Santorum and Intelligent Design

Now that a federal judge has slapped down the Dover (Pa.) Area School District's intelligent design policy, Sen. Rick Santorum (R-Pa.) has left the advisory board of the Thomas More Law Center, the policy outfit that fought the district's case in court.

Santorum says the center picked a bad case to litigate because the Dover district mandated intelligent design instruction rather than leaving it up to the teachers to mention the "controversy of evolution" to students.

By controversy Santorum evidently means the ongoing debate between Rick Santorum and Rick Santorum.

Comments

[thoreau]

So that's what the creationists have devolved into? The option of briefly mentioning controversy in class?

You know, it's kind of pathetic. The Mighty God of the Gaps was once an awesome sight to behold. Nowadays, he's nothing more than a quick mention of a controversy.

And yet the creationists continue to fight.

It's sad.

[Herrick and His Balls]

Huh huh huh, you said santorum.

[Rich Ard]

Did I just see testicles make fun of someone?

[NoStar]

Thoreau,

Would you do me a big favor and tell me if this means anything?

It purports to discredit evolution and has something to do with folding and unfolding proteins. To mangle a famous quote "Any advanced science will appear as goobledeegook to an airhead, but then so can goobledeegook."

http://www.cs.unc.edu/~plaisted/ce/blocked.html

Can you tell me if this is science or not science?
I don't have anyone else to ask and I do respect your opinion.

Thanks,
NoStar

[Proctor Silex]

There must be some mistake -- a Santorum entry without 'frothy mix' in the headline?

Who gave who the day off?

[thoreau]

NoStar-

The intro knocks down some strawmen. But I skimmed ahead a little farther anyway. It's not my field, but I encountered something about protein structure and hydrophobic vs. hydrophilic groups. I have done a little work with amphiphilic molecules, so I read that paragraph. I don't know a lot about the amphiphilic aspects of proteins, so I can't comment authoritatively, but he seems to misunderstand a few things.

Maybe I'll read more later, but it seems pretty weak.

[Herrick and His Balls]

I actual research protein folding and misfolding, so I might be able to give a response to NoStar's link if it wasn't so damn long. Can I get a paraphrasation?

[Herrick and His Balls]

That should be an "actually" above. Oh man, too much egg nog, which is my second favorite milky fluid.

[Warren]

No Star,
I'm not thoreau but I'll tell you what I think anyway. The article you link to is too long and difficult to parse for me to 'read for comprehension'. So I can not say for sure if there is anything of interest or not. There are a couple of things in the opening paragraphs that make me skeptical. First of all the article starts out with a lengthy discussion of what it is not. The author talks about other, unrelated arguments and why this argument is "more scientific". Such a discussion would have no place in a scientific paper. So we conclude that this is a non-scientific article about a scientific article. Which is perfectly fine, but it is completely lacking in form and structure. There are no paragraph or chapter headings, to assist the reader. This makes it very difficult if not impossible for the reader to comprehend. That of course is a hallmark of pseudo science.

As the author tells it, this work 'proves' that certain evolutions of proteins are impossible. I've seen other work with similar claims such as "the probability of the base pairs randomly occurring is?" with some small number indicating that the universe would have to be millions of times older before it could be expected to happen once. These arguments make a couple of errors. First of all they assume that everything must happen at once. That you have to jump from one form of protein to the next without any intermediary form. This of course ignores the fundamental quality of evolution. Another problem with this type of argument is that the author assumes he knows the circumstances that it must have occurred in. However there are many process in nature (freezing, pressure heating, etc.) where chemical reactions take place that can yield results not reproducible in a bowl of soup. (Creationists often have this idea that evolution starts out with a warm soupy ocean and later a mud puppy crawls out.)

However, it is clear that the author is well versed in his subject matter. From what I can tell the mathematics presented not erroneous.

My greatest skepticism stems from the repeated claims of the nature "it therefore follows that in order to achieve such and such, it must have been accomplished by this and that" where I do not see how it "follows" at all, but then I am outside my field of expertise.

It looks like crap to me, but I can't pull it apart far enough to point to something I can positively identify as poo.

[Herrick and His Balls]

Also, if this really did disprove evolution, I'd think it might be in Nature or Science instead of on a student web page

[thoreau]

Herrick-

It can't really be summarized, because it doesn't have a central thesis. It's a rambling run through a wide range of issues in protein folding, purportedly showing how none of this could have come about through the accumulation of small changes. I don't know much about the field, but I noticed 3 things:

1) Strawmen in the intro
2) Some questionable statements about amphiphilic molecules. It isn't pivotal to his case, but if I find an expert in another field making mistakes that even I can catch, I become much more skeptical.
3) He cites the Sacramento Bee as one of his references. (I'm sure it's a fine newspaper, but it's not the place I'd look for info on protein folding.)

Three strikes and this article is out of credibility as far as I'm concerned.

[thoreau]

instead of on a student web page

Actually, he's a computer science professor.

The biggest mistake that non-biologists make is thinking that we're smarter than biologists. I've been disabused of that notion. I do think that I have something to contribute, but I don't labor under the illusion that I'm smarter than them. Anyway, it's no surprise to me that he thinks he can debunk them. But it's sad that he writes like a crank, as Warren said: Long paragraphs, no headings, bold claims, etc.

I'm sure he's very good at what he does, but he's showing all the signs of a crackpot when he steps outside his field.

Sad.

