Flagella - Real and Fictional

| 273 Comments

Intelligent Design advocates are fond of using the bacterial flagellum as, in Dembski’s words, a “mascot” of the Intelligent Design movement. In particular, during the recent TV debate between Behe and myself, Behe showed pictures of flagella and triumphantly asserted that they looked exactly like man-made machines, and therefore they must be designed. What ID advocates, including Behe, fail to mention is that the images of flagella they endlessly demonstrate are heavily doctored, and that the real observed flagella do not look like “machines” at all. In fact the structure of flagella is more typical of a bacteriophage virus. Seeing the actual cryogenic electron micrographs of flagella, as well as the images derived from X-rays analysis immediately reveals that showing artificial machine-like images of flagella, without explaining the degree of idealization applied, is sometimes perilously close to committing a fraud.

Read Flagella – Real and Fictional, at Talk Reason.

273 Comments

I’m amazed that they still cling to the bacterial flagellum.

“A fanatic is one who can’t change his mind and won’t change the subject.

- Winston Churchill

Would love to hear or view the debate with between you and Behe. Is there a link anywhere?

without explaining the degree of idealization applied, is sometimes perilously close to committing a fraud.

Sometimes?

Perakh’s point that illustrations of flagella look more artificial, more “designed,” than actual flagella is well-taken. A pity that to get to it, one must wade through his plodding, wordy attack on Bessette’s claim that the existence of theistic Great Scientists of ages past and of an alleged 40% theism rate among modern US scientists is “inconvenient” for atheists. A silly claim, true, but Perakh is capable of equal silliness. He rears up at Bessette’s claim to know what atheists are thinking –

“How could Bessette know that atheists indeed construe his two facts (assuming they are true) as ‘inconvenient’? Has he conducted a poll of the atheistic scientists?”

– but then goes into a mind-reading act of his own, a few lines later:

“ … those 40% of contemporary [theistic] scientists in the USA … overwhelmingly inherited their faith from their parents and adhere to it throughout their lives because of having emotionally absorbed it in their childhood.”

Since turnabout is fair play, how does Perakh know that continued adherence to some form of religious belief is causally explained across the whole group of US theistic scientists by their “having emotionally absorbed it in their childhood”? How does he rule out a contribution from mature mental and emotional processes to ongoing religiosity, possibly including reason, volition, and adult religious experience? To paraphrase his own question, has he conducted a poll of the theistic scientists?

I doubt he has. What I think is that a double standard has just flashed. I think that to Perakh all religion is utterly absurd by definition, so it is simply self-evident that any scientist who professes religious belief must do so “because of having emotionally absorbed it in their childhood.” Just as, apparently, when Bessette would like to think that atheists find certain facts “inconvenient,” no evidence is necessary for him, either.

The level of discourse here is, let’s say, lower than it might be. Perakh emits a strong whiff of that true-believer funk so often emitted by those who have decided that Religion Is the Enemy and that they, themselves, are the true Warriors of Light.

LG

Perhaps it’s fraud, or perhaps it’s merely the fact that IDologists, not being scientists in spirit, do not have any motivation to dig deeper when they see something that appears to support their agenda.

Severino wrote: “Would love to hear or view the debate with between you and Behe. Is there a link anywhere?” To my knowledge, no links are available. If somebody is indeed very much interested in that debate, perhaps a DVD could be requested from Larry Kane’s program. However, the arrangements I described made the debate of a rather limited interest as I had no way to adequately respond to Behe whose posters I did not see, nor himself or the moderator. It was about 30 min long, with several commercial breaks, so not much could be discussed anyway. My position has been explained in detail more than once (for example see my post here or those posts referred as [20, 21, 22} in this article, or in chapter 2 of my book Unintelligent Design.

arent these the same people who are always complaining about haeckel diagrams?

I appreciate time and effort Larry Gilman has put into his comment. Yes, Larry, like Bessette, I did not conduct a survey of scientists, I just evinced my opinion with which you are free to disagree.

