# Faith in mechanisms that would be outside our reach and understanding (as a matter of principle)

**URL:** <https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557>\
**Category:** Side Conversation\
**Tags:** Theology\
**Created:** [February 11, 2020, 1:52pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557 "2020-02-11T13:52:03Z")\
**Posts on this page:** 20\
**Page:** 8

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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:** [February 12, 2020, 8:58pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/141 "2020-02-12T20:58:05Z")

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> [@T\_aquaticus](#):
>
> I made the original claim that you have to know all of the parameters and number of trials before you can claim that an outcome is improbable, and I used the lottery as an analogy to illustrate that point.

The outcome is improbable based on all the available data we have today. For your claim to have any merit life would have to be much simpler than Venters minimum and you are not willing to make a positive claim in this direction.

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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:** [February 12, 2020, 9:00pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/142 "2020-02-12T21:00:19Z")

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> [@colewd](#):
>
> The outcome is improbable based on all the available data we have today.

You have yet to present that data.

> [@colewd](#):
>
> For your claim to have any merit life would have to be much simpler than Venters minimum and you are not willing to make a positive claim in this direction.

Again, you are shifting the burden of proof. YOU are the one claiming that life couldn’t be simpler than the bacteria that Venter used in his study, and you need evidence to back this up with evidence.

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**Author:** ![Timothy\_Horton](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/timothy_horton/32/9410_2.png) [@Timothy\_Horton](https://discourse.peacefulscience.org/u/Timothy_Horton)\
**Post date:** [February 12, 2020, 9:00pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/143 "2020-02-12T21:00:42Z")

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> [@colewd](#):
>
> You are assuming it was different without evidence.

The work of Dr. Joe Thornton in reconstructing ancient proteins is evidence life was simpler in the past. Bill loses again.

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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:** [February 12, 2020, 9:02pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/144 "2020-02-12T21:02:56Z")

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> [@colewd](#):
>
> The outcome is improbable based on all the available data we have today.

No, what you mean to say is that the claim that the outcome is improbable is based on the **assumption** that life could not be simpler than what we observe today, and that it had to sort of spontaneously assemble as if a tornado in a junkyard.

Yet you have conceded you do not know whether this assumption is true. You appear to just believe it.

> [@colewd](#):
>
> For your claim to have any merit life would have to be much simpler than Venters minimum and you are not willing to make a positive claim in this direction.

That’s because it is a genuine unknown. When we don’t know something we shouldn’t be making claims about it. We shouldn’t be claiming to know that it’s not possible when we don’t actually know that.

I don’t know how simple life can get because I simply don’t know all the forms that life can take. Hence I can not actually calculate a probability for the origin of life, since I lack the relevant information that would be required to make such a calculation.

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**Author:** ![Timothy\_Horton](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/timothy_horton/32/9410_2.png) [@Timothy\_Horton](https://discourse.peacefulscience.org/u/Timothy_Horton)\
**Post date:** [February 12, 2020, 9:03pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/145 "2020-02-12T21:03:17Z")

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> [@colewd](#):
>
> You made the original claim that the lottery fallacy solved the abiogenesis problem. .

Heh. Look at Bill trying to shift the burden of proof. Bill is the one who claimed the lottery example showed abiogenesis to be too improbable to occur. It was demonstrated Bill’s lottery example was based on a logical fallacy.

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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:** [February 12, 2020, 9:06pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/146 "2020-02-12T21:06:40Z")

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> [@T\_aquaticus](#):
>
> Again, you are shifting the burden of proof. YOU are the one claiming that life couldn’t be simpler than the bacteria that Venter used in his study, and you need evidence to back this up with evidence.

I claimed that I think it was not much different then what we see in Venters lab. If you cannot make a positive counter claim then we what are we really discussing?

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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:** [February 12, 2020, 9:07pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/147 "2020-02-12T21:07:59Z")

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> [@colewd](#):
>
> I claimed that I think it was not much different then what we see in Venters lab. If you cannot make a positive counter claim then we what are we really discussing?

One is not obliged to prove your assumption wrong. All it is, is an assumption you make.

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**Author:** ![Timothy\_Horton](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/timothy_horton/32/9410_2.png) [@Timothy\_Horton](https://discourse.peacefulscience.org/u/Timothy_Horton)\
**Post date:** [February 12, 2020, 9:09pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/148 "2020-02-12T21:09:11Z")

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> [@colewd](#):
>
> I claimed that I think it was not much different then what we see in Venters lab.