[Jeff P.]

My proteins are folded to the point of creasing. Can I iron them without damaging them?

[jimmyboy]

Did anyone go to this guy's homepage?

http://www.cs.unc.edu/~plaisted/ce/index.html

I tried to read the article and my eyes glazed over--I am just not sufficiently knowlegdeable in biochem to follow his arguments. This does not even include folowing his references to see if he has taken liberties with them.

However his home page makes his perspective clear--which does not necessarily invalidate his argument--he is not a disinterested onlooker however.

On one occasion, long ago, I had the pleasure on a discussion board of having the book on hand from which one of these guys was citing, and I nailed him--but his arguments were much more simpistic and straightforward. Again, this doesn't mean they all do this but I am skeptical of claims as sweeping as those he makes in his last sentence:

"Unless the evolution of proteins of new shapes is possible, evolution is blocked. All scenarios for protein evolution have been shown to be mathematically impossible, under reasonable assumptions."

That sure ends the conversation.

He is a computer scientist (this reminds me of a book by Updike which I read a long time ago--I think it is called "Roger's Version"-- in which a Theology Prof takes on a grad student who wishes to disprove evolution by making these probablistic arguments. Not much science in it but a cool novel.

[jimmyboy]

Here's an interesting quote from his site:

Instead of postulating that an intelligent designer was involved in the origin of life, one can simply hypothesize that highly non-random events contributed to the origin of life. Stated another way, from time to time the laws of probability are suspended and events that may seem to have a purpose simply happen, for reasons that we do not fully understand. This approach does not say what the cause of this nonrandomness is, but only that it sometimes takes place. Of course, the intervention of an outside intelligence could have contributed to such nonrandom events, but this need not be mentioned in the classroom.

I like this because I'm willing to bet that this is the kind of tactic that might be expected from the creation/ID people now that it seems that the Dover endeavor has been stifled.

What is interesting is how much ground these guys have ceded. Even ID--what I've read of it--does not contest the idea of an old earth or of evolution. They merely assert thate it must be guided. It seems to me that there is no way of reconciling ID with the theology of, say, the southern Baptists. These folks reject evolution because it is irreconcilable with the idea that death was introduced inte world by original sin. If they appear to support ID, they do so with something else in mind, I think.

[Jennifer]

This was the only quote from his site that I needed to see:

We do not mean to criticize those who support the theory of evolution, but for one who is willing to accept the possibility of supernatural intervention, we believe that a creation theory is an acceptable alternative.

If you are willing to accept the possibility of supernatural intervention to explain natural processes, then, at least in regards to those processes, you're not a scientist.

[cell biologist]

While I agree with all that's been said about the sloppiness, straw men, etc, I actually don't think the guy's a total kook--after the non-random quote above he goes on to say:

"It is true that one cannot give a scientific explanation for such nonrandom events, or demonstrate them in the laboratory. However, there are many aspects of science that are not yet understood, so this lack of an explanation and reproducibility should not be a reason for rejecting this theory. "

Not unreasonable, it seems to me. He also seems to understand the key scientific issues re: testable/falsifiable hypotheses, micro vs. macro evolution, etc, and to be genuinely engaged in a search for some actual answers, unlike the bulk of the ID folks who simply want to shove their own god down everyone else's throats.

All that said, I think he's wrong about the protein evolution, first for assuming that proteins are the main engines of evolution (as opposed, for instance, to catalytic RNAs), second for not talking about gene duplication (at least as far as I could tell by skimming), which allows a duplicate gene to randomly wander into either non-function or new function while the original retains its function.

[Rick Barton]

This is evidence that Santorum has some regard for choice.

On the cited critique of protein evolution:

The critique makes the mistake of looking at forms of proteins and then calculating astronomical odds against chance producing the transition from older to current forms. The problem is that this approach ignores intermediate forms, which conferred function for the organism. The author does not consider that the process coulda been step-wise, thereby reducing the improbability of the earlier forms morphing into the current forms.

I've encountered this type of error before in evolution critiques. It's covered in the book: Finding Darwin's God: A Scientist's Search for Common Ground Between God and Evolution by Kenneth Miller. The volume is a defense of evolution by a Bio prof. who is a serious Catholic.

[Rick Barton]

Jennifer:

If you are willing to accept the possibility of supernatural intervention to explain natural processes, then, at least in regards to those processes, you're not a scientist.

Yeah, and just what is "supernatural"? It sems like an impossible concept. I don't think that there is any supernatural. There is only what we don't understand.

[toxic]

If a guy is preempting any attempt to produce, you know, actual evidence (i.e. reproducability) ... quack quack quack, if you know what I mean.

I had a science teacher in junior high who thought he'd figured out how to debunk relativity.

Smart guy. Bet this guy is smart too.

[Dave W.]

So that's what the creationists have devolved into? The option of briefly mentioning controversy in class?

"Devolved into?" I guess. Sounds like they are figuring that the ID meme is dead and that they have to focus on stuff that is more important, true and real -- like the spiel we worked on together yesterday, T. Santorum says "evolution controversy," I say "limits of science." Amounts to the same. I certainly hope Santorum doesn't get too involved. Things were going so much smoother when it was just u & me and besides Santorum is just awful on gay issues. I think he is like a fundie or something.

[Dave W.]

Actually, I think he is Catholic, IIRC. The old fashioned kind, like one of my parents. But ???, really.

