Self replicating and evolving RNA molecule created...

[John Larkin]

On Thu, 24 Mar 2022 17:26:41 +0000, Martin Brown
<\'\'\'newspam\'\'\'@nonad.co.uk> wrote:

On 24/03/2022 16:20, jlarkin@highlandsniptechnology.com wrote:
On Thu, 24 Mar 2022 15:37:59 +0000, Martin Brown
\'\'\'newspam\'\'\'@nonad.co.uk> wrote:

On 23/03/2022 16:02, Tom Gardner wrote:
On 23/03/22 14:43, jlarkin@highlandsniptechnology.com wrote:

That couldn\'t have been an incremental process.

Why not?

Because he doesn\'t understand what incremental means.

Because a non-functional complex system is not improved by random
mutation and selection.

You start with the simplest systems of all and slowly build ever more
complicated systems up from them. Diffusion limited chemical reactions
can do quite astonishing things even in purely inorganic chemistry.

You demand that a complex eukaryote springs out of nowhere and insist
that the probability of that happening is essentially zero. Fair enough
because that is almost certainly *not* how it happened.

The way it happened is that a simple replicator got ever more diverse
and complicated. Eventually isolated itself from its environment with a
semipermeable lipid membrane so that there was the very first cell.

That\'s one idea, popular but improbable.

Why are other improbable ideas off-limits?

--

If a man will begin with certainties, he shall end with doubts,
but if he will be content to begin with doubts he shall end in certainties.
Francis Bacon

 

[David Brown]

On 24/03/2022 17:14, jlarkin@highlandsniptechnology.com wrote:

On Thu, 24 Mar 2022 10:00:26 +0100, David Brown
david.brown@hesbynett.no> wrote:

On 23/03/2022 20:32, John Larkin wrote:
On Wed, 23 Mar 2022 17:46:28 +0000, Tom Gardner
spamjunk@blueyonder.co.uk> wrote:

The Blind Watchmaker

I read that, and The Selfish Gene. They were qualitative, repetitious,
and boring. A few pages could have made all his points. Hardly subtle.


And yet you missed all his points.

He only had a couple, none original. Maybe you can summarize his many
original ideas for us.

I have not suggested that he had many ideas. Nor have I suggested that
any of his ideas are original. (Nor am I suggesting that he /hasn\'t/
had many original ideas.)

I merely said you missed his points.

The main point of \"The Blind Watchmaker\" is that there is no such thing
as \"irreducible complexity\" - complex things can evolve from simple
things. Things that might look \"all or nothing\" at first sight, can
develop through evolution. The classic example is the eye.
\"Intelligent design\" fans like to claim \"there\'s no use for half an eye,
therefore the eye could not have evolved\" - but they are totally and
completely wrong, which is easy to demonstrate by looking at the range
of currently living organisms with sight organs that are at different
places on the path between light-sensitive chemicals and advanced eyes.

That is definitely /not/ an original Dawkins idea - Darwin considered it
too, along with every biologist in between.

Apparently, however, it still baffles you.

Dawkins is a self-admitted agressive atheist.

You make that sound like a bad thing.

Yes. Strong emotions constrain logical thinking.

Atheism is restricted to logical thinking, precisely because it does not
accept illogical and unjustified arguments. (It is happy to accept \"we
don\'t know\".) If you have ever actually read things he has written, or
listened to him talk, or watched a Youtube video of him, you\'ll notice
he does not get emotionally worked up or make unsubstantiated appeals to
supposed authority, as some of his debate opponents do.

Call Dawkins boring, or repetitive, or unoriginal if you like. But
suggesting he can\'t think logically because of strong emotions is laughable.

That corrals all his
thinking.


It means he /thinks/. People following religious dogma avoid thinking
by getting their unquestionable answers presented to them. They are
encouraged /not/ to think too deeply, because then they\'d see all the
inconsistencies and how the answers they\'ve been given don\'t actually
match the questions. Atheists, on the other hand, /do/ get to think,
learn and discover things, because they accept that we don\'t have all
the answers.

Why is anti-religious dogma any better than religious? Both put some
ideas off-limits.

I agree - dogma is not good. Scientists don\'t go in for dogma. They
expect theories to be very well justified with solid evidence,
experiments and theoretical backing before they accept them as
\"scientific fact\". And even then, it is only as \"the current best
theory\" which every scientist would love to prove wrong.

 

[Joe Gwinn]

On Thu, 24 Mar 2022 21:54:53 +0100, David Brown
<david.brown@hesbynett.no> wrote:

[snip]

I agree - dogma is not good. Scientists don\'t go in for dogma. They
expect theories to be very well justified with solid evidence,
experiments and theoretical backing before they accept them as
\"scientific fact\". And even then, it is only as \"the current best
theory\" which every scientist would love to prove wrong.

I beg to disagree - some scientists do issue dogma, by that name:

..<https://www.yourgenome.org/facts/what-is-the-central-dogma>

..<https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology>


Joe Gwinn

 

[John Larkin]

On Thu, 24 Mar 2022 21:54:53 +0100, David Brown
<david.brown@hesbynett.no> wrote:

On 24/03/2022 17:14, jlarkin@highlandsniptechnology.com wrote:
On Thu, 24 Mar 2022 10:00:26 +0100, David Brown
david.brown@hesbynett.no> wrote:

On 23/03/2022 20:32, John Larkin wrote:
On Wed, 23 Mar 2022 17:46:28 +0000, Tom Gardner
spamjunk@blueyonder.co.uk> wrote:

The Blind Watchmaker

I read that, and The Selfish Gene. They were qualitative, repetitious,
and boring. A few pages could have made all his points. Hardly subtle.


And yet you missed all his points.

He only had a couple, none original. Maybe you can summarize his many
original ideas for us.


I have not suggested that he had many ideas. Nor have I suggested that
any of his ideas are original. (Nor am I suggesting that he /hasn\'t/
had many original ideas.)

I merely said you missed his points.