Look at Bill ignore the evidence life was simpler in the past. 🙂

[Thornton Labs: molecular mechanisms of evolution](https://voices.uchicago.edu/thorntonlab/research-2/)

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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:** [February 12, 2020, 9:11pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/149 "2020-02-12T21:11:48Z")

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> [@Rumraket](#):
>
> That’s because it is a genuine unknown. When we don’t know something we shouldn’t be making claims about it. We shouldn’t be claiming to know that it’s not possible when we don’t actually know that.
> 
> I don’t know how simple life can get because I simply don’t know all the forms that life can take. Hence I can not actually calculate a probability for the origin of life, since I lack the relevant information that would be required to make such a calculation.

We do know a lot at this point Rum. We know the basic chemicals of life. We know how proteins are formed. We know how energy is produced. We know a lot about the cell cycle. This is not at all the mystery it was 150 years ago. We also have done experiments to determine the minimum gene set to get growth in a population. There is a lot of data to work with to make a reasonable estimate on the probabilistic resources required for what we are observing if random change is the mechanism that built this.

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**Author:** ![Timothy\_Horton](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/timothy_horton/32/9410_2.png) [@Timothy\_Horton](https://discourse.peacefulscience.org/u/Timothy_Horton)\
**Post date:** [February 12, 2020, 9:13pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/150 "2020-02-12T21:13:45Z")

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> [@colewd](#):
>
> We do know a lot at this point Rum.

We know the existing molecular evidence shows your claim is wrong. That’s the evidence you refuse to look at of course. So what else is new? 🙂

> [@colewd](#):
>
> There is a lot of data to work with to make a reasonable estimate on the probabilistic resources required for what we are observing if random change is the mechanism that built this.

Those are the probability calculations Bill keeps claiming but can never produce. What a surprise. 🙂

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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:** [February 12, 2020, 9:18pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/151 "2020-02-12T21:18:29Z")

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> [@colewd](#):
>
> We do know a lot at this point Rum. We know the basic chemicals of life.

We know the chemicals of extant life.

Does that prove simpler forms of life could not exist, or that it was not simpler in the past?

> [@colewd](#):
>
> We know how proteins are formed.

Yeah they evolve. What does that have to do with how simple life was in the past, or how simple it could be?

> [@colewd](#):
>
> We know how energy is produced.

What does that have to do with how simple life was in the past, or how simple it could be?

> [@colewd](#):
>
> We know a lot about the cell cycle.

What do we know about the cell cycle that allows us to conclude something about how simple life was in the past, or how simple it could be?

> [@colewd](#):
>
> This is not at all the mystery it was 150 years ago.

I agree, we know more today than we did 150 years ago. What does that have to do with how simple life was in the past, or how simple it could be?

> [@colewd](#):
>
> We also have done experiments to determine the minimum gene set to get growth in a population.

Are you talking about Venter’s experiments again?

Explain how it follows from venter whittling away genes until he fails to detect growth, that no simpler forms of life are possible?

> [@colewd](#):
>
> There is a lot of data to work with to make a reasonable estimate on the probabilistic resources required for what we are observing if random change is the mechanism that built this.

But you just can’t seem to tell us what that data is. You can mention this supposed data in a vague and handwavy way over and over again.

Your post is _all_ just wave handwaving again Bill.

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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:** [February 12, 2020, 9:30pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/152 "2020-02-12T21:30:54Z")

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> [@colewd](#):
>
> I claimed that I think it was not much different then what we see in Venters lab.

Can you please show us the evidence that led you to believe that the first life was not much different than _Mycoplasma mycoides_?

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**Author:** ![Rich\_Hampton](https://avatars.discourse-cdn.com/v4/letter/r/a88e4f/32.png) [@Rich\_Hampton](https://discourse.peacefulscience.org/u/Rich_Hampton)\
**Post date:** [February 12, 2020, 10:51pm UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/153 "2020-02-12T22:51:55Z")

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About the Craig Venter experiment

> Venter’s minimal cell is a product not just of its environment, but of the entirety of the [history of life on Earth](https://www.quantamagazine.org/20150716-how-did-life-begin-on-earth/). Sometime in biology’s 4-billion-year record, cells much simpler than this one must have existed. “We didn’t go from nothing to a cell with 400 genes,” [Jack Szostak](http://molbio.mgh.harvard.edu/szostakweb/) said. He and others are trying to [make more basic life-forms](https://www.quantamagazine.org/20160317-david-deamer-origins-of-life/) that are representative of these earlier stages of evolution.