[Dave W.]

supernatural intervention to explain natural processes

What if the hand of God did indeed place the sun so that it would shine on the balls of some homo habilus in just such a way that his daughter would be true man? Would this hypothetical intervention be a supernatural intervention or a natural intervention? Would the fact that God used the Sun's rays make the intervention natural, instead of supernatural? Is there a meaningful distinction between natural and supernatural, or are these terms more like poles of a continuous spectrum?

[The Great Ape]

under reasonable assumptions."

The guys from what used to be Long Term Capital Management would have a few things to say about dependence on 'reasonable assumptions' to prove a point.

[quasibill]

It's been a few years since I was actively involved in biochem, but my quick scan threw up a few red flags, most of which have been mentioned above.

The one concept which he seems to be missing is a concept which is somewhat fringe but currently working its way to greater acceptance: evolution is in itself, a problem solving process. Not that it is conscious, or even an individual intelligence as we define it, but as the result of coordinated decisions and results of relatively large populations, the best solution to a given challenge IS likely to be accomplished, especially, as many have noted, when intermediates provide noticeable improvements in survivability and/or reproduction.

It's kinda the same argument about the superiority of free markets v. planned markets. Many independent agents making decisions and taking risks solve the problem faster and cheaper than a top-down, focused, risk averse process.

So his arguments about improbability are addressed by some real science, that real scientists are testing according to the scientific method. Probability, like all mathematics, is a nice tool, but it is highly dependent on the starting assumptions.

[Isaac Bartram]

Actually, I think he is Catholic, IIRC.

You do recall correctly.

http://www.vote-smart.org/bio.php?can_id=H3521103

What I find interesting is the extent to which catholic politicians find a need to pander to what they belive are the beliefs of the core supporters of the party.

After all Santorum and Pat Buchanan do not need to believe in creationism in order to be in good standing as catholics. The Pope stamped evolution as A-OK years ago. So it occurs to me that they can hardly claim that their belief in creationism comes from the teachings of their church.

Now, what about their positions on capital punishment?

[Randolph Carter]

My favorite moment that's come from this was some Fox News reporter outside a courthouse saying (completely without irony), "Well, Shepart, we don't know everything right now, but this is a story that continues to evolve."

[thoreau]

Dave W.-

Actually, yesterday, when you wanted to talk about the limits of science, you asserted that nobody knows how mutations come about. I said that physical chemistry actually has something to say about it.

Don't claim that you and I are reaching a consensus if you're leaving out key parts of the exchange.

cell biologist-

I agree, the guy isn't a total crank. But he shows signs of amateurism in his critique. It's sad, because you'd expect a professor to at least put more polish on it.

[Mo giggity]

Number of legit scientific results from ID = number of legit scientific results from astrology.

Teach the controversy.

[Son of a!]

Number of legit scientific results from ID = number of legit scientific results from astrology.

Teach the controversy.

"There is a continuing and ongoing debate in which many people continue to believe that the positions of the planets and stars can influence one's personal life."

Only the ignorant and intellectually-dishonest actually believe any of this (either astrology or ID). The "controversy" is that there continue to be such people in the world.

[Warren]

Hey I just realized that I made reference to poo in my comment last night and didn't even make a tie in with Santorum. Santorum-poo hee

The Senator is such a total asshat. I hope they snicker at his funeral.

[Jennifer]

Yeah, and just what is "supernatural"? It sems like an impossible concept. I don't think that there is any supernatural. There is only what we don't understand.

In context, I think the guy meant supernatural to mean not "what we don't understand," but what we CAN'T understand. Ever.

Think of this: before the discovery of nuclear energy nobody could figure out how the sun worked--according to all available scientific knowledge, it should have burned out after just a few centuries. But a true scientist would have said, "We don't understand how the sun works, but in time we will probably make more discoveries in that area." Whereas an ID/supernatural proponent would say "It's God who does it, and we will never be able to understand it, because God doesn't conform to mathematics and equations."

When this guy said "supernatural," he meant "something above and beyond all natural laws," not "something which we currently do n ot understand."

[Dave W.]

Actually, yesterday, when you wanted to talk about the limits of science, you asserted that nobody knows how mutations come about. I said that physical chemistry actually has something to say about it. Don't claim that you and I are reaching a consensus if you're leaving out key parts of the exchange.

Uhh, okay. We haven't gotten to a concensus yet. Our work is co-operative and ongoing. We are making some good headway now that we are lissening 2 each other!

[jkp]

And what the hell is with National Review Online metaphorically sucking ID cock nowadays? (Other than Derbyshire, who remains entertainingly curmudgeonly anti-idiotarian, even if we don't always understand why he says the things he does.)

[NoStar]

Dear Thoreau, Rick Barton, Warren, Jimmyboy, Cell Biologist, and everyone who commented on my question,

Thank you. Your specific concerns give strength to my vague feeling of unease with the article.

I love Hit&Run for the interesting mixture of serious discussion and smart assed retorts. I apologize that I am usually able to provide the latter and not enough of the former.

Merry Christmas to you all.

NoStar

[Rick Barton]

Jennifer,

Yeah, I'm hep that he meant "something above and beyond all natural laws," not "something, which we currently do not understand." My point was that the idea of "supernatural" forces does not make sense if they are being alleged to interact with and thus affect the natural world.

[Rick Barton]

No star,

Merry Christmas to you as well! Thanks for all your input, including this matter.

