Do Self-replicating Motors Exist?

[swamidass (S. Joshua Swamidass)]

Which brings us of course to the “argument by conflation”.

Is there an official established fallacy on this?

[Frank_robert (Retired Psychologist)]

This seems to fit:

The fallacy of ambiguity, or polysemy.

This fallacy includes the fallacies of equivocation, conflation, composition and such as well as your case of mixing technical terminology and ordinary usage. Conflation can also be considered a continuum or equivocation fallacy, but in particular conflation is the merging of two different things. Ambiguity, being open to more than one interpretation, more accurately describes the general fallacy.

Depending on the argument, the mis-use of technical jargon can also be an argument from false authority, or an example of a rhetorical device of “argumentum ad ignorantiam” which relies upon the audience’s ignorance. Stating “gravity is just a theory” is not, however, an argument.

An argument that

1. gravity is a theory, and,
2. all theories are opinions, therefore
3. gravity is an opinion

…is an example of an informal fallacy, i.e. a valid and unsound argument predicated upon a fallacy of ambiguity that misrepresents the truth.

[scd]

@Michael_Okoko

In addition we can know the minimum number of parts to remain to preserve certain cellphone functions. If I only needed a cellphone to make or receive calls, then I could remove the camera, flashlight and other parts not relevant to that function

great. and this is also true for a minimal olfactory system. we need not only the part that can detect an odor molecule, but also a part that can process it for the organsm benefit. i think that at least 2-4 parts are required for that minimal olfactory system. exactly like what we need for a minimal cellphone which can receive calls.

@Michael_Okoko

I never claimed that evolutionary biologists argue that the flagella completely evolved neutrally

i also never said you claimed. that was a question. either way, i dont think that issue is relevant to the discussion above.

[Faizal_Ali]

@scd

we need not only the part that can detect an odor molecule

What is an “odor molecule”?

@scd

i also never said you claimed. that was a question.

However, you did make the statement below:

@scd

@Michael_Okoko

Its certainly possible. There is nothing in evolutionary biology that says selection must be present at every step leading to a some feature.

so why do you think that no biologist claims that the flagellum evolved by neutral steps?

In context, you appear to be saying that no biologists claim there were any steps in the evolution of the flagellum that were not selected. Is that what you meant to say? And, if so, are you able to defend that claim?

[scd]

@Faizal_Ali

What is an “odor molecule”?

basically any molecule that can be detected by the olfactory system to give us the sense of smell. there are many types of such molecules:

(image from https://www.scienceinschool.org/2007/issue6/scents)

@Faizal_Ali

In context, you appear to be saying that no biologists claim there were any steps in the evolution of the flagellum that were not selected. Is that what you meant to say?

no.

[Faizal_Ali]

@scd

basically any molecule that can be detected by the olfactory system to give us the sense of smell. there are many types of such molecules:

That doesn’t really answer the question.

How would an “odour molecule” be defined if there were no organisms possessing olfactory systems that could be stimulated by certain molecules to produce the sensation of smell?

@scd

no.

OK.

[Michael_Okoko]

@scd

great. and this is also true for a minimal olfactory system.

No its not. You can have a minimal or reduced (with fewer parts) olfactory system, but that’s not what you are arguing for. You are arguing that since we can take away several parts of an olfactory system and still have a functional remnant, therefore, the olfactory system is IC which is nonsensical. If an olfactory system is IC in the same sense as the mousetrap, then removing any of its parts contributing to its basic function (in this case, to sense smells), should cripple that function. However, as we have seen taking away several parts (like the nose and apparently olfactory bulbs) of an olfactory system like the one in humans doesn’t eliminate its function, although it might compromise that function to some extent. That disqualifies an olfactory system where this can happen as IC.

This talk about what is or is not IC is really secondary, what matters in whether they can evolve and the answer to that is a big, resounding yes.

@scd

@Michael_Okoko

I never claimed that evolutionary biologists argue that the flagella completely evolved neutrally

i also never said you claimed. that was a question. either way, i dont think that issue is relevant to the discussion above.

Oh no it is highly relevant here, because you are always asking us to show how each step leading to a flagella or fan could be selected for or against given the flagella is IC. This question is based on a strawman reasoning because it assumes natural selection is the only mechanism that can generate molecular complexity, an evidently false assumption. The bottom line is that some of the evolutionary steps that produced the flagella could have been neutral, while the others adaptive.

[scd]

@Michael_Okoko

You can have a minimal or reduced (with fewer parts) olfactory system, but that’s not what you are arguing for.

this is indeed what im arguing for: a minimal olfactory system, which requires at least few parts for its function. if such a system cant evolve stepwise then the IC argument is true. i dont care about some specific olfactory systems which we can remove some parts from. i only care about the minimal system, and that system indeed exist.

[Faizal_Ali]

@scd

i only care about the minimal system, and that system indeed exist.

Please show us this system.

[Witchdoc]

@scd

i think that at least 2-4 parts are required for that minimal olfactory system. exactly like what we need for a minimal cellphone which can receive calls.

No.

A minimal olfactory system requires one part- a G-protein coupled receptor.

