Reaping the Whirlwind: protein function without stable structure

[Raymond_Isbell]

@Chris_Falter

The mathematical foundation of evolutionary biology is the simultaneous optimization of a set of slowly changing stochastic probability density functions. The fact that you are looking for a deterministic prediction from a set of conditions shows that you have profoundly misunderstood the whole enterprise from the get-go.

What you’re failing to recognize is that the PDF’s are models. Models are only as good as the correctness of the assumptions on which they’re built, the understanding of the modeler (for the cell it is seriously limited) and when you don’t have a complete understanding of the system, the model will reflect such. Will I use the model’s predictions to determine my beliefs? Only to the extent that I’m confident the model has captured a correct and complete picture of the reality the model represents. Are you that confident about your understanding of the cell? Even Matheson admitted that much of our understanding of cell function is still unknown and is the topic of robust research. So a model of a system where an unknown level of its function is still unknown should not be the basis for any dogmatic conclusions on a topic like evolution that should require a much greater knowledge and understanding than we currently have. Have you every modeled complex electronic circuits? I have, and guess what. The first thing you learn is that the VI characteristics of the components are not linear. The models needed to predict their behavior become too complex to solve, not to mention algorithmic problems with digitizing it. Ever hear of numerical instability? It will bite you hard when you try to model anything other than simple linearized systems. Ever write and try to solve a systems of non-linear differential equations? I have, and my computer would lock up every time due to the amount of calculations needed to be performed.

The sad part of all of this is that you guys apparently don’t know or appreciate what you don’t know. You fail to see that your overly simple models of cell function with large numbers of unknowns should not be trusted especially on such an important topic as evolution. Get it wrong and if affects your entire and very important world view. I’m suggesting in all of this that you give more thought about what you don’t know (the C4 functionality in the cell just for starters) and show and give heed to the improbability of evolution (macro). James Tour is a voice you should pay attention to, not to mention the other brilliant folks in the ID movement. You’re living in a dream world that doesn’t exist. Be very, very careful. Enough said.

[Bill_II]

@Raymond_Isbell

The sad part of all of this is that you guys apparently don’t know or appreciate what you don’t know. You fail to see that your overly simple models of cell function with large numbers of unknowns should not be trusted especially on such an important topic as evolution.

If this was the only thing we have that supports evolution you might have a point, but it isn’t.

[Chris_Falter]

@Raymond_Isbell

Are you that confident about your understanding of the cell?

I am confident that the biological community has figured it out well enough, Raymond. In particular, they have built a reliable PDF of DNA sequence changes. The fact that you and I are alive even after 18,000 sequence changes over the past 6000 years of our ancestry is powerful empirical proof that the biology community’s perspective on mutations and evolution is well-founded, and that yours is not.

Yours,
Chris

[Chris_Falter]

@Raymond_Isbell

Will I use the model’s predictions to determine my beliefs? Only to the extent that I’m confident the model has captured a correct and complete picture of the reality the model represents. Are you that confident about your understanding of the cell?

Hi Raymond,

You are laboring under the misconception that a model needs to be well-understood to be trusted. Advances in artificial intelligence over the last 10 years demonstrate that a model can be very well trusted even if humans cannot understand it.

GoogleMind researchers can tell you some generalizations about AlphaGo.They cannot say, however, what calculation path it followed to select any particular move. Nevertheless, AlphaGo is stronger than any human player who relies on having a complete understanding of the game’s logic.

Examples abound! The world of AI is full of poorly understood models that are nevertheless relied upon:

• Convolutional neural nets that identify human faces better than any human–but no human understands the details of the math they use.
• Reinforcement learning networks that can autonomously drive a vehicle, in spite of the fact that no human can tell you the details of the mathematical calculations used to accomplish any particular driving task.
• Recurrent neural nets that can transcribe and translate spoken words as well as any human–yet once again, no human can tell you the details of the calculations used to transcribe and translate any particular sentence.

I know from my own experience that these models are not built in a deterministic fashion. A team of data scientists has to do a lot of trial-and-error to decrease the objective loss before a model can be deemed reliable. A biologist would say, I think, that this trial-and-error process resembles the processes of evolution. Biologists (@sfmatheson, @glipsnort, @DennisVenema, etc.), please correct me if I am misrepresenting what biologists believe.

Thanks,
Chris

[Raymond_Isbell]

@Chris_Falter

You are laboring under the misconception that a model needs to be well-understood to be trusted.

No, I’m referring to the reality behind the model. Remember, a model represents what the modeler understands. In the case of the cell, that understanding is a far cry from reality. When we have major gaps in our understanding of that reality (full cell functionality and interdependence of the cell proteins and collections of proteins (subsystems)), then we can be confident of concepts like evolution. If you really believe that you understand it that well, then your confidence in evolution is justified. However, you, I and the others know better. Remember, pride goes before the fall.

[Chris_Falter]

@Raymond_Isbell

Remember, a model represents what the modeler understands.