Merry Chritsmas-Happy Chanukah(sp?)-Happy Holidays, everyone!

[Jennifer]

My point was that the idea of "supernatural" forces does not make sense if they are being alleged to interact with and thus affect the natural world.

Which meshes with my earlier point, that anyone "willing to consider supernatural intervention" is NOT a scientist.

[Rick Barton]

Jennifer,

Yep, I think your point is strong. When someone posits supernatural intervention, it's like they're saying; "I have this hypothesis, but you can't test it." That's definitely not science.

[Rick Barton]

...Now positing a God that had to obey phycical law with its divine intervention, as opposed to supernatural intervention, would be more defensible. But then what kind of a God would we have? What would "God" mean in this context?

[NoStar]

Rick and Jennifer,

The supernatural exists in the 7 dimensions that exist from whence comes the foam that gives rise the m-branes that created our 4D universe.

See, cutting edge physics allows for a place for God to exist.

[NoStar]

correction: ...that gives rise TO the m-branes...

[Rick Barton]

To say this one in a little more rigorous fashion: When someone posits supernatural intervention, it's like they're saying; "I have this hypothesis, but *by nature* you can't *ever* test it."

[Rick Barton]

NoStar,

Yeah, I think that a criticism of string theory is that seems kinda like religion.

[thoreau]

String theory is NOT religion!

I'm just not sure that it's science either.

There are more than 2 options, you know. It could be "none of the above."

[zach]

The supernatural exists in the 7 dimensions that exist from whence comes the foam that gives rise the m-branes that created our 4D universe.
See, cutting edge physics allows for a place for God to exist.

God always has a place to exist in uncertainty, and science will always have an abundance of that. But I don't see why a reasonable mind would decide to call the first four dimensions "natural" and the last three "supernatural" (even assuming the accuracy of string theory). Unless your definition of the word were something like "really nifty".

[joshua corning]

"String theory is NOT religion!

I'm just not sure that it's science either.

There are more than 2 options, you know. It could be "none of the above.""

This is why god invented Science Fiction.

[Rick Barton]

thoreau,

I didn't say that a criticism of string theory is that it IS religion. I said "kinda like". Perhaps the critique derives from the un-testability of some of its hypotheses. Why do you say that you're just not sure that it's science?

[NoStar]

Zach,
It has nothing to do with what a reasonable mind would call it, but everything to do with common usage of an existant word.

Supernatural:
1 : of or relating to an order of existence beyond the visible observable universe; especially : of or relating to God or a god, demigod, spirit, or devil
2 a : departing from what is usual or normal especially so as to appear to transcend the laws of nature b : attributed to an invisible agent (as a ghost or spirit)

Part of the definition ("of or relating to an order of existence beyond the visible observable universe" and "departing from what is usual or normal especially so as to appear to transcend the laws of nature") need not include god.

As I understand it, certain forces like gravity from an object in the upper 7 dimensions will affect the space/time/matter/energy in our 4D universe. Things we cannot see or detect could be making our universe less homogenous than current scientific assumptions have it. For instance, the speed of light may not be the same constant in all parts of the 4D universe due to an undetectable thing in the other 7 dimensions.

To call this undetectable thing God is unscientific. To say it is not God is also unscientific. It is unknown.

So, until the conditions in the other seven dimensions are understood, they remain a part of the supernatural (that is, of course if the 11 dimensional string theory pans out. If it does not, then in the words of Emily Letella: Never mind.)

[joshua corning]

"On the cited critique of protein evolution:

The critique makes the mistake of looking at forms of proteins and then calculating astronomical odds against chance producing the transition from older to current forms. The problem is that this approach ignores intermediate forms, which conferred function for the organism. The author does not consider that the process coulda been step-wise, thereby reducing the improbability of the earlier forms morphing into the current forms."

yeah that isn't the problem...the problem there just has not been enough time for all the gene sequences to have occured in one line of genes throughout history (4-5 billion years)...what they really neglect (and evolutionary biologist also neglect) is that the mutations did not occure in one line...becouse orginisms could did and still exchange genetic material...so now you have multiple lines of genes producing novel and useful genetic material.

it is the difference between one computer solving a problem step by step and a cluster of trillions of computers doing all the steps all at once.

[NoStar]

joshua corning,

WOW! I don't think certain fundamentalists will like the implications of different species swapping genetic information (anymore than they like evolution), but it sounds like the makings of a fantastic science fiction/porno movie.

[thoreau]

Why do you say that you're just not sure that it's science?

In principle, of course, it is science: They have made an educated guess about the natural world, and there are some observations that would enable us to test the idea.

The problem is that those observations seem very unlikely to be possible in the forseeable future. Now, some versions of string theory may be ruled out by current observations (e.g. there's a group in Seattle that performs gravitational measurements on sub-millimeter scales, ruling out the possibility of macroscopic extra dimensions), but there are plenty of other versions that can't be ruled out.

And even if they obtain some glimpse of unexpected particle physics at high enough energies in the next decade, those energies are still so far below the Planck energy (the energy scale where string theory effects manifest most clearly) that those observations couldn't really be seen as confirmation of string theory. Those observations may be used to rule out more versions of string theory, but they won't provide any sort of clear, direct testing of the basic idea.

In short, any forseeable experiments in the near future will only serve to rule out particular versions of string theory. The string theorists can always change things around to accomodate those observations. The fundamental ideas will remain untestable in the forseeable future.

