# The Extra Face in Mount Rushmore

**URL:** <https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067>\
**Category:** Side Conversation\
**Tags:** Design\
**Created:** [January 25, 2019, 2:31am UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067 "2019-01-25T02:31:33Z")\
**Posts on this page:** 20\
**Page:** 8

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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:** [January 31, 2019, 3:38pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/143 "2019-01-31T15:38:56Z")

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@Kirk

> [@Kirk](#):
>
> The have been attempts in the literature to define FI. Here is my attempt [Measuring the functional sequence complexity of proteins](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2217542/) and here is another from Hazen et al. [Functional information and the emergence of biocomplexity](https://www.pnas.org/content/104/suppl_1/8574)

From my understanding, both of those papers measure mutual information, not functional information.

> [@Kirk](#):
>
> I would not want to automatically reject natural processes as being able to produce FI. Rather, I think we need to limit our options to what we can empirically verify as having an ability to produce FI. If there is a natural process that we can empirically verify as doing it, then my earlier hypothesis is falsified. We would then be left with two options, rather than just one.

You may want to check out my thread on catalytic antibodies:

> [@Are Catalytic Antibodies Evidence for Evolution of New Function?](https://discourse.peacefulscience.org/t/are-catalytic-antibodies-evidence-for-evolution-of-new-function/4158):
>
> One of the common claims heard in these debates is that there is a low probability of random sequence having function. Catalytic antibodies may offer a good way of testing this claim. During embryonic development, B-cells go through a process where segments of DNA are randomly shuffled and stitched together (VDJ recombination) to make the variable regions of antibodies, the sections of the antibody that are responsible for sticking to bacteria, viruses, and other antigens. Each B-cell lineage has just one combination of this shuffled DNA, and there are about 100 million B-cell lineages in each human being and in other mammalian species [NOTE: I’m not sure how this may or may not work in more distantly related vertebrate species, so I am sticking with mammals]. So what are the chances that these randomly shuffled bits of DNA will have enzyme activity? As it turns out, antibodies with enzyme function are relatively common. The following review article discusses several different c…

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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:** [January 31, 2019, 5:29pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/144 "2019-01-31T17:29:09Z")

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> [@Kirk](#):
>
> It appears to me that you are using the “no true Scotsman” approach for what defines a testable hypothesis.

No, I am using the “testable hypothesis” approach.

> [@Kirk](#):
>
> As for using “appear” in a hypothesis, it depends whether a person likes to overstate things, or err on the side of caution.

You’ve got it backwards, Kirk. To be useful, your hypothesis needs to make empirical predictions that allow you no interpretive wiggle room. You’re supposed to be trying to falsify it, not keep it alive. If, after you bash it diligently and ruthlessly, it is still standing, then you’ve got something!

I really don’t get this idea that the hypothesis is the product.

> [@Kirk](#):
>
> If you are suggesting that hypotheses of the form “Y is a unique property of X” is not useful, then I’m afraid you are tossing a great deal of science out the window. In a lab, you would not have a clue what you are working with, nor it’s properties when you conduct an experiment.

I’m afraid that I would disagree and note that what you wrote makes no sense. I respectfully suggest that you consult my publication record to see that I do have a clue:

> **[My Bibliography - NCBI](https://www.ncbi.nlm.nih.gov/sites/myncbi/1zE_dLhLdmxAf/bibliography/45268294/public/?sort=date&direction=ascending)**
>
> Django project django-bibliography

> [@Kirk](#):
>
> This isn’t a simple matter of “cataloguing”, it is essential for understanding, testing, and predicting processes, field effects, and outcomes.

As you’ve presented it, cataloguing is all it is. There’s nothing mechanistic.

> [@Kirk](#):
>
> What I would rather see from you, is a mathematical approach to distinguishing examples of intelligent design from non-designed objects and effects …

Why me?

> [@Kirk](#):
>
> What method, including equations, would you provide that is not purely subjective?

I would rigorously test hypotheses regarding when the hypothetical design occurred.

> [@Kirk](#):
>
> Throwing up one’s hands and standing slack-jawed, criticizing other scientists actually working on the problem, is not the way science advances.

I agree that you should stop doing that. 😄

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<div class="post-metadata">

**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:** [January 31, 2019, 5:38pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/145 "2019-01-31T17:38:57Z")

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> [@Kirk](#):
>
> Here is my attempt [Measuring the functional sequence complexity of proteins](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2217542/)

It’s nonsensical. Absolutely nonsensical. Why the fork and knife should the “functional sequence complexity” of a protein depend on how many such similar proteins can be found in PFAM? What does that tell us? That just makes FSC a measure of a completely arbitrarily defined quality, partly constrained by historical circumstance (how many genomes have been sequenced and properly annotated, for example).

Why not count how many birds passed by your window in the last hour before, dividing it by the length of the protein in picometers, multiplied by the logarithm of it’s weight on Jupiter, and then have that be it’s “functional sequence complexity”? What is that a measure of? What does it tell us, other than you have created some nonsensical mathematical relationship to … look clever?