The main point of \"The Blind Watchmaker\" is that there is no such thing
as \"irreducible complexity\" - complex things can evolve from simple
things. Things that might look \"all or nothing\" at first sight, can
develop through evolution. The classic example is the eye.
\"Intelligent design\" fans like to claim \"there\'s no use for half an eye,
therefore the eye could not have evolved\" - but they are totally and
completely wrong, which is easy to demonstrate by looking at the range
of currently living organisms with sight organs that are at different
places on the path between light-sensitive chemicals and advanced eyes.

That is definitely /not/ an original Dawkins idea - Darwin considered it
too, along with every biologist in between.

Apparently, however, it still baffles you.

There is a clear evolutionary path for an eye, with many actual living
examples along the way.

The replication mechanism for DNA is not so friendly to incremental
design

https://www.youtube.com/watch?v=fpHaxzroYxg

Fun stuff at 9:00.

Dawkins is a self-admitted agressive atheist.

You make that sound like a bad thing.

Yes. Strong emotions constrain logical thinking.


Atheism is restricted to logical thinking, precisely because it does not
accept illogical and unjustified arguments. (It is happy to accept \"we
don\'t know\".) If you have ever actually read things he has written, or
listened to him talk, or watched a Youtube video of him, you\'ll notice
he does not get emotionally worked up or make unsubstantiated appeals to
supposed authority, as some of his debate opponents do.

Call Dawkins boring, or repetitive, or unoriginal if you like. But
suggesting he can\'t think logically because of strong emotions is laughable.


That corrals all his
thinking.


It means he /thinks/. People following religious dogma avoid thinking
by getting their unquestionable answers presented to them. They are
encouraged /not/ to think too deeply, because then they\'d see all the
inconsistencies and how the answers they\'ve been given don\'t actually
match the questions. Atheists, on the other hand, /do/ get to think,
learn and discover things, because they accept that we don\'t have all
the answers.

Why is anti-religious dogma any better than religious? Both put some
ideas off-limits.

I agree - dogma is not good. Scientists don\'t go in for dogma. They
expect theories to be very well justified with solid evidence,
experiments and theoretical backing before they accept them as
\"scientific fact\". And even then, it is only as \"the current best
theory\" which every scientist would love to prove wrong.

There is no solid evidence or experiment that shows a path from
inorganics to DNA based living cells. But RNA World is accepted and
suggestions that there could be other paths are mocked. Lots of people
hate their work to be proven wrong. I\'ve been to some scientific
conferences where people were very unwilling to be wrong. Viciously
so.

Scientists have emotions too. \"Science progresses one funeral at a
time.\"




--

If a man will begin with certainties, he shall end with doubts,
but if he will be content to begin with doubts he shall end in certainties.
Francis Bacon

 

[John Larkin]

On Thu, 24 Mar 2022 17:26:31 -0400, Joe Gwinn <joegwinn@comcast.net>
wrote:

On Thu, 24 Mar 2022 21:54:53 +0100, David Brown
david.brown@hesbynett.no> wrote:

[snip]

I agree - dogma is not good. Scientists don\'t go in for dogma. They
expect theories to be very well justified with solid evidence,
experiments and theoretical backing before they accept them as
\"scientific fact\". And even then, it is only as \"the current best
theory\" which every scientist would love to prove wrong.


I beg to disagree - some scientists do issue dogma, by that name:

.<https://www.yourgenome.org/facts/what-is-the-central-dogma

.<https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology


Joe Gwinn

Crick created and named the Central Dogma, which was obviously wrong.
His explanation is that \"I just didn\'t know what dogma meant.\"

As if.

--

If a man will begin with certainties, he shall end with doubts,
but if he will be content to begin with doubts he shall end in certainties.
Francis Bacon

 

[Joe Gwinn]

On Thu, 24 Mar 2022 16:06:41 -0700, John Larkin
<jlarkin@highland_atwork_technology.com> wrote:

On Thu, 24 Mar 2022 17:26:31 -0400, Joe Gwinn <joegwinn@comcast.net
wrote:

On Thu, 24 Mar 2022 21:54:53 +0100, David Brown
david.brown@hesbynett.no> wrote:

[snip]

I agree - dogma is not good. Scientists don\'t go in for dogma. They
expect theories to be very well justified with solid evidence,
experiments and theoretical backing before they accept them as
\"scientific fact\". And even then, it is only as \"the current best
theory\" which every scientist would love to prove wrong.


I beg to disagree - some scientists do issue dogma, by that name:

.<https://www.yourgenome.org/facts/what-is-the-central-dogma

.<https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology


Joe Gwinn

Crick created and named the Central Dogma, which was obviously wrong.
His explanation is that \"I just didn\'t know what dogma meant.\"

Nahh. He was just joking, but the term \"central dogma\" did go into
bio-speak anyway. It was a dramatic clarification of multiple
mysteries in a single stroke.

And he very much knew about the gaps and asterisks. His Intro to
Biology textbook (now obsolete) is in paragraph outline form, and
there are lots of places where he summarizes what is known, and says
that we really don\'t know what\'s going on there. I guess that tenured
nobelists can admit ignorance.

Joe Gwinn

 

[Anthony William Sloman]

On Friday, March 25, 2022 at 3:14:11 AM UTC+11, jla...@highlandsniptechnology.com wrote:

On Thu, 24 Mar 2022 10:00:26 +0100, David Brown <david...@hesbynett.no> wrote:
On 23/03/2022 20:32, John Larkin wrote:
On Wed, 23 Mar 2022 17:46:28 +0000, Tom Gardner <spam...@blueyonder.co.uk> wrote:

<snip>

Dawkins is a self-admitted agressive atheist.

You make that sound like a bad thing.

Yes. Strong emotions constrain logical thinking.

John Larkin\'s vanity seems to be remarkably effective at preventing him from following the kind of logical argument that suggests that he\'s ever got anything wrong.

That corrals all his thinking.

It means he /thinks/. People following religious dogma avoid thinking
by getting their unquestionable answers presented to them. They are
encouraged /not/ to think too deeply, because then they\'d see all the
inconsistencies and how the answers they\'ve been given don\'t actually
match the questions. Atheists, on the other hand, /do/ get to think,
learn and discover things, because they accept that we don\'t have all
the answers.