Also worth noting

> Venter is careful to avoid calling syn3.0 a universal minimal cell. If he had done the same set of experiments with a different microbe, he points out, he would have ended up with a different set of genes.
> 
> In fact, there’s no single set of genes that all living things need in order to exist. When scientists first began searching for such a thing 20 years ago, they hoped that simply comparing the genome sequences from a bunch of different species would reveal an essential core shared by all species. But as the number of genome sequences blossomed, that essential core disappeared. In 2010, [David Ussery](http://gst.tennessee.edu/faculty/Ussery.php), a biologist at Oak Ridge National Laboratory in Tennessee, and his collaborators [compared 1,000 genomes](https://www.ncbi.nlm.nih.gov/pubmed/20093288). **They found that not a single gene is shared across all of life. “There are different ways to have a core set of instructions,”** Szostak said.

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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:** [February 13, 2020, 12:28am UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/154 "2020-02-13T00:28:27Z")

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That last quote appears to refer “only” to protein coding genes though. I’m quite certain that all known life shares genes encoding core RNA components of the translation system.

> **[Translation: The Universal Structural Core of Life](https://academic.oup.com/mbe/article/35/8/2065/5000151)**
>
> Abstract. The Universal Gene Set of Life (UGSL) is common to genomes of all extant organisms. The UGSL is small, consisting of \<100 genes, and is dominated

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**Author:** ![stcordova](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/stcordova/32/2030_2.png) [@stcordova](https://discourse.peacefulscience.org/u/stcordova)\
**Post date:** [February 13, 2020, 1:08am UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/155 "2020-02-13T01:08:15Z")

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> [@T\_aquaticus](#):
>
> Why not? Because you say so?

In a raffle type lottery the probability of a winning ticket is based on the number of entries. In origin of life you don’t count the number of entries for starters, the probabilities are built from combinatorial principles, raffle type lottery probabilities aren’t. I could go on, but that’s the start of the problems…

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**Author:** ![stcordova](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/stcordova/32/2030_2.png) [@stcordova](https://discourse.peacefulscience.org/u/stcordova)\
**Post date:** [February 13, 2020, 1:10am UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/156 "2020-02-13T01:10:18Z")

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> [@Rich\_Hampton](#):
>
> **They found that not a single gene is shared across all of life. “There are different ways to have a core set of instructions,”**

Orhpan genes all over the place. This isn’t exactly good either for the pro-evolution case.

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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:** [February 13, 2020, 1:49am UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/157 "2020-02-13T01:49:39Z")

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> [@Rumraket](#):
>
> Does that prove simpler forms of life could not exist, or that it was not simpler in the past?

It’s the data we have. On what bases do you believe life forms were simpler?

> [@Rumraket](#):
>
> Yeah they evolve. What does that have to do with how simple life was in the past, or how simple it could be?

Proteins a formed from DNA sequences translated to Amino Acid sequences. Proteins evolving is an evolutionary \ assumption which has little empirical support.

> [@Rumraket](#):
>
> What does that have to do with how simple life was in the past, or how simple it could be?

The process of converting an energy source like glucoses to to generating ATP is complex.

> [@Rumraket](#):
>
> I agree, we know more today than we did 150 years ago. What does that have to do with how simple life was in the past, or how simple it could be?

We know what the cell looks like across many species and there is little fundamental variation on energy conversion and protein synthesis.

> [@Rumraket](#):
>
> Explain how it follows from venter whittling away genes until he fails to detect growth, that no simpler forms of life are possible?

It shows a real limitation for increasing populations.

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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:** [February 13, 2020, 2:19am UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/158 "2020-02-13T02:19:29Z")

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> [@colewd](#):
>
> > [@Rumraket](#):
> >
> > We know the chemicals of extant life.
> > 
> > Does that prove simpler forms of life could not exist, or that it was not simpler in the past?
> 
> It’s the data we have.

So what? Please explain how it follows from the fact that life today is made of these chemicals, that it had to begin with 470 genes?

> [@colewd](#):
>
> On what bases do you believe life forms were simpler.

