Science v Intelligent Design: The reducible bacterial flagella

| 36 Comments

flunked.jpgMy second example in this very educational series is how science explains the origin of the bacterial flagella.

Science Explains

Erv asks and Science explains. First of all thanks to Erv for providing us with a ‘transcript’ of Dembski’s lecture

“Evolution in (Brownian) space: a model for the origin of the bacterial flagellum” Nick Matzke 2003

Background to “Evolution in (Brownian) space: a model for the origin of the bacterial flagellum” Nick Matzke

Pallen MJ, Matzke NJ. “From The Origin of Species to the origin of bacterial flagella.” Nature Reviews Microbiology, 4(10), 784-790. October 2006. (pdf)

Intelligent Design Explains

William Dembski, 2007 in Dembski v the masked man

36 Comments

W. Ford Doolittle and Olga Zhaxybayeva (2007). “Reducible Complexity - The Case for Bacterial Flagella.” Current Biology, 17(13), R510-R512. July 3, 2007.

Apel D, Surette MG. Bringing order to a complex molecular machine: The assembly of the bacterial flagella. Biochim Biophys Acta. 2007 Jul 24;

The bacterial flagellum is an example of elegance in molecular engineering. Flagella dependent motility is a widespread and evolutionarily ancient trait. Diverse bacterial species have evolved unique structural adaptations enabling them to migrate in their environmental niche. Variability exists in the number, location and configuration of flagella, and reflects unique adaptations of the microorganism. The most detailed analysis of flagellar morphogenesis and structure has focused on Escherichia coli and Salmonella enterica. The appendage assembles sequentially from the inner to the outer-most structures. Additionally the temporal order of gene expression correlates with the assembly order of encoded proteins into the final structure. The bacterial flagellar apparatus includes an essential basal body complex that comprises the export machinery required for assembly of the hook and flagellar filament. A review outlining the current understanding of the protein interactions that make up this remarkable structure will be presented, and the associated temporal genetic regulation will be briefly discussed.

The bacterial flagellum, singular; bacterial flagella, plural. C.f. bacterium, bacteria. Unless it’s “the bacterial flagella were harvested.”

It’s bacterial flagella, just like punctuated equilibria, plural.

Nice article with pictures

Revealing the mystery of the bacterial flagellum — A self-assembling nanomachine with fine switching capability —

Ah, biological nanomachines in all their efficient glory. (While human micromachines have yet to overcome ubiquitous frictional sticking problems.)

Keiichi Namba Wrote:

On one hand you have such things as this efficiency or the elegant built in assembly line for the flagellar filament. Fortunately on the other hand you have the stupid locally suitable solutions that shows you evolution is the thoughtless tinkerer theory says it is, like blood vessels and nerves that loops over other organs.

For a probable example just in the news is the idea that the human bodyplan may be dated to at least 21 Ma, and that it may have been a sudden defect that forced “hominiform” ancestors to stand upright:

The mechanical effect of the transposition was to make horizontal or quadrupedal stance inefficient. “Any mammal with this set of changes would only be comfortable standing upright. I would envision this malformed young hominiform - the first true ancestral human - as standing upright from a young age while its siblings walked around on all fours.”

The earliest example of the transformed hominiform type of lumbar spine is found in Morotopithecus bishopi an extinct hominoid species that lived in Uganda more than 21 million years ago. “From a number of points of view,” Filler says, “humanity can be redefined as having its origin with Morotopithecus. This greatly demotes the importance of the bipedalism of Australopithecus species such as Lucy (Australopithecus afarensis) since we now know of four upright bipedal species that precede her, found from various time periods on out to Morotopithecus in the Early Miocene.”

Poor bast…, um, malformed thing!

Oh, and there is a bit of irony in that Lucy may eventually be demoted from her pivotal role, considering her recent and controversial world tour. (She is of course still an impressive specimen to see close up, I’ve seen a replica.)

Dembski may actually be “getting it” (hmm, maybe an inappropriate phase…)

Several months ago, while scanning Uncommon Descent (banned on my first post!), I noticed a thread that considered the question: Should we change our mascot [i.e., the flagellum] to the Ribosome? Obviously, this question would not arise if the flagellum were still considered a viable talking point.

The response seemed to be: No, because most people know what a flagellum is, but don’t have any idea what a ribosome is.…

Typical.

The response seemed to be: No, because most people know what a flagellum is, but don’t have any idea what a ribosome is….

