Sunday, March 28, 2010

The Axe-Meyer Axis.

This is an attempt to state more clearly what I tried to say before...
How is Axe's published work relevant to ID?

Past posts for reference:
I was thinking...
J.Mol.Biol- 2000 -301-585-595
Controversial paper
Appearance of design


Making a functional protein from scratch is difficult. This is relevant in two situations(a) In a prebiotic soup making a protein to help stabilise or increase the function of a precellular replicon.
(b) after the origin of life the development of a brand new structural or functional protein which enhances the reproductive capacity of the organism.

The following argument is my version of what Stephen Meyer says on p206 and following in Signature in the Cell.

Most functional proteins are over 150 amino acids long. The average is estimated at around 300 amino acids long. With 20 different amino acids a protein 150 amino acids long gives a very large number of possible sequences - 10195 (which is a pretty big number)

Firstly in a prebiotic soup with an abundance of amino acids there are a number of possible ways in which amino acids can link up- however to get a folding protein we need peptide bonds. The probability of forming a peptide link is about 1 in 2.

To get a 150 amino acid molecule with peptide bonds the whole way along will be a probability of 1 in 1045.

Secondly in a prebiotic soup there will be 2 optical isomers of each amino acid. All the functional proteins in nature use only L isomers.

To get a 150 amino acid molecule with only L isomers the probability is also 1 in 10 45.

Thirdly there are constraints in terms of the exact order of amino acids that will produce a protein that can fold into a globular shape with the possibility of having a function.

Fourthly there are constraints in terms of the exact order of amino acids that will produce a protein that has a function.

The fourth issue was investigated by Robert Sauer in the late 1980's at MIT. Cassette mutagenesis was used to examine the tolerance to sequence change at a number of locations in a variety of proteins.

The results showed that the probability of acheiving a functional sequence in several small proteins was very low. In other words there are very few different combinations of amino acids that allow the function to be maintained.

The chance of hitting on one of these by chance was about 1 in 1063.

Doug Axe was interested in Sauer's work and began to wonder if he had underestimated how much protein sequences can vary and still retain function.

He developed a more rigorous mechanism to test this. The results in a paper published in 2004 were particularly important. On the basis of these results Axe was able to demonstrate that the ratio of functional sequences to non functional sequences for the enzyme beta-lactamase was 1 functional sequence to every 1 x1077.

Axe's work also allowed him to calculate the probabilities of finding any functional sequence amongst the possible sequences. This was done by looking at the probability of sequences being able to form stable folds (a necessary pre-requisite for stable 3D structure)

On the basis of his work he calculated the ratio of sequences able to form stable 3D structures to those which were not able to as 1 to 10 74.


A comparison of these odds:

The odds of finding a 150 amino acid sequence able to fold into a stable 3D shape is equivalent to finding a single marked atom out of all the atoms in a a billion Milky Ways (that is the galaxy[this is the star system rather than the chocolate bar] rather than the chocolate bar)

These are unpromising odds to say the least.

For a functional protein in a prebiotic soup the odds are considerably worsened.

For a complex of functional proteins occuring at the same time the odds are also considerable worsened.

The odds of a 150 amino acid protein with stable 3D shape in a prebiotic soup is 1 in 10 to 164 this is well below the entire probabalistic resources of the entire history of the entire universe.

19 Comments:

Blogger Paul (probably - maybe Liz) said...

You can use html tags to show powers. The tags are sup and sub. They don't work in comments, so I can't demonstrate.

11:24 pm  
Blogger Paul (probably - maybe Liz) said...

Hi, Andrew. Further, with regard to the actual subject matter.... Unfortunately, this is a dead end. It was one of the issues that I tried to pursue several years ago on my blog - what it will lead to is opponents of ID saying that simple catalytic functionality doesn't require high specification - 10-12 amino acid sequences can provide a level of functional catalysis, and is adequate for the early stages of natural selection. Axe's work is invalid at least in part because he is a proponent of ID. It must also be invalid because evolution happened, didn't it? So the maths must be wrong.

Over the couple of years I spent debating ID, I became convinced that the real issue was one of presuppositions. The naturalistic perspective on design in life, fine tuning, morality etc etc etc is profoundly unsatisfactory. However, if you presuppose the lack of a God, then it's the only real game in town. Ergo, it must be defended.

11:31 pm  
Blogger Human Ape said...

