# Great Example of the Appropriate Use of Algorithmic Mutual Information in Biology

**URL:** <https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188>\
**Category:** Conversation\
**Tags:** Science\
**Created:** [January 31, 2019, 11:53pm UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188 "2019-01-31T23:53:49Z")\
**Posts on this page:** 20\
**Page:** 1

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [January 31, 2019, 11:53pm UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/1 "2019-01-31T23:53:50Z")

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> **[Discovering dependencies via algorithmic mutual information: A case study in DNA...](https://link.springer.com/article/10.1007/BF00993378)**
>
> Algorithmic mutual information is a central concept in algorithmic information theory and may be measured as the difference between independent and joint minimal encoding lengths of objects; it is...

> **[Sequence Alignment, Mutual Information, and Dissimilarity Measures for...](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014373)**
>
> Background Existing sequence alignment algorithms use heuristic scoring schemes based on biological expertise, which cannot be used as objective distance metrics. As a result one relies on crude measures, like the p- or log-det distances, or makes...

Given all the conversation we have had about information theory and biology, I thought I’d post a couple articles that show how algorithm mutual information (somewhat related to ASC) can be appropriately applied to biology. Note, it is not at all useful for detecting design.

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**Author:** ![Patrick](https://avatars.discourse-cdn.com/v4/letter/p/b2d939/32.png) [@Patrick](https://discourse.peacefulscience.org/u/Patrick)\
**Post date:** [February 1, 2019, 12:00am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/2 "2019-02-01T00:00:35Z")

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Our main result uses algorithmic (Kolmogorov) information theory, but we show that similar results can also be obtained from Shannon theory.

@EricMH care to comment?

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [February 1, 2019, 1:15am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/3 "2019-02-01T01:15:23Z")

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That is right. Algorithmic Mutual Information is, essentially, a type of similarity metric.

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**Author:** ![EricMH](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/ericmh/32/679_2.png) [@EricMH](https://discourse.peacefulscience.org/u/EricMH)\
**Post date:** [February 1, 2019, 4:22pm UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/4 "2019-02-01T16:22:34Z")

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> [@swamidass](#):
>
> Note, it is not at all useful for detecting design.

Can you explain this statement? How does “not used to detect design in this example” imply “not at all useful for detecting design”?

Aleksandar Milosavljević’s work is great. He also invented a metric very similar to ASC.

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**Author:** ![gbrooks9](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/gbrooks9/32/7979_2.png) [@gbrooks9](https://discourse.peacefulscience.org/u/gbrooks9)\
**Post date:** [February 1, 2019, 5:03pm UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/5 "2019-02-01T17:03:45Z")

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> [@EricMH](#):
>
> Can you explain this statement? How does “not used to detect design in this example” imply “not at all useful for detecting design”?

@ericMH

The former lends itself to showing the latter.

It doesnt prove it by itself… but it certainly doesnt support its use as something that can detect design.

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**Author:** ![EricMH](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/ericmh/32/679_2.png) [@EricMH](https://discourse.peacefulscience.org/u/EricMH)\
**Post date:** [February 1, 2019, 5:15pm UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/6 "2019-02-01T17:15:48Z")

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> [@gbrooks9](#):
>
> it certainly doesnt support its use as something that can detect design.

That’s about all you can conclude from this example.

Now that we’ve established AMI is practically useful, we can appropriately apply the LoING and use it to detect design.

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**Author:** ![gbrooks9](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/gbrooks9/32/7979_2.png) [@gbrooks9](https://discourse.peacefulscience.org/u/gbrooks9)\
**Post date:** [February 1, 2019, 5:19pm UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/7 "2019-02-01T17:19:43Z")

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> [@EricMH](#):
>
> Now that we’ve established AMI is practically useful, we can appropriately apply the LoING and use it to detect design

@EricMH,

This is EXACTLY why @swamidass  
stated the former!

