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Monday, September 12, 2005

Hang your head in shame, Grauniad!

The Guardian has published a pathetic interview with Behe. The interviewer, John Sutherland, is clearly out of his depth and allows real howlers to slide by, and in a few cases, even helps Behe along.

But the question is: exactly how did life get here? Was it by natural selection and random mutation or was it by something else? Everybody - even Richard Dawkins - sees design in biology. You see this design when you see co-ordinated parts coming together to perform a function - like in a hand. And so it's the appearance of design that everybody's trying to explain. So that if Darwin's theory doesn't explain it we're left with no other explanation than maybe it really was designed. That's essentially the design argument.

Yes it is; things "look" like they were designed. That's all there is to design, so can we be done with it now? People also see Jesus in a potato chip, but no one with any sense takes that as a credible, legitimate sort of evidence.

JS: Why do you think we should replay the Darwinian controversies of 1860 and the 1925 Scopes monkey trial? MB: Because we have new data. It's because science has advanced since then. We now know what the very foundation of life looks like. It's made up of molecules. Not just molecules but sophisticated molecular machinery.

This is another tired ploy out of the creationist playbook: it "looks" like design, and molecules "look" like machines! Reifying analogies is not a sensible way to do science, Dr Behe.

Irreducible complexity is a problem for Darwinian evolution. Whenever we see these complex functional systems we realise that they have to be designed.

Aaaargh. This is not true: irreducible complexity is not a problem for evolution, even the Darwinian kind. It's been explained before, it's in the FAQ, so it's annoying to see it repeated again and accepted without question by this clueless interviewer. I'm going to explain it one more time. Here's why IC is not a problem and even an accepted outcome of normal genetic processes.

Here's a pathway. Gene product A activates gene product B, which has some autocatalytic function (it activates itself) and which then activates gene product C. Nothing unusual here, this arrangement can be found all over cellular biochemistry, and Behe must know it.

IC evolution

Here's another common event: a gene duplication. An error in replication has made a copy of B, called B'. It's initially identical to B, has the same inputs and outputs, and basically acts like a simple redundant copy. This is probably a neutral event, but can also affect the activity of the pathway.

IC evolution

With a redundant copy, selective constraints are removed from evolution. If B' has a mutation that makes it unreceptive to activation from A (the red arrow from A to B'), the system still works. If that happened in the original pathway, there'd be no way to get to C from A…it would destroy the pathway. With that extra copy, though, there is an alternative path that allows the circuit to reroute around the damage.

IC evolution

Accumulate enough small changes, for instance knocking out all of the red arrows above, and a new, irreducibly complex pathway exists:

A → B → B' → C

Duplication plus loss of function is the simple recipe for getting irreducibly complex systems. Behe looks at that and claims there is no way it can evolve. I've just shown you how it can evolve.

The conclusion of the interview is dazzling in its hubris, and Sutherland obligingly feeds him the creationist position.

JS: Has the National Academy of Science taken an interest?

MB: It takes a position strongly condemning it. The recently retired president, Bruce Albert, sent a letter to all 2,000 members of the NAS essentially naming me.

JS: Did Galileo come to mind?

MB: Yeah. In a way it's flattery.

Galileo? Why does every kook with a stupid idea that gets rejected by scientists compare himself to Galileo?

That statement that he's 'flattered' is remarkable. The letter from Bruce Albert to the NAS is not at all flattering—here's the part where he mentions Behe:

On February 7, 2005, Michael Behe, a founder and leading proponent of the Intelligent Design (ID) movement, published a long Op-Ed in the New York Times in response to an editorial that the Times had released the previous week. In that letter, Dr. Behe claimed that some words I wrote support his view that scientific explanations for the evolution of life on the Earth need to be modified to insert the work of an "intelligent designer".

