Genomes as events in a trial

Incl. intelligent design, belief in divine creation

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Re: Genomes as events in a trial

#41  Postby Rumraket » Jun 06, 2017 8:51 pm

OrdinaryClay wrote:
Rumraket wrote:
OrdinaryClay wrote:
Rumraket wrote:
Sure, the space of potential, probably never realized genomic sequences, is enormous. Much greater than the sampled one.

What is an unrealized genomic sequence? Still borne?

I just mean one that never came to exist. In this sense I would say that technically a stillborn, or dead-on-arrival organism (that died due to lethal mutations), is still a realized genomic sequence. It existed in reality once upon a time.

The set that has never come to exist is calculable and so large as to beyond even the time scales of the universe. That set is not relevant.

Relevant to what?

OrdinaryClay wrote:My discussion is restricted to the set that has existed. That's the sample space I'm talking about.

Okay. What about that space? The set of genomic sequences that has existed, what are you saying about it?

OrdinaryClay wrote:
Rumraket wrote:But at the phenotypic level I believe it is more common than at the genetic level, because for the most part, we inhabit similar environments and are subject to similar selective pressures. And there are usually many different genetic pathways to the same phenotypic result.

There are many examples of convergent evolution. Then why are there not more phenotypes that map their own genomes.

I'm not convinced there is a "why" there. Your question seems to me to have the same intellectual content as "why is the world so made so that we see blue in the way we see blue and don't see green in it's place, and blue in the place of green?".

Would you expect there to be more phenotypes that map their own genomes among the set of realized phenotypes? Or less? And if so, why? I presume you're asking because you're suprised. Why are you suprised?
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Re: Genomes as events in a trial

#42  Postby Thommo » Jun 06, 2017 8:54 pm

OrdinaryClay wrote:
Thommo wrote:
OrdinaryClay wrote:So here is my question and where I'm positive there will great gnashing of teeth ... Does this not give evolutionary biologists pause, at least ones with statistical training, when you look at that space and see only one species that has mapped it's own genome. For a materialists what is the explanation they use for why it happened just once? Just "shit happens"?


I don't get the question or why you'd expect there to be gnashing of teeth.

We haven't established what proportion of the sample space can be swept out in a given time, we haven't established what proportion of the sample space would allow for a species to map its own genome.

Are we supposed to be surprised because a genome mapping species arrived slower than expected, or because a genome mapping species arrived faster than expected?

Presumably we'd need a comprehensive estimate of how fast we expected it to arrive before we were surprised either way, wouldn't we? Even then we'd have huge problems with generating a meaningful expectation because we have a non valid sample size (of just 1 successful result), a questionably chosen sample space (it doesn't allow for the anthropic principle) and a post hoc definition of the desirable outcomes.

If you look at physiological complexity then we are at least as genetically complex as a bat or a bird, yet bats and birds have convergent evolution with regard to flight. When a phenotype has advantages evolution tends to converge on a good solution. If you consider humans as an outlier then you see ten of millions of years of convergent evolution between mammals and theropods.

Faster or slower is not the question. The surprise should be that it occurred only once.


That's not an answer to the question that I can see. Why should I be surprised that it happened only once?

First off it's not clear that it* has happened only once (the Neanderthal genome has been explored in this random walk of ours, for example) and second of all for any number of happenings there must be a first time. Asking this question after this first time should elicit no particular surprise.

OrdinaryClay wrote:Humans are clearly an outlier. Normal statistical analysis would tend to throw them out of the sample if analysis was interested in tool use. There are many species that use tools, yet the degree and kind of tool use in humans is so different as to be an outlier.


No, I don't think any of this is right. We haven't described a variable or an experimental methodology for throwing out data. If we took a 5% trimmed mean based on some approximation of cognitive power then humans would be an "outlier" and thrown out. If we took a standard mean then humans would not be.

Normally in statistics one would have to have a reason to justify removing data points from a set, such as risk of experimental error. Throwing out data you don't like the look of tends to introduce bias rather than limit it.

*It here referring to one side of the blurred lines between genomes and the actions of the organisms carrying those genomes as pointed out above by NineBerry.
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Re: Genomes as events in a trial

#43  Postby Pebble » Jun 06, 2017 8:56 pm

Science starts by identifying the underlying patterns and working to explain those patterns. Looking for the outliers and trying to explain them without having understood the underlying pattern in the first place is a fool's errand that can only end with magical explanations.
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Re: Genomes as events in a trial

#44  Postby Rumraket » Jun 06, 2017 9:03 pm

OrdinaryClay wrote:The surprise should be that it occurred only once.