The only reason I know what a flagellum is, is because of the arguments about it. Would a ribosome be any different in that respsect, once the arguments got started?

Henry

That would be a bad move, since the ribosome is the poster child for the RNA world theory.

Oh rats, I forgot to use the spell checker…

Would a ribosome be any different in that respsect, once the arguments got started?

No, I think PvM tries to tell us that this larger problem may be in the process of being plausibly attacked.

This is clearly the death nail to ID. This classical creationist approach of putting their god in the gaps of science knowledge is plain idiocy.

It really does become silly when they retreat into the increasing small gaps as the evolution of the flagellum is worked out.

If they beleive in god it is sad they beleive in such a flimsy god that god is marginalized into nothingness by the ordinary persuits of humans.

PvM:

It’s bacterial flagella, just like punctuated equilibria, plural.

[grammar pedantry] But your grammar is wrong if you intended the plural case. You should have omitted the definite article and said, “…the origin of bacterial flagella.” Using “the” means you should also use a singular noun. [/pedantry]

I believe science has a great message which is not always communicated well outside a ‘select group’. And yet, great ‘stories’ arise from this research which ID attempts to denigrate using terminology like ‘just so stories’, when in fact they are exactly that. Just so stories, aka scientific hypotheses take a combination of speculation and foundational principles, combine them with known constraints and reconcile them with available data to attempt to explain a particular phenomenon and generate additional hypotheses and research. In other words, just so stories generate a research programme. I believe that science has great stories to tell and a willing audience that is interested in hearing more. Science needs to be embarassingly honest about the limitations and the many speculative aspects involved while at the same time be willing to propose and stand by its explanations and defend until a better explanation is found.

I also believe that ID has at best a very minor role to play, not particularly related to ID but related to ‘keeping science honest’. Until ID is willing and able to generate scientific hypotheses which can compete with the ‘just so stories’ of science, it is doomed to remain scientifically without much content.

There are many indicators that suggest that ID is retreating from its grandiose claims to an entrenched position of ‘teach the controversy’ which is based on a flawed assumption that there is a controversy beyond the usual scientific speculations and competing ideas and concepts. These are not weaknesses of science but strengths and educating people how science works does more to expose ID. So by all means ‘teach the controversy’, educate our children as to the fascinating world of science and ID will be forced to live in ever smaller gaps, doomed to an existence of irrelevance.

Why do the IDers focus on areas of ignorance such as the origin of life, the genetic code, the Cambrian ? Simple, because they believe that they can compete with ‘we don’t know’ but this requires them to ignore and deny the existence of countless scientific hypotheses about the origin of life, the origin of the translation mechanisms, the transition of RNA to DNA world, the Cambrian explosion, and so on.

It is science’s task to share these stories with the world, story tellers used to be a very important profession to share information, values, knowledge across large distances and across time. It’s time for science to take on again this important tradition and be very straightforward about the limitations and assumptions of their work. And who knows, there may be even a role for ID

Well said PvM.

Torbjörn Larsson quoted Keiichi Namba (above) as writing:

…the flagellum..rotates at around 20,000 rpm, at energy consumption of only around 10-16 W…

16 watts can’t be right! Is that milliwatts or microwatts or nanowatts or picowatts…? Or am I missing something here?

The link provides the answer

10^-16

Yeah, gotta watch those disappearing exponential operators. That seems to happen fairly often when somebody pastes stuff.

Henry

PvM Wrote:

And who knows, there may be even a role for ID.

I have argued locally that ID/Creationism would make a nice case study on the abuse of science in a course on critical thinking. Not in a high school science class however. If any of the activities of our local ID/Creationists are any indication, placing these discussions in, say, a high school biology class would provide them with the perfect opportunity to chew up all the time needed to teach legitimate science.

But as a case study in critical thinking, it might be just the antidote needed to drive the stake through the heart of this ugly beast. They themselves have provided more material to shoot themselves in the head than we have. It’s all on record, and it serves as a great prototype example of the kinds of propaganda that so disrupts reasoned thinking and fact finding in public and political arenas. Including a few broadcasts from the Coral Ridge Hour’s attempts to portray itself as a sectarian view supported by science and a bastion against evolution would provide some humor as well.

Why do the IDers focus on areas of ignorance such as the origin of life, the genetic code, the Cambrian ?

I think it’s because the areas of non-ignorance do not support their Creationist conclusions.

