Genomes as events in a trial

Incl. intelligent design, belief in divine creation

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Re: Genomes as events in a trial

#21  Postby NineBerry » Jun 06, 2017 7:31 pm

This argument has been debunked a million times.

There are two major problems:

1. Because of the deterministic parts of evolution, the sample space is not as big as you would want us to believe.

2. You talk about the possibility of achieving a very specific genome when the relevant question is what is necessary to achieve any genome. When rolling a dice, the chance to role a six is close to 1/6, but the chance to role any number is close to 1/1.
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Re: Genomes as events in a trial

#22  Postby OrdinaryClay » Jun 06, 2017 7:32 pm

Cito di Pense wrote:
OrdinaryClay wrote:
Cito di Pense wrote:
OrdinaryClay wrote: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.


Wait. You're using human beings' opinions of themselves as some kind of yardstick for 'something unusual'. Get a second opinion. Then another. When you have an adequate sampling of species with self-opinions, then you can talk about 'unusual'. This means you shouldn't restrict yourself to considering life forms you find only on this planet.

What I'm saying is that your question is an entirely vacuous opinion based on limited data.

Oh yes, the "can't define unique or special" canard. Now that's vacuous.

Probability proves you wrong.


What do you know about sample spaces, OrdinaryClay? Nothing, that's what's evident on the face of your bullshit.

What is erroneous with what I've posted regarding sample spaces in this thread?
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Re: Genomes as events in a trial

#23  Postby Cito di Pense » Jun 06, 2017 7:36 pm

NineBerry wrote:This argument has been debunked a million times.

There are two major problems:

1. Because of the deterministic parts of evolution, the sample space is not as big as you would want us to believe.

2. You talk about the possibility of achieving a very specific genome when the relevant question is what is necessary to achieve any genome. When rolling a dice, the chance to role a six is close to 1/6, but the chance to role and number is close to 1/1.


That's not the only fallacy OrdinaryClay is committing. He can also sample longitudinally, in say, the last 100 million years and find only what he's looking for just at the time he's doing the study. How convenient for that tower of bullshit.
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Re: Genomes as events in a trial

#24  Postby Cito di Pense » Jun 06, 2017 7:37 pm

OrdinaryClay wrote:
Cito di Pense wrote:
OrdinaryClay wrote:
Cito di Pense wrote:

Wait. You're using human beings' opinions of themselves as some kind of yardstick for 'something unusual'. Get a second opinion. Then another. When you have an adequate sampling of species with self-opinions, then you can talk about 'unusual'. This means you shouldn't restrict yourself to considering life forms you find only on this planet.

What I'm saying is that your question is an entirely vacuous opinion based on limited data.

Oh yes, the "can't define unique or special" canard. Now that's vacuous.

Probability proves you wrong.


What do you know about sample spaces, OrdinaryClay? Nothing, that's what's evident on the face of your bullshit.

What is erroneous with what I've posted regarding sample spaces in this thread?


See my comment immediately preceding this one. You claim "can't define unique or special" is some canard. At least I'm trying to poke a hole in it, if it is one. What're you up to? Internet woofing.
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Re: Genomes as events in a trial

#25  Postby OrdinaryClay » Jun 06, 2017 7:38 pm

NineBerry wrote:This argument has been debunked a million times.

There are two major problems:

1. Because of the deterministic parts of evolution, the sample space is not as big as you would want us to believe.

2. You talk about the possibility of achieving a very specific genome when the relevant question is what is necessary to achieve any genome. When rolling a dice, the chance to role a six is close to 1/6, but the chance to role and number is close to 1/1.

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?

Regarding 1: You are hand waving. The deterministic parts don't restrict the size of the space. It changes the probability for each event in the space for example, the bias on distribution.

Regarding 2: Your statement makes no sense.
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Re: Genomes as events in a trial

#26  Postby Fenrir » Jun 06, 2017 7:41 pm

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Re: Genomes as events in a trial

#27  Postby Cito di Pense » Jun 06, 2017 7:41 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?


