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Friday, April 6, 2007
He's got to be joking
Dembski's latest proof that ID is taking the scientific establishment by storm? this paper. Here's the abstract:
The extraordinary properties of natural proteins demonstrate that life-like protein engineering is both achievable and valuable. Rapid progress and impressive results have been made towards this goal using rational design and random techniques or a combination of both. However, we still do not have a general theory on how to specify a structure that is suited to a target function nor can we specify a sequence that folds to a target structure. There is also overreliance on the Darwinian blind search to obtain practical results. In the long run, random methods cannot replace insight in constructing life-like proteins. For the near future, however, in enzyme development, we need to rely on a combination of both. Dembski just doesn't get science does he? The authors aren't suggesting that proteins were designed or that evolution is false, they're talking about the relative merit of different protocols for rational protein design. I suppose if you squint really hard and have no idea of what the science involves you could read it that way, but sheesh. What a moron. And what a nice example of selectivity. **Update - added link to UC** Labels: Evolution denialism, william dembski |
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29 Comments:
It's funny, though, that folks like Dembski and Darwin Denier can
1. whine about how research that "challenges the Darwinistic paradigm" or whatever gets rejected by the Evul Atheistic Evolushunary Establishment;
and
2. crow about how research that challenges Darwinism is getting published all the time, thus showing how the edifice is crumbling
... pretty much within the same breath.
Also, if this indicates that ID is such a fruitful line of research, why aren't Dembski, Behe, or the others actually getting their feet wet with similar honest-to-god lab research?
Why just point to the work of real scientists and say "Oh yeah, we totally predicted that" after the fact?
Is it because bencjwork takes too much time away from the crucial job of making fart-noide Flash animations?
April 6, 2007 1:39 PM,
Damn typos.
"bencjwork" = benchwork,
"noide" = noise
Though I'm sure you could have figured that out. Well, any ID-sympathetic readers may not have been able to figure out "benchwork" since they don't seem aware of how to do it.
April 6, 2007 1:40 PM,
I thought this was going to be a site that talked about real issues. Instead, it's just another "panda's thumb" clone site. When will you guys grow up and come up with something more substantive than "IDiots are just poopy-heads"? It makes one wonder if that's all you're capable of.
You talk about "denialism" in a broad sense but all you seem to do is rant on creation/evolution and global warming stuff. Nothing new here. Nothing useful either.
April 6, 2007 8:07 PM,
This post has been removed by the author.
April 6, 2007 8:43 PM,
Are you familiar with the term "garbage in, garbage out"? Maybe if the ID crowd could get off their asses and
* come up with an actual theory of ID
* come up with a testable hypothesis
* TEST that hypothesis in the lab,
we might have some actual meat to chew on.
Until then I see no problem with pointing and laughing at the Emperor's swinging package.
QUESTION: If we made a fart-noise Flash animation would that make us more legitimate in your eyes Y/N?
April 6, 2007 9:29 PM,
"If we made a fart-noise Flash animation would that make us more legitimate in your eyes Y/N?"
I'm still not convinced you older than 15. Does that answer your question?
April 7, 2007 1:22 AM,
I think saying that PT is somehow a negative comparison is a sure sign of being a crank. PT is an amazing, informative and thorough site run by extremely knowledgeable scientists.
There's this funny idea that Al and disappointed seem to have that one should always stay completely civil and calm about this stuff, but that's sometimes just not possible or desirable. People who lie about science to advance their agenda should piss you off. And when they make such ridiculous arguments, as Dembski does in this case, you don't need a point-by-point rebuttal. You only need to point and laugh. This is just ridiculous.
I mean accusing protein designers of being pro-ID because they design proteins rationally? Those are some rose-colored glasses he's reading the literature with. This assertion is beneath contempt, it strains credulity, and it doesn't desrve to be dignified with an endless rebuttal.
Nor do denialists deserve this in general. We're talking about how you identify cranks here, and how it's a waste of time to spend time arguing with them. Sure, you should always try to straighten out the record when they fudge it, but in the end they're cranks, they will never be convinced of anything but what they believe because cranks don't believe in data, and it's ultimately futile to engage in some kind of civil argument with them. They won't listen.