Why? Why is that surprising?

Humans are clearly an outlier.

There isn't really any objective scale by which we can measure "outlierness" in this sense. You're essentially just saying that you feel like humans are super special. Okay, cool. Good for you. And?

Normal statistical analysis would tend to throw them out of the sample if analysis was interested in tool use.

Under what objective measure of tool use?

There are many species that use tools, yet the degree and kind of tool use in humans is so different as to be an outlier.

Even supposing you could come up with some sort of objective measure of "degree and kind" of tool use, okay. But outliers happen. So what?

Are we now supposed to relegate outliers to divine intervention? I'm guessing that's where you want to go.
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Re: Genomes as events in a trial

#45  Postby Calilasseia » Jun 06, 2017 9:06 pm

OrdinaryClay wrote:If you look at physiological complexity then we are at least as genetically complex as a bat or a bird


How is this defined, let alone measured? Only I'm aware of several serious problems with the elementary metrics frequently proposed for this, including those that have in the past been proposed by actual biologists. A nicely detailed exposition thereof can be found here.

OrdinaryClay wrote:yet bats and birds have convergent evolution with regard to flight.


So what? Insects got there first. Furthermore, insects have entirely different anatomical structures facilitating their ability to fly, form those seen in vertebrates, so whilst there is convergent evolution with respect to locomotive capability, there isn't any convergent evolution with respect to detailed anatomy. Insect wings are completely separate entities, distinct from their limbs, whilst vertebrate wings are forelimb modifications, and furthermore, forelimb modifications that took different paths.

OrdinaryClay wrote:When a phenotype has advantages evolution tends to converge on a good solution.


Correction. Evolution converges on a working solution. Whether that solution is in any way "optimal" is frequently an entirely different topic. There are plenty of examples of working solutions that make no sense whatsoever, from the standpoint of any assertions about their being the product of purported rational, planned, sentient input. I'm minded to bring those embarrassing Carabid beetles to the table once more to illustrate this.

OrdinaryClay wrote:If you consider humans as an outlier then you see ten of millions of years of convergent evolution between mammals and theropods.


In what respect? This assertion is not only questionable per se, but lacks the detail required to test it properly.

OrdinaryClay wrote:Faster or slower is not the question. The surprise should be that it occurred only once.


That what occurred "only once"? Again, detail is missing here from your assertion.

OrdinaryClay wrote:Humans are clearly an outlier.


Again, in what respect? Once again, detail, please?

OrdinaryClay wrote:Normal statistical analysis would tend to throw them out of the sample if analysis was interested in tool use.


Another questionable assertion lacking proper substantive detail. Provide some.

OrdinaryClay wrote:There are many species that use tools, yet the degree and kind of tool use in humans is so different as to be an outlier.


Is it?
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Re: Genomes as events in a trial

#46  Postby Rumraket » Jun 06, 2017 9:09 pm

Pebble wrote:Science starts by identifying the underlying patterns and working to explain those patterns. Looking for the outliers and trying to explain them without having understood the underlying pattern in the first place is a fool's errand that can only end with magical explanations.

Heh, yeah. And magical explanations invariably fail to explain anything when it comes down to it. They usually amount to the platitude "It is the way it is because God did it that way". Oh, well fuck me. There isn't anything that couldn't be "explained" by that.

Suppose life didn't exist at all. Why would things be the way they are then? Well if God made it so, then it would be true in the exact same sense. "It is the way it is because God did it that way".

Suppose every planet, moon, asteroid or even stars had life on them. Suppose there was an infinite number of universes with an infinite variety of physical laws and arrangements, and with an infinite diversity of life among them. Why would things be the way they are then? Well if God made it so, then it would be true in the exact same sense. "It is the way it is because God did it that way".

The God-did-it "explanation" has no actual explanatory power in the sense that term is used in philosophy. Nothing is actually explained. It's just a platitude. A band-aid you put on things you don't really know how to answer.
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Re: Genomes as events in a trial

#47  Postby Thommo » Jun 06, 2017 9:26 pm

Suppose we build a maze:-
Image

It has a start point and an end point built of clear plastic. All the other walls are made of opaque plastic. We fill it with gallons of water.

Now we introduce many millions (but still a minuscule number relative to the volume of fluid) of molecules of dye to the water at the start point of the maze. We track the molecules (somehow, perhaps we just run a computer simulation of the whole thing) and at the point the first one reaches the exit we pause the whole experiment.