The topic is called 'population dynamics'. That should get you started.
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Re: Genomes as events in a trial

#28  Postby Rumraket » Jun 06, 2017 7:42 pm

OrdinaryClay wrote:
Rumraket wrote:
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?

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 explanation for why what in particular just happened once? I'm not sure I understand the question.

What: An intellectual achievement such as mapping the genome of it's own species.

I don't actually know it to be the case that only one species has mapped it's own genome. For the species that live on Earth, sure. But I don't know whether it has happened elsewhere in the universe.

Regardless, I take your point. Why has it only happened once on Earth? Historical contingency. Yesterday is for the most part the cause of why today is the way it is. And the day before yesterday is mostly the cause of the way yesterday was. And so on.

Do you think convergent evolution is common or rare?

Well depends of course by where you put the line between rare and common, and in what exact sense something is thought to be convergent.

Speaking colloquially, at the genetic level I think convergence in nucleotide sequence is rare, with it's rarity growing in proportion to the length of the convergent sequences. There are mechanisms known that make it likely that two distinct species might suffer the same mutation(s) in some particular set of genes. Though those would be rare exceptions. Stated another way, most organisms are not genetically convergent for most of their genes. Their similarities owe mostly to shared descent, not independent convergence.

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.
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Re: Genomes as events in a trial

#29  Postby OrdinaryClay » Jun 06, 2017 7:46 pm

Cito di Pense wrote:
NineBerry wrote:This argument has been debunked a million times.

There are two major problems:

1. Because of the deterministic parts of evolution, the sample space is not as big as you would want us to believe.

2. You talk about the possibility of achieving a very specific genome when the relevant question is what is necessary to achieve any genome. When rolling a dice, the chance to role a six is close to 1/6, but the chance to role and number is close to 1/1.


That's not the only fallacy OrdinaryClay is committing. He can also sample longitudinally, in say, the last 100 million years and find only what he's looking for just at the time he's doing the study. How convenient for that tower of bullshit.

Huh?

Anyway, there is no need to change the sample period, though I did earlier to just include chordates, because we are still the only genome to map itself ever.
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Re: Genomes as events in a trial

#30  Postby Cito di Pense » Jun 06, 2017 7:49 pm

OrdinaryClay wrote:
Cito di Pense wrote:
NineBerry wrote:This argument has been debunked a million times.

There are two major problems:

1. Because of the deterministic parts of evolution, the sample space is not as big as you would want us to believe.

2. You talk about the possibility of achieving a very specific genome when the relevant question is what is necessary to achieve any genome. When rolling a dice, the chance to role a six is close to 1/6, but the chance to role and number is close to 1/1.


That's not the only fallacy OrdinaryClay is committing. He can also sample longitudinally, in say, the last 100 million years and find only what he's looking for just at the time he's doing the study. How convenient for that tower of bullshit.

Huh?

Anyway, there is no need to change the sample period, though I did earlier to just include chordates, because we are still the only genome to map itself ever.


So you say. As I suspected, you know fuck all about sample spaces. For your next trick, you should try to say something intelligent about population dynamics. Then give your tie in with deterministic processes. That will shut you up for awhile, unless you care, as expeccted, to go on making stupid statements on topics you cannot show you know anything about.

Remember? You asked the question in the OP. Your tone there implied you know what you're talking about.
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Re: Genomes as events in a trial

#31  Postby Thommo » Jun 06, 2017 7:53 pm

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.
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Re: Genomes as events in a trial

#32  Postby Cito di Pense » Jun 06, 2017 7:57 pm

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


Probably because of the post hoc declaration of the desirable/unusual outcome. You said it better than I could, and now I can say why i'm gnashing my teeth, aside from the delicate odour of hosiery.
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Re: Genomes as events in a trial

#33  Postby NineBerry » Jun 06, 2017 8:05 pm

Genomes don't sequence genomes. Technology does.
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Re: Genomes as events in a trial

#34  Postby Cito di Pense » Jun 06, 2017 8:10 pm

NineBerry wrote:Genomes don't sequence genomes. Technology does.