Disappointed, tim is actually a very mature scientist who is mocking the IDists for their rebuttal of the Dover decision which famously was just a flash animation with a bunch of fart noises over the voices of ID's detractors. No matter how uncivil we may get here, tim is right, that would be hard to beat.
April 7, 2007 5:34 AM,
I'm still not convinced you older than 15. Does that answer your question?
Not sure. Is that older or younger than someone who thinks that fart-noise Flash animations constitute legitimate scientific arguments?
April 7, 2007 7:52 AM,
In response to the lack of need for substantive responses...
"ID will win because the pro-Darwin crowd is acting like a bunch of losers.
"Ewww...intelligent design people! They're just buck-toothed Bible-pushing nincompoops with community-college degrees who're trying to sell a gussied-up creationism to a cretinous public! No need to address their concerns or respond to their arguments. They are Not Science. They are poopy-heads."
There. I just saved you the trouble of reading 90% of the responses to the ID position. Vitriol, condescension, and endless accusations of bad faith all characterize far too much of the standard pro-Darwinian response to criticism. A reasonable observer might note that many ID advocates appear exceptionally well-educated, reasonable, and articulate; they might also note that ID advocates have pointed out many problems with the Darwinist catechism that even pro-Darwin scientists have been known to concede, when they think the Jesus-kissing crowd isn't listening. And yet, even in the face of a sober, thoughtful ID position, the pro-Darwin crowd insists on the same phooey-to-the-boobgeois shtick that was tiresome in Mencken's day. This is how losers act just before they lose: arrogant, self-satisfied, too important to be bothered with substantive refutation, and disdainful of their own faults. Pride goeth before a fall."
http://techcentralstation.com/100705C.html
I guess not everyone is impressed by the "extremely knowledgeable scientists" at PT. In short, this juvenile attitude is what will sink our ship. We need to either take these guys seriously or folks will stop taking us seriously.
April 9, 2007 2:21 PM,
You know why the response IDers get is one of contempt? You know why people treat ID as a pack of lies?
Because they deserve it. Because they are liars. Their own documents prove that the reason for their existence is to reintroduce creationism into schools. They were called liars by a federal judge in Dover v. Kitzmiller. Their response? Fart sounds over flash animation.
I do not understand why there is this idea that we have to remain calm and respectful to a group that exists to confuse established science. We have to be civil to proven liars who have no honest contribution to debates, just an agenda of sowing confusion and introducing religion into science class? Really?
Sorry, the contempt they get is deserved. That TCS link was as much proof as anyone needed (for more laughs go check out their reasoning for why ID will win).
Scientific theories are not popularity contests in which uninformed citizens get to choose what is true based on what makes them feel good or what is consistent with their dogma (contrary to what TCS suggests). Scientific theories are based on facts and data, of which the DI and ID supporters have none. Smart and nice people might believe it, but that doesn't make them less wrong. And the liars who propagate the misinformation that confuse people about the science don't deserve anything but contempt.
It's easier though, I guess, to whimper and cry to mommy that the mean scientists have hurt your feelings rather than actually provide data or do real bench work. Yes, they can milk sympathy that the big bad scientists were mean to them, but does that mean we should stop?
I think it would be worse to treat them like honest brokers. It's worse to act as if they can make some substantive contribution to the discussion. They are known, proven liars, and denialists. Should we be nice and respectful to the HIV/AIDS denialists too? Should we be so worried about hurt feelings that we should be sweet to the holocaust deniers?
Denialists deserve contempt. They do not deserve parity. They do not deserve to be treated as honest brokers in a debate. This desire to be nice to them is misguided. To take them seriously is the exact opposite of what denialism.com is about. Denialism.com is about how to identify denialism to make sure it is dismissed and ignored as the lies and BS that it is.
April 9, 2007 2:40 PM,
This is how losers act just before they lose
Hmm. How many court cases has ID won, again?
guess not everyone is impressed by the "extremely knowledgeable scientists" at PT.
Tech Central Station is a haven for cranks and publishes ID-friendly stuff regularly. They're not a neutral audience, they're not who we're here to persuade, and it's not like they'll listen.
April 9, 2007 7:47 PM,
Tim wrote:
"How many court cases has ID won, again?"