Why is anti-religious dogma any better than religious? Both put some ideas off-limits.

The problem is dogma - which does put some ideas off-limits. Atheists aren\'t dogmatically anti-religion - they are against the kind of religion that postulates gods. That\'s not so much dogma as an aversion to non-evidence-based theories.

Agnostics are slightly more cautious - they merely say tat nobody has produced any reliable evidence of the existence of any god yet.

--
Bill Sloman, Sydney

 

[Anthony William Sloman]

On Friday, March 25, 2022 at 5:17:29 AM UTC+11, John Larkin wrote:

On Thu, 24 Mar 2022 17:26:41 +0000, Martin Brown
\'\'\'newspam\'\'\'@nonad.co.uk> wrote:

On 24/03/2022 16:20, jla...@highlandsniptechnology.com wrote:
On Thu, 24 Mar 2022 15:37:59 +0000, Martin Brown
\'\'\'newspam\'\'\'@nonad.co.uk> wrote:

On 23/03/2022 16:02, Tom Gardner wrote:
On 23/03/22 14:43, jla...@highlandsniptechnology.com wrote:

That couldn\'t have been an incremental process.

Why not?

Because he doesn\'t understand what incremental means.

Because a non-functional complex system is not improved by random
mutation and selection.

You start with the simplest systems of all and slowly build ever more
complicated systems up from them. Diffusion limited chemical reactions
can do quite astonishing things even in purely inorganic chemistry.

You demand that a complex eukaryote springs out of nowhere and insist
that the probability of that happening is essentially zero. Fair enough
because that is almost certainly *not* how it happened.

The way it happened is that a simple replicator got ever more diverse
and complicated. Eventually isolated itself from its environment with a
semipermeable lipid membrane so that there was the very first cell.

That\'s one idea, popular but improbable.

Popular, feasible and probably probable enough if you wait long enough.

> Why are other improbable ideas off-limits?

Mostly because they aren\'t feasible. Your \"improbable ideas\" merely divert the question about the origin of our form of life to the origin of some other form of life which intelligently designed ours, which means that your idea is incomplete, and you haven\'t noticed - which is a higher level incompetence.

--
Bill Sloman, Sydney

 

[Anthony William Sloman]

On Friday, March 25, 2022 at 8:26:59 AM UTC+11, Joe Gwinn wrote:

On Thu, 24 Mar 2022 21:54:53 +0100, David Brown
david...@hesbynett.no> wrote:

[snip]

I agree - dogma is not good. Scientists don\'t go in for dogma. They
expect theories to be very well justified with solid evidence,
experiments and theoretical backing before they accept them as
\"scientific fact\". And even then, it is only as \"the current best
theory\" which every scientist would love to prove wrong.

I beg to disagree - some scientists do issue dogma, by that name:

.<https://www.yourgenome.org/facts/what-is-the-central-dogma

.<https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology

Francis Crick had a lively sense of humour, and it was a ironic joke. At the time he articulated it -1958 - it was a speculation, if a rather well-founded and perceptive one. Subsequent authors have shown their appreciation by repeating the irony.

--
Bill Sloman, Sydney

 

[Anthony William Sloman]

On Friday, March 25, 2022 at 10:06:53 AM UTC+11, John Larkin wrote:

On Thu, 24 Mar 2022 17:26:31 -0400, Joe Gwinn <joeg...@comcast.net
wrote:
On Thu, 24 Mar 2022 21:54:53 +0100, David Brown
david...@hesbynett.no> wrote:

[snip]

I agree - dogma is not good. Scientists don\'t go in for dogma. They
expect theories to be very well justified with solid evidence,
experiments and theoretical backing before they accept them as
\"scientific fact\". And even then, it is only as \"the current best
theory\" which every scientist would love to prove wrong.


I beg to disagree - some scientists do issue dogma, by that name:

.<https://www.yourgenome.org/facts/what-is-the-central-dogma

.<https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology

Crick created and named the Central Dogma, which was obviously wrong.

His Central Dogma turned out to be entirely correct, though it was a speculation when he first published it

> His explanation is that \"I just didn\'t know what dogma meant.\"

Probably untrue. Francis Crick did have sense of humour, and enjoyed maklng jokes at journalists expense. \"I just didn\'t know what dogma meant\" is shorter and much easier for a not-too-well-informed English-language science journalist to accept. It\'s also funny, which you seem to have missed.

> As if.

So you haven\'t entirely missed the point.

--
Bill Sloman, Sydney

 

[whit3rd]

On Thursday, March 24, 2022 at 9:20:55 AM UTC-7, jla...@highlandsniptechnology.com wrote:

On Thu, 24 Mar 2022 15:37:59 +0000, Martin Brown
\'\'\'newspam\'\'\'@nonad.co.uk> wrote:

On 23/03/2022 16:02, Tom Gardner wrote:
On 23/03/22 14:43, jla...@highlandsniptechnology.com wrote:

That couldn\'t have been an incremental process.

Why not?

Because he doesn\'t understand what incremental means.
Because a non-functional complex system is not improved by random
mutation and selection.

False, of course. It can be improved, or unchanged, or worsened by
a mutation, and it might be that a dozen \'unchanged\' mutations followed
by an \'improved\' is rewarded by selection.

You can\'t insist on single-step improvement many times in a row, nor
on \'worsened\' and extinction as the only alternatives. It wouldn\'t be random
if such simplifications were imposed.

By one assessment, your genome is likely to have four lethal (but recessive)
genes. Unless you marry a close relative, there\'s no problem for you or your progeny,
But, there\'s a lottery win possible, as well as lottery loss, depending on what combination
comes up. And, that win needn\'t be only ONE mutation away from the general-population-average
genome; it could include (for instance) four lethal, but recessive, genes.

