, they constantly used the word creationist (they used that term far more often than ID)...to confuse the reader into thinking ID is creationism. the one guy is quoted as saying that similar elements in all life supports common descent, but clearly thats his interpretation and you can much easier see that as common DESIGN. as the above poster pointed out- thats the way designers work. they use much of the same stuff to build vastly different items. there are items in calculators that are used in space shuttles- are we to infer that the calculator slowly changed into a space shuttle? no. no steps have lead to any of that. they were both designed...yet designers use the same parts all the time! the other person quoted mentioned that a designer wouldnt do this and that...but thats not science! getting into the mind of an intelligent designer of life is a philosophical issue...and he has nothing to stand on when he makes claims of what the designer would and would not do. its already clear that a HUMAN designer would do precisely what he said the ultimate designer would NOT do. elephants trunks and antlers cannot be reduced to just the same genes expressing themselves differently as the authors claim. if that were the case, you could easily insert dna programs from an elephant into an animal with antlers, and instead of antlers youd get a tusk! thats not what happens...it cannot be reduced to that level, and its quite obvious that genes do not, alone, make a rabbit a rabbit or a dog a dog. its much more than that, and a lot of it is a mystery. the writer of the piece claims that creationists claim that the fossil record is the only evidence for mud to man evolution, but the fact is- creationists point to that and say the opposite! the fossil record does NOT show gradual change over long periods of time...it shows complex body forms fully formed in the record with no traces of any ancestor! the fossil record doesnt support the model at all. the other areas they claim support evolution dont support it much either- scientists still cannot even create the simple building blocks of life...and they cannot break any type of species barrier by ratcheting up the mutation rates in e coli and fruit flies. which shows us that its much more than genes and mutations that make a fly a fly and a bacteria a bacteria. genetics doesnt support the model, in the end. closely formed life would be closely related dna wise with a common designer...so you can easily see the evidence as that and NOT common descent. these guys have way too many presuppositions and refuse to see anything outside of the light of randomness, chance, purposeless, etc. its like they refuse to let go of the dogma for fear their worlds will come crashing down around them. follow the EVIDENCE, i say...sadly too few scientists are willing to do that with this issue. jboze3131
"It still puzzles me why some biologists bring up the origins of life as unexplainable by current biology principles." That's probably because you are ignorant. Perhaps these articles will help you. http://www.arn.org/docs/odesign/od171/rnaworld171.htm http://www.grisda.org/origins/20045.htm MGD
Kirschner and Gerhart say this situation has now changed. Organisms, they assert, have a far greater capacity to generate rapid and complex variations than even biologists had previously supposed.
Has it ever been demonstrated (rather than merely supposed) that organisms can generate rapid, complex, and adaptive (non-harmful) variations? Or do I have ill intentions for asking the question? TomG
> Those who study biological systems should spend more time with engineers who actually design other physical systems. There are significant parallels with biological systemsthat would illuminate their understanding of designed systems. For example, electronic systems are made up of collections of the same basic device types connected together. Everything from TVs to computers to clocks to toasters are composed of the same basic types of parts. It is knowing which specific ones to use and how to connect them together to achieve a particular purpose that is important. > Smart engineers make use of existing designs as much as possible to create new ones. It saves much time and money to adapt known good ideas and to use parts already in the catalog. That is why you can buy many different models of radios or automobiles or whatever from a given manufacturer. Very little of each model is different from the others of its type. Biological systems exhibit the same parsimony of effort, and it is a mark of good design. It is also a mark of good design to provide for variation from basic functionality. "Plug-n-play" technology in desktop computers is a good example of this. Aquila
First they ignore you, then they ridicule you, then they fight you, then you win. I've always heard it attributed to Gandhi though I'm sure others have said it. I'm wondering when they'll realize that the smartest thing they can do is shut down something like a Panda's Thumb or a Dawkins and actually address the issues. You can only ridicule the people who are paying the bills for so long. Jon Jackson

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