If Larry Gilman objects to making statements not based on a thorough investigation, why did he resort in a similar fashion to stating an opinion of my attitude to religion? If he wanted to know my view of religion, rather than asuming what it is, based on just one sentence relating to that question in passing, he could have looked up my essays dealing in a more detailed way with that topic, some of which are posted on Talk Reason in the pertinent section. I regret that Larry Gilman does not like the parts of my article dealing with religious scientists. I guess having perused my more detailed essays on that topic, he still would not like my views, but it can’t be helped. I don’t mind learning about Larry Gilman’s views being contrary to those of mine, but hopefully I am entitled to my own views as well. Ironic (or rather condescending) statements about delusional self-confidence of supposed “Warriors of Light” while testifying to Larry’s sense of humor, are hardly convincing.

Ironically, yes they are. But somehow fraud is not fraud when it serves one’s purpose and yet when it comes to Haeckel, they seem to refuse to do an in-depth analysis of these drawings and their relevance to evolutionary theory. However, the accusation of fraud still hangs over Haeckel. A better example would be the ‘staged photographs’ of the peppered moth, which some ID creationists consider a blatant example of fraud… I wonder how they feel about the ‘staged’ representation of the flagellum?

snex said:

arent these the same people who are always complaining about haeckel diagrams?

I think that this shows that the flagellum really is a perfect mascot of ID. More so and in more ways than I think they intend though…

And of course even did flagella “look like a machines,” such would be irrelevant to whether they were evolved structures. (“Looking like a machine” is an awfully underspecified property.) So the argument’s a fraud times two.

Larry Gilman wrote:

how does Perakh know that continued adherence to some form of religious belief is causally explained across the whole group of US theistic scientists by their “having emotionally absorbed it in their childhood”? How does he rule out a contribution from mature mental and emotional processes to ongoing religiosity, possibly including reason, volition, and adult religious experience? To paraphrase his own question, has he conducted a poll of the theistic scientists?

.

Since Larry most probbaly will not search for my essays dealing with this matter, I’ll provide here a very brief exposition of an argument in support of my thesis rejected by Larry Gilman. If you wish, consider it as a “theory,” so, if desired you may dismiss it as “just a theory” like ET has been regularly rejected by creos. My point is, though, that like in the case of ET, and unlike Larry Gilman references to various factors which may be responsible for religious faith, other than being emotionally absorbed in childhood, my theory is based on evidence. To explain what I mean, let me ask Larry Gilman a question: Can you predict, with an overwhelming probability, what the religious affiliation will be of a boy born today in Islamabad? And what the religious affilation will be of a boy born today in Tel-Aviv? Or of a girl born in a rural Russian village? Or of a boy borh in a village in Sicily? With a very few exceptions, such a prediction can be made with a little risk of a mistake. Does not this undisputable evidence testify that faith to a very large extent originates in childhood emotional experience? All those other factors listed by Larry Gilman, even if present, more often than not are just devices utilized, often subconsciously, to support in a supposedly rational way, the faith absorbed in childhood, and to exclude all other faiths. Why almost every person born to a Muslim family believes in the stories told in the Quran, but disdainfully dismisses the stories told, say, by Bahais or Druses? Why, on the other hand, say, Druses, generation after generation, with a great confidence assert the truth of their beliefs which the mainstream Muslims consider bizarre and heretical? My “theory” is supported by these facts. The rare exceptions to the general rule (as when,say, an adult converts to another religion, most often because of a social pressure from the surrounding majorities - as in the case of Jews for Jesus)only confirm the well known notion that no theory is perfect and each has exceptions. Larry Gilman is entitled to his disagreeement with me (albeit it hardly justifies his angry and demeaning words about my “plodding wordy attack” upon Bessete’s review), but his assertions do not seem to be supported by evidence.

Religious conversion by adults is itself a fascinating topic. I wonder if some qualified person has ever explored it in depth.

Behe has often referred to the bacterial flagellum as the equivalent of an outboard motor. However, his analogy is flawed because the “motor” that turns the flagellum is INSIDE of the cell wall of the bacterium. The proper analogy would be to a boat with an inboard motor that powers a propeller that is outside of the boat’s hull. (In the case of a jet drive, the motor and propeller may both be inside of the boat’s hull.)

Scott Beach said:

Behe has often referred to the bacterial flagellum as the equivalent of an outboard motor. However, his analogy is flawed because the “motor” that turns the flagellum is INSIDE of the cell wall of the bacterium. The proper analogy would be to a boat with an inboard motor that powers a propeller that is outside of the boat’s hull.