 

[David Brown]

On 24/03/2022 19:13, John Larkin wrote:

On Thu, 24 Mar 2022 10:23:14 +0100, David Brown
david.brown@hesbynett.no> wrote:

On 24/03/2022 04:52, jlarkin@highlandsniptechnology.com wrote:
On Wed, 23 Mar 2022 20:35:52 +0100, David Brown
david.brown@hesbynett.no> wrote:

On 23/03/2022 18:46, Tom Gardner wrote:
On 23/03/22 17:24, jlarkin@highlandsniptechnology.com wrote:



Non-Darwinian evolution, jumping genes, epigenetics were not much
welcomed.

Eh? Jumping genes and epigenetics are part of Darwinian evolution.
They are just additional complications to the mechanisms of biological
evolution as we have it in life on earth - they fit within standard
Darwinian evolution. They don\'t fit neatly within the simple model of
getting your traits via genes from your parents - but biologists are
used to things being more complicated when examined more closely.


Viruses use reverse transcription to insert their genome into a host\'s
DNA, who then builds move viruses.

Some viruses do that, but most do not. Retroviruses are only a small
proportion of virus families. (The family includes some big names, like
HIV and hepatitis, but it is only one of many different types of virus.)

RT is used to make cells produce
useful products like insulin.

It is useful in all kinds of artificial genetic modification, as it
provides a pathway for altering the DNA of a cell.


Why would we allow RT to work if all it does is enable viruses?


Are you really suggesting that the cells of eukaryotes evolved (or were
\"designed\") specifically to enable reverse transcription to work,
putting up with some 450 million years of virus infections, just so that
one day humans would evolve and advance enough to be able to use RT to
make insulin?

I am suggesting that reverse transcription may be useful, so was not
eliminated by evolution.

Let me try to be clear about what you are saying. Reverse transcription
has been beneficial to retroviruses, so they have kept it as a method
for reproduction. That much is obvious. So you must be talking about
the eukaryote side - the vulnerability to reverse transcription from
retroviruses.

There you are wrong on multiple counts, due to your fundamental lack of
understanding of evolution and biology.

First, evolution is random mutation and natural selection. It is not
guided. It does not in any way move towards optimal solutions to
problems, and certainly not \"big picture\" solutions. At best, it can
lead to local maxima - which can also mean it gets stuck there. Every
lifeform has vast numbers of traits that are not useful overall, but are
artefacts of our evolutionary history.

(We have kept our vulnerability to all sorts of diseases, not just
retroviruses, despite the cost.)

Secondly, whatever biochemical pathways make us vulnerable to reverse
transcription could be essential to other mechanisms that are more
important. You can\'t have mail without being vulnerable to junk mail -
maybe you can\'t have DNA replication without being vulnerable to reverse
transcription.

Thirdly, if there is enough evolutionary pressure to lead to changes to
a particular problem (i.e., if retroviruses were a major cause of
death), then there is no particular reason for any one given technique
for reducing the problem. A better immune system that stops the
retroviruses is just as good as a way to block the reverse transcription.


All in all, it is clear that there is no reason to suppose that
vulnerability to reverse transcription is at all \"useful\" in itself in
terms of being preserved by evolution. If it turns out to be useful 450
million years later, that is happy chance - not a feature of evolution.

It has been suggested that viruses assist
horizontal evolution, for one. I can imagine other uses for RT.

You don\'t mean \"horizontal evolution\", you mean \"horizontal gene
transference\" - it is still normal Darwinian evolution. And yes,
viruses are a mechanism for horizontal gene transfer in eukaryotes
(prokaryotes have other mechanisms that are vastly more common, but
viruses could also theoretically transfer genes there). RT is not the
only way a gene could be transferred horizontally. (I don\'t know if
sexual reproduction could be considered \"horizontal transfer\", but we\'ll
leave that one out!)

But even if RT /were/ the only way to transfer genes horizontally, and
horizontal gene transfer lead to useful new traits, susceptibility to RT
would not confer an /evolutionary/ advantage. Evolution works by
natural selection - first think how likely are you to pass on your genes
to viable offspring that pass them on again? Then consider those
probabilities as statistics over a population, and that gives you the
likelihood of particular characteristics being passed on. Horizontal
gene transfer in eukaryotes is extremely rare, especially more complex
ones. And like all types of mutations, the vast majority are directly
harmful or deadly (local transfer of genes by RT viruses is a big cause
of cancer), or at best harmless. It\'s extremely rare that you get
something useful - such as the genes for the placenta in early mammal
precursors.

Evolution is /not/ going to select for RT susceptibility on the basis of
it being useful for horizontal gene transfer. It has no effect on the
timescale of the natural selection function, and in the long run is
mostly detrimental. Evolution does not plan for the future.


Now, as for your imagination, would you care to expand on \"other uses
for RT\" ? Please /justify/ your suggestions.

People didn\'t invent Reverse Transcriptase and we don\'t have
antibodies that destroy it.

You are mixing up two meanings of \"people\" here. Please don\'t do that.
You already have a reputation for being thoroughly confused, and don\'t
need to make it worse. First /think/ clearly. Then /write/ clearly.

Reverse transcriptase evolved in retroviruses. Modern scientists
discovered it when examining such viruses, and found it useful as a
genetic engineering tool.

We (and I don\'t know how broad you are going here - humans, mammals,
complex eukaryotes - it doesn\'t really matter) don\'t have antibodies
against RT because it is a protein found /inside/ a cell under attack by
a retrovirus. We make antibodies against the viruses themselves.

Don\'t discuss, start the mocking. That\'s what you do to unauthorized
ideas.

I have tried hard here. I hope you appreciate it.

When someone has an idea, it needs to be evaluated for how it fits
reality and how useful it might be. If it doesn\'t fit, and is leading
nowhere, it must be rejected to make room for better ideas. It\'s a
dog-eat-dog world for ideas.

Ideally, the person having the ideas can do the basic filtering
themselves. You seem to be missing such filtering ability. But I\'ve
gone through the process for you here. You can take what\'s left and try
to refine it into something better - that\'s one way progress is made.
You can accept that the idea doesn\'t pan out, and drop it - then you can
make progress on something else.