In my response to the Times, I pointed out that, while my words are reflected correctly in Behe's column, he completely misrepresents the intent of my statement. This is a common tactic among those who are attempting to introduce religious views of the origins of life into the public schools -- or who are trying to undermine the teaching of evolution because of purported "weaknesses" in the theory.

So Behe misinterprets and misrepresents a scientist's work, and when the scientist calls him on the outrage, Behe compares himself to Galileo and is flattered. Why, if he put on clown shoes and mumbled gibberish, and an audience of scientists laughed and threw overripe tomatoes at him, maybe he could get a promotion and be just like Newton and Einstein. Doesn't their fame rest on vacuous pronouncements and garbled scholarship, after all?


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Comments:
#39664: — 09/12  at  01:40 PM
With no selective 'advantage', how does it get passed down?

You see, when a mommy and a daddy love each other very much...



#39666: — 09/12  at  02:01 PM
@ NatureSelectedMe

I think you have that reversed. It should be that descendents with a selective DISadvantage tend to NOT survive. In evolutionary terms, neutral changes are a wash.

Duplication of pathway protiens allows for more variance in the organism. With only a single pathway, there can only be so much change before a 'hard wall' is reached and the organism dies because the pathway breaks apart.



#39667: — 09/12  at  02:35 PM

#39629: mark — 09/12 at 10:37 AM
The second quote seems to imply that the "new data" we have might have been obtained by Creationi, errr..., ID kids, and that evolutionary theory still depends on the observations made by Darwin over 150 years ago. Well, Behe is right that we do have more data, but these data are collected by scientists doing research in evolution, and the results provide even more support for evolutionary theory and our understanding of the processes of evolution.

They should have asked him about the new data just on systems he labeled "irreducibly complex" in his book, which shows that the IR claims are bogus.



Trackback: The Guardian's Unintelligent Design Tracked on: Andrew Jaffe: Leaves on the Line (209.68.1.99) at 2005 09 12 15:27:56
I was enjoying the new, redesigned Guardian newspaper today, until I came to the end of the new G2 features section, and an offensive interview with chief Intelligent Design crackpot Michael Behe, under the inappropriate banner, "Ideas". Offensive because interviewer John Sutherland doesn't call Behe on any of his flagrant misstatements (I hesitate to call them lies since that implies that Behe is smart enough to know he's wrong, and anyway I do give him the benefit of the doubt…



#39676: — 09/12  at  03:39 PM
There's a fundamental arrogance to the ID argument, the way I see it. I don't read enough to know whether this is a common observation, but here's my take:

The claim "it's too complicated, it must have been designed" seems nearly the same as saying "I don't understand it, so God must have designed it." This latter is equivalent to "Only a God could fool me. I'm too smart for just ordinary Nature. So if I'm fooled, there must be a God!"

Much as I like to think of myself as pretty smart, I have to concede that Nature gets the better of me routinely. Thus, ID doen't persuade me.



#39679: — 09/12  at  04:10 PM
39666: linnen — 09/12 at 02:01 PM
I think you have that reversed. It should be that descendents with a selective DISadvantage tend to NOT survive. In evolutionary terms, neutral changes are a wash.

No, I have this quote from the man himself.
I have called this principle, by which each slight variation, if useful, is preserved, by the term natural selection, in order to mark its relation to man's power of selection. But the expression often used by Mr. Herbert Spencer, of the Survival of the Fittest, is more accurate, and is sometimes equally convenient.

So I think my butchering is more accurate than yours.
Duplication of pathway protiens allows for more variance in the organism.

How can it allow for more variance when there is no selective constraint? The organism is only using one of the pathways. Isn't the duplicate 'hidden' until it's more useful?



#39685: — 09/12  at  04:39 PM
Don't take that Guardian piece in the back of the G2 "magazine" section too seriously. All the British papers fill their barely-news magazines with a lot of fluff and nonsense. Behe's interview was done under the "Ideas" banner which I think is a new section for the newly redesigned Guardian (today was the first issue). No idea what the next "Ideas interview" will be, but I'm willing to bet it will be equally unchallenging and uncritical.