Since when do the courts decide what counts as science? This is the silliest argument I've ever heard. At no point in the history of science has anyone ever appealed to a court of law to determine what counts as science.
Based on this line of thinking, OJ really didn't do it (in a criminal sense) because the courts acquitted him.
It's a pretty sad day when "scientists" choose to hide behind the black robes of judges.
April 9, 2007 8:00 PM,
Since when do the courts decide what counts as science? This is the silliest argument I've ever heard. At no point in the history of science has anyone ever appealed to a court of law to determine what counts as science.
Maybe you should at least google things like this before you make a total ass of yourself. Ever hear of the lemon test? The whole point of the DI, according to their own internal wedge document, is that they exist to subvert the legal definition of science so taht creationism can be taught in the classroom.
Anyway, this is all just a distraction. No one is talking about whether or not this paper really suggests a pro-ID viewpoint. It doesn't. Pretty much all anyone can do is distract, distract.
Enough already denialists. We don't really care what you think. It's always just more BS anyway. quit thinking that you have a chance to win in a fair fight with people who know what they're talking about.
April 9, 2007 8:53 PM,
And really, the courts were the only arena where the ID'ers had the opportunity to win or lose. You can't win if you don't try, and they sure haven't tried do do anything within the realm of science. No theory, no hypotheses, no labwork...
Who's hiding, now?
April 9, 2007 9:13 PM,
I don't suppose any of you sheep happened to notice that one of the authors, Matti Leisla is listed as a from evolution? That kinda means that it's pretty likely that Dembski is right.
April 11, 2007 12:57 AM,
That's interesting. Leisola is listed as a denier but Turunen is not listed (might not mean he's not).
But I'm confused. How does that make rational protein design have anything to do with disproving evolution? Is this another one of those pathetic probability arguments in the making? Dembski's previous attempts at the maths have been little more than a joke to tear apart.
This could actually end up being really interesting. If the IDers try to attack evolution by contributing to protein science rather than just endlessly misrepresenting other science, maybe they'll actually discover something useful entirely by accident. It still won't make Dembski's argument any less of a loser.
April 11, 2007 7:13 AM,
So if Matti Leisola is a creationist, his paper is therefore... creationist? Isn't that an ad hominem? Shouldn't you argue whether the content of the paper supports creationism?
Not to mention that he's clearly not the senior scientist in that laboratory, whose name is always listed last (with some exceptions). Regardless of who wrote the article, a scientific paper must always represent the lab head's POV. If Turunen is not a creationist, then chances are (to put it mildly) quite good that he would not want to advance a creationist viewpoint.
As another example, Todd Wood, baraminologist, wrote this paper, entitled "Evolution of protein sequences and structures". This was written while working in the lab of Bill Pearson, who is not a creationist of any stripe and in fact has written commonly-used software that explicitly works from an 'evolutionist' viewpoint. The paper, similarly, works from the viewpoint that protein evolution happened and says nothing to contradict it -- indeed, it contradicts one recent ID talking-point which attempts to make the claim that even small mutations can entitrely scupper a protein's structure and function.
Wood and Leisola may be adopting similar positions here, working within a scientific framework which they deny in order to obtain their degrees. Compartmentalizing their beliefs from the science they practice.
But I guess we'll never know for certain if the denialists don't want to discuss the content of the paper.
April 11, 2007 7:40 AM,
It's interesting you say that tim. I was just thinking about Todd in this context.
And as a matter of due diligence I did contact Leisola to ask if he wanted to discuss the paper or indicate if he feels it disproves evolution. He did not reply.
April 11, 2007 7:44 AM,
Tim wrote:
"So if Matti Leisola is a creationist..."
Who said anything about being a creationist? Lynn Margulis (endosymbiosis) disagrees with much of Darwinian evolution but that doesn't make her a creationist. Similarly, Michael Behe doesn't appear to be anything nearing a creationist. It's extremely over-simplistic to suggest that one must either be a creationist or an evolutionist (unless you define the terms so broadly as to loose their meaning).
dd
April 11, 2007 7:14 PM,
I'm not going to waste my time going into the voluminous data linking ID to creationism with a staunch denialist, so -- for the duration of this argument only, and to try to steer you back onto topic -- I will concede.