Odour sensing proteins are G protein coupled receptors, also known as seven transmembrane receptors, which also occur and do the same role even in single celled organisms like yeast or slime mold.

G protein-coupled receptor

By the way, if you’re interested in learning more, a first year university biology textbook should have information on G protein coupled receptors - and much more fascinating stuff, like receptor tyrosine kinases, zinc finger proteins.

For example, Campbell Biology is a great textbook - super pretty pictures with an amazing wealth of information which is absolutely not too dry to read. If the eleventh ed is too pricy for reading for funsies, buy an older edition for dirt cheap - there really aren’t too many differences between editions.

I managed to read mine in a couple of months when I in year 10 of high school IIRC.

https://www.amazon.com/Campbell-Biology-11th-Lisa-Urry/dp/0134093410

[scd]

@Witchdoc

A minimal olfactory system requires one part- a G-protein coupled receptor.

first, do you have an example of such OR that can be functional by itself without any additional parts? in addition, as i said above: even a single OR contain 3 parts. so even if its possible to start with a single protein we are still talking about IC system.

[Witchdoc]

@scd

first, do you have an example of such OR that can be functional by itself without any additional parts?

Well.

Doesn’t technically detect odours, but rhodopsin is a seven transmembrane protein that detects light.

By the way, what’s your definition of “without extra parts”?

Does the cell itself count?

The cell wall?

Cytoplasm?

Other proteins in the cell?

[Witchdoc]

G protein coupled receptors / 7TM proteins are a fascinating rabbit hole to go down.

Thanks @scd for bringing us down this hole.

Here are a bunch of more GPCRs/7TMs -

https://www.nature.com/articles/s41598-017-15707-9/figures/5

And it is fun to look at how similar they are

https://www.nature.com/articles/s41598-017-15707-9/figures/6

Source article

https://www.nature.com/articles/s41598-017-15707-9

The sheer number and variety of GCPRs also proves creationist numbers about improbability of functional proteins in sequence space grossly wrong.

I wonder if @John_Harshman wants to add/discuss anything about GPCRs.

[scd]

@Witchdoc

Doesn’t technically detect odours,

so it cant be a part of the olfactory system.

@Witchdoc

Other proteins in the cell?

yep. mostly.

[Witchdoc]

@scd

so it cant be a part of the olfactory system.

…

I gave rhodopsin as an example to demonstrate how ubiquitous they are.

Which is very well explained from an evolutionary POV.

If you want another proper “olfactory” example, yeast “smelling” glucose with a glucose GCPR.

yep. mostly.

So you’re goalpost moving your example of what is IC from olfaction to the cell?

It’s kinda similar to making someone move the
definition of the minimal lung itself to having to include Earth’s atmosphere as part of a minimal lung to work…

[Faizal_Ali]

@scd

so it cant be a part of the olfactory system.

So suppose we have a functional system of multiple parts all of which arose thru unguided evolution. However, this system is not an olfactory system.

Then another part is added, also thru unguided evolution, and the system is now converted into an olfactory system.

If you remove that last part, the system no longer functions as an olfactory system.

Would this olfactory system then be considered IC?

If so, then it is clear that IC systems can evolve.

[scd]

@Witchdoc

I gave rhodopsin as an example to demonstrate how ubiquitous they are.

so? they are still IC.

@Witchdoc

If you want another proper “olfactory” example, yeast “smelling” glucose

can they detect odor molecules?

@Witchdoc

definition of the minimal lung itself to having to include Earth’s atmosphere as part of a minimal lung to work

since earth’s atmosphere isnt a part of an organism this isnt true.

@Faizal_Ali

Would this olfactory system then be considered IC?

yes. since it could supposedly be made by small steps from other systems. but this isnt what Witchdoc showed.

[Witchdoc]

@scd

can they detect odor molecules?

Palm, meet face.

First, define “odor molecule” please or we will just waste everyone’s time, yours and mine.

Also, I really should go sleep, it’s way past the time I should have started sleeping. Goodnight.

P. S. you might find you cannot define odors exclusive of the receptors themselves, in the same way we cannot define color independent of our light receptors.

The yeast does, indeed, “smell” glucose.

Does it bother you that some organisms can see colors we cannot see, and many organisms can “smell” molecules we cannot?

Does it bother you that light sensing, olfaction sensing, a wide variety of molecule sensing such as amine sensing, pepetide sensing, hormone sensing, are all a very short (mutational) distance away from glucose sensing?

[scd]

@Witchdoc

The yeast does, indeed, “smell” glucose.

no problem. are we talking here about a single protein which is requires for that function, or at least few proteins are needed?

@Witchdoc

Does it bother you that light sensing, olfaction sensing, a wide variety of molecule sensing such as amine sensing, pepetide sensing, hormone sensing, are all a very short (mutational) distance away from glucose sensing?

no. and how close by the way? 10 amino acids? 20? 30?

[John_Harshman]

@Witchdoc

I wonder if @John_Harshman wants to add/discuss anything about GPCRs.

Not remotely my field. The closest I’ve ever come is sequencing some rhodopsin introns for phylogenetic purposes.