#39693: — 09/12  at  05:15 PM
No, I have this quote from the man himself.

The man himself had no idea about neutral mutations or genetic drift. The existence of a second pathway would not be removed by natural selection, since it does nothing harmful. However, in a small enough population, such neutral mutations can still be spread throughout the population by random drift.



#39709: — 09/12  at  08:15 PM
A single pathway would be able to vary so far before it could no longer function. Duplication and reduncancy (sp?) would allow wider variance since B could go to the limit in one direction and teh B` variant could approach the limit in the other direction.

As for selective constraints, the only constraint is that the organism survives. That is the hard wall (constraint) that evolution enforces. If the organism benifits, all that better to force the neutral mutations out of the environment.

An (imperfect) example would be malaria and sickle-cell anemia. If a person carries two genes for sickle-cell, that persons chance to survive to reproduce is greatly hindered. BUT carrying only one gene, while slightly reducing that person's survivability, allows that person to survive malaria.



#39716: — 09/12  at  08:49 PM
The man himself had no idea about neutral mutations or genetic drift.

I'm sure he didn't, but he knew how to state his own theory.
As for selective constraints, the only constraint is that the organism survives. That is the hard wall (constraint) that evolution enforces. If the organism benifits, all that better to force the neutral mutations out of the environment.

No, the constraint is that the organism is 'more fit' and survives. We're talking about evolution here. Why did the organism change? Because it's more fit. What you're getting at is a tautology, if I'm not mistaken. You're saying the ones that survive are survivors.



#39721: Narc — 09/12  at  09:30 PM
I'm sure he didn't, but he knew how to state his own theory.

Perhaps, but I assume we are discussing the modern theory of evolution, not a revealed, unchanging Truth passed down on tablets of stone.

No, the constraint is that the organism is 'more fit' and survives.

No. If the A -> (B/B') -> C mutation is entirely benign, it won't get selected for. But it does allow the A->B->C pathway to mutate further without harming the individual, because it still has the A-B'-C pathway to produce C. The original organism does not, and a change in B could cause it to be unable to produce C.



#39730: — 09/12  at  10:52 PM
Perhaps, but I assume we are discussing the modern theory of evolution, not a revealed, unchanging Truth passed down on tablets of stone.
Don't you read all comments? I was referring to:
It should be that descendents with a selective DISadvantage tend to NOT survive.

Isn't that opposite from the standard description of Natural Selection?
No. If the A -> (B/B') -> C mutation is entirely benign, it won't get selected for

Why won't it get selected for? Because it's benign and doesn't give an advantage, which is what I stated. The problem I have with this 'duplicated gene' is that there is no selective advantage between the time it's a benign duplicate until it's useful adaptation. What intrigues me is the recent chimpanzee genome project. Comparing that with humans they can actually see these duplicates. Or not.



#39732: — 09/12  at  11:08 PM
How can it allow for more variance when there is no selective constraint? The organism is only using one of the pathways. Isn't the duplicate 'hidden' until it's more useful?
Yes, the duplicate (B') is in an "evolutionary vacuum," where its (potentially or would-have-been) deleterious mutations are not (necessarily) placing a disadvantage on the organism.

The problem I have with this 'duplicated gene' is that there is no selective advantage between the time it's a benign duplicate until it's useful adaptation.
It's true, that even if B' has "bad" mutations that are disadvantageous to the organism, the organism(s) will likely keep B'. Evolution doesn't always have the luxury of being able to just get rid of things when they aren't advantageous.

If the organism is able to survive long enough, long enough for B' to acquire an advantageous function, B' will be kept. Of course, if B' mutates into something that isn't advantageous in the long run, it's likely that it will continue to adapt through natural selection so that B' (whatever it may be) will provide the best likelihood for survival (whatever that may be).

By that time, it's too late for B' to just disappear. Nature has do the the best with what she's got.

