Saturday, December 24, 2005

The Ribosome.


The Ribosome is perhaps the most complex machine at the centre of life. It is the place where proteins are assembled by putting together the 20 different amino acids in a specific order coded by information "photocopied" from the cell's "hard drives" - the DNA molecules.


Bruce Alberts is the President of the National Academy of Science in the US and organisation which thrown its weight behind the campaign to exclude consideration of Intelligent Design from Science.

In his huge textbook on Molecular and cellular biology he says this about the ribosome:

“The complexity of a process with so many interacting components has made many biologists despair of ever understanding the pathway by which protein synthesis evolved.”

He goes on to argue that RNA in the ribosome (the factory for assembling amino acids into long chains in the correct order using the code message copied from the DNA) provides a clue to its simple evolutionary precursors.

The important point is that Bruce Alberts here acknowledges a real and serious problem. He goes on to suggest some hope for Darwinists but it is a clutching at straws sort of hope.

Biologists have really serious problems with explaining complexity using chance and selection but they are determined to teach our children that no other more appropriate causes of complexity can be seriously considered.

11 Comments:

Blogger Jeffahn said...

http://www.talkorigins.org/indexcc/CB/CB010_2.html

" 1. Biochemistry is not chance. It inevitably produces complex products. Amino acids and other complex molecules are even known to form in space.

2. Nobody knows what the most primitive cells looked like. All the cells around today are the product of billions of years of evolution. The earliest self-replicator was likely very much simpler than anything alive today; self-replicating molecules need not be all that complex (Lee et al. 1996), and protein-building systems can also be simple (Ball 2001; Tamura and Schimmel 2001).

3. This claim is an example of the argument from incredulity. Nobody denies that the origin of life is an extremely difficult problem. That it has not been solved, though, does not mean it is impossible. In fact, there has been much work in this area, leading to several possible origins for life on earth:

* Panspermia, which says life came from someplace other than earth. This theory, however, still does not answer how the first life arose.
* Proteinoid microspheres (Fox 1960, 1984; Fox and Dose 1977; Fox et al. 1995; Pappelis and Fox 1995): This theory gives a plausible account of how some replicating structures, which might well be called alive, could have arisen. Its main difficulty is explaining how modern cells arose from the microspheres.
* Clay crystals (Cairn-Smith 1985): This says that the first replicators were crystals in clay. Though they do not have a metabolism or respond to the environment, these crystals carry information and reproduce. Again, there is no known mechanism for moving from clay to DNA.
* Emerging hypercycles: This proposes a gradual origin of the first life, roughly in the following stages: (1) a primordial soup of simple organic compounds. This seems to be almost inevitable; (2) nucleoproteins, somewhat like modern tRNA (de Duve 1995a) or peptide nucleic acid (Nelson et al. 2000), and semicatalytic; (3) hypercycles, or pockets of primitive biochemical pathways that include some approximate self-replication; (4) cellular hypercycles, in which more complex hypercycles are enclosed in a primitive membrane; (5) first simple cell. Complexity theory suggests that the self-organization is not improbable. This view of abiogenesis is the current front-runner.
* The iron-sulfur world (Russell and Hall 1997; Wächtershäuser 2000): It has been found that all the steps for the conversion of carbon monoxide into peptides can occur at high temperature and pressure, catalyzed by iron and nickel sulfides. Such conditions exist around submarine hydrothermal vents. Iron sulfide precipitates could have served as precursors of cell walls as well as catalysts (Martin and Russell 2003). A peptide cycle, from peptides to amino acids and back, is a prerequisite to metabolism, and such a cycle could have arisen in the iron-sulfur world (Huber et al. 2003).
* Polymerization on sheltered organophilic surfaces (Smith et al. 1999): The first self-replicating molecules may have formed within tiny indentations of silica-rich surfaces so that the surrounding rock was its first cell wall.
* Something that no one has thought of yet. "

Also, from Kenneth Miller's testimony in Dover:

"Q. Now let me just stop you. Just because science today cannot explain something, does that mean it can never be explained?

A. Of course not. And if it did, no one would do scientific research. What attracts scientists to research is the lure of the unknown. There is nothing more dreadful than to wake up one morning and think that all the fundamental problems in your field has been solved. On the day that I think all fundamental problems in cell biology have been resolved, I will retired to Sussex and keep bees, as Sherlock Holmes once said.

You want unsolved problems. You're attracted to them. I'll just give you a very simple example. Proteins are built by hooking together strings of amino acid, almost like beads on a string. The machine that does that building is called a ribosome. We have worked for years to understand the detailed molecular structure of the ribosome.

As a result of work that's been published in the last couple years, we know the internal structure of the ribosome down to the atomic level. We can now look inside it, and we can see the molecular details of how these two amino acids are brought into very close proximity.

But do you know what? There's still an unsolved problem. We still don't understand the chemistry that forges the link between those two beads on a chain. There was a very popular hypothesis that was put forward by Peter Moore at Yale University. But in the last year, a number of experimenters, including Al Dahlberg at my own university, has shown that Moore's ideas are wrong.

So what scientists everywhere realize is, there's a great prize to be won. That's very exciting. To find the mechanism by which these are joined together. What no one is doing is to say, we'll never solve it, we're going to attribute the formation of the bond between amino acids to an unseen outside force operating beyond nature and, therefore, any chemical explanation is doomed to failure.

That's something we never say in science, because if we did, it would be a research stopper. It would tell us, give up, go home, we'll never figure it out."

Why just give up and say that the ribosome was created supernaturally?

12:49 pm  
Blogger Andrew Rowell said...

Hello Jeff,

I am not saying "I know for certain you will never find a solution to the origin of life" (personally I think a chance solution will never be found) BUT I am saying that scientists have absolutely no right to say that "we know for certain that a natural chance solution will be found eventually if we keep looking hard enough" BOTH statements shut down possible answers which have not been ruled out.

