# Intelligent design and "design detection"

**URL:** <https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132>\
**Category:** Side Conversation\
**Tags:** Design\
**Created:** [June 10, 2023, 1:37pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132 "2023-06-10T13:37:54Z")\
**Posts on this page:** 20\
**Page:** 3

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [June 15, 2023, 3:12pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/41 "2023-06-15T15:12:58Z")

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> [@John\_Harshman](#):
>
> Well, similarity to human genes is an odd measure of sequence conservation, since human genes are not primitive. All it’s really measuring is genetic distance, which has something to do with conservation but more to do with time since divergence. And why choose humans as the reference sequence? Pinnacle of creation, or what?

The focus on human genes is probably heavily influenced by various religious beliefs, although non-religious people are just as susceptible to ego as anyone else.

From my understanding, the argument boils down to the probability of producing a highly conserved protein sequence. Their claim is that only that sequence could have carried out that function which is evidenced by how highly conserved it is. What they don’t seem to consider is contingency through time. Protein interactions can cement the importance of a specific sequence _after_ it has appeared, especially if multiple proteins interact with the same target. It’s a bit like being amazed that the hole in the ground exactly fits the shape of the water in the hole.

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [June 15, 2023, 3:19pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/42 "2023-06-15T15:19:06Z")

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> [@T\_aquaticus](#):
>
> From my understanding, the argument boils down to the probability of producing a highly conserved protein sequence.

But Gpuccio isn’t even measuring conservation. He’s measuring similarity to the human sequence. Not in any way the same thing.

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [June 15, 2023, 3:21pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/43 "2023-06-15T15:21:42Z")

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> [@John\_Harshman](#):
>
> But Gpuccio isn’t even measuring conservation. He’s measuring similarity to the human sequence.

If an orthologous sequence is 99% similar between sharks, frogs, birds, and humans then that would be a highly conserved sequence.

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [June 15, 2023, 3:26pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/44 "2023-06-15T15:26:47Z")

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> [@T\_aquaticus](#):
>
> If an orthologous sequence is 99% similar between sharks, frogs, birds, and humans then that would be a highly conserved sequence.

For sure. But that isn’t what’s happening there. The comparison is only between some species and humans. Chimps, by that measure, would have almost every sequence highly conserved, while sharks would have very few.

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [June 15, 2023, 3:39pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/45 "2023-06-15T15:39:34Z")

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> [@John\_Harshman](#):
>
> For sure. But that isn’t what’s happening there. The comparison is only between some species and humans. Chimps, by that measure, would have almost every sequence highly conserved, while sharks would have very few.

I think I am confusing things in my mind. I am remembering arguments based on a single or handful of strongly conserved genes, but that doesn’t appear to be the argument being cited here. Apologies.

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**Author:** ![Art](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/art/32/3805_2.png) [@Art](https://discourse.peacefulscience.org/u/Art)\
**Post date:** [June 15, 2023, 6:01pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/46 "2023-06-15T18:01:04Z")

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> [@John\_Harshman](#):
>
> He’s measuring similarity to the human sequence. Not in any way the same thing.

IIRC, Gpuccio was plugging the bit values from BLAST alignments into Szostak’s equation(s) and claiming “information” or something like that.

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [June 15, 2023, 6:49pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/47 "2023-06-15T18:49:37Z")

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> [@Art](#):
>
> IIRC, Gpuccio was plugging the bit values from BLAST alignments into Szostak’s equation(s) and claiming “information” or something like that.

Clearly he doesn’t understand Szostak’s definition. But the graph that’s been shown doesn’t even use an equation. It just reports the bit values.

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**Author:** ![Faizal\_Ali](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/faizal_ali/32/12416_2.png) [@Faizal\_Ali](https://discourse.peacefulscience.org/u/Faizal_Ali)\
**Post date:** [June 15, 2023, 7:01pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/48 "2023-06-15T19:01:50Z")

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The graph is meant for people like @Giltil, not for anyone who has the first frigging clue. So, as we can see, it is a very good graph in terms of achieving its intended goal.

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [June 15, 2023, 7:38pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/49 "2023-06-15T19:38:14Z")

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> [@Dan\_Eastwood](#):
>
> The obvious flaw here is that archaeologists _assume humans are the designers_ of artifacts - they do not infer the existence of humans from the artifacts.

What you call a “flaw” maybe simply that the analogy is not exactly the same as the original claim. If it was exactly like the original claim would it be an analogy?

What would be your argument that it is “flawed” or a poor analogy?

In one case we know the existence of the designer in the other we need to infer existence. While direct evidence of the designer would be preferred does lack of direct evidence really nullify the inference?

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**Author:** ![Dan\_Eastwood](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dan_eastwood/32/2368_2.png) [@Dan\_Eastwood](https://discourse.peacefulscience.org/u/Dan_Eastwood)\
**Post date:** [June 15, 2023, 8:00pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/50 "2023-06-15T20:00:46Z")

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> [@colewd](#):
>
> In one case we know the existence of the designer in the other we need to infer existence. …

Exactly that.

> While direct evidence of the designer would be preferred does lack of direct evidence really nullify the inference?

Yes.

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [June 15, 2023, 8:42pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/51 "2023-06-15T20:42:44Z")

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> [@Dan\_Eastwood](#):
>
> Yes.