Or, true to form, you can ignore all the facts, information and
evidence, and continue to propound your idea as if it were the best
thing since sliced bread. And then you will be upset at the mocking it
gets.

https://en.wikipedia.org/wiki/Reverse_transcriptase#History

\"Valerian Dolja of Oregon State argues that viruses, due to their
diversity, have played an evolutionary role in the development of
cellular life, with reverse transcriptase playing a central role.\"

Yes. So?

Killing off the occasional individual is a small price to pay for
accelerating species evolution. In that sense, viruses are our
friends.

Evolution does not plan.

For much of the history of the earth, life was very simple and changed
very little. It was quite stable. Evolution does not easily lead to
big changes if there is little need (it happens occasionally - it is the
nature of randomness to have extreme events happen sometimes). It takes
major changes to the environment to give more rapid evolution - mass
extinction events, or \"arms races\" between predators and prey.

If you look at things from a purely self-centred viewpoint, and think
the purpose of life on earth was to produce /you/, then you can well say
that viruses are your friends. But evolution does not have a purpose.
If there hadn\'t been factors challenging the survival of early microbes,
life on earth would still be mats of slime - because that\'s how
evolution works.

Oops, another idea. Sorrrry.

It is not your worst idea - at least it is not \"aliens did it\". But on
closer examination, it goes to the reject pile. It\'s a pity you still
don\'t understand the fundamentals of evolution and still don\'t
self-filter these things. That\'s why you end up with the mocking.

 

[David Brown]

On 24/03/2022 22:26, Joe Gwinn wrote:

On Thu, 24 Mar 2022 21:54:53 +0100, David Brown
david.brown@hesbynett.no> wrote:

[snip]

I agree - dogma is not good. Scientists don\'t go in for dogma. They
expect theories to be very well justified with solid evidence,
experiments and theoretical backing before they accept them as
\"scientific fact\". And even then, it is only as \"the current best
theory\" which every scientist would love to prove wrong.


I beg to disagree - some scientists do issue dogma, by that name:

.<https://www.yourgenome.org/facts/what-is-the-central-dogma

.<https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology

To quote from the Wikipedia link
<https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology#Use_of_the_term_dogma>
:

\"\"\"
Use of the term dogma

In his autobiography, What Mad Pursuit, Crick wrote about his choice of
the word dogma and some of the problems it caused him:

\"I called this idea the central dogma, for two reasons, I suspect. I
had already used the obvious word hypothesis in the sequence hypothesis,
and in addition I wanted to suggest that this new assumption was more
central and more powerful. ... As it turned out, the use of the word
dogma caused almost more trouble than it was worth. Many years later
Jacques Monod pointed out to me that I did not appear to understand the
correct use of the word dogma, which is a belief that cannot be doubted.
I did apprehend this in a vague sort of way but since I thought that all
religious beliefs were without foundation, I used the word the way I
myself thought about it, not as most of the world does, and simply
applied it to a grand hypothesis that, however plausible, had little
direct experimental support.\"

Similarly, Horace Freeland Judson records in The Eighth Day of Creation:[19]

\"My mind was, that a dogma was an idea for which there was no
reasonable evidence. You see?!\" And Crick gave a roar of delight. \"I
just didn\'t know what dogma meant. And I could just as well have called
it the \'Central Hypothesis,\' or — you know. Which is what I meant to
say. Dogma was just a catch phrase.\"

\"\"\"


Despite the name, it is not \"dogma\". When it was formed, the authors
did not have enough nearly evidence to call it a \"theory\". And like all
science, it will be changed or replaced as soon as anyone finds clear
evidence that contradicts it.

It turns out that individual scientists are humans too - they use words
incorrectly, or where the interpretations could be different. They pick
names that sound good, even though they are not precise. (\"String
theory\" is /very/ far from being a scientific theory.)

 

[Tom Gardner]

On 25/03/22 07:48, David Brown wrote:

<snipped many accurate and relevant points>

It is not your worst idea - at least it is not \"aliens did it\". But on
closer examination, it goes to the reject pile. It\'s a pity you still
don\'t understand the fundamentals of evolution and still don\'t
self-filter these things. That\'s why you end up with the mocking.

John\'s attitudes and beliefs are akin to those that annoy
engineers.

John rightly gives short shrift to his (potential)
customers that articulate classic nonsense such as:
- mechanical: it is only few bits of string and bent metal
- software: it is only a few lines of code, so you can
work around deficient hardware
- hardware: is is only a few wires and a micro
- rf: it is only a few diodes and tracks on a PCB
- comms: faster is simply a matter of more power or sensitivity

John should either accept the inverse or show intellectual humility.

 

[David Brown]

On 24/03/2022 23:58, John Larkin wrote:

On Thu, 24 Mar 2022 21:54:53 +0100, David Brown
david.brown@hesbynett.no> wrote:

On 24/03/2022 17:14, jlarkin@highlandsniptechnology.com wrote:
On Thu, 24 Mar 2022 10:00:26 +0100, David Brown
david.brown@hesbynett.no> wrote:

On 23/03/2022 20:32, John Larkin wrote:
On Wed, 23 Mar 2022 17:46:28 +0000, Tom Gardner
spamjunk@blueyonder.co.uk> wrote:

The Blind Watchmaker

I read that, and The Selfish Gene. They were qualitative, repetitious,
and boring. A few pages could have made all his points. Hardly subtle.


And yet you missed all his points.

He only had a couple, none original. Maybe you can summarize his many
original ideas for us.


I have not suggested that he had many ideas. Nor have I suggested that
any of his ideas are original. (Nor am I suggesting that he /hasn\'t/
had many original ideas.)

I merely said you missed his points.

The main point of \"The Blind Watchmaker\" is that there is no such thing
as \"irreducible complexity\" - complex things can evolve from simple
things. Things that might look \"all or nothing\" at first sight, can
develop through evolution. The classic example is the eye.
\"Intelligent design\" fans like to claim \"there\'s no use for half an eye,
therefore the eye could not have evolved\" - but they are totally and
completely wrong, which is easy to demonstrate by looking at the range
of currently living organisms with sight organs that are at different
places on the path between light-sensitive chemicals and advanced eyes.