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**Author:** ![T.j\_Runyon](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t.j_runyon/32/9662_2.png) [@T.j\_Runyon](https://discourse.peacefulscience.org/u/T.j_Runyon)\
**Post date:** [January 31, 2019, 5:47pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/146 "2019-01-31T17:47:11Z")

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> [@Rumraket](#):
>
> Why the fork and knife

Stealing this

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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:** [January 31, 2019, 5:49pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/147 "2019-01-31T17:49:18Z")

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> [@T.j\_Runyon](#):
>
> Stealing this

I can’t claim credit. Got it from _The Good Place_.

[![](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/3X/6/5/65a0fe46fa9f1df1eb7e9ade27dc1427ab143b5c.jpeg "What the Fork Is This Fake Cursing Bullshirt?! - The Good Place (Mashup)") ](https://www.youtube.com/watch?v=QPXsYOPex4s)

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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, 5:53pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/148 "2019-01-31T17:53:09Z")

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> [@Kirk](#):
>
> The research question is, “what can produce FI?”. Thus far, there is only one thing we have ever observed that can actually produce it … intelligence.

The evolution of cancer can produce FI, quite a bit of it. So, therefore, we know intelligence is not the only source. I’m not sure, for that matter, you have even demonstrated intelligence can produce FI. See here: [Computing the Functional Information in Cancer](https://discourse.peacefulscience.org/t/computing-the-functional-information-in-cancer/1646).

> [@Kirk](#):
>
> What I would rather see from you, is a mathematical approach to distinguishing examples of intelligent design from non-designed objects and effects … there is a difference between a laptop and a rock in the bush. What method, including equations, would you provide that is not purely subjective? Throwing up one’s hands and standing slack-jawed, criticizing other scientists actually working on the problem, is not the way science advances.

@Kirk what if the task you are undertaking is (logically or practically) impossible? What if it is like trying to make a perpetual motion machine? How would you know? Perhaps continuing to try is just waisting you effort. How would you be able to avoid that waiste?

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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:** [January 31, 2019, 6:50pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/149 "2019-01-31T18:50:13Z")

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> [@Rumraket](#):
>
> It’s nonsensical. Absolutely nonsensical. Why the fork and knife should the “functional sequence complexity” of a protein depend on how many such similar proteins can be found in PFAM? What does that tell us? That just makes FSC a measure of a completely arbitrarily defined quality, partly constrained by historical circumstance (how many genomes have been sequenced and properly annotated, for example).

Rum he is measuring conservation of a site similar to the way gpuccio measures it. Does a particular site tolerate substitution.

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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, 6:51pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/150 "2019-01-31T18:51:47Z")

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> [@colewd](#):
>
> Rum he is measuring conservation of a site similar to the way gpuccio measures it. Does a particular site tolerate substitution.

@Rumraket is correct @colewd. FSC is not FI, and FSC is essentially an arbitrarily defined quantity. It is not the measure of how many functional sequences there are, nor is it a measure of how difficult it is to evolve something.

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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:** [January 31, 2019, 6:57pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/151 "2019-01-31T18:57:27Z")

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> [@swamidass](#):
>
> @Rumraket is correct @colewd. FSC is not FI, and FSC is essentially an arbitrarily defined quantity. It is not the measure of how many functional sequences there are, nor is it a measure of how difficult it is to evolve something.

Are you saying that the paper Kirk posted should have called it FI instead of FSC?

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<div class="post-metadata">

**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, 6:59pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/152 "2019-01-31T18:59:59Z")

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> [@colewd](#):
>
> Are you saying that the paper Kirk posted should have called it FI instead of FSC?

I’m saying he measured an arbitrary quantity that he called FSC, and posited that it equaled FI despite overwhelming evidence to the contrary. FSC is not and never has been a measure of FI.

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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:** [January 31, 2019, 7:02pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/153 "2019-01-31T19:02:54Z")

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> [@swamidass](#):
>
> I’m saying he measured an arbitrary quantity that he called FSC, and posited that it equaled FI despite overwhelming evidence to the contrary. FSC is not and never has been a measure of FI.

So you believe that his method of measurement and calculation does not estimate FI?

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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, 7:04pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/154 "2019-01-31T19:04:15Z")

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> [@colewd](#):
>
> So you believe that his method of measurement and calculation does not estimate FI?

That is correct.

I’ve also provided an alternative approach to computing the difficulty of evolvability, that does not suffer from the same problems as FSC (and, for that matter, FI).

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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:** [January 31, 2019, 7:10pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/155 "2019-01-31T19:10:19Z")

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> [@swamidass](#):
>
> I’ve also provided an alternative approach to computing the difficulty of evolvability, that does not suffer from the same problems as FSC (and, for that matter, FI).

Is this in the cancer discussion?

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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, 7:18pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/156 "2019-01-31T19:18:09Z")

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> [@colewd](#):
>
> > I’ve also provided an alternative approach to computing the difficulty of evolvability, that does not suffer from the same problems as FSC (and, for that matter, FI).
> 
> Is this in the cancer discussion?