There are philosophical differences between string theory and ID, of course: String theory is still grounded in ideas that have proven themselves fruitful in other areas of physics. String theory is still at least hypothetically testable. (ID can't be tested without either a time machine or God making an appearance and setting the record straight.) And string theorists at least appreciate the need to elucidate predictions that can be tested in the near future. They strive mightily to accomodate the needs of particle experimentalists, observational astrophysicists, and experimental gravity groups. They have a long way to go, but at least they're making progress.

So, I would say that string theory is closer to science than ID, but it is not even close to the same league as, say, electromagnetism or relativity or thermodynamics.

[joshua corning]

"WOW! I don't think certain fundamentalists will like the implications of different species swapping genetic information (anymore than they like evolution)"

Yeah what I am saying is that different species swapping genetic information is part of evolution...ever hear of sexual reproduction? Anyway my point is that the ID guys (even though god didn't create all the birds and bees) did bring up an important point about how classicle evolutionary theory is flawed...but everyone is ignoring it simply becouse it was the god folk who brought it up...this is why I see little differance in the science faithful and the god faithful.

[Rick Barton]

thoreau,

Alota the proponents of ID have their minds made up due to the implications for creationism. So, they don't approach ID scientifically. Even the article in the cited link seems to lack for some genuine curiosity. But on the other hand, cuz of the folks who are pushing it, the ID conjecture might be unfairly demeaned as unworthy for consideration.

I would say that string theory is closer to science than ID, but it is not even close to the same league as, say, electromagnetism or relativity or thermodynamics.

I concur with that hierarchy, and I think that ID deserves its "least scientific" ranking due to the dearth of evidence, not cuz the consideration of ID is not scientific, as opposed to considerations of the supernatural. Although, it would be interesting to hear an ID proponent explain how that ID came to engineer life sans the supernatural. (see my next comment for the moral dilemma that creationists face.)

...ruling out the possibility of macroscopic extra dimensions

It doesn't really rule em out, does it? It just indicates that the gravity is not slipping into extra dimensions. So don't these measurements fail to show evidence for extra dimensions rather then ruling em out?

ID can't be tested without either a time machine or God making an appearance and setting the record straight.

It seems that you're raising the bar way too high. We know what systems that are the result of ID look like and how they behave, so we can look at life for the same attributes. I think that life doesn't show key attributes of these systems but does show evidence of evolution, pitiless evolution.

[Rick Barton]

The dilemma of morals that creationists must answer:

Creationists have some splainin to do. What kind of mean, creepy God would design life that on occasion suffers so, solely as a result of the design?? This God is either not a perfect designer, or it's malicious!

[Rick Barton]

joshua corning:

Yeah what I am saying is that different species swapping genetic information is part of evolution...ever hear of sexual reproduction?

What evidence is there of inter-species procreation and that those offspring thrived as a new population?

Anyway my point is that the ID guys (even though god didn't create all the birds and bees) did bring up an important point about how classicle evolutionary theory is flawed...

And what is that important point that they brought up?

[thoreau]

It doesn't really rule em out, does it? It just indicates that the gravity is not slipping into extra dimensions. So don't these measurements fail to show evidence for extra dimensions rather then ruling em out?

Well, the 3 other major forces don't slip into extra dimensions, or at least they don't need extra dimensions to explain them in any of the experiments conducted thus far. If gravity doesn't slip into extra dimensions either, then there isn't really a point to those extra dimensions.

The point of the extra dimensions is that gravity does go into them. The other interactions may or may not, but gravity definitely goes into them. Under some versions of string theory, the other interactions (or at least the electromagnetic interaction, which we understand better than the others) are confined to our 4D universe (3D + time) so we wouldn't notice, say, an extra dimension that's 1mm in size. We'd only notice it with very sensitive gravitational measurements. But those measurements are being done and so far nothing has turned up. So we're left to conclude that the extra dimensions must be even smaller.

As to ID: You're right, it's at least hypothetically conceivable that a testable form of ID could be devised. It hasn't yet, but I've discussed ways that they might at least move toward validation. My concern remains that they'll never come up with a fundamental, quantitative test for their theory. So it will always come down to "Well, we couldn't think of any other way that this might happen, so it must be an intelligent intervention."

As long as their arguments boil down to limited imagination, the only way to test it will be a time machine or God showing up to clarify matters. Or, for Agent Mulder, the aliens landing and admitting that they engineered life on earth.

[Pirate Jo]

"...Now positing a God that had to obey phycical law with its divine intervention, as opposed to supernatural intervention, would be more defensible. But then what kind of a God would we have? What would "God" mean in this context?"

Exactly! If the natural universe makes up "all that exists," and supernatural means something outside the natural universe, there can be no such thing that exists and is also supernatural. God would then be a natural being, just like (although maybe a lot smarter or long-lived or different than) us. But to de-mystify God, and acknowledge that he would be just another life form dwelling someplace in the universe, having mass and matter, taking up space - that's precisely what freaks out the religious.

They need to believe that God gives their lives meaning, that he has a purpose for them, that he'll send them someplace nice after they die, etc. etc. He NEEDS to be un-knowable, or else he couldn't be whatever they want him to be. At the bottom of all that religious stuff isn't a real desire to find truth, it's a need to have truth be what you want it (or need it) to be. What Rick Barton said - a hypothesis that by its very nature can't EVER be tested. Which means it will last and endure forever in its present state.

