Thursday, March 18, 2010

The appearance of Design.

The universe itself and living organisms in particular have the appearance of being designed. Human intelligence from very early times has concluded from this appearance of design that there must be a designer.
Darwin’s theory was an alternative seeking to explain the appearance of design without an actual designer.

In terms of biology ID writers suggest three key areas for investigation that interest me.
1. The origin of life itself.
2. The origin of new functional proteins
3. The origin of interdependent proteins where multiple proteins are fine tuned for a particular function and all are required simultaneously for minimal function.
With regards to area 1 I am interested in working through Stephen Meyers recent book – Signature in the Cell.
With regards to area 2 the key research is the investigation of the relative quantities of functional to non-functional proteins amongst all possible proteins. How easy is it to produce an entirely new functional protein? I am not talking about variants within a protein family but the production of an entirely new structure with a new function with no amino acid sequence homology to any other functional protein.
One way to investigate this is to ask how easily protein structure and function degrades when you change one or more amino acids around the active site of an enzyme or elsewhere in its structure.

This gives an increasingly clear picture of the size of the islands of protein functionality in the vast ocean of possible protein amino acid sequences.
It is this kind of experiment that Doug Axe did at Cambridge.

Some previous posts on this:

How big is the hole?
I was thinking..
Axe's paper
Axe's paper
Which Golf Course?

9 Comments:

Blogger Psiloiordinary said...

Hi Andrew,

Excellent suggestions for further work.

Of course scientists are already investigating all these areas and there is a large pile of published work giving lots of detail about all three of you suggestions. None of them involve either the supernatural or meddling aliens.

In particular 2 and 3 both have quite a long list of experimental data where such things have been observed.

Are you not aware of this?

Regards,

Psi

4:57 pm  
Anonymous Cedric Katesby said...

19/March/2010

...asking the question- How easy is it to produce an entirely new functional protein? - Is directly relevant to the issue of detecting design in biology.

Ok.
How?

How do you go about "detecting design" in nature...using the question....

How easy is it to produce an entirely new functional protein?

or this question...

...how easily protein structure and function degrades when you change one or more amino acids...?

You said...

This gives an increasingly clear picture of the size of the islands of protein functionality...

I don't get it. What does this have to do with ID? Can you give a practical example?

It is this kind of experiment that Doug Axe did at Cambridge.

Axe did some protein folding.
That's wholely unremarkable.
Scientists do that on a regular basis.

How do you go from doing routine protein folding to detecting design?

Axe himself does not seem to know.
Axe has done nothing with the paper since.
That was six years ago, for goodness sake.

No "ID scientist" has done anything with it, either inside the world of peer-review or on some anonymous ID-friendly blog somewhere.

Axe's paper was a damp squib.
I'm not saying that just to be nasty.
My personal opinion doesn't count.

I'm saying that because if Axe's paper was productive or even a little bit exciting then...there would be some follow-up.
You'd expect to see some movement somewhere.
Somebody taking their queue from Axe's work and doing...something.
Anything.
That's not what happened.
It just faded away.

It was not through lack of publicity. It was not through lack of finance. It was not through lack of time.

It was through lack of interest.
Not even "ID scientists" did anything.
That's the very model of a damp squib.

I can't think of a better way to investigate ID.

Nobody else can either. Nobody can even do the first step and give a scientific definition of what is ID.

5:31 pm  
Anonymous Cedric Katesby said...

19/March/2010

...scientists are already investigating all these areas...

Therefore, those scientists are ID scientists!

And the work they do is "relevent to ID"!!!

So ID is really scientific after all.

Take that you scientific gatekeepers, you!!!!!!!!

:)

5:40 pm  
Anonymous Cedric Katesby said...

Posted twice about twenty-four hours ago.
I have no idea what happened but I'm confident that you didn't make them vanish.
I'll wait a day longer to make sure and then re-post.
Cheers.

12:01 pm  
Anonymous Cedric Katesby said...

27/March/2010

Andrew, sorry for the long delay.
Life got in the way.
Didn't mean to leave you hanging.
On with the show!

............................


Asking the question- How easy is it to produce an entirely new functional protein? - Is directly relevant to the issue of detecting design in biology.

I don’t get it.
I’m not baiting you, I swear I’m not.
I just don’t get it.
I have no idea how you go about “detecting design”.

I have no problem with doing scientific research on proteins but there’s no link that I can see between that and ID.

Ask how easily protein structure and function degrades when you change one or more amino acids around the active site of an enzyme or elsewhere in its structure.

Ditto for this one too.

This gives an increasingly clear picture of the size of the islands of protein functionality in the vast ocean of possible protein amino acid sequences.

Yep. I’m completely lost.
Even if we’re given a wonderfully clear picture on sizes of proteins, when do we get to the part about “detecting design” or ID?

It is this kind of experiment that Doug Axe did at Cambridge.

Which was accepted but considered to be completely unremarkable by the scientific community. No scientist nor "ID scientist" ever did anything with it.
It just stopped.
There was no further interest. It was not productive.

I can't think of a better way to investigate ID.

Nobody else can either. That’s why there is no work being done.
Remember Mike’s suggestion that he just made up on the spot?

Here's an idea- Gene knockout experiments these could test the assertion of irreductable complex structures and functions within the cell.

That’s about as good as it’s going to get. Empty, useless sciencey sounding waffle. Nobody is going to take that into a lab. Ever.
It's a total turkey.

This time next year, the situation will be exactly the same.
Andrew, there are no all-powerful, all-seeing “scientific gatekeepers” sabotaging any work on ID.

There’s nothing to sabotage. There is simply no work to be done.

In terms of biology ID writers suggest three key areas for investigation that interest me.
1. The origin of life itself.
2. The origin of new functional proteins
3. The origin of interdependent proteins.


Making idle suggestions in books is a poor substitute for actual work.
Nothing stops these “writers” from getting together with an “ID scientist” and thrashing out their “suggestions” in detail and…doing some work.

None of the fields you mention are being ignored by biologists.
ID, however, contributes nothing.

The best it can do is to wait around for somebody else to do something and then cling to their shirt-tails claiming vindication for ID.
That’s parasitic and dishonest.

2:24 pm  
Anonymous Suyuti said...

I would like to report the incident that a few months ago an American final year PhD student in biology studying proteins was expelled from Oxford University(UK) because in the Thesis that he submitted, he had a line saying that all proteins are unique because God created them. There were two months of negotiation but the university did not allow him back.
Perhaps you can investigate this further.

Kind regards,
Mirza

2:31 pm  
Blogger Andrew Rowell said...

Mirza,

I think it is unlikely to be as simple as that... I have not heard anything about it as yet.

9:35 pm  
Blogger Mirza said...

Have you contacted Oxford uni for what happened?
I have first hand sources so I have confirmed what happened.
He tried to negotiate for 2 months with procters but he still wasn't allowed.
Remember that this is university is where Dawkins was the head of!

Mirza

5:51 pm  
Blogger Andrew Rowell said...

Mirza,
Dawkins was never the "head" of Oxford Uni. He was a professor there.

I would need more details to make an enquiry.

1:23 pm  

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