Now we start an internet thread on a forum asking why it is that only one molecule of the dye is at the exit and whether people are surprised. We might point out that several other dead ends of the maze have been reached independently by other molecules of dye as well.

What kind of answers would we get, from evolutionary biologists or statisticians? What would the correct response to the assertion that we should ignore the molecule that reached the end as a statistical outlier be?

Obviously those are semi-rhetorical questions. But my suspicion is that the answers to this question and those expanded on through this thread are remarkably similar.
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Re: Genomes as events in a trial

#48  Postby Pebble » Jun 07, 2017 7:52 am

Thommo wrote:Suppose we build a maze:-
Image

It has a start point and an end point built of clear plastic. All the other walls are made of opaque plastic. We fill it with gallons of water.

Now we introduce many millions (but still a minuscule number relative to the volume of fluid) of molecules of dye to the water at the start point of the maze. We track the molecules (somehow, perhaps we just run a computer simulation of the whole thing) and at the point the first one reaches the exit we pause the whole experiment.

Now we start an internet thread on a forum asking why it is that only one molecule of the dye is at the exit and whether people are surprised. We might point out that several other dead ends of the maze have been reached independently by other molecules of dye as well.

What kind of answers would we get, from evolutionary biologists or statisticians? What would the correct response to the assertion that we should ignore the molecule that reached the end as a statistical outlier be?

Obviously those are semi-rhetorical questions. But my suspicion is that the answers to this question and those expanded on through this thread are remarkably similar.


Yes I should have said "an outlier" rather than outliers. In order to have outliers you must have some sort of model in your head. If there are many outliers, your model is obviously incorrect, and looking for patterns among the outliers is how you improve the model.
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Re: Genomes as events in a trial

#49  Postby LucidFlight » Jun 07, 2017 8:07 am

Ah, but why the maze, Thommo? Why the maze? It's because God made it that way.
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Re: Genomes as events in a trial

#50  Postby DavidMcC » Jun 07, 2017 11:38 am

NineBerry wrote:No, because evolution is not a random trial, but a mechanism that includes random trials but also non-random elements.

You may be answering the wrong question, because the OP made on mention of whether the trial was picked at random.
Also, it is too vague, IMO, to talk of "non-random elements". You need to be more specific. Reference to selection being on the (non-random) basis of what gives the most descendants would be better.

EDIT: The OP was also too vague, in talking only of "trials", not random genomic changes (mainly genetic mutations).
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Re: Genomes as events in a trial

#51  Postby NineBerry » Jun 07, 2017 12:05 pm

What leads to the existence of a specific individual genome is mostly non-biological mechanisms.
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Re: Genomes as events in a trial

#52  Postby DavidMcC » Jun 07, 2017 2:27 pm

NineBerry wrote:What leads to the existence of a specific individual genome is mostly non-biological mechanisms.

That's what I call a half-truth. The whole truth is that it is a combinatoon of mainly non-biological factors (which help determine the selection factors) and the biological response to them.
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Re: Genomes as events in a trial

#53  Postby Just A Theory » Jun 09, 2017 4:49 am

Of all the supernova remnants in all of the galaxies in the observable universe, why is it that there is only one example of a conglomeration of such remnants that is capable of observing the universe and commenting on discussion forums?
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Re: Genomes as events in a trial

#54  Postby Cito di Pense » Jun 09, 2017 7:06 am

Just A Theory wrote:Of all the supernova remnants in all of the galaxies in the observable universe, why is it that there is only one example of a conglomeration of such remnants that is capable of observing the universe and commenting on discussion forums?


You're a deep thinker, indeed, JAT, but the depth of your thinking is vastly exceeded by the depth of your ignorance about what goes on in the rest of the universe you clearly acknowledge is not a figment of the imagination of God. What I mean is that you don't know enough to claim what you are claiming. Why don't you avoid complex topics like this one if all you can produce are lame plagiarisms of Jehovah's Witnesses Watchtower tracts?

If you're not intimidated by that, perhaps you could comment on why you think remarks in discussion forums are all that impressive. Get a second opinion, like, you know, from somebody who doesn't speak your feeble language.