Replace "creationist" with "ID supporter" and my point still stands. If the paper supports ID, you should be able to do so by specifically pointing out how the data does so, not by screeching about the author's affiliations.
Can you do so?
April 11, 2007 9:14 PM,
Tim,
The paper makes the distinction between blind darwinian processes and the directed, "darwinian inspired" methods they employed. Unless you are prepared to say that darwinian mechanisms can be explicitly teleological, then this becomes ID. Indeed, they were using these directed methods to pursue specific ends, which, again darwinian evolution does not do.
Indeed, we are reminded of this in the review of Michael Behe's new book:
"Although Behe writes with passion and clarity, his calculations of probability ignore biologists' rejection of the premise that evolution has been working toward producing any particular end product." (emphasis added)
dd
April 12, 2007 1:12 AM,
DD,
It makes no such distinction at all, actually. It is a review article comparing two methods of protein engineering: one which uses evolution in the lab, and "rational design", an emerging idea for engineering proteins out of whole cloth based on what we know about relationships between protein folding, structure, and function -- information that, the authors state, we don't have enough of yet. So much of the paper is in fact devoted to successes of the evolutionary method.
There really is no distinction between directed evolution and evolution in the wild, vis a vis the role of randomness versus selection. The mutagenesis portion is random, but that is filtered through a process of selection for specific traits. From the article:
"Random or directed evolution methods involve a set of techniques to create random changes in a protein structure by genetic methods and selection of new protein variants. The gene of interest is diversified through mutations, and the created library of mutated genes is tested against a specific selection pressure, for example a particular property of a protein. The best variants are iteratively subjected to a new round of mutations."
Mutation plus selection? That sounds like conventional evolution to me. Evolution in the wild does have a "target," and that is "anything that will give me a competitive advantage of some sort." Exactly the same principle applies here, it's just that the selective pressure is determined by the scientists themselves.
Funny thing is, even the "rational design" method may start from broad strokes of structural data and computations, but still requires screening (selecting) lots of individual variants.
The authors do explore some shortcomings of directed evolution (after discussing its successes), having primarily to do with unsuccessful applications of some known mutational mechanisms in the lab specifically for the purpose of protein engineering. There is a crucial difference between that and the origination of traits in biological systems, which the authors briefly make note of. There is a brief statement of the incompleteness of some ideas in explaining the origination of certain structural features:
"It is often said that random genetic methods to improve enzyme properties "rely on simple but powerful Darwinian principles of mutation and selection" (Johannes and Zhao 2006). We agree. It is also said that "every protein has become adapted by step-by-step improvement and refinement of its function over millions of years" (McLachlan 1987). The present theories, however, only partly explain the protein diversity, although a recent study (Poelwijk et al. 2007) shows that even the key-lock dilemma can be resolved by the Darwinian approach when the operation field for random search is within the same protein family, and the new key-lock pair closely resembles the original (ancestral)."
... yet nowhere in the paper do they tout "design" principles in the wild, only in the lab.
Furthermore, after that passage the authors go on to explore the advantages and weaknesses of finding novel traits through directed evolution in the lab, in addition to just refining current traits. That is what they were referring to in the abstract about an "overreliance on Darwinian methods" in protein engineering; it can hamstring our ability to design new proteins, something that can only be achieved if we more fully understand the relationship between structure, folding and function -- which is something no "evolutionist" would deny in the slightest. But nowhere in the paper do they even suggest that this means proteins with novel functions cannot emerge in the wild -- indeed this would be a silly position to take, given that it is contradicted by empirical evidence (nylonase, for one).
In short, as near as I can tell, Dembski has claimed this paper for ID simply because it uses the term "design." Well, yeah, we design things in the lab. That's what we do in science, just like we design experiments that mimic evolution in the wild. It's not evidence in the slightest that ID was responsible for the "design" of the proteins in our bodies and the authors make that pretty darn clear.
April 12, 2007 8:56 AM,
Nice job tim.
But, Dembski's still harping on it.
Once again, I'm not patient enough to go through and show why he's wrong, he's doing more or less the same thing though. Conflating lab designed experiments with design and blathering about teleology.
This is one instance in which he might as well just quit and say he goofed. It reminds me of the Princess Bride for some reason, "this paper, I do not think it means what you think it means."