Sorry, I'm tired...

Once in a while you get shown the light, in the strangest of places if you look at it right.

-Jerry Garcia



#39735: — 09/13  at  12:42 AM
I've just sent this to the readers' editor:

Dear Sir,

In yesterday's Guardian you quote with approval Alan
Rusbridger's comments about the paper's main relationship
being with its readers. As a loyal one of those readers,
I would like to say that I think as journalists your
relationship with the truth is even more important, and
that sadly in the very first appearance of the new G2
"Ideas" section that relationship seems to have become
very strained indeed.

John Sutherland's interview with "Intelligent Design"
proponent Michael Behe is a travesty of journalistic
standards. Sutherland allows him to make factually
incorrect statements (that the neo-Darwinian synthesis
cannot explain the evolution of various molecular
structures in cells) and peddle logical fallacies (chiefly
the false dilemma -- if evolution is wrong, this one
particular other theory must be right) without once
challenging them, instead playing up to Behe's excessively
large martyr complex (he even _invites_ him to compare
himself to Galileo, long a favoured identificiation figure
for scientific cranks). Sutherland does not give the
appearance of having done any research into the situation,
seeming to accept ID's arguments at face value without
having investigated the well-established and well-publicised
evolutionary counterarguments. Less than an hour spent on
the Internet would have led him to a wide variety of
websites where he could have understood the flaws in the
Intelligent Design position.

One thing I would like to know is _why_ John Sutherland
was selected to perform this interview. I find it hard
to imagine that (for instance) Ben Goldacre, your columnist
on "bad science", would be sent to interview some
controversial literary critic -- why then send your
columnist who is a literary critic to interview an
extremely controversial figure, widely regarded by his
peers as a very bad scientist indeed?

Two notions in particular concern me. First, the
possibility that Behe only consented to be interviewed by
someone whose eyes he could easily pull the wool over (in
which case you should have simply not interviewed him in
my opinion), and secondly and even more worryingly,
that this piece is somehow "balance" for the excellent
Richard Dawkins/Jerry Coyne piece in the 1st September
edition of Life, which accurately skewered the Intelligent
Design movement's unscientific aims, flawed metholodogies
and entirely religious and political motivations. Good
science is not simply a matter of opinion, and frankly I
expect better of the Guardian than to give such an easy
ride to someone who in the most charitable interpretation
possible is utterly and hopelessly wrong.

Yours sincerely,
Brendan Hogg

(Though frankly I don't know _why_ I expect better, given that they have a homeopathy column every weekend in their glossy lifestyle magazine thing.)



#39741: — 09/13  at  02:15 AM
Today's Guardian has this: http://www.guardian.co.uk/comment/story/0,3604,1568491,00.html

on "the anthropic principle, which starts from the fact of our existence and then argues backwards to claim that the precise properties of the universe that emerged from the big bang had to be those that made the eventual emergence of humans inevitable. The unique properties of water depend on an exquisite level of fine tuning of the fundamental constants. So why are these constants just right? Because if they weren't we wouldn't be here. [...] scientists are wary [because] it seems to reverse the Copernican revolution and place humankind at the centre of the universe. Even worse, it could allow creationists to bring the G word back into science: a God to tweak all those knobs to make life possible. But if God is needed to tweak the universe's knobs then who was there to tweak God's knobs?"

This guy is a professor of molecular genetics. I'm mainly willing to give him the benefit of the doubt and assume he's just expressing himself badly -- though the ID crowd will just love lines like "why are these constants just right? Because if they weren't we wouldn't be here", especially taken out of context. But where does "it seems to reverse the Copernican revolution and place humankind at the centre of the universe" come from? OK, if the laws of physics were not as they are, we wouldn't have fluffy kittens. Does that place fluffy kittens at the centre of the universe?



#39743: — 09/13  at  02:47 AM
Nice letter Brendan.