I wrote a few things about Stephen Meyer and his everything-is-magic book in my blog.

http://darwin-killed-god.blogspot.com/

Do you ever get tired of being at war with the entire scientific community?

Stephen Meyer, by the way, is not part of the scientific community, because never once in his life has he ever contributed anything important to science. His customers are non-scientists, and he makes a living from spreading lies about the discoveries of real scientists. His Christian creationist organization (the Discovery Institute) exists for one reason only - to dumb down science education to accommodate the childish religious beliefs of uneducated Christians.

Comment moderation has been enabled. All comments must be approved by the blog author.

Well then we will soon find out what kind of person you are.

5:05 am  
Blogger Andrew Rowell said...

Paul,
Thanks for the sup!

7:56 am  
Blogger Andrew Rowell said...

Paul,

All kinds of molecules can provide a level of functional catalysis but that is a world away from the specific & efficient 3D structure catalysis provided by proteins.

Even if this is adequate for the early stages of natural selection (I am not convinced BTW) there must still at some point be the switch to proteins and the same obstacle applies.

I am not convinced that all atheists will be happy with the
"It must also be invalid because evolution happened, didn't it? So the maths must be wrong" argument.

8:02 am  
Anonymous Cedric Katesby said...

30/March/2010

I am not convinced that all atheists will be happy with the
"It must also be invalid because evolution happened, didn't it? So the maths must be wrong" argument.


Props for pointing out a strawman, Andrew.
Thanks.

Though you must know that it's got nothing to do with "atheism".
There are plently of devout, sober-minded Christians out there who are brilliant mathematicians.
They are NOT wasting any time churing out any experiments or work as a follow-up to Axe.

The "atheists" don't have an all powerful monopoly in the field of mathematics or science in general.
Never did. Never will.
It's impossible.
The Hindus would have to vanish, for a start!

Oh, and this one was a goodie too:

Axe's work is invalid at least in part because he is a proponent of ID.

Pure gold.
Poe worthy.

The scientific gatekeepers strike again. How do they do it?
The fiends!!!!
;)

But how accurate is the ID whining that science unfairly rules out, a priori, supernatural or non-material explanations? As with everything else in ID "theory", this claim is based solely on deception and hand-waving.

The scientific method is very simple, and consists of five basic steps. They are:

1) Observe some aspect of the universe
2)Form a hypothesis that potentially explains what you have observed
3) Make testable predictions from that hypothesis
4) Make observations or experiments that can test those predictions
5) Modify your hypothesis until it is in accord with all observations and predictions

Nothing in any of those five steps excludes on principle, a priori, any "supernatural cause". Using this method, one is entirely free to invoke as many non-material pixies, ghosts, goddesses, demons, devils, djinis, and/or the Great Pumpkin, as many times as you like, in any or all of your hypotheses. And science won't (and doesn't) object to that in the slightest. Indeed, scientific experiments have been proposed (and carried out and published) on such "supernatural causes" as the effects of prayer on healing, as well as such "non-materialistic" or "non-natural" causes as ESP, telekinesis, precognition and "remote viewing". So ID's claim that science unfairly rejects supernatural or non-material causes out of hand on principle, is demonstrably quite wrong.

Link

Over the couple of years I spent debating ID, I became convinced that the real issue was one of presuppositions.

You "debate" ID, do you?
Wonderful.

Is ID a scientific theory?
If so, how?

5:33 pm  
Anonymous Anonymous said...

I've been in ID-evo debates for +/- 4yrs & I spot here the same old pattern.

ID offers rational arguments (this doesn't mean they are right). Evos do not have rational arguments (doesn't follow they are wrong)

The 6 posts above show this well. Thus the only focus of evo proponents is personalities or labels i.e.

(1) Meyer (not his points) is this, that & the other.

(2)I.D. is not Science (as if labelling it non-science makes it false or there's a demarcation - science vs non-science)

I know it's the side I'm on but on reason alone ID has a case & evo hasn't.

Could the evos please say what's wrong with Meyer's arguments, not Meyer the man? Also, what's logically or empirically wrong with ID, not what label shall we stick on it? I'd like to think if evo presents a sound argument, I'll buy it.

5:33 pm  
Anonymous Cedric Katesby said...

Also, what's logically or empirically wrong with ID...?

What do you mean when you say "ID"?

Nobody seems to know.

ID is meaningless.
It's an empty buzzword.
Nobody around here seems very willing to explain it in a straight-forward scientific way.
Odd that.

For example: Is ID a scientific theory?

Either it is or it isn't.