Actually, artificial intelligence has already undermined this bare assertion of yours. The machine learns the model (hence the term: machine learning). A neural network starts with random parameters, then tunes them by back-propagating prediction error against the training set. By monitoring the model’s success against a validation set after each training epoch, the data science team ascertains when the model is optimized. They deploy that model into a production environment when it is optimized, and the business or agency becomes more effective.

And no one–not even the data science team–understands the details of the math in the model.

Object recognition, language translation, and vehicle driving are realities, are they not?

They are represented by neural network models, are they not?

Those models are poorly understood, are they not?

Secondly, the fundamental issue you continue to refuse to discuss is that the validity of a scientific model is based on the empirical success of its predictions. The theory of evolution has produced oodles (that’s 10^oodles, in case you’re wondering) of well-validated predictions. Meanwhile, the only prediction I am aware of having been produced by ID is Martin Ewert’s modularity hypothesis, and that flamed out quite spectacularly. Moreover, Ewert acknowledged that the scope of his hypothesis, unsuccessful as it turned out, was quite narrow–completely unable to make sensible predictions for the vast majority of scientific data in the field of biology.

Is evolution imperfect? Sure. So is theology. So is mathematics. So is physics. So is systems engineering.

However, contrast the usefulness of evolution with ID. You can’t even use ID to account for the simple fact of ~18,000 mutations in your DNA from your/our ancestors 240 generations ago, Raymond. You still refuse to acknowledge the reality of those 18,000 mutations. It seems quite odd that you have refused to even discuss these data.

Meanwhile, the theory of evolution can and does explain those 18,000 mutations.

That’s just one example of why I join 99% of biologists in accepting the theory.

@Raymond_Isbell

Remember, pride goes before the fall.

You would agree that this truth applies to each and every one of us who have been participating in the discussion, right?

Is there any possibility that it might apply to you?

If so, what is the utility of citing it?

Good night and God bless,
Chris

[Raymond_Isbell]

@Chris_Falter

Actually, artificial intelligence has already undermined this bare assertion of yours.

Actually it hasn’t since AI is not even applicable to our discussion and reveals that you still don’t understand (won’t accept is closer) my point or the point of ID in general. Your bringing it up in this discussion tells me that you’re failing to understand how AI can be used legitimately. You clearly don’t understand it’s limitations. (Remember, before I retired I was a Research Scientist working with AI.) You misunderstand it at a fundamental level. You sound pedantic.

What I seem to have forgotten is that you guys are dug into the evolution position like an Alabama Tick, and all the King’s men and all the King’s horses will not dislodge you. I think it’s time to move on.

[Mervin_Bitikofer]

@Raymond_Isbell

…you guys are dug into the evolution position…

Yep. Just like we’re also dug into things like the “round earth” theory or the germ theory of diseases, and we do at times tend to get cranky and impatient with people who still willfully dabble in the various denialisms that are easily seen by everybody else to have been long ago rubbished.

@Raymond_Isbell

I think it’s time to move on.

An apt observation.

[Christy (Christy Hemphill)]

@T.j_Runyon

Are you kidding me? Moderators, how long are you going to let this guy continue?

@sfmatheson

To be fair, the forum’s goals include the notion of attempting to reach skeptics, and that means entertaining crudely dismissive comments like Raymond’s (and plenty of others) while attempting to discourage/disallow dehumanizing or personally disrespectful behavior.

The forum’s goals also include providing diversion to certain kinds of people, and if you are still reading this thread at post 629, and claim all it has been is frustration and hardship, I call B.S. You must find it entertaining at some level.

If you diagnose yourself as perhaps not in the healthiest place as far as the kind of amusement you get sucked into and how much of your life you spend reading and responding to the repetitive claims of people bent on not learning anything from you, that really isn’t the moderators’ problem. Own your own stuff, people.

And as for the guideline:

State your case and then respect other people’s right to agree or disagree. Avoid repeating the same ideas over and over because you have failed to convince everyone to accept your viewpoint.

It seems to me that to get to post 629, it’s not just Raymond being repetitive and unsatisfied with lingering disagreement. We generally give people one thread to go nuts on with whatever idea they feel compelled to pontificate on, and as long as people are entertained, (i.e. continuing to respond), they can be repetitive.

Where we are going to step in is when people start posting a bunch of different threads harping on the same topic that has already been hashed out. Or when people show up every two months to ask about self-replicating machines or other such nonsense.

So, you are all free to not read any of this thread and you are all free never to answer Raymond’s assertions again. Have fun, forum junkies. I am now going to watch Stranger Things.

[sfmatheson]

@Christy

If you diagnose yourself as perhaps not in the healthiest place as far as the kind of amusement you get sucked into and how much of your life you spend reading and responding to the repetitive claims of people bent on not learning anything from you, that really isn’t the moderators’ problem. Own your own stuff, people.

I realize that I read this 5 minutes after @Christy posted it. Please, I assure you, this is pure coincidence.