We went boating this afternoon (it was a nice day here) and I held a flagellum in my hands in the water behind the boat. Nothing happened… Turned on the boat’s inboard engine, and off we went for a wonderful day on the water. So I Scientifically tested Behe’s comparison, and it failed.

Don’t the creos always whine that seeing is believing? You showed them Mark, excellent images.

Flint Wrote:

Religious conversion by adults is itself a fascinating topic. I wonder if some qualified person has ever explored it in depth.

Many years ago I read The Varieties of Religious Experience: A Study in Human Nature by William James.

No doubt there have been more recent studies, but James still seems to have had some pretty good insights.

This study also looks interesting. Thanks.

Even the images in Perakh’s essay somewhat overstate the “machine-like” aspects of flagellar structure, because these are idealized optimized structures, most of them presented at the somewhat abstracted level of ribbon diagrams, with all of the subunits in identical conformations. If one has never seen molecular dynamics simulations, it is easy to think of these as rigid parts, rather than molecules with a huge number of rotatable bonds in constant Brownian motion, looking not so much like an engine as like a shaken Jello dessert.

Obligatory post kudos - it is a good topic.

As the peppered moth illustrations were mentioned, in my layman opinion I suspect the photographs tells us very little about the real structural behavior of the flagellum.

The fixation process is rapid freeze cryogenic for a reason, resolution problems abound, and in a sense it is giving as much or more of a false impression to show electron microscopy for persons untrained in the differences to light photography than an idealized sketch. (Not that this heavily referenced Talk Reason article should be expected to do so.)

IMHO what would be really impressive would be to show an animation of proteins being pushed about in the cellular environment, stochastically working through a mechanic function while going through any possible conformation changes they may have. Or at least taking the idealized structure diagrams of figure 5-7 and randomize distances and angles in and between molecules according to a freeze frame of the real distribution.

Data comparing man made “macromachine” and micromachine tolerances and work cycle efficiency with biochemical machines would also be telling.

Meanwhile EM pictures is a great antidote for claims of perfection.

Btw, Bessette’s argument from authority seems even sillier to me than mentioned here. If it had any value at all, it would be that the trend has been for more scientists being or becoming atheists, especially among the great authorities I believe.

But as it has no relevance for the discussed science outside of what motivates ID advocates attacking it, these statistics are best forgotten. Practically it is a problem for me if a paper is written in french, not if it is written by a buddist. [Disclaimer for french readers: I’m a language agnostic, and “freedom for language” is no problem for me - but I haven’t absorbed french in my childhood.]

oops, trrll was faster on the images and simulation.

wow whining about overstated flagellum complexity. and like the NCSE made clear it only took four mutations to make the eye(didn’t hear anyone blogging that oversimplification). everything is simple, the cell is so simple! time and frothy bubbles concentrating.…compacting and wham!! simple. wait the frothy bubbles had to mutate! simple happens all the time(although never observed). Observation, that isn’t a necessary step in the scientific process is it? Repitition? who needs it? so simple indeed.

Mark Perakh said:

let me ask Larry Gilman a question: Can you predict, with an overwhelming probability, what the religious affiliation will be of a boy born today in Islamabad?

I shouldn’t wade into this, but how would you respond to the similar observation that the overwhelming majority of people accept what they were taught in science class. If 9th grade science books teach that there are three phases of mater, then people think there are three phases of mater. If four, then four. etc. To compound the problem, people who are serious about science and write those book assert that the majority of people are woefully scientifically ignorant. Similarly, the people who write books about religion, and teach religion classes assert that average people are woefully theologically ignorant.

While I understand that you are making an argument that religion is accepted not on the basis of a rational argument, but on shared cultural values, it seems to me that such values can also emphasize critical thinking and the scientific method (they did in my family at least). As Dawkins nearly points out, the vast majority of people have the same political affiliation as their parents as well. Does this imply that there is no rational discourse in politics?

I have certainly never observed rational debate in politics. I have hear rumors of such debate, but have found the evidence of it to be sadly unconvincing. A friend of a friend saw two people talking intelligently, someone wrote it down the next day after hearing it, but no one seems to ever have a tape recorder on while these rational people talk. Any person who says that logic and reason play any part in public policy, life, sex, rhetoric, or really anything more exiting and productive than checkers is clearly been spending too much time reading and should not be trusted. Especially if they have glasses. Glasses are a dead give away of these academic types. I say if someone doesn’t have enough decency to get a pair of contacts, then they are probably a communist agitator. In closing, reading is bad for you, go watch some tv. And send me a dollar.