Really, I'd love to see a knock-down argument that the universe spent 13.6 billion years and hundreds of billions of cubic parsecs evolving simply to produce us. I wish I was as impressed with us as you appear to be. But I'm not, and your lame rhetoric is not helping to reverse that (for you) inconvenient condition.
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Re: Genomes as events in a trial

#55  Postby LucidFlight » Jun 09, 2017 7:46 am

I bet they're asleep on Gliese 667Cc. I bet they're asleep all over the galaxy. Of all the supernova remnants in all of the observable universe, this discussion forum had to come into existence here.
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Re: Genomes as events in a trial

#56  Postby Cito di Pense » Jun 09, 2017 7:48 am

LucidFlight wrote:I bet they're asleep on Gliese 667Cc. I bet they're asleep all over the galaxy. Of all the supernovas in all of the observable universe, this discussion forum had to come into existence here.


We'll always have Wolf 359. 'Cos, y'know, it's a red dwarf. Here's lookin' at you, kid.
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Re: Genomes as events in a trial

#57  Postby sdelsolray » Jun 09, 2017 2:45 pm

OrdinaryClay wrote:rumraket, good info and I'll go there in a minute.

Second observation, which to me seems completely non-controversial whether you are a materialist or not. The sample space over the entire history of life on the earth is staggeringly enormous (yes I'm completely on board with the 3.8 BY give or take trajectory of life). No? Even if you restrict this set to chordates, which given my next points we pretty much have to, the set is huge.

So here is my question and where I'm positive there will great gnashing of teeth ... Does this not give evolutionary biologists pause, at least ones with statistical training, when you look at that space and see only one species that has mapped it's own genome. For a materialists what is the explanation they use for why it happened just once? Just "shit happens"?


Once events occur, prior probabilities adjust or dissipate. Blame Time's Arrow and the 2nd LoT.
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Re: Genomes as events in a trial

#58  Postby Just A Theory » Jun 10, 2017 10:03 am

Cito di Pense wrote:
Just A Theory wrote:Of all the supernova remnants in all of the galaxies in the observable universe, why is it that there is only one example of a conglomeration of such remnants that is capable of observing the universe and commenting on discussion forums?


You're a deep thinker, indeed, JAT, but the depth of your thinking is vastly exceeded by the depth of your ignorance about what goes on in the rest of the universe you clearly acknowledge is not a figment of the imagination of God. What I mean is that you don't know enough to claim what you are claiming. Why don't you avoid complex topics like this one if all you can produce are lame plagiarisms of Jehovah's Witnesses Watchtower tracts?

If you're not intimidated by that, perhaps you could comment on why you think remarks in discussion forums are all that impressive. Get a second opinion, like, you know, from somebody who doesn't speak your feeble language.

Really, I'd love to see a knock-down argument that the universe spent 13.6 billion years and hundreds of billions of cubic parsecs evolving simply to produce us. I wish I was as impressed with us as you appear to be. But I'm not, and your lame rhetoric is not helping to reverse that (for you) inconvenient condition.


Clearly my sarcasm was not evident enough :(

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Re: Genomes as events in a trial

#59  Postby Cito di Pense » Jun 10, 2017 10:45 am

Just A Theory wrote:
Cito di Pense wrote:
Just A Theory wrote:Of all the supernova remnants in all of the galaxies in the observable universe, why is it that there is only one example of a conglomeration of such remnants that is capable of observing the universe and commenting on discussion forums?


You're a deep thinker, indeed, JAT, but the depth of your thinking is vastly exceeded by the depth of your ignorance about what goes on in the rest of the universe you clearly acknowledge is not a figment of the imagination of God. What I mean is that you don't know enough to claim what you are claiming. Why don't you avoid complex topics like this one if all you can produce are lame plagiarisms of Jehovah's Witnesses Watchtower tracts?

If you're not intimidated by that, perhaps you could comment on why you think remarks in discussion forums are all that impressive. Get a second opinion, like, you know, from somebody who doesn't speak your feeble language.

Really, I'd love to see a knock-down argument that the universe spent 13.6 billion years and hundreds of billions of cubic parsecs evolving simply to produce us. I wish I was as impressed with us as you appear to be. But I'm not, and your lame rhetoric is not helping to reverse that (for you) inconvenient condition.


Clearly my sarcasm was not evident enough :(

I blame Poe's Law. You may, of course, peruse my post history on this forum to see my opinion on pseudoscientific woo.


Oops. Sorry. I'll change my book on you. I should have remembered you at least from the EE thread.
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Re: Genomes as events in a trial

#60  Postby Shrunk » Jun 10, 2017 12:24 pm

OrdinaryClay wrote:Really? Then it should be trivially easy for you to point me to a thread, a paper, a blog post a book that deals with the subject. Can you?


Scientific journals are not in the habit of posting articles debunking obvious bullshit. I reckon there are no articles in mathematics journals stating that circles are not squares.
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