April 12, 2007 9:40 AM,
"There really is no distinction between directed evolution and evolution in the wild, vis a vis the role of randomness versus selection."
Except for the "directed" part. Are movies "directed" by unconscious forces that don't have specific outcomes in mind? Are orchestras?
For something to be directed, it must have a director. For something to be directed involves teleology. Reading Gould or Dawkins or Mayr or Miller or Pinnock makes it clear that evolution has do director and is not teleological, not one bit. Or did I miss the memo that non-material causes directing evolution towards specific ends is now an allowable explanation?
dd
April 12, 2007 1:37 PM,
I think you missed the part where I explained that environmental selection imparts the "direction" in nature as well as the lab.
See, take a relatively inefficient, but crucial, enzyme. Like nylonase, which was adapted from a completely different protein and hence is rather slow and inefficient in its task. Now say that nylon is suddenly in short supply, which provides the environmental pressure. A mutation that improves its efficiency, even by a tiny increment, will confer an advantage to its possessor by allowing the bacterium to assimilate more nylonase and grow faster. So the presence of that allele within a population will spread. Successive generations, and succesive mutation/selection steps, will further refine the nylonase to become more efficient.
This is basic stuff and apparently the only reason I need to go over it is that creationists keep reading superfluous teleology into it. It's no more teleological a process than a ball rolling downhill (Intelligent Falling!).
Also, humans would definitely fall into the category of "material causes."
But I'm curious about Dembski's sudden position on "directed evolution"... doesn't that imply theistic evolution, which he's previously pooh-poohed as a "cowardly" stance?
April 12, 2007 2:55 PM,
Tim,
What your analogy was missing was any sense that the activity was directed. Indeed, it was no more directed than a ball rolling down a hill.
That notwithstanding, to say that evolution is directed towards greater fitness (or any end) is to say that critters are evolving torwards greater fitness, which is an inherantly teleological statement. It implies that the purpose for certain mutations becoming fixed in a population is to infer greater reproductive success to the bearer of those mutations. Teleology has been consistantly rejected by evolutionary theoriticians. This can't be surmounted by simply suggesting that directed (or teleological) evolution isn't teleological.
Of course, you also have the problem of whether or not natural selection can truly be considered a "cause" in the formal sense. If it can't be considered a cause then it can't direct anything. This is one of those times where it's all too easy to skip the heavy lifting done by the philosophers of science but this is exactly what is at issue.
Also, it's not at all clear that humans always count as material causes (sensu Tim). For example, if a carpenter reads a blueprint and then erects a frame in accordance with the specs contained therein, it's obvious that the blueprint is the formal cause and the wood, nails, screws, ect are the material cause (sensu Aristotle). However, what is the efficient cause? The efficient cause is the carpenter mentally translating the lines on the blueprint into actual materials, amounts, dimensions, etc to build the frame. This is a form of mental causation. It is in no way clear nor self evident that mental causation is material.
There are other forms of human causation that would be even more difficult to categorize as material causes (sensu Tim). For example, if you watch an advertisement or read a book and, based on what you see or read decide to adopt a different mode of thinking on a particular topic, there is no material cause (sensu Tim) at work (indeed, no material effect need have taken place either).
dd
April 12, 2007 4:44 PM,
What your analogy was missing was any sense that the activity was directed. Indeed, it was no more directed than a ball rolling down a hill.
That notwithstanding, to say that evolution is directed towards greater fitness (or any end) is to say that critters are evolving torwards greater fitness, which is an inherantly teleological statement.
Not at all. Selection is highly dependent on environmental pressures; remove the pressure (say, a return to an abundance of nylon), and there is no longer any significant advantage to accruing positive mutations. Not to say that they won't (and this simple analogy leaves out neutral mechanisms; we're addressing selection, not evolution as a whole).
But it certainly doesn't imply some striving for some Platonic-ideal protein; it's just an accumulation of positive changes that happen to end up that way. Think of the old joke about two guys running from a hungry bear: you don't have to be Ben Johnson, you just have to be faster than the other guy. ;)
The only real difference between natural selection and artificial selection is that humans are setting the parameters of success. Otherwise the process -- iterative increases in efficiency -- is identical.