Yes. The right measure is KL divergence, not delta entropy (which is what @Kirk uses for FSC). KL divergence measure how close new functions are to the starting point. Notice how @Agauger and Axe make their argument:

1. Evolution of new protein functions requiires design IF…
2. Function is exceedingly RARE in sequence space AND…
3. Function is exceedingly ISOLATED in sequence space.

FSC, at best, only measures #2, the rarity of function in sequence space. (Note: It does not even accomplish this). It does not measure #3, how separated functions are in sequence space. Neither FI or FSC, even in principle, measure #3. Both #2 and #3 have to be true for the Axe-@agauger argument to work.

KL-divergence measures #3, which is a better way to measure how difficult it is to evolve a new function, and it is measured in bits too. So we can understand it as the amount of information required to evolve a new function. Using KL divergence, we find out that new functions require far less bits than @Kirk calculates, and we can demonstrate dramatic increases in functional information (as measured by KL-divergence) in natural systems (such as cancer). So less bits are required, and we have direct evidence that natural process can produce them.

The argument fails. I think @kirk is sincere and doing his best here, but it seems he is working towards a desired conclusion, regardless of the evidence. It looks very much like a quest for a perpetual motion machine to me.

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<div class="post-metadata">

**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:** [January 31, 2019, 7:18pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/157 "2019-01-31T19:18:39Z")

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> [@colewd](#):
>
> Are you saying that the paper Kirk posted should have called it FI instead of FSC?

No, I’m saying he hasn’t measured a property of the protein at all. The relationship by which he defines FI, or FSC, or whatever you might want to call it, is fictional and arbitrary.

No conclusion about the protein’s origin or function can be reached from the data used to compute it’s “FSC”. Because it is computed from measures that aren’t actually measures of the proteins attributes, but things entirely unrelated to it. Like how many OTHER proteins with similar sequences that humans have decided to put into the PFAM database.

In other words, Kirk is essentially saying that we can infer something about the protein’s origin and history by, among other things, seeing _how industrious_ human biochemists have been at sequencing and annotating genomes.

Clearly, CLEARLY we aren’t measuring a property of one my genes by considering how often biochemists have sequenced similar genes in other species and uploaded their sequences to PFAM. That should go without saying. That’s before we even begin to consider whether such a value (whatever it might be) should be multiplied, taken the square-root or base-2 log of, or divided by yet another measure.

It’s numerology. It looks fancy and technical, but it’s nonsense.

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<div class="post-metadata">

**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [January 31, 2019, 7:43pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/158 "2019-01-31T19:43:59Z")

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> [@swamidass](#):
>
> - Evolution of new protein functions requiires design IF…
> - Function is exceedingly RARE in sequence space AND…
> - Function is exceedingly ISOLATED in sequence space.

I don’t know why they make the argument like this as there is lots of function in Axe’s experiment. The issue is does the ratio of function to total sequence space allow for the number of evolutionary experiments available. I understand you and Rum are questioning if the measurement has validity.

If an experiment shows function is rare does it matter if it is isolated? While this can show evolution inside a protein family is possible it does not show how a new protein family with very different sequences is formed.

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<div class="post-metadata">

**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, 7:56pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/159 "2019-01-31T19:56:13Z")

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> [@colewd](#):
>
> If an experiment shows function is rare does it matter if it is isolated?

Yes it does. Because if isn’t isolated, we can change from one function to another very easily. @Agauger and Axe know this, and go to lengths to argue that function is isolated because they know this is central to the argument.

> [@colewd](#):
>
> I don’t know why they make the argument like this as there is lots of function in Axe’s experiment.

That is a good question for you understand. Axe argues (approx) that function is 10^-77 rare, but comparable experiments that directly test this show that funciton is more like 10^-10 rare. Everyone agrees it is rare (10^-8 is rare), but there is a big different between those numbers. One is easy to evolve, and the other is more difficult (though not impossible!).

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<div class="post-metadata">

**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:** [January 31, 2019, 8:27pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/160 "2019-01-31T20:27:58Z")

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> [@colewd](#):
>
> Rum he is measuring conservation of a site similar to the way gpuccio measures it. Does a particular site tolerate substitution.

Can you explain why natural selection would not be able to conserve sequence that is required for function? If functional information is simply sequence conservation then it is exceedingly obvious that natural selection can produce functional information.

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<div class="post-metadata">

**Author:** ![T.j\_Runyon](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t.j_runyon/32/9662_2.png) [@T.j\_Runyon](https://discourse.peacefulscience.org/u/T.j_Runyon)\
**Post date:** [January 31, 2019, 8:39pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/161 "2019-01-31T20:39:24Z")

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> [@swamidass](#):
>
> Because if isn’t isolated

Can you explain the difference between rare and isolated? Want to make sure I’m grasping that correctly.

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<div class="post-metadata">

**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [January 31, 2019, 9:00pm UTC](https://discourse.peacefulscience.org/t/the-extra-face-in-mount-rushmore/4067/162 "2019-01-31T21:00:52Z")

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> [@T\_aquaticus](#):
>
> If functional information is simply sequence conservation then it is exceedingly obvious that natural selection can produce functional information.

Functional information and sequence conservation are different things.

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