[This post has been typed purely for my own amusement, and should in now way be taken as a serious intellectual discourse]

[Enable javascript to see this email address.] said: like the NCSE made clear it only took four mutations to make the eye

??? There is an NCSE video about the eye which shows a series of states in the process of eye evolution. But did anyone mention “four mutations”? The eye and its development comprises a whole lot of genes, so it is likely a large amount of genome change involved even though the phenome change seems small between states.

The “one gene, one trait” idea, isn’t that a really old hypotheses, found to be most often wrong several decades ago?

Observation, that isn’t a necessary step in the scientific process is it? Repitition? who needs it?

As I suspect you have watched the above video, you should know that they mentioned observations and repetitions, including repetitions from disparate areas of phylogeny and development.

Your strawman of the science is really funny as eyes have developed independently a large number of times, so there is plenty of phylogenetic repetition already there. What where you thinking?

what was that movie that Behe and expelled allegedly stole from? the one about the cell?

Torbjorn: you are a man of precision. Have you ever researched this mutation bizzo? I have heard - and I have every reason to believe it to be true - that the genetic damage constantly downgrading the clarity of genetically transmissible information in all higher life forms including Man, if it continues, will ultimately render higher life inoperable. I know for a fact that our genetics are getting worse. So, evolution through mutation cannot happen amongst higher life-forms, IN THE ENVIRONMENT IN WHICH WE CURRENTLY LIVE.

Do common descent advocates get around this by hypothesizing a different world in the past, or do they simply ignore the facts? And have you got anything authoritative on the rate of genetic damage?

Philip Bruce Heywood said:

I have heard…that the genetic damage constantly downgrading the clarity of genetically transmissible information in all higher life forms including Man, if it continues, will ultimately render higher life inoperable.

Why?

Philip Bruce Heywood said:

I know for a fact that our genetics are getting worse.

How do you know that “for a fact”? What evidence do you have to support this claim?

Philip Bruce Heywood said:

So, evolution through mutation cannot happen amongst higher life-forms, IN THE ENVIRONMENT IN WHICH WE CURRENTLY LIVE.

Why?

Larry Gilman Wrote:

[Perakh] rears up at Bessette’s claim to know what atheists are thinking –

“How could Bessette know that atheists indeed construe his two facts (assuming they are true) as ‘inconvenient’? Has he conducted a poll of the atheistic scientists?”

– but then goes into a mind-reading act of his own, a few lines later:

“ … those 40% of contemporary [theistic] scientists in the USA … overwhelmingly inherited their faith from their parents and adhere to it throughout their lives because of having emotionally absorbed it in their childhood.”

Since turnabout is fair play, how does Perakh know that continued adherence to some form of religious belief is causally explained across the whole group of US theistic scientists by their “having emotionally absorbed it in their childhood”? How does he rule out a contribution from mature mental and emotional processes to ongoing religiosity, possibly including reason, volition, and adult religious experience? To paraphrase his own question, has he conducted a poll of the theistic scientists?

Although, Larry, you appear to have failed to notice how Mark then (quite rightly) dismissed all of these arguments from authority as irrelevant. The way I took Mark’s objection was not as a genuine counter-point, but as an illustration of the folly of making such arguments based on opinion polls or references to authority. His comment about why an alleged 40% of scientists in the USA are religious is an interesting point, perhaps, but scarcely central to Mark’s argument.

Some comments on the whole 40% thing. First of all, this statistic is used by TEs such as Collins and myself to let lay people know that evolutionary biology is not some atheistic plot. Atheistic scientists aren’t really the audience here. Also, last time I checked 40% is not a majority and it also refers to generic theists and not particular faiths. Another interesting thing is that a similar survey at the beginning of the 20th Century showed the same 40/60 split between theist/atheist. So, despite all that has happened in the last 100 years this hasn’t moved. So much for the self-serving conspiracy theories of ID or the New Atheists.