And absent any a priori assumptions about unevidenced non-material mental phenomena, humans should be considered material causes. You seem to be confusing non-observable with non-material, and that because you can't "read" thoughts, mind is a non-material cause (apologies if I misunderstand). However, we do know that physically screwing with the human brain can destroy that carpenter's ability to read the instructions, or the motor skills to wield his tools, or so on. Advances in neuroscience mean that we can identify portions of the brain directly involved in spatial interpretation, language, motor skills, and that firing of those neurons correspond with those activities.
You may not personally find the evidence for a material mind conclusive, but on the other hand there is zero evidence to conclude any mysterious non-material causes for thought. Therefore it is not a useful scientific model. If you could show me someone capable of thought without brain activity, you might be on to something. As it stands, it's superfluous, like proposing that a ghost pulled that ball downhill.
April 12, 2007 6:25 PM,
Tim,
The fact that thoughts and brain activity occur together in no way means that brain activity is sufficient to explain thought any more than your foot pressing on the gas peddle occuring together with your car accellerating makes your foot pressing the accellerator sufficient to explain your car accellerating.
Getting back on point, neither your example nor your explanation said anything about the activity being directed. However, when you talked about the difference between natural and artificial selection, you hit it squarely on the head. In artificial selection, the end is in mind, directing the progress of evolution. In natural selection, there is no end in mind and, therefore no direction. A breeder has specific ends in mind (calves with lower birth weights but higher weaning weights, for example) but natural selection has no such ends in mind.
You may retort that the end being "sought" is fitness but this isn't really an end any more than flowing water is seeking an end. Both are simply following the path of least resistence, which is not purposeful, not teleological and, therefore not directed.
dd
April 12, 2007 7:06 PM,
Hi DD,
You're right that we're getting off topic, and the topic is this: the Turunen paper creates no distinction between "directed evolution" and evolution "in the wild". This much is clear even in the abstract Mark posted, where they use "directed evolution" interchangeably with "Darwinian methods". The entire point of the paper is to review directed evolution and compare its strengths and weaknesses to rational protein design.
Seeking support for your (or Dembski's) position with this paper is therefore a nonstarter, because they simply do not address these issues. Directed evolution is Darwinian in the context in which they discuss it, and they make no distinction between evolution in the lab vs in the wild, and certainly are not criticizing any aspect of the latter.
If you can point out any particular passages in the paper that you feel supports your position, please quote them and we can discuss. Otherwise I think we can consider that topic settled.
That said, I love debate too much to ignore the derail, so I'd be happy to continue with that, if you wish.
Anyway, what I have been trying to say is, neither directed evolution nor "undirected" evolution have any specific endpoint in mind. In each generation, a variant/allele which is superior to the others will be found in greater proportions in subsequent generations. Repeated iteratively over many generations, the variant will improve -- that is the "direction" in which evolution proceeds, as long as environmental pressures apply. This will continue until no further improvements can be made, at which point the population may compete over some other trait (in the wild) or the researchers declare it a success (in the lab).
Note that last bit: the researchers did not have a specific goal in mind. As with nature, the only goal was to find the one variant within the immediate population that was better than its neighbors. The researchers didn't know quantitatively how the enzyme would behave, they didn't know what the sequence would be, or really anything specific. If they did, they'd be doing rational protein design instead.
Rational protein design is the method that really does start with a more specific goal in mind, drawing on knowledge of structure and folding to build a better protein from the ground up. Basically evolution, both "directed" and "natural", works by co-option and jerry-rigging, making the best of what you start out with. As the authors point out, this doesn't result in a "perfect", 100% efficient protein because the range of structures it can adopt will be constrained by its original structure. Folding and structure tends to be pretty resistant to the sort of small-scale point mutations employed in the lab (large-scale structural changes can happen spontaneously in the wild: the authors in fact explicitly acknowledge this, but state that our ability to replicate these processes for the purpose of directed evolution has met with only limited success).
Thus, directed evolution, as currently practiced, can only result in limited changes to the overall structure. At least, it's not practical or cost-efficient to count on the sort of large-scale changes that can happen in the wild. Therefore the authors compare that to rational protein design, which starts with a backbone (and endpoint) that will be most efficiently suited to the intended task.
April 13, 2007 4:18 PM,
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