Certainty that a natural solution will be found is just as wrong as certainty that a natural solution will not be found.

I am convinced that there never will be a natural solution based solely on chance. I am convinced that the origin of life reserachers are barking up the wrong tree and will eventually get tired of it.

(Just as I am convinced that Richard Faragher will not solve the problem of ageing and death before he and I and you die)

Saying an intelligent designer did it is not a research stopper. This is one of the strong points that Steve Fuller is making from the history of science. The idea of an intelligent designer was perhaps the greatest stimulus to the origin of science.

My point was that Bruce Alberts acknowledges the real problem but insists on shutting out the possibility that philosophical naturalism may actually be wrong.

BTW I hope you have a great Christmas!

Thanks for your interest and comments.

1:22 pm  
Blogger Kingfisher said...

Just wanted to say that I follow this blog closely and really enjoy the posts and the discussion. You seem to have a higher level of civility than exists on many of the sites discussing this issue.

5:39 pm  
Blogger Andrew Rowell said...

Hello Kingfisher,

You live in a beautiful part of the world... some wonderful pictures on your blog!

Thank you for your interest...have a happy Christmas.

9:36 pm  
Anonymous Anonymous said...

"Nobody denies that the origin of life is an extremely difficult problem. That it has not been solved, though, does not mean it is impossible."

If it has not been solved, then the idea that we all came to be from matter with no intervention by any intelligent agent should not be held with the kind of confidence that is now customary.

3:03 am  
Anonymous Anonymous said...

"But do you know what? There's still an unsolved problem. We still don't understand the chemistry that forges the link between those two beads on a chain."

This is not AT ALL analogous to the ID case.

We know there must be chemical bonds between those two molecules, even if we don't understand them at present, because we have tons and TONS of EXPERIMENTAL evidence that such chemical bonds govern interaction between molecules.

We do not have anything like that kind of evidence for the view that unintelligent forces can produce irreducible complexity, because the only times when we are able to trace the causes of an irreducibly complex structure, we find that someone did it.

It is therefore entirely reasonable to doubt that unintelligent forces could account for the origin of irreducible complexity.

3:12 am  
Blogger DaveScot said...

jeffahn

"1. Biochemistry is not chance. It inevitably produces complex products. Amino acids and other complex molecules are even known to form in space."

Dude! DNA is a digital code. Biochemistry doesn't produce digital codes. Digital coders to that. As far as I know all the digital coders, myself included, are categorically classified as intelligent agents.

Nice try though! Or rather, nice try by the computer science illiterate that wrote the talkorigins entry you quoted...

6:50 pm  
Blogger Jeffahn said...

DaveScot said...
jeffahn

"1. Biochemistry is not chance. It inevitably produces complex products. Amino acids and other complex molecules are even known to form in space."

Dude!

DaveScot, dude, please stuff yourself back up Dembski's ass, along with the rest of your merry band of front-loading, creationist crank/moron buddies.

DNA is a digital code.

No, it merely is merely similar to digital code in some respects and in fact completely different in other respects.

Biochemistry doesn't produce digital codes.

Biochemistry doesn't need to produce digital codes.

Digital coders to that. As far as I know all the digital coders, myself included, are categorically classified as intelligent agents.

So, Dave, who then is the original "digital coder" according to you? He doesn't exist according to your much beloved Dembski, did you know that? Demski said that the only source of CSI is "intelligent agents", and all "intelligent agents", by definition, have CSI, so how could CSI then arise from nowhere?

Nice try though! Or rather, nice try by the computer science illiterate that wrote the talkorigins entry you quoted...

This is rich coming from somebody who knows nothing about both biological evolution and computer science. I suppose you would also accuse all of Mark Isaak's sources of being part of the conspiracy against ID aswell?

Again, back up Dembski's ass where you belong.

7:23 pm  
Blogger Andrew Rowell said...

Jeff,

You said:
"So, Dave, who then is the original "digital coder" according to you? He doesn't exist according to your much beloved Dembski, did you know that? Demski said that the only source of CSI is "intelligent agents", and all "intelligent agents", by definition, have CSI, so how could CSI then arise from nowhere?"

It seems to me that we either assume
(a) eternal (unless you believe that nothing can produce something)unintelligent, self existent matter created everything

OR

(b) eternal intelligence created matter and all that followed.

Who is to say which is a more logical assumption? Intelligence first or matter first. That really is the crunch between atheism and theism.

8:53 am  
Blogger beervolcano said...

Andrew Rowell,

Certainty that a natural solution will be found is just as wrong as certainty that a natural solution will not be found.

I don't think anyone is absolutely certain that a "natural" solution must be found. It's just that there are two options. Keep working to try to find a naturalistic answer or give up.

Or, if you think you can detect the supernatural through forensic science and you can get funding for it, good for you, you've got a paycheck. Now, if you can do that and manage to publish actual results that are reproducible then it might be on the road to being taught to kids in public schools.

5:12 am  
Blogger beervolcano said...

Sorry for the double post, but:

It seems to me that we either assume
(a) eternal (unless you believe that nothing can produce something)unintelligent, self existent matter created everything

OR

(b) eternal intelligence created matter and all that followed.



OK, you or I or anyone else can assume anything we like. We can philosophize about things like this, but science has little if any way in which to adress such questions. Is all of existence eternal? Is there a first cause? Science as we know it has no way of even broaching the subject.

The limit, for now, is being able to hypothesize about things beyond this universe (universe not being the cosmos) based on existing science. It still has to fit existing data and be mathematically sound. Regardless, it remains an untested and perhaps untestable hypothesis.

5:21 am  

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