Fear of change is a constant theme among the religious, especially when it comes to changes in the world they live in. No matter how much better, longer, and healthier their lives are than those of people who lived 200 years ago, things are always "worse" or "going downhill" because of something like Grand Theft Auto or homosexuals or punk rock or marijuana. Religion that evolves over time is watered-down or selling out - the hallmark of a true religion is that it never changes, since it represents absolute truths and those don't change over time.

I believe religions come from the very flawed but human desire for certainty - to have all the answers in one place - and that is something which science (by its very nature) won't accept. No matter how certain you are of something, some new evidence will probably come along and blast all your ideas out of the water. And you'd better be prepared for that - no clinging to the old ideas just because you know them really well. You always have to be open to an upgrade. I see this as the real bottom-line divide between science and religion. One person's progress is another person's breakdown of decency or moral decay.

[joshua corning]

"What evidence is there of inter-species procreation and that those offspring thrived as a new population?"

mitocondria...in every animal alive today.

plants have something similar cloroplasts or something.

bacteria share DNA all the time both through evolved psudo-sexual mechanisms and through phages.

there is this example of speciasisation..only one i am aware of and thing the only one ever observed in science. Some lab had a bunch of fruit flies..one batch suddenly could only breed with its own batch. They did some dna work and discovered that the flies were infected with a virus that changed thier dna...wammo bammo a new species is born.

[biologist]

Rick Barton:

a number of lizards and salamanders that reproduce parthenogenetically (parthenos = Gr. virgin; genesis = origin), that is to say, without sexual reproduction and only females are known appear to be result of hybridization between related species that weren't fully genetically compatible, and homologous chromosome pairs failed to separate during meiosis (gamete formation). also, see the discussion of wheat that Ron Bailey posted the day before yesterday. mitochondria and chloroplasts aren't quite the same phenomenon, but somewhat similar, that symbiotic intracellular bacteria became imtimately associated with the host cell to the point that they lost their ability to grow independently outside the cell, or the host cell developed mechanisms to enslave them for energy production.

[biologist]

NoStar et al.:

if you're still reading this thread, my take on NoStar's link is that people who aren't biologists who want to criticize any area of biology, not just evolutionary theory, really ought to consult with a biologist (or in this case, a biochemist) to see if they actually have an idea worth feces.

one of our chemists has proposed similar nonsense to what this guy proposes, trying to estimate the probability of amino acids assembling themselves by random into useful proteins. there are a few problems with this.

first, the probability of a particular amino occurring at any point in a protein chain is 1/20, since there are 20 naturally occurring amino acids that the genetic code codes for (I'm simplifying a bit here). of course, since some amino acids are chemically similar, more than one amino acid could occur in any particular position without affecting the protein function and/ or folding to any great degree. of course, if it does, and the effect is negative, natural selection will eliminate the individual from the gene pool. if the effect is positive, the individual will have higher fitness, leave more offspring, and the gene will spread through the population (assuming the individual doesn't die prematurely for reasons unrelated to this new, excellent protein). the practical upshot is, point mutations can act to fine-tune a protein's function by changing a single amino acid at a single position. the author of the link is right that point mutations by themselves are unlikely to lead to whole new proteins with whole new functions.

luckily, in eukaryotes (all organisms except bacteria), the genes are broken up into regions that code for amino acid sequences (exons) and regions that don't code for amino acid sequences (intervening sequences, or introns). apparently, the exons represent coding for major protein structures (alpha helices, beta pleated sheets, beta barrels, etc.) that can be rearranged and swapped whole between different gene regions, allowing whole functional parts of proteins to be copied over to other proteins.

basically, we don't know enough about the way gene regulation works to say with any certainty what the probabilities are.

finally, proteins don't assemble randomly, they follow the rules of chemistry just like all the other chemicals in the universe (caveat: as far as we know).

[NoStar]

Thanks, biologist.

[Jon]

See http://saveliberty.blogspot.com/2005/12/whopper-of-week.html for the hyperlinks.

Santorum 2002: "Intelligent design is a legitimate scientific theory that should be taught in science classes" (Washington Times op-ed).

Santorum 2005: "I'm not comfortable with intelligent design being taught in the science classroom" (BBC).

Hat tip: Will Saletan.

See more on Santorum here and here.

[joshua corning]

"if you're still reading this thread, my take on NoStar's link is that people who aren't biologists who want to criticize any area of biology, not just evolutionary theory, really ought to consult with a biologist (or in this case, a biochemist) to see if they actually have an idea worth feces."

nice do you get robes like priests with that biologist?

what a crock of shit.

It is good to know my point about science as method and science as faith is holding up well.

[joshua corning]

"one of our chemists has proposed similar nonsense to what this guy proposes, trying to estimate the probability of amino acids assembling themselves by random into useful proteins. there are a few problems with this."

so it is just BS becouse you say so...without actually saying why.

oh wait you do and here it is...only after 500 words of stuff that has nothing to do with the argument.

"basically, we don't know enough about the way gene regulation works to say with any certainty what the probabilities are."

yup but you can measure how long it takes....insert e-coli with gene that can create a protein that matabolozes a certian type of suger exept it has one codon wrong. Put e-coli in dish with lots of that type of sugar and a little of a type it can motobolize...count how long it takes until a mutation occures that allows the e-coli to matabolize the sugar...now we know how long it takes for a useful mutation to occure...and we know how many genes are in a bacteria...and now we can calculate how long it would take to make all those genes...and we know there is not enough time since life started on the panet (4-5 billion years) to create all those useful gene sequences...opps current theory of evolution has a BIG BIG problem...to bad people like biologist are to busy hateing IDers to recognize it.