Let me show you the use of this statistic in its context. For example, Collins used this statistic in the AAAS video on YouTube which is a response to Expelled to show that Evolution was not *necessarily* atheistic. (Actually a pre-response because the video was shot long before the movie.) The NAS in their statement on evolution and creationism also noted this. The bottom line here is scientists who believe Evolution and believe in God exist and not that we are some sort of majority. N.B. my use of prepositions in my previous sentence.

One book that was not reviewed that also dealt with this statistic was The Reason for God by an evangelical pastor and theologian by the name of Tim Keller. He had an interesting and in my opinion on target interpretation of the statistic. Neither side is going away. We are neither moving to a “godless nation” nor to a “theocracy”. I guess we will just need to learn to live with each other.

trrll said:

Even the images in Perakh’s essay somewhat overstate the “machine-like” aspects of flagellar structure, because these are idealized optimized structures, most of them presented at the somewhat abstracted level of ribbon diagrams, with all of the subunits in identical conformations. If one has never seen molecular dynamics simulations, it is easy to think of these as rigid parts, rather than molecules with a huge number of rotatable bonds in constant Brownian motion, looking not so much like an engine as like a shaken Jello dessert.

Trrll, this is a good point. Something that X-ray crystallographers must constantly be aware of is that the crystallisation procedure that is necessary to freeze the motion of the protein and thus allow capture of the diffraction pattern may also result in a non-native conformation of the protein. Some published X-ray structures have gaps, where portions of the polypeptide have not been immobilised in the crystal and are thus not resolved in the electron-density map.

Bobby said: Perhaps it’s fraud, or perhaps it’s merely the fact that IDologists, not being scientists in spirit, do not have any motivation to dig deeper when they see something that appears to support their agenda.

Bobby, this is very revealing. After the ID advocates have been whining on and on and on about how ID is science and not based on religion (oh, no, siree), even their own supporters are now admitting that they are not scientists.

Whether this was a deliberate fraud or the result of academic incompetence is only a small difference. It illustrates the inherent hypocrisy of the entire ID movement. They are happy to accuse science of irrelevant wrongdoing (e.g. over Haeckel’s embryo images, that were revealed to be wrong by scientists working about 100 years ago and are only included in textbooks to provide some historical perspective; and over the peppered moth images, which nicely illustrate the moths’ camouflage irrespective of whether they are photographed on a tree trunk or a branch), but are not prepared even to attempt to meet the standard they publicly expect others to meet.

Nigel, thanks for the thorough explanation, and for clearing up some confusions of mine re reproductive success.

I can see the feedback clearly, though not the loop as you describe it. There are feedback loops when the change in traits change the environment (coevolution, ecology, et cetera), obviously.

Eric said: Torbjorn (sorry about the missing umlaut), while I don’t disagree with you, there is a much simpler response to the fine tuning argument. To whit: any idiot can see that the universe isn’t fine tuned for our type life at all.

Consider; the % volume of the universe consisting of earth-like planet surfaces is, what? 0.000000000001%?

Oh, I agree, it certainly is a valid response when religious people claim that the universe is finetuned for life, as they often do (and really conflate it with). If you google it you can see I used it the other day in such a case. (IIRC on Bad astronomer.)

But when they discuss finetuning in general, and finetuning in theories specifically (“physical” finetuning, for example the ridiculously low cosmological constant of 10^-120 relative, when normalized constants naturally are ~ 1), I want to use the correct answer for that.

bigbang said: Well, perhaps you don’t realize it, but, based on the currently available science and evidence, most agree that the universe that we find ourselves in is around 14 billion years old.

Either you didn’t read my comment, or couldn’t. I explained why a local observable age doesn’t preclude an infinite volume nor eternal time (for example, as future infinite time). In fact, the current cosmology predicts that the universe is eternal. (Or “will be”, if you want to use local coordinates.)

As I was correcting a detail in science, I fail to see what relevance any wider absence of belief would have. Btw, atheism isn’t a religion, you don’t need freedom of religion to abstain from expressing religion. You just need right to life and liberty.

Henry J said:

without explaining the degree of idealization applied, is sometimes perilously close to committing a fraud.

Sometimes?

Isn’t the flagellum graphically portrayed in textbooks in this ‘machine-like’ manner?

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This page contains a single entry by Mark Perakh published on May 12, 2008 9:44 AM.

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