To discourage a category error.

The fact it has any use does not make it applicable to detect Design as well.

# This has been explained to you constantly. Please desist.

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**Author:** ![EricMH](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/ericmh/32/679_2.png) [@EricMH](https://discourse.peacefulscience.org/u/EricMH)\
**Post date:** [February 2, 2019, 1:26am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/8 "2019-02-02T01:26:32Z")

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> [@gbrooks9](#):
>
> This has been explained to you constantly. Please desist.

Then I guess you all don’t want me to comment 😃

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [February 2, 2019, 1:29am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/9 "2019-02-02T01:29:30Z")

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> [@EricMH](#):
>
> > This has been explained to you constantly. Please desist.
> 
> Then I guess you all don’t want me to comment 😃

You are welcome. @gbrooks9 does not speak for me on shushing you.

> [@EricMH](#):
>
> Now that we’ve established AMI is practically useful, we can appropriately apply the LoING and use it to detect design.

Non sequitur. I’ve always maintained that AMI is useful, and I have in fact published on it. The fact that it is useful for some purposes does not mean it is useful for your purposes. Just because nail clippers are useful for clipping nails does not make them effective at propelling you to the moon. One does not follow from the other.

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**Author:** ![EricMH](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/ericmh/32/679_2.png) [@EricMH](https://discourse.peacefulscience.org/u/EricMH)\
**Post date:** [February 2, 2019, 1:33am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/10 "2019-02-02T01:33:38Z")

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> [@swamidass](#):
>
> Just because nail clippers are useful for clipping nails does not make them effective at propelling you to the moon. One does not follow from the other.

Certainly, never said it did. But, the converse also does not apply. Just because metal is used in nail clippers does not mean metal is not effective for getting us to the moon.

Just because AMI is used in a non design detecting setting does not mean it is useless for detecting design.

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**Author:** ![Patrick](https://avatars.discourse-cdn.com/v4/letter/p/b2d939/32.png) [@Patrick](https://discourse.peacefulscience.org/u/Patrick)\
**Post date:** [February 2, 2019, 1:46am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/11 "2019-02-02T01:46:31Z")

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> [@EricMH](#):
>
> Certainly, never said it did. But, the converse also does not apply. Just because metal is used in nail clippers does not mean metal is not effective for getting us to the moon.
> 
> Just because AMI is used in a non design detecting setting does not mean it is useless for detecting design.

@EricMH science follows the evidence. It doesn’t assume a conclusion first and then try to make the data fit the conclusion. That is dishonest. You have concluded that ID is true. And you are 100% biased in looking at the data and in doing research. You should recluse yourself from scientific research on this subject because you are not credible nor honest.

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [February 2, 2019, 1:47am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/12 "2019-02-02T01:47:42Z")

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> [@Patrick](#):
>
> You should recluse yourself from scientific research on this subject because you are not credible nor honest.

It isn’t dishonest. It is, rather, a conflict of interest, and it isn’t how science works.

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**Author:** ![Patrick](https://avatars.discourse-cdn.com/v4/letter/p/b2d939/32.png) [@Patrick](https://discourse.peacefulscience.org/u/Patrick)\
**Post date:** [February 2, 2019, 1:49am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/13 "2019-02-02T01:49:03Z")

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> [@swamidass](#):
>
> It isn’t dishonest. It is, rather, a conflict of interest, and it isn’t how science works.

If you know you have a COI and you continue anyway, that’s dishonest.

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**Author:** ![EricMH](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/ericmh/32/679_2.png) [@EricMH](https://discourse.peacefulscience.org/u/EricMH)\
**Post date:** [February 2, 2019, 2:34am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/14 "2019-02-02T02:34:04Z")

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> [@Patrick](#):
>
> That is dishonest. You have concluded that ID is true.