Some people may disagree with this as it would disqualify the use of abductive and inductive reasoning 😉

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**Author:** ![Joe\_Felsenstein](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/joe_felsenstein/32/8176_2.png) [@Joe\_Felsenstein](https://discourse.peacefulscience.org/u/Joe_Felsenstein)\
**Post date:** [June 16, 2023, 8:03pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/52 "2023-06-16T20:03:37Z")

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I was one of many who participated in the long and very tedious discussion of gpuccio’s functional information criterion. In fact I wrote two posts at TSZ ([here](http://theskepticalzone.com/wp/does-gpuccios-argument-that-500-bits-of-functional-information-implies-design-work/) and [here](http://theskepticalzone.com/wp/does-gpuccios-150-safe-thief-example-validate-the-500-bits-rule/)) that led to discussion on that. In the end we found that _unlike Szostak_ he was assuming that all sequences that had less functionality than the one which we saw, were so much less functional that there was no evolutionary path to the observed sequence. This is _way_ different from Szostak and Hazen’s FI. They were not even attempting to use FI to discuss whether evolution could reach that sequence.

BTW, I am failing to access TSZ, there is some 404 problem.

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**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [June 16, 2023, 8:37pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/53 "2023-06-16T20:37:15Z")

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The links work fine for me right now.

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**Author:** ![Giltil](https://avatars.discourse-cdn.com/v4/letter/g/5f8ce5/32.png) [@Giltil](https://discourse.peacefulscience.org/u/Giltil)\
**Post date:** [June 17, 2023, 1:00pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/54 "2023-06-17T13:00:44Z")

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> [@John\_Harshman](#):
>
> I only vaguely remember gpuccio’s arguments, but didn’t he produce a graph purporting to show increase in functional information over time, which was basically a line showing time since divergence from humans? Do you have a link to his very sciency publication?

You will find such a graph at post 78 of this thread

> [@Gpuccio: Functional Information Methodology](https://discourse.peacefulscience.org/t/gpuccio-functional-information-methodology/7549):
>
> Gpuccio is a poster at Uncommon Descent who published a blog article at UD arguing that proteins have high functional information (FI), and must have been designed. His work is commonly referenced by ID proponents. This is his post: We asked for him to explain his methodology further. @colewd asked him (comment 343), and gpuccio gave a response (comment 356). He has agreed to respond to reasonable critique. OK, so here is a brief primer about my methodology to measure Functional Information in proteins: a) I use Blast to measure sequence homology between proteins, in bits. I take the bitscore from the Blast algorithm as it is, with some consideration of the number of identities and similarities, too. b) I am interested in homologies that are conserved throughout long evolutionary periods. I consider that kind of homology as a very good estimator of FI. The reason is very simple: a specific sequence can be conserved for those long time windows only if it is under very strong fu…

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [June 17, 2023, 1:07pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/55 "2023-06-17T13:07:14Z")

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> [@Giltil](#):
>
> You will find such a graph at post 78 of this thread

Best read the posts that follow that one.

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**Author:** ![Giltil](https://avatars.discourse-cdn.com/v4/letter/g/5f8ce5/32.png) [@Giltil](https://discourse.peacefulscience.org/u/Giltil)\
**Post date:** [June 17, 2023, 1:17pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/56 "2023-06-17T13:17:54Z")

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> [@John\_Harshman](#):
>
> For sure. But that isn’t what’s happening there. The comparison is only between some species and humans. Chimps, by that measure, would have almost every sequence highly conserved, while sharks would have very few.

The comparison Gpuccio is interested in is between species whose common ancestor lived a long time ago because in that case, the similarities denote conservation throughout long evolutionary time.

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**Author:** ![Giltil](https://avatars.discourse-cdn.com/v4/letter/g/5f8ce5/32.png) [@Giltil](https://discourse.peacefulscience.org/u/Giltil)\
**Post date:** [June 17, 2023, 1:25pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/57 "2023-06-17T13:25:37Z")

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> [@John\_Harshman](#):
>
> > [@Giltil](#):
> >
> > You will find such a graph at post 78 of this thread
> 
> Best read the posts that follow that one.

Already done

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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [June 17, 2023, 2:26pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/58 "2023-06-17T14:26:54Z")

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> [@Giltil](#):
>
> > [@John\_Harshman](#):
> >
> > Best read the posts that follow that one.
> 
> Already done

Then why did you make the blatantly false claim that @gpuccio used Szostak’s definition?

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**Author:** ![Giltil](https://avatars.discourse-cdn.com/v4/letter/g/5f8ce5/32.png) [@Giltil](https://discourse.peacefulscience.org/u/Giltil)\
**Post date:** [June 17, 2023, 3:06pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/59 "2023-06-17T15:06:30Z")

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> [@Mercer](#):
>
> Then why did you make the blatantly false claim that @gpuccio used Szostak’s definition?

FI=-log2(target space /search space).  
This is the definition Gpuccio uses, which is also Szostak’s definition.

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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [June 17, 2023, 3:11pm UTC](https://discourse.peacefulscience.org/t/intelligent-design-and-design-detection/16132/60 "2023-06-17T15:11:31Z")

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> [@Giltil](#):
>
> FI=-log2(target space /search space).  
> This is the definition Gpuccio uses, which is also Szostak’s definition.

Utterly false. @gpuccio has done nothing to measure either space. Looking only at existing sequences, particularly only consensus ones, tells you nothing.

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