That is definitely /not/ an original Dawkins idea - Darwin considered it
too, along with every biologist in between.

Apparently, however, it still baffles you.

There is a clear evolutionary path for an eye, with many actual living
examples along the way.

Yes.

It\'s important to remember that the current living examples show how the
current human eye (for example) /might/ have evolved - not how it /did/
evolve. We can look at a nautilus with a \"pin-hole camera\" eye and
understand that was a likely stage in the evolution of the lens eye, but
we did not evolve from modern-day nautiluses.

The replication mechanism for DNA is not so friendly to incremental
design

\"Design\" is a loaded word here - if you used it to mean \"actively
designed by something or someone\", you\'re showing that you still don\'t
grok evolution. If you really meant \"incremental evolution\", then don\'t
write \"design\". Your reputation for confusion, misunderstanding, and a
belief it \"God did it\" precedes you - if you don\'t want to provoke
mocking, be more accurate in what you write.


What makes you say that the current modern mechanism for DNA replication
is not \"friendly\" to incremental evolution? All you can say is that no
one has proposed a plausible development pathway so far - or at fact,
merely none that /you/ have heard of. (I haven\'t heard of one either,
but I know the sum of human knowledge extends somewhat beyond my own
personal knowledge.)

There are three big challenges in looking at the evolutionary history
here. One is that this is all done at the molecular level and happens
fast - it is experimentally extremely challenging to observe what is
really happening.

Secondly, DNA as a genetic structure is extraordinarily successful. If
the RNA World hypothesis is a good approximation of the early life on
earth, then once DNA systems evolved they out-competed RNA-based
lifeforms so completely that there are no traces left (found so far) in
the modern ecosystem. There could have been all sorts of basis for life
in the early history of the earth - we only know about the ones that
survived.

Thirdly, the organisms of that time were very small, and there can be no
fossil records as direct evidence. We have a few ancient rocks where
certain minerals or patterns in the rocks can reasonably be interpreted
as evidence of early microbial life, but that\'s the best we can get -
there is no conceivable way to know if they used DNA or some precursor.


We can, however, look at DNA replication mechanisms in different living
organisms to get some ideas. Roughly speaking, prokaryote and eukaryote
DNS replication has some major differences as well as many similarities.
There are also differences between some groups of prokaryotes. This
gives a good starting point for the evolution from our common ancestor
going forward. We can also look at organisms that have slightly
different variations of the usual DNA base pairs (such as some
bacteriophages that have an alternative form of the \"A\" letter). All
these variations makes it clear that what we have in our own cells is
most certainly not \"irreducible complexity\" or \"all or nothing\".


So how did DNA replication evolve? The correct answer is we don\'t know,
and probably never will know how it /did/ evolve. But we can work
towards better answers for how it /might/ have evolved.

Throwing our arms up and saying \"it\'s all so amazing - it must have been
a god\" is not helpful. (And I don\'t care if you refer to a Christian
god, a Hindu god, an alien robot, intelligent DNA, conscious electrons,
or any other super-natural super-powerful super-intelligent
super-designer - it\'s all the same principle with different names and
different details.)

https://www.youtube.com/watch?v=fpHaxzroYxg

Fun stuff at 9:00.

Yes, it\'s amazing stuff, and fun to watch. It does not in any way
collaborate your idea.

I hesitate a little with this analogy, because I fear you may
misinterpret it, but let\'s look at something that very clearly /was/
designed - because it is man-made. Have you ever watched a modern
pick-and-place machine in action? You have a big device that is placing
millimetre-sized components at rates of 30 per second. The machine is
dependent on a whole range of subsystems - feeders, arms, control
boards, visual inspection systems. Remove or change any one of these,
and it won\'t work. But would you consider it \"irreducible complexity\"?
Would you say it was designed as a whole, from scratch? No - you can
understand how it \"evolved\" from previous generations of pick and place
machines, going back to earliest models that were using ideas and
designs from completely different systems. The ratchet mechanism used
to feed from component rolls can be traced back to pendulum clocks - an
utterly different kind of usage. The placement arms can be traced back
to human arms.

The point is, just because something is impressive and complex, does not
remotely suggest that it cannot have developed gradually from simpler
systems.

Dawkins is a self-admitted agressive atheist.

You make that sound like a bad thing.

Yes. Strong emotions constrain logical thinking.


Atheism is restricted to logical thinking, precisely because it does not
accept illogical and unjustified arguments. (It is happy to accept \"we
don\'t know\".) If you have ever actually read things he has written, or
listened to him talk, or watched a Youtube video of him, you\'ll notice
he does not get emotionally worked up or make unsubstantiated appeals to
supposed authority, as some of his debate opponents do.

Call Dawkins boring, or repetitive, or unoriginal if you like. But
suggesting he can\'t think logically because of strong emotions is laughable.


That corrals all his
thinking.


It means he /thinks/. People following religious dogma avoid thinking
by getting their unquestionable answers presented to them. They are
encouraged /not/ to think too deeply, because then they\'d see all the
inconsistencies and how the answers they\'ve been given don\'t actually
match the questions. Atheists, on the other hand, /do/ get to think,
learn and discover things, because they accept that we don\'t have all
the answers.

Why is anti-religious dogma any better than religious? Both put some
ideas off-limits.

I agree - dogma is not good. Scientists don\'t go in for dogma. They
expect theories to be very well justified with solid evidence,
experiments and theoretical backing before they accept them as
\"scientific fact\". And even then, it is only as \"the current best
theory\" which every scientist would love to prove wrong.

There is no solid evidence or experiment that shows a path from
inorganics to DNA based living cells.

Correct. There is solid evidence, experiments and plausible pathways
for many parts of the journey, but far from all of it. Science is a
work in progress - but that doesn\'t mean you get to fill in the gaps
with fairy tales.

> But RNA World is accepted

It is accepted as a work-in-progress hypothesis - because that is what
it is.

and
suggestions that there could be other paths are mocked.

No, there are other work-in-progress hypotheses for abiogenesis. I
think the RNA World is probably the front-runner, but it is not the only
one being considered and no doubt other ideas will be considered in the
future.