So let's have it.

Is ID a scientific theory?
Yes or no?

6:50 am  
Blogger Andrew Rowell said...

ID is a scientific idea/hypothesis. I would hesitate I think to call it a theory.

7:14 am  
Anonymous Cedric Katesby said...

I would hesitate I think to call it a theory.

Good call.
Fools rush in and all that...

ID is not a scientific theory.
Never has been, never will be.

When an ID supporter calls ID a theory, they are either dupes that fell for Discovery Institute propoganda or they are simply lying.
It's that simple.

"Let's be blunt. There is no scientific theory of ID. When pressed, the most that IDers can do is recite a long list of criticisms of evolution -- all of which are untrue, none of which is accepted by the scientific body at large, and most of which are simply restatements of the same tired old "criticisms" that creation "scientists" have been making for almost 40 years now. By declaring that "evidence against evolution, equals evidence for design", the IDers are just continuing the very same "two models" idea that the creation "scientists" tried to argue. Unfortunately for them, the "two models" argument was decisively and explicitly rejected by the 1982 Maclean v Arkansas case, and also in the 1987 Edwards v Aguillard Supreme Court ruling."
Link

ID is a scientific idea/hypothesis.

Hmm.
Don't have a clue what you mean by "scientific idea". Sounds a little vague.

However, you think that ID is a...hypothesis?
A scientific hypothesis?
Ok.
Let's work with that.

Honestly explain to me how ID is a scientific hypothesis.
No waffle.
No hand-waving.

If it's a hypothesis then...let's have it.

If ID (whatever it is) is indeed a hypothesis...then we need testable predictions from that hypothesis.

Do you have any?

Have you ever heard of anybody anywhere at any time making any such "testable predictions"?

Feel free to use any blog, Discovery Institute press release, forum comment or fortune cookie you like as your source material. No restrictions at all.
It's all good.

If ID is really and truely a hypothesis (no foolin') then somebody needs to get out there and roll up their sleeves and...actually...MAKE observations or experiments that can test those predictions.
Right?

They need to actually DO something.
They need to MAKE something.
Experiments and/or observations.
Tests.

For over 20 years, what experiments or observations have been done to test "Intelligent Design"?
By anybody?
Ever?

To the best of your knowledge, has anybody ever even PROPOSED such a thing and scribbled it down on a napkin somewhere?

After over twenty years and the millions of dollars that have been soaked up, ID believers are entitled to look expectantly at their watch and ask themselves "What's the holdup?"

I see a lot of propoganda, press releases, coffee table books and solicitaions for more money but...I can honestly say that I don't see a scientific hypothesis.

Do you really believe that there is such a creature?
Really?

6:24 pm  
Blogger Andrew Rowell said...

Cedric,

I will attempt to reply to some of your concerns in a new post dealing with chapters 6 and 7 from Stephen Meyer's book "Signature in the cell"

9:04 pm  
Anonymous Anonymous said...

The pro-Evo post says nothing about the FACTS or TRUTH of ID. It focuses only on what LABEL ID should/shouldn't have.

This confirms suspicion there's no factual or empirical counter to ID. If there were, somebody would have come with it/them by now.

However we label it, science or stamp-collecting, ID seems closer to truth about nature than evolutionism. Surely what matters is what's true, not the name.

7:31 pm  
Anonymous Cedric Katesby said...

30/May/2010

...says nothing about the FACTS or TRUTH of ID.

What do you mean when you say "ID"?


...there's no factual or empirical counter to ID.

Yeah, but...what do you mean when you say "ID"?

(Think about it)

Difficult to talk about "emperical evidence" for ID or "facts" about ID when...you don't have a definition of ID.
(Kinda short-circuits any rational discussion.)

However we label it, science or stamp-collecting, ID...

This is not about "labels".
This is about meaning.
This is about ID.

What is it?
What do you mean by "ID"?
How do you define it?

Do you want to define it as stamp-collecting?
Then do so.

Do you want to assert that ID is really and truely science?
Then do so.
Explain yourself.

Or is ID...without meaning?
Is ID meaningless?
Undefinable?
Vague and wispy and forever just out of reach?

So far, nobody knows what you mean by ID.
(shrug)

11:44 am  
Anonymous Anonymous said...

Cadrec Katesby
I note you have not given a empirical or logical argument reason why evolutionism is a true account of nature. This is my point exactly.

10:18 pm  
Anonymous Cedric Katesby said...

