Hunt's 2007 Critique of Axe

Hi Art
First I have read your 2007 critique of the ID use of Doug Axe’s work that I thought was highly useful. There were a couple of comments you made in the discussion that I disagreed with, and one which contradicts your 2003 panda’s thumb article.

  1. Your claim that the ubiquitin system doesn’t look designed because of the destruction of proteins as a mechanism.

  2. That there is very little or no information content in proteins. Your 2003 article shows a range of significant information content in proteins.

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@colewd, can you link to the main article? Great questions.

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That looks familiar.

Bill, I don’t understand your first question. The second flags an issue that is a never-ending discsussion. Basically, when I state that there is no “information” content in proteins, I am referring to the concept of CSI spelled out a long time ago by Dembski. In my essay about Axe’s work, I was just working with ratios.

I apologize if that doesn’t help clear things up. I tried to be precise in the essay, which wasn’t possible at the Biola event.

Hi Art
The first question was about the ubiquitin system and whether design is a reasonable analogy for this system. In the video you called it something very different then human design. I would disagree as it is an example of a self regulating system that we have many examples of. No real need to respond here. I think the understanding of this system has improved since this discussion in 2010 :slight_smile:

As far a your critique of Axe I agree that the information content of proteins may not be classic CSI but it is functional information per Szostak’s description in his 2003 paper written with Hazen.

I know you understand that functional space is a fraction of total sequence space and this ratio is a challenge for protein evolution.

I thought your 2003 article was well written and very helpful for me trying to understand the issues. I continue to use it as a reference in discussions.

I can’t believe that you are asking about something that happened 15 years ago. Was this book review some kind of milestone of ID history because it sure wasn’t a milestone in the history of science.

No, it was Art’s critique of the ID interpretation of Doug Axe’s paper on rarity of protein folds. I don’t believe that data has changed substantially since this discussion but if you do please update.

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I believe I am supposed to summarize the points in my essay that Axe still hasn’t addressed, 11 years on and counting.

I will get to it. Classes start this week and I probably need to get things squared away before I indulge myself too much here. But I will get to it.

Dr Hunt - Why does ID deserve any explanation? ID and DI has been putting out garbage for nearly two decades. They are not taken seriously by the entire scientific community. Why give them any of your time and effort?

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Why the continued attempt to cut off discussion on ID? I know several scientists that find the idea interesting. It is not well developed yet but so what.

Because ID is not science. ID is creationism disguised as science. ID and DI have been discredited time and time again by mainstream science and the courts. It is not legitimate science. If you know several scientists who find the idea interesting, have them publish on what they find interesting about ID. Who are these several scientists? Are they afraid to come forth and speak about the idea that they find interesting?
We are 13 years past Dover, ID and DI is merely a cult of a failed ideology. Let it die a natural death like all bad ideas in the history.

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It has political advocates just like evolution does. I don’t think what happened in Dover is not going to end people pushing the concept. We are 12 years later and there still are new books a few new papers. I was against it for a while because it was a dead end as far as science goes but now find the concept interesting. It is no more than a discussion of the evidence of design as a cause of nature.

It may not be science but at the end of the day whats important is if it is a viable inference. At this point I think it is. Are you afraid it is a threat to your freedom from religion project?

No, we have ourselves busy now with the disturbing raping of children institutionalized by the Catholic Church

Better priority.


Um so linking to a Panda’s Thumb’s article and parodying Patrick’s claims that DI and ID are garbage means that

“Your post was flagged as spam : the community feels it is an advertisement, something that is overly promotional in nature instead of being useful or relevant to the topic as expected.”.

Linking to Panda’s Thumb is OK has long as it is the right article. Very, very interesting. Clearly ideas not orthodox are immediately censored and dialogue means groupthink. Worrying but sadly predicable.

@theman8469 you can link to an article. You cannot add the this link with insults.

Why does Dr Hunt/Panda’s Thumb deserve any explanation? Hunt and Panda’s Thumb’s has been putting out garbage for nearly two decades. They are not taken seriously by anyone with a triple digit IQ. Why should we give Dr Hunt any of your time and effort?

I’ve told you before that this is not a debate site. Insults not welcome here and I’m seeing you throw them around with increasing frequency. The IQ statement was way out of line.

In my experience, the major problem with this ID argument is that it reeks of the Sharpshooter Fallacy. Each and every evolutionary change is going to be extremely improbable by its very nature which is often ignored by ID researchers. The other problem is that Axe only tests for one function instead of the billions of possible functions that a protein can have. Of the proteins that lacked beta-lactamase activity, how many interacted with other proteins in a new way? Did they bind to and change other substrates? Also, there is the obvious possibility that proteins with very different folds and primary sequence could have beta-lactamase activity.

Quite frankly, I don’t see how you can say that a protein is non-functional if you only test for beta-lactamase activity. If this same test were used for human proteins you would conclude that no human proteins have function.


The big question is in what area of thought is ID a viable inference. For biologists, ID isn’t a viable inference in their scientific work because it really doesn’t help us understand anything about biology in a scientific sense. ID could still be a viable inference at the level of philosophy or theology, but it isn’t very useful in scientific applications. A better way to put it is that the theories we have now (i.e. evolution) explain the data really, really well and ID just doesn’t explain that data. For example, how does ID explain sequence conservation of exons compared to introns? How does ID explain the pattern of nested hierarchy at the sequence level? How does ID explain the bias of mutations towards CpG and transition mutations seen between species? If I want to find functional sequence in a genome, what tools does ID give me? When you get down to the nitty gritty of the science of biology, ID isn’t useful, at least in my experience.


To build a living organism you need high interdependence of proteins and other small molecules. The interdependence is fundamental to life. The “any function will do” argument while interesting is not relevant to living organisms.

In biology we see evidence of complex functional systems. The ubiquitin system is an example. Coming at this from a design perspective is helpful as it emulates certain human designs like feedback regulation systems.