[biologist]

joshua:

actually, that other stuff does have to do with the argument, you just verified that you don't understand my point. neither does the computer scientist that wrote that page. therefore, all his probability calculations will be off.

I'll try to simplify it for you:

the probability of any amino acid occurring at a given position in a protein by random chance is 1/20. however, since other amino acids could fulfill the same function at that position, the probability of getting an amino acid at a given position that will permit the protein to fold and/ or function is higher than 1/20. also, not every amino acid is necessary for the functioning or has an effect on the folding of the protein. therefore, in certain positions in the sequence, any amino acid could be inserted, and the protein would still work. therefore, the probability of a getting an amino acid that allows the protein to fold and function at those positions (the positions that don't affect the folding and functioning of the protein) is 20/20, since any amino acid will do. there is a lot more detail that a biochemist or cell biologist could provide, but that isn't really my area of expertise. notice I don't have much opinion on the details of whether certain quantum electrodynamic models or string theory models or computer programming languages are right or wrong because (insert drum roll here)...they are outside my area of expertise. everyone seems to have an opinion about evolutionary theory, even though their training consists of watching the NOVA evolution special.

I don't have a robe...I have a degree in biology (from an accredited university, no less), which is more than most anti-evolutionists can say. so, if you have a criticism of evolution that you've read that you think is valid, let's hear it. be specific, not "go read Michael Behe's Darwin's Black Box". if ID'ers have any valid criticisms to make, I'm open to hearing them, which is why I took the time to read Behe. in my opinion, it is crap.

I have faith in the scientific method, not in humans, invisible imaginary friends, or in any particular scientific theory. I'll drop my adherence to evolutionary theory as soon as someone comes up with a better explanation.

finally, whether you agree with evolution or not, I'd be more likely to listen to you if there weren't so damn many misspellings in all of your comments.

[joshua corning]

"so, if you have a criticism of evolution that you've read that you think is valid, let's hear it"

i have said it like 5 times on this blog but the best description was my last one in my last post that you ignored..here it is again for postarity:

"yup but you can measure how long it takes....insert e-coli with gene that can create a protein that metabolizes a certain type of sugar except it has one codon wrong. Put e-coli in dish with lots of that type of sugar and a little of a type it can metabolize...count how long it takes until a mutation occurs that allows the e-coli to metabolize the sugar...now we know how long it takes for a useful mutation to occur...and we know how many genes are in a bacteria...and now we can calculate how long it would take to make all those genes...and we know there is not enough time since life started on the planet (4-5 billion years) to create all those useful gene sequences for all the orginisms on the planet...opps current theory of evolution has a BIG BIG problem...to bad people like biologist are to busy hating IDers to recognize it."

and bebe did talk about this in his book darwins black box.

And i to belive evolution to be the best model for explaining the origin and adaptation of life on this planet...i just think it needs to be tweeked a bit....but until Reason decides to include a spell checker you are stuck with having read misspelled words.

[biologist]

joshua:

that would indeed allow you to estimate how long it takes for evolution to generate a useful gene by point mutations (changing one DNA base at a time, which sometimes results in a codon that changes which amino acid occurs in that position in the protein). however, as I stated:

"...luckily, in eukaryotes (all organisms except bacteria), the genes are broken up into regions that code for amino acid sequences (exons) and regions that don't code for amino acid sequences (intervening sequences, or introns). apparently, the exons represent coding for major protein structures (alpha helices, beta pleated sheets, beta barrels, etc.) that can be rearranged and swapped whole between different gene regions, allowing whole functional parts of proteins to be copied over to other proteins...

Comment by: biologist at December 24, 2005 03:06 PM

therefore, evolution can occur by rearrangements of exons within genes. if the genes are duplicated, redundant genes that still have their control sequences attached, then evolution of protein products of genes can proceed much more rapidly than just by point mutations.

also, the model you propose apparently assumes that there is only one chain of species formation, so that all evolutionary developments must occur in series. however, in bacteria, there is gene exchange between individual cells of different taxa. so, different evolutionary adaptations can develop in different lineages, then lateral transfers of genes can cause accumulations of the adaptive genes in a single lineage. symbiosis would work similarly, as in the mitochondrial example you yourself cited. the harnessing of endosymbionts for energy production may have occurred more than once independently.

some eukaryotes (all organisms other than bacteria) can tranfer genes laterally, and if these horizontal transfers occur across different taxonomic groups, then adaptive genes can accumulate by this mechanism in eukaryotes also.

sexual reproduction across different lineages is known in animals (even across different genera), so again, this is a plausible mechanism for accumulation of adaptive genes. the opposite is also known, where hybrids have lower fitness than their parents. it usually isn't possible to know in advance whether the hybrid will have higher fitness or lower fitness than the parents

finally, evolutionary time is better measured in generations, not absolute time. bacteria and simpler eukaryotes have very short generation times. under optimal conditions, E. coli divides every 20 minutes and Bacillus stearothermophilus divides every 11 minutes. since their reproduction is clearly base two logarithmic, a very large number of lineages, all running evolutionary experiments in parallel, can be generated very quickly.