Not even technology is enough for some folks. There has to be a ghost in the machine.
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Re: Genomes as events in a trial

#35  Postby OrdinaryClay » Jun 06, 2017 8:23 pm

Rumraket wrote:
OrdinaryClay wrote:
Rumraket wrote:
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?

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.

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


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.
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Re: Genomes as events in a trial

#36  Postby OrdinaryClay » Jun 06, 2017 8:24 pm

Cito di Pense wrote:
OrdinaryClay wrote:
Cito di Pense wrote:
NineBerry wrote:This argument has been debunked a million times.

There are two major problems:

1. Because of the deterministic parts of evolution, the sample space is not as big as you would want us to believe.

2. You talk about the possibility of achieving a very specific genome when the relevant question is what is necessary to achieve any genome. When rolling a dice, the chance to role a six is close to 1/6, but the chance to role and number is close to 1/1.


That's not the only fallacy OrdinaryClay is committing. He can also sample longitudinally, in say, the last 100 million years and find only what he's looking for just at the time he's doing the study. How convenient for that tower of bullshit.

Huh?

Anyway, there is no need to change the sample period, though I did earlier to just include chordates, because we are still the only genome to map itself ever.


So you say. As I suspected, you know fuck all about sample spaces. For your next trick, you should try to say something intelligent about population dynamics. Then give your tie in with deterministic processes. That will shut you up for awhile, unless you care, as expeccted, to go on making stupid statements on topics you cannot show you know anything about.

Remember? You asked the question in the OP. Your tone there implied you know what you're talking about.

I say because you are engaging in non-relevant gobbledygook instead of showing where I misused the term sample space.
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Re: Genomes as events in a trial

#37  Postby NineBerry » Jun 06, 2017 8:31 pm

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Re: Genomes as events in a trial

#38  Postby OrdinaryClay » Jun 06, 2017 8:42 pm

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.

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.
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Re: Genomes as events in a trial

#39  Postby NineBerry » Jun 06, 2017 8:46 pm

Why are blue whales so much bigger than other animals? A clear outlier. God must love them very much.
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Re: Genomes as events in a trial

#40  Postby Calilasseia » Jun 06, 2017 8:50 pm

Problem number one.

If a given mutation arises in some of the offspring of a lineage, but that mutation results in those offspring being prevented from producing offspring of their own, then the probability of that mutation being disseminated further is precisely zero.

Problem number two.

There does not exist a one to one correspondence between sequence and function. Many sequences can produce the same working function. See: insulin. Consequently, it's possible for a mutation to occur, even in a critical gene, and for that gene still to work. The manner in which such mutations are disseminated through a lineage forms a fair part of the basis of molecular phylogeny.

Problem number three.

Not all parts of a genome correspond to protein coding sequences. Some are regulatory sequences, for example, and yet others are pseudogenes - genes that once worked in the past, but which don't work in the present. Then you have such entities as endogenous retroviral insertions to consider - previously active, but now silenced, gene sequences from retroviral infections in the past. Which tend to be left in place, because [1] lineages examined thus far don't possess specific endogenous retroviral DNA excision enzymes, at least none I'm aware of from the literature, and [2] once those sequences are silenced by other means, their removal is largely surplus to requirements, and organisms have a habit of not acquiring superfluous features unless there's a driver mechanism at work facilitating this.

Problem number four.

It doesn't ultimately matter what probability is attached to random events, if the products of those random events are then subject to subsequent partial elimination by a filter. If a well-defined subset of those random products are eliminated by the filter, on the basis of non-random criteria, then that subset simply won't contribute to future interactions. Ignoring the presence of any filters that may be present is a serious error.
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