#39749: — 09/13  at  06:27 AM
Many years (and two Guardian format changes) ago my pre-university summer was largely spent playing "Diplomacy" at a friend's house. They took The Guardian and I spent more time reading than playing the game. I discovered that newspapers were actually interesting - we were a Sunday Express household so I'd not seen one before. wink

I bought the yesterday's paper having seen that the Behe piece was there over someone's shoulder on the bus to work.

Now I'm just saddened.



#39773: — 09/13  at  09:19 AM
>>With a redundant copy, selective constraints are removed from evolution

>That's the part I don't get. With no selective 'advantage', how does it get passed down? You know, the descendents with an selective advantage tend to survive.

NSM,

It might be useful to go back to this point, as this it seems to be the source of your confusion. The quote at the top doesn't mention 'advantage,' that's something you seem to be reading into it. It's not that the duplicate lacks or doesn't lack selective advantage. (We're assuming it's more or less neutral.)

However, it is free of the selective constraint that is on the original. It is free to aquire mutations that change its function, without disrupting the origianl A->B->C pathway. B' can take on *new* functions, even though in doing so it may become unable to do the same task as B. If only B were present, with no duplicate, any mutation would be constrained by the fact that it would affect the pathway.

[Another (minor) point that is missing from the comments is that, in this scenario, we are assuming that the duplication has, through chance, spread through the population widely enough and long enough to acquire mutations. This is neutral selection, yes?]



's avatar #39895: — 09/13  at  03:46 PM
Eleanor:

The anthropic principle are whrought with controversy and confusion.

Much of the confusion stems from that it is not a welldefined concept. Wikipedia (http://en.wikipedia.org) mentions four of them, ranging from truisms ("If something must be true for us, as humans, to exist; then it is true simply because we exist.") to faithbased. Some of these work equally well with kittens. wink

These principles have apparently been mentioned in different theories in the hope of restricting or pinning parameters. As far as I know they have not been successful.

I think you are correct to be concerned about the risk faithbased nonfalsifiable variants to be privateered by IDiots.



's avatar #39896: — 09/13  at  03:48 PM
Errr... "... risk _for_ faithbased ...".



#39906: — 09/13  at  04:58 PM
Ginger -- thanks! I got a very prompt reply from Myers saying he'd "make my views known" to Katz, so it looks like you were right in your suggested targeting after all.



#39934: — 09/13  at  09:43 PM
<cite>With no selective 'advantage', how does it get passed down?</cite>

In the normal way? smile It's not that every mutation must confer a selective advantage in order to be passed down at all; but if it does confer selective advantage, the mutant's offspring (provided they inherit it too) will be more likely to survive and/or have more offspring--that is the driving force for evolution. If it provides no particular advantage, there are no unusual barriers to its being passed down.

Or so I understand it. I'll add the disclaimer that I'm a layman as well...



#39937: — 09/13  at  10:00 PM
And apparently dense enough to have missed the last page of comments. Never mind....



#39964: — 09/14  at  03:15 AM
Torbjorn, thanks for the link. I sent Professor McFadden a "huh?" email and got a nice friendly reply arguing that "we're forced to view the principle from the perspective of what makes us possible". I don't feel particularly forced to view it in any way, since one of the basic attractions of science for me is that it gives us broader and further-reaching perspectives than our own personal/anthropocentric ones...

(Sorry PZ, going off topic, will stop now.)



's avatar #40040: — 09/14  at  04:07 PM
Eleanor, my pleasure.

McFadden may have answered as he did because if everything else fails to decide parameters, anthropic principles may be used as parts of a larger (falsifiable) theory, even when the particular variant is nonfalsifiable. A current example is in theoretical physics string theory.

I have been against anthropic principles wholesale earlier but has come to accept their use as above. However:
- I am not sure if I feel comfortable with them in a full (without ad hocs) theory.
- I don't think any use has so far resulted in anything reliable.
- As you yourself argue well, they will be misapprehended into faithbased theories or arguments.



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