I hope this addresses your stated concern about evolutionary theory.

[zach]

NoStar,

To call this undetectable thing God is unscientific. To say it is not God is also unscientific. It is unknown.

To bring God into the question at all is unscientific. An idea only earns a place in a scientific discussion with evidence. You can call a theoretical dimension supernatural, or even Heaven, if you want, but it doesn't change its meaning to anything but a theoretical dimension.

So, until the conditions in the other seven dimensions are understood, they remain a part of the supernatural.

By no stretch of the imagination does "supernatural" mean "not yet understood". Again, you really are saying that these theoretical dimensions are just really nifty. Attaching the title "supernatural" frankly just seems like a sad attempt to connect them to old beliefs.

[NoStar]

Zach,
People make many assumptions. In the face of limited knowledge, there is no other choice. However, many assumptions are not warranted.

One assinine assumption is that the laws of nature are the same everywhere. Many people who consider themselves "scientific" make this assumption. But cosmologist admit that at or near the point of singularity, say the big bang or a black hole, the physical laws as we understand them break down.

Questions like what were the conditions on the other side of the big bang?, what happens to matter, energy, space and time inside a black hole? or what is it like in the other 7 dimensions? cannot be answered with current scientific understanding. This does not make the questions bad or wrong headed, just outside the realm of science. It also does not mean that laws or conditions do not exist in these strange places or time, but it does place them in the "supernatural", that is, above and beyond the current probing of science.

I am glad that science has been able to push the boundaries of understanding so that what is supernatural no longer includes things like thunderbolts and earthquakes.

I do not think my use of the word supernatural is outside the norm of current usage. I am sorry that you take offense in that I take some comfort in seeing in my understanding of string theory a possible location of God's heaven. I do not attempt to call my conjecture science.

On the otherhand, you have a limited understanding of the word supernatural to mean anything that is in the realm of fairy tales, ghosts, and the non-existant. Using that definition, nothing supernatural can exist. I guess you might find comfort in that tautology, just as I find comfort in my belief that heaven could exist in a 7 dimensional space.

When I was growing up, the "Static State" universe was still widely held by people who called themselves scientific. This theory was used as a slap in the face to those who believed in a Biblical creation. Low and behold, science came around to a more biblical point of view.

I don't begrudge scientists their views when they disagree with my theology. Sometimes science affects the way I interpret the Bible and the Bible affects the way I look at science. If God created this world, the job of science is to discover and teach us how it was done. The job remains the same even if God didn't exist.

[zach]

NoStar, I obviously don't take offense to you seeing anything in anything, I'm simply pointing out what I feel is a logical mistake on your part in trying to find God wherever there's uncertainty. I realize you don't call this science, but it's not logic, either. It's a classic example of starting from a conclusion and waiting for the evidence to support it, rather than starting with no conclusion and forming one from scratch, based on the evidence. By your own admission, the way you look at the Bible affects the way you look at science, and to me this approach automatically invalidates any scientific pursuit, since science is supposed to be unaffected by anything but evidence. Naturally this is not always the case, but it's the goal; for you it is not even the goal. The goal is to further inform the forgone conclusion that God created the universe.

I'm also pointing out a misuse of the word supernatural, but you seem intent on it, so I'm wasting my time. Suffice it to say that the commonly held definition of supernatural does not include undiscovered subeterranean life, which yours would; nor according to the commonly held definition does something change from supernatural to natural once scientists sufficiently understand it. Indeed, science can only ever understand that which is already natural.

[NoStar]

Ah, but the boundaries of the natural are expanded and the supernatural becomes natural or debunked.

That science proceeds from evidence as a starting point is a gross misunderstanding of what really happens. Wild ass guesses are often reformulatd as hypothesis. The bible has been the precursor, inspiration or impetus for many discoveries including an expanding universe (He stretches out the heavens like a curtain), the idea that time itself along with space has a beginning (In the beginning...) and Matthew Fontaine Maury's understanding of Psalms 8:8 (..the paths of the seas...) lead him to research oceanic currents.

Science once existed as a subset of Philosophy, but the divorce is pretty much complete and some would place science above everything else. As a former worshipper at the alter of man's intellect, I know that science can be easily become a religion itself. Just watch what happens when its sacred cows are attacked.

[zach]

Ah, but the boundaries of the natural are expanded and the supernatural becomes natural or debunked.

You make me want to worship at the altar of man's stubbornness. I know you are smarter than this.

That science proceeds from evidence as a starting point is a gross misunderstanding of what really happens. Wild ass guesses are often reformulatd as hypothesis.

Science indeed proceeds from an hypothesis as a starting point for experimentation. Scientific conclusions proceed from evidence gleaned from said experimentation. Conclusions not based on evidence have no place in the process, except to be discredited. Your examples referring to the bible have no bearing on what we're talking about.

[NoStar]

Zach,
I'm sorry I missed something earlier:

"I'm simply pointing out what I feel is a logical mistake on your part in trying to find God wherever there's uncertainty."

That's not exactly how it works. My reasons for knowing God exists are quite personal and admittedly anecdotal. Nevertheless, having had a burning-bush or road-to-Damascus experience I have no need to find God. He is not lost and I feel His presence daily.

I do find it exiting that there is a possibility that a far out, albeit, speculative scientific theory has the potential to bring a 7 dimensional heaven (e.i. 7th heaven) from the realm of the supernatural to within our understanding of what is in fact natural.