Perhaps if you are going to accuse me of dishonesty you can cite where I conclude ID is true? If memory serves, I have gone out of my way on this forum to state I am very happy to be convinced otherwise that ID is false, and spent over a month trying to ferret such an argument out of the interlocutors here. But, perhaps I have stated somewhere that ID is definitely true, in which case if you can find a citation I will retract it. If not, then perhaps it is not appropriate to accuse me of being dishonest?

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**Author:** ![Patrick](https://avatars.discourse-cdn.com/v4/letter/p/b2d939/32.png) [@Patrick](https://discourse.peacefulscience.org/u/Patrick)\
**Post date:** [February 2, 2019, 2:42am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/15 "2019-02-02T02:42:02Z")

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> [@EricMH](#):
>
> Perhaps if you are going to accuse me of dishonesty you can cite where I conclude ID is true? If memory serves, I have gone out of my way on this forum to state I am very happy to be convinced otherwise that ID is false, and spent over a month trying to ferret such an argument out of the interlocutors here. But, perhaps I have stated somewhere that ID is definitely true, in which case if you can find a citation I will retract it. If not, then perhaps it is not appropriate to accuse me of being dishonest?

I will go further and accuse you, your university, and your advisor of inserting creationism into the secular science of Information Theory.

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [February 2, 2019, 2:43am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/16 "2019-02-02T02:43:09Z")

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@EricMH, I hope you realize that @patrick is now just messing around with you. I suggest you don’t take it too seriously.

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**Author:** ![Patrick](https://avatars.discourse-cdn.com/v4/letter/p/b2d939/32.png) [@Patrick](https://discourse.peacefulscience.org/u/Patrick)\
**Post date:** [February 2, 2019, 2:45am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/17 "2019-02-02T02:45:31Z")

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> [@swamidass](#):
>
> I hope you realize that @patrick is now just messing around with you. I suggest you don’t take it too seriously.

No, I am not just messing with @EricMH I am investigation whether US Air Force funds were used to research ID.

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**Author:** ![EricMH](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/ericmh/32/679_2.png) [@EricMH](https://discourse.peacefulscience.org/u/EricMH)\
**Post date:** [February 2, 2019, 2:45am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/18 "2019-02-02T02:45:52Z")

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> [@swamidass](#):
>
> @EricMH, I hope you realize that @patrick is now just messing around with you. I suggest you don’t take it too seriously.

Ok…at any rate I don’t know how this is productive. He asked me to weigh in on this topic, and now is suddenly accusing me of dishonesty and such. It strikes me as odd.

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [February 2, 2019, 2:46am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/19 "2019-02-02T02:46:50Z")

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> [@Patrick](#):
>
> I am investigation whether US Air Force funds were used to research ID.

You already know the answer is “yes.” What exactly is your goal here?

> [@EricMH](#):
>
> > @EricMH, I hope you realize that @patrick is now just messing around with you. I suggest you don’t take it too seriously.
> 
> Ok…at any rate I don’t know how this is productive. He asked me to weigh in on this topic, and now is suddenly accusing me of dishonesty and such. It strikes me as odd.

It should just strick you as “@patrick trying to push your buttons”. This may be surprising to you, but I think he is doing this playfully. Don’t tell anyone, but I’m pretty sure he kinda likes you.

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**Author:** ![EricMH](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/ericmh/32/679_2.png) [@EricMH](https://discourse.peacefulscience.org/u/EricMH)\
**Post date:** [February 2, 2019, 2:47am UTC](https://discourse.peacefulscience.org/t/great-example-of-the-appropriate-use-of-algorithmic-mutual-information-in-biology/4188/20 "2019-02-02T02:47:19Z")

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> [@Patrick](#):
>
> No, I am not just messing with @EricMH I am investigation whether US Air Force funds were used to research ID.

☝ so seems like he has the ulterior motive I mentioned before. Using this forum to find an excuse to bring lawsuits against people. @swamidass does this strike you as behavior that encourages peaceful discourse?

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