But scientists don\'t bother with \"I give up\" as an answer. \"We don\'t
know\" is fine, as long as it is \"We don\'t know /yet/\" - with \"We will
probably never know for sure, but we can maybe find plausible
hypotheses\" as a fall-back. Science does not bother with \"God did it\"
or other kinds of magic - if you want that, find (or found) a suitable
religion.

Lots of people
hate their work to be proven wrong. I\'ve been to some scientific
conferences where people were very unwilling to be wrong. Viciously
so.

Scientists have emotions too. \"Science progresses one funeral at a
time.\"

Yes, scientists are human, and usually dislike been proven wrong. They
/do/ like proving other scientists wrong. But the emphasis is on the
word \"prove\". Random thoughts do not /prove/ anything. None of your
\"ideas\" has had the faintest shred of evidence. The RNA World
researchers are unlikely to find much evidence for what /did/ happen,
but at least they find evidence for what /might/ have happened or
/could/ have happened. And if anyone finds evidence - historical or
experimental - that contradicts it, the hypothesis will be disproved.

Come back to us when you have /evidence/ for your ideas. \"I can\'t
imagine how that would have evolved\" is only evidence for your own lack
of knowledge and imagination - it is not evidence for your ideas or
evidence against real research hypotheses.

And remember - extraordinary claims require extraordinary evidence. If
you want to prove conventional theories of Darwinian evolution are
wrong, you\'ll need overwhelmingly strong evidence to counter the vast
evidence we have that supports it. And when you come with absolutely
nothing, you can expect to be mocked.

 

[David Brown]

On 24/03/2022 16:37, Martin Brown wrote:

ISTR there is a conjecture that the presence of the moon and so lunar
month influence on daily tidal range may have played a part in the
initial phase of abiogenesis. Isolated rock pools warmed in the sun and
concentrated are apparently just right for one of the combination steps.

https://www.scientificamerican.com/article/moon-life-tides/

It has also been suggested that the moon has played a major part in the
development of life beyond the microbial. As well as tides giving a
good balance between relatively stability in coastal environments with
enough mixing to spread nutrients and useful chemicals, the moon has
kept the earth\'s rotation balanced and the 23° tilt stable. Modelling
has shown that this tilt would have varied far more chaotically over
earth\'s history - causing disruption in the seasons and climate.
Advanced life - and especially intelligent life - probably requires
stable periods.

(Asimov used that idea in his Foundation series. When people were
trying to find the ancient birth planet of the human race, the legends
told of a planet with a huge moon - something they found hard to believe.)

 

[David Brown]

On 24/03/2022 19:17, John Larkin wrote:

On Thu, 24 Mar 2022 17:26:41 +0000, Martin Brown
\'\'\'newspam\'\'\'@nonad.co.uk> wrote:

On 24/03/2022 16:20, jlarkin@highlandsniptechnology.com wrote:
On Thu, 24 Mar 2022 15:37:59 +0000, Martin Brown
\'\'\'newspam\'\'\'@nonad.co.uk> wrote:

On 23/03/2022 16:02, Tom Gardner wrote:
On 23/03/22 14:43, jlarkin@highlandsniptechnology.com wrote:

That couldn\'t have been an incremental process.

Why not?

Because he doesn\'t understand what incremental means.

Because a non-functional complex system is not improved by random
mutation and selection.

You start with the simplest systems of all and slowly build ever more
complicated systems up from them. Diffusion limited chemical reactions
can do quite astonishing things even in purely inorganic chemistry.

You demand that a complex eukaryote springs out of nowhere and insist
that the probability of that happening is essentially zero. Fair enough
because that is almost certainly *not* how it happened.

The way it happened is that a simple replicator got ever more diverse
and complicated. Eventually isolated itself from its environment with a
semipermeable lipid membrane so that there was the very first cell.

That\'s one idea, popular but improbable.

What is your basis for calling it \"improbable\"? Ignorance? Something
you read in one of your \"intelligent design\" books by authors looking
for new guidable pundits when their homeopathy business is waning?
Something you saw online that had lots of big numbers and calculations,
so you assume it must be right?

Why are other improbable ideas off-limits?

Improbable ideas can be considered, if they give something useful, have
evidence, are rational, and might lead somewhere. Impossible or magic
ideas with no evidence or justification need not apply.

 

[Tom Gardner]

On 25/03/22 10:19, David Brown wrote:

Come back to us when you have/evidence/ for your ideas. \"I can\'t
imagine how that would have evolved\" is only evidence for your own lack
of knowledge and imagination - it is not evidence for your ideas or
evidence against real research hypotheses.

I don\'t think John realises that in science the prize does /not/
go to the originator of an idea.

The prize goes to the person(s) that provide /evidence/ that
/convinces/ others.

And that\'s as it should be, since the alternatives are unworkable.

 

[server]

On Fri, 25 Mar 2022 11:19:49 +0100, David Brown
<david.brown@hesbynett.no> wrote:

On 24/03/2022 23:58, John Larkin wrote:
On Thu, 24 Mar 2022 21:54:53 +0100, David Brown
david.brown@hesbynett.no> wrote:

On 24/03/2022 17:14, jlarkin@highlandsniptechnology.com wrote:
On Thu, 24 Mar 2022 10:00:26 +0100, David Brown
david.brown@hesbynett.no> wrote:

On 23/03/2022 20:32, John Larkin wrote:
On Wed, 23 Mar 2022 17:46:28 +0000, Tom Gardner
spamjunk@blueyonder.co.uk> wrote:

The Blind Watchmaker

I read that, and The Selfish Gene. They were qualitative, repetitious,
and boring. A few pages could have made all his points. Hardly subtle.


And yet you missed all his points.

He only had a couple, none original. Maybe you can summarize his many
original ideas for us.


I have not suggested that he had many ideas. Nor have I suggested that
any of his ideas are original. (Nor am I suggesting that he /hasn\'t/
had many original ideas.)

I merely said you missed his points.