6/June/2010

I note you have not given a empirical or logical argument reason why evolutionism is a true account of nature.

Evolutionism?
Huh?
I thought you wanted to talk about Intelligent Design?

"Let's be blunt. There is no scientific theory of ID. When pressed, the most that IDers can do is recite a long list of criticisms of evolution..."

Yep. I think I can see where this conversation is going.
:)

You wanted to talk about ID before.
So I asked you to tell me what you meant by ID.
Remember?

Then (mysteriously, suddenly) you drop ID like a hot potato and now you want to talk about "evolutionism" or something.
Oh dear.

:)

You have fallen for the false dichotomy fallacy.

Epic logic fail.

Try harder.
Focus on the topic at hand.

Remember the name of this very blog?

It's called "ID in the UK" for a reason.

It's not called "Uninformed, clueless gripes about 'evolutionism' in the UK."

So what's the topic at hand?
Forgotten again?
Let me spell it out for you.

I.N.T.E.L.L.I.G.E.N.T
(big breath)
D.E.S.I.G.N.

THAT's the topic of discussion.
ID.
You brought it up.
ID.
As in 'Intelligent Design'.

So let's have it.
No more hapless hand-waving and painfully obvious evasion.

What do you mean when you say ID?

Or is ID doomed to remain a meaningless phrase?
Forever wispy and vague and functionally useless?
So useless, in fact, that even SUPPORTERS OF ID are TOTALLY INCAPABLE of giving a scientific definition when pressed?

Say it ain't so!

3:34 pm  
Anonymous Anonymous said...

Caderic Katesby
Thanks for your comments. Is there any factual claim about biology by ID that you think is false?

9:43 pm  
Anonymous Cedric Katesby said...

8/July/2010

Is there any factual claim about biology by ID that you think is false?

I'm happy to discuss ID with you.
I really am.

If you have something to say about ID then I am all ears.

So....what do you mean when you say "ID"?
Give the phrase "Intelligent Design" actual meaning.
Define it.

Without a scientific definition, ID is just a meaningless buzzword.

Is it a hypothesis?
An actual scientific theory?
A vague and fuzzy warm feeling deep inside?
What?

Seriously, what do you mean when you say...ID?

5:52 am  
Anonymous Anonymous said...

Rightly or wrongly, I've concluded you do not actually have any empirical facts. You'd have spelled them out by now.

7:57 pm  
Anonymous Cedric Katesby said...

(repost from a few days ago. The other one has become lost)

9/June/2010

Rightly or wrongly, I've concluded you do not actually have any empirical facts.

"empirical facts"?

That's not what we are talking about.

Me having "empirical facts" or not having "empirical facts" has got nothing to do with anything.
Wierd.

The discussion is Intelligent Design.
Remember?
ID?

You brought it up as a subject.
You get to define it.
Stop the wriggling.
It won't work with me.
I have no intention of letting you of the hook.

The part were ID goes from being a meaningless buzzword to taking on form and substance remains suspiciously blank.

Remember this?

ID offers rational arguments...

ID.
ID offering rational arguments?
Wow.
Cool.
So...what's ID?

The pro-Evo post says nothing about the FACTS or TRUTH of ID.

ID.
The FACTS/TRUTH of ID (in allcaps no less!).
Ok.
So what do you mean when you say ID?

ID seems closer to truth about nature...

ID
ID is closer to truth about nature?
Well, well, well.
Sounds interesting.
So, um, what exactly is ID?

Is there any factual claim about biology by ID...

ID.
Factual claims by ID?
A bold assertion.
But what do you mean when you say "ID"?

I'm happy to discuss ID with you.
I really am.

If you have something to say about ID then I am all ears.

Let's have a good, solid, reasonable, polite and friendly discussion about ID.
Let's get to the meat of it.
Reveal all.
Use any and all sources of information that you like.
No restrictions at all.
You have a completely free hand.
Nobody will censor you or avoid the topic of ID around these here parts.

Let's talk about ID.
Let's do it!

ID.
Yes.

What do you mean when you say ID?

I've been in ID-evo debates for +/- 4yrs...

Then you are the perfect person for the job then!
Talk about being overqualified.
:)
In all that time, you must have found out an awful lot about ID.
Excellent.
Share your wealth of knowledge.

Give us a definition of ID.
Please.

So far, nobody knows what you mean by ID.

That's your problem, not mine.
Your words are empty and without meaning.
So far, you are only talking nonsense and playing games.

4:00 am  

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