A non-biological attempt: Iron as an example of ID

God is rather hard to miss in the universe he has created. A thoughtful professor of engineering just recently pointed out in a conversation that the unexpected changing structure of iron when heated, which allows atoms of other elements to slip into the lattice, seems to have had steelmaking in mind. And iron just happens to be the most abundant metal in the earth’s crust. Steel is the metallic foundation of modern civilisation. The Professor sees God in iron and we got to talking about this anthropic principle in nature - the idea growing in ‘scientific’ respectability that a super mind designed a world to be inhabited and used by creative humans.

More embarrassment for rational engineers. Gotta love those scare quotes on ‘scientific.’

Why do the IDers focus on areas of ignorance such as the origin of life, the genetic code, the Cambrian ?

I think it’s because the areas of non-ignorance do not support their Creationist conclusions.

Yeah, that and the fact that their premise doesn’t answer any questions about details. (Or deheads, either.)

Henry

wamba:

A non-biological attempt: Iron as an example of ID

God is rather hard to miss in the universe he has created. A thoughtful professor of engineering just recently pointed out in a conversation that the unexpected changing structure of iron when heated, which allows atoms of other elements to slip into the lattice, seems to have had steelmaking in mind. And iron just happens to be the most abundant metal in the earth’s crust. Steel is the metallic foundation of modern civilisation. The Professor sees God in iron and we got to talking about this anthropic principle in nature - the idea growing in ‘scientific’ respectability that a super mind designed a world to be inhabited and used by creative humans.

More embarrassment for rational engineers. Gotta love those scare quotes on ‘scientific.’

Except that aluminum is the most abundant metal in the earth’s crust. Still useful though, but people should get facts correct.

I believe science has a great message

AH HAH! So science IS just another Religion!

*chokes*

I believe science has a great message

AH HAH! So science IS just another Religion!

“Preachers in pulpits talked about what a great message is in the book. No matter what you do, somebody always imputes meaning into your books.”

Theodore Geisel (a.k.a. Dr. Seuss) (1904-1991)

That would be a bad move, since the ribosome is the poster child for the RNA world theory.

In their role as ribozymes.

Crowther attemtps

Video: Molecular Machines and the Death of Darwinism

In this excerpt from “Molecular Machines and the Death of Darwinism,” CSC senior fellow and mathmatician William Dembski explains how Darwinists use complex living systems like the mammalian eye to support Darwinian evolution without supplying adequate sequential evidence. In response, Dembski says, ID proponents focus on molecular machines such as the bacterial flagellum to understand their complexity and directly address Darwinist claims.

From this we learn that 1) ID is based on an argument that science does not provide adequate sequential information but it has become clear that Dembski would never accept the information presented as sufficient 2) ID is based on complexity even though Darwinian theory seems sufficient to explain information and complexity.

So how does ID explain? We may never know. But ID seems to be more and more an emperor without any clothes.

Isn’t ID fascinating, accusing Darwinian theory of using complexity without providing sufficient steps…

Does anyone fail to understand the incredible amount of irony here?

ID abuses the concept of complexity to argue for design while presenting NO steps for its claims beyond “I am not convinced…”

What a crock

It’s bacterial flagella, just like punctuated equilibria, plural.

Sigh. You got it right with “Ken Miller on the flagellum”. “the flagella” refers to a concrete collection of flagella, but is incorrect when referring to the abstract class.

[grammar pedantry] But your grammar is wrong if you intended the plural case. You should have omitted the definite article and said, “…the origin of bacterial flagella.” Using “the” means you should also use a singular noun. [/pedantry]

First, plural isn’t a case. Second, it’s wrong when used in the abstract, as here. But “The bacterial flagella were barely discernible on the slide” would be proper grammar.

And yet, great ‘stories’ arise from this research which ID attempts to denigrate using terminology like ‘just so stories’, when in fact they are exactly that. Just so stories, aka scientific hypotheses take a combination of speculation and foundational principles, combine them with known constraints and reconcile them with available data to attempt to explain a particular phenomenon and generate additional hypotheses and research.

I would make a distinction between inferred historical sequences that are firmly grounded in logic and multiple threads of evidence, and “just so stories” which grounded only in one’s desire for them to be true – like “God did it”.

Just so stories, aka scientific hypotheses

Um, what PG said. Most often defined as “an unverifiable and unfalsifiable narrative explanation”.

Henry J:

Thanks for the correction! I usually checks for those things…

About this Entry

This page contains a single entry by PvM published on October 10, 2007 10:25 PM.

Judgement Day: Intelligent Design on Trial November 13, 2007 was the previous entry in this blog.

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