The main point of \"The Blind Watchmaker\" is that there is no such thing
as \"irreducible complexity\" - complex things can evolve from simple
things. Things that might look \"all or nothing\" at first sight, can
develop through evolution. The classic example is the eye.
\"Intelligent design\" fans like to claim \"there\'s no use for half an eye,
therefore the eye could not have evolved\" - but they are totally and
completely wrong, which is easy to demonstrate by looking at the range
of currently living organisms with sight organs that are at different
places on the path between light-sensitive chemicals and advanced eyes.

That is definitely /not/ an original Dawkins idea - Darwin considered it
too, along with every biologist in between.

Apparently, however, it still baffles you.

There is a clear evolutionary path for an eye, with many actual living
examples along the way.


Yes.

It\'s important to remember that the current living examples show how the
current human eye (for example) /might/ have evolved - not how it /did/
evolve. We can look at a nautilus with a \"pin-hole camera\" eye and
understand that was a likely stage in the evolution of the lens eye, but
we did not evolve from modern-day nautiluses.

The replication mechanism for DNA is not so friendly to incremental
design

\"Design\" is a loaded word here - if you used it to mean \"actively
designed by something or someone\", you\'re showing that you still don\'t
grok evolution. If you really meant \"incremental evolution\", then don\'t
write \"design\". Your reputation for confusion, misunderstanding, and a
belief it \"God did it\" precedes you - if you don\'t want to provoke
mocking, be more accurate in what you write.


What makes you say that the current modern mechanism for DNA replication
is not \"friendly\" to incremental evolution? All you can say is that no
one has proposed a plausible development pathway so far - or at fact,
merely none that /you/ have heard of. (I haven\'t heard of one either,
but I know the sum of human knowledge extends somewhat beyond my own
personal knowledge.)

There are three big challenges in looking at the evolutionary history
here. One is that this is all done at the molecular level and happens
fast - it is experimentally extremely challenging to observe what is
really happening.

Secondly, DNA as a genetic structure is extraordinarily successful. If
the RNA World hypothesis is a good approximation of the early life on
earth, then once DNA systems evolved they out-competed RNA-based
lifeforms so completely that there are no traces left (found so far) in
the modern ecosystem. There could have been all sorts of basis for life
in the early history of the earth - we only know about the ones that
survived.

Thirdly, the organisms of that time were very small, and there can be no
fossil records as direct evidence. We have a few ancient rocks where
certain minerals or patterns in the rocks can reasonably be interpreted
as evidence of early microbial life, but that\'s the best we can get -
there is no conceivable way to know if they used DNA or some precursor.


We can, however, look at DNA replication mechanisms in different living
organisms to get some ideas. Roughly speaking, prokaryote and eukaryote
DNS replication has some major differences as well as many similarities.
There are also differences between some groups of prokaryotes. This
gives a good starting point for the evolution from our common ancestor
going forward. We can also look at organisms that have slightly
different variations of the usual DNA base pairs (such as some
bacteriophages that have an alternative form of the \"A\" letter). All
these variations makes it clear that what we have in our own cells is
most certainly not \"irreducible complexity\" or \"all or nothing\".


So how did DNA replication evolve? The correct answer is we don\'t know,
and probably never will know how it /did/ evolve. But we can work
towards better answers for how it /might/ have evolved.

Throwing our arms up and saying \"it\'s all so amazing - it must have been
a god\" is not helpful. (And I don\'t care if you refer to a Christian
god, a Hindu god, an alien robot, intelligent DNA, conscious electrons,
or any other super-natural super-powerful super-intelligent
super-designer - it\'s all the same principle with different names and
different details.)



https://www.youtube.com/watch?v=fpHaxzroYxg

Fun stuff at 9:00.



Yes, it\'s amazing stuff, and fun to watch. It does not in any way
collaborate your idea.

You\'re not interested in biology or cool mechanisms or design,
electronic or other wise. You certainly don\'t delight in ideas or fun
machines, or much of anything as far as I can tell.

You hate ideas and speculation.

You seem to delight only in insults. You are just a bitchy old hen.

Maybe you are sick or something. That makes people depressed and
crabby.



--

I yam what I yam - Popeye

 

[server]

On Fri, 25 Mar 2022 08:48:33 +0100, David Brown
<david.brown@hesbynett.no> wrote:

On 24/03/2022 19:13, John Larkin wrote:
On Thu, 24 Mar 2022 10:23:14 +0100, David Brown
david.brown@hesbynett.no> wrote:

On 24/03/2022 04:52, jlarkin@highlandsniptechnology.com wrote:
On Wed, 23 Mar 2022 20:35:52 +0100, David Brown
david.brown@hesbynett.no> wrote:

On 23/03/2022 18:46, Tom Gardner wrote:
On 23/03/22 17:24, jlarkin@highlandsniptechnology.com wrote:



Non-Darwinian evolution, jumping genes, epigenetics were not much
welcomed.

Eh? Jumping genes and epigenetics are part of Darwinian evolution.
They are just additional complications to the mechanisms of biological
evolution as we have it in life on earth - they fit within standard
Darwinian evolution. They don\'t fit neatly within the simple model of
getting your traits via genes from your parents - but biologists are
used to things being more complicated when examined more closely.


Viruses use reverse transcription to insert their genome into a host\'s
DNA, who then builds move viruses.

Some viruses do that, but most do not. Retroviruses are only a small
proportion of virus families. (The family includes some big names, like
HIV and hepatitis, but it is only one of many different types of virus.)

RT is used to make cells produce
useful products like insulin.

It is useful in all kinds of artificial genetic modification, as it
provides a pathway for altering the DNA of a cell.


Why would we allow RT to work if all it does is enable viruses?


Are you really suggesting that the cells of eukaryotes evolved (or were
\"designed\") specifically to enable reverse transcription to work,
putting up with some 450 million years of virus infections, just so that
one day humans would evolve and advance enough to be able to use RT to
make insulin?

I am suggesting that reverse transcription may be useful, so was not
eliminated by evolution.

Let me try to be clear about what you are saying.

Why start now?


--

I yam what I yam - Popeye