Phylogenetic evidence, as I already explained to you. The very same evidence you use to try to estimate FI of some protein sequence, and you use to try to infer conservation over some time period. Compare gene sets and gene sequences of different organisms, map them onto a phylogenetic tree, and infer the history of change from that. The exact same thing shows that life used to be simpler than what it is today. That metabolic pathways used to be simpler, that the translation system used to be simpler, that individual proteins and the molecular machines we see in extant organisms used to be simpler.  
We can even infer the ancestral distribution in the frequency of amino acids used in the oldest known proteins(some of them from a time before the last universal common ancestor), and it is a remarkable fact that the distribution as we go further and further back in time increasingly reflects the distribution we get when scientists simulate abiotic chemical reactions such as in spark-discharge experiments, simulated hydrothermal systems, and found in carbonaceous chondrite meteorites.  
For the latter part about amino acids see for example:  
[Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code](https://academic.oup.com/mbe/article/19/10/1645/1258758).  
[A universal trend of amino acid gain and loss in protein evolution](https://www.nature.com/articles/nature03306).  
[A Thermodynamic Basis for Prebiotic Amino Acid Synthesis and the Nature of the First Genetic Code](https://www.liebertpub.com/doi/10.1089/ast.2008.0280).

> [@colewd](#):
>
> > [@Rumraket](#):
> >
> > Yeah they evolve. What does that have to do with how simple life was in the past, or how simple it could be?
> 
> Proteins a formed from DNA sequences translated to Amino Acid sequences. Proteins evolving is your assumption which has little empirical support.

This is nothing short of denial of observational reality Bill. There [are](https://discourse.peacefulscience.org/t/de-novo-gene-birth/9535) numerous [threads](https://discourse.peacefulscience.org/t/de-novo-emergence-of-adaptive-membrane-proteins-from-thymine-rich-genomic-sequences/9531) on this very forum that shows how proteins can evolve [by empirical experiment](https://discourse.peacefulscience.org/t/optima-in-evolution/9323/186). So no, it’s not an assumption.

So I ask again, what is it about proteins evolving that makes you think that you can assume life had to start with 470 genes?

> [@colewd](#):
>
> > [@Rumraket](#):
> >
> > > [@colewd](#):
> > >
> > > We know a lot about the cell cycle.
> > 
> > What does that have to do with how simple life was in the past, or how simple it could be?
> 
> The process of converting an energy source like glucoses to to generating ATP is complex.

So what? You are aware that many organisms live without glucose, right?

You’re not even trying to answer the questions I put to you now. You’re _just saying stuff_ that doesn’t even appear tangentially relevant.

> [@colewd](#):
>
> > [@Rumraket](#):
> >
> > I agree, we know more today than we did 150 years ago. What does that have to do with how simple life was in the past, or how simple it could be?
> 
> We know what the cell looks like across many species and there is little fundamental variation on energy conversion and protein synthesis.

Again you’re just waving your hand vaguely. Explain what it is about “energy conversion and protein synthesis” that makes you think life had to start out with 470 genes please.

You’re just making stuff up now Bill, saying whatever random nonsense that appears to come to your mind.

> [@colewd](#):
>
> > [@Rumraket](#):
> >
> > Are you talking about Venter’s experiments again?
> > 
> > Explain how it follows from venter whittling away genes until he fails to detect growth, that no simpler forms of life are possible?
> 
> It shows a real limitation for increasing populations.

There’s a limit to how many genes you can remove from some organism before it stops being able to grow. I agree. How does it follow from that, that life had to start out with 470 genes?

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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:** [February 13, 2020, 2:21am UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/159 "2020-02-13T02:21:57Z")

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> [@stcordova](#):
>
> Orhpan genes all over the place. This isn’t exactly good either for the pro-evolution case.

That can only be a problem for people who want to deny the observational reality that functional proteins can evolve from non-coding DNA.

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<div class="post-metadata">

**Author:** ![stcordova](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/stcordova/32/2030_2.png) [@stcordova](https://discourse.peacefulscience.org/u/stcordova)\
**Post date:** [February 13, 2020, 2:35am UTC](https://discourse.peacefulscience.org/t/faith-in-mechanisms-that-would-be-outside-our-reach-and-understanding-as-a-matter-of-principle/9557/160 "2020-02-13T02:35:36Z")

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> [@Rumraket](#):
>
> Phylogenetic evidence, as I already explained to you.

Phylogeny only says something evolved, it doesn’t explain why it is reasonable from physics and chemistry. That’s why bio-chemists like Michael Behe realized it was a non-explanation from chemistry and physics, it was just a bald assertion that evolutionary transformations can happen naturally.

Phylogeny isn’t physics and chemistry.

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