DNA animation

[Tim Williams]

"John Larkin" <jjlarkin@highlandtechnology.com> wrote in message
news:hfi8ded0igs8l5e2ipidus433l19ra5mr4@4ax.com...

Most evolutionary algorithms seek a pre-defined goal, and have metrics
for measuring progress along the way. This is intelligent design for
sure.

Critters don't quite work that way.

In the absence of a pre-defined goal, the implicit goal is survival.

This has been reproduced time and time again, even with extremely simple
computational models (cellular automata where each cell runs its code,
interacts with its neighbors, and reproduces under natural selection
conditions). After thousands of generations, some "species" seems to take
over; then after a while with no change, random mutations accumulate to
cause another tipping point and speciation occurs.

It's really quite obvious. If a thing ceases to exist, it ceases to exist.
It can only continue to persist if it persists. In the presence of
competition, we call this natural selection.

Tim

--
Seven Transistor Labs, LLC
Electrical Engineering Consultation and Design
Website: https://www.seventransistorlabs.com/

 

[John Larkin]

On Thu, 9 May 2019 04:26:31 -0500, "Tim Williams"
<tiwill@seventransistorlabs.com> wrote:

"Rick C" <gnuarm.deletethisbit@gmail.com> wrote in message
news:979b244c-1168-45f3-9661-1952dda50fc1@googlegroups.com...
I recall an evolutionary experiment which I believe was done in an analog
circuit simulation, I don't recall for sure.
snip


It was in an FPGA -- think the goal was to make an oscillator, without any
particular design constraints as we would think. I don't recall if outputs
driving outputs were prohibited, or if it went ahead with such abuse
regardless.

The result was very fragile too, AFAIK.

Most evolutionary algorithms seek a pre-defined goal, and have metrics
for measuring progress along the way. This is intelligent design for
sure.

Critters don't quite work that way.

There have been attempts at automated, evolutionary topological (not
just value tuning) circuit design, with hilarious results. Even value
tuning of a given circuit is hazardous.


--

John Larkin Highland Technology, Inc

lunatic fringe electronics

 

[Martin Brown]

On 09/05/2019 15:42, Rick C wrote:

On Thursday, May 9, 2019 at 12:31:11 AM UTC-4, Jasen Betts wrote:
On 2019-05-08, John Larkin <jjlarkin@highland_snip_technology.com> wrote:
On Wed, 8 May 2019 16:54:08 +0100, Martin Brown
'''newspam'''@nezumi.demon.co.uk> wrote:


There is still a lot of hand waving. As in

"it is fruitful to consider the alternative possibility that RNA was
preceded by some other replicating, evolving molecule, just as DNA and
proteins were preceded by RNA."

Its entirely reasonable to try and find the simplest possible canonical
thing that can be said to meet the minimum requirements for "life".

Is that a fact? In modern life, DNA builds RNA.

Reverse transcriptase does the opposite.

but the RNA for that is found in retroviruses so it could be argued that
it's not "life", weasel words that pomoters of that claim may cling
to.

Really? There are people who claim viruses are not life? I don't know what they think viruses are then.

They can only reproduce by hijacking the cellular apparatus of a
suitable host. They sit in the DMZ between life and non-life.

Viroids specific to plants are even smaller and still less like life.
They are in essence small loops of RNA that catalyse making copies of
themselves once they find the right host.

https://www.sciencedirect.com/topics/neuroscience/viroids

Shortest are under 500 base pairs and they are infectious agents for the
very specific plant that they target. Transposons are even more curious.

https://www.sciencedirect.com/topics/medicine-and-dentistry/transposon

They are very much a double edged sword.

--
Regards,
Martin Brown

 

[Martin Brown]

On 09/05/2019 16:04, Rick C wrote:

On Thursday, May 9, 2019 at 4:21:54 AM UTC-4, Martin Brown wrote:
On 08/05/2019 17:38, R Collins wrote:
On Wednesday, May 8, 2019 at 7:42:36 AM UTC-4, Bill Sloman
wrote:
On Wednesday, May 8, 2019 at 7:25:05 PM UTC+10, Martin Brown
wrote:
On 08/05/2019 05:24, John Larkin wrote:


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

This is insane. This is impossible.

It is an impressive animation of the the copying and transfer
of DNA is actually occurring at a molecular level inside
every cell. Thanks for sharing. It is a shame that you cannot
be bothered to understand it.

Asking him to understand it is trifle unreasonable - he hasn't
got the education on which an understanding might be built.
And while we can probably understand the transcription from DNA
to messenger RNA (which is presumably what was being animated)
the business of getting from there to protein synthesis is
trickier.

-- Bill Sloman, Sydney

I find it hard to believe the transcription was a real time
video. The bases find the enzyme via diffusion which I would
think would not be that fast. But then the distances are very
tiny so maybe my sense of how fast diffusion can work is the
unrealistic part of it all. The video makes it look like there is
a current funneling the bases into the enzyme.

The video is strictly classical in terms of ball and spoke models
of the various components and their lock and key behaviour.
Diffusion would be good enough for things to work but there may be
a little bit of quantum mechanics helping things along as well.

No one said anything about it not working. The speed is the issue.
Diffusion is not directed and not fast. The Brownian motion seen in
the video is the basis of the random movements of various reactants.
New bases are not "propelled" as the video seems to show. It
actually shows bases streaming into the work area as if forced into a
funnel. Most quantum mechanical forces are much shorter range than
that.

That is a simplification more for clarity. It would be a mess if all the
other molecules jostling for position were also shown. I expect it is
truly diffusion limited if there is a long sequence of just one base.

It is probably no coincidence that a quantum Turing machine would
have four rather than two "binary" states since in the quantum
world a single comparison allows you to branch four ways. DNA and
RNA may well be in effect a Turing machine of sorts exploiting
quantum mechanics.

What four way branch does quantum mechanics provide?

I'm struggling to find an explanation that isn't far too mathematical
but this is the best I have been able to find in a quick search.

https://physics.stackexchange.com/questions/164155/what-is-the-difference-between-a-bit-and-a-qubit

I know there is a better one somewhere that showed how well you could do
with anything up to 4 quantum comparison branches nested but its URL
eludes me. It is more than a decade since I last looked at this stuff.

In a handwaving sort of way a qubit can represent 2 conventional bits at
once. This is a little bit more technical without going overboard:

http://www.thphys.nuim.ie/staff/joost/TQM/QvC.html

All the other treatments I can find use advanced inpenetrable notation
for generalised rotations which have a steep learning curve. I know
there was a nice table for comparisons somewhere but right now I can't
find it.

In a similar fashion the number of amino acids is suspiciously
close to the number of ways you can branch in three quantum
comparisons. If there is a role for quantum effects in life then it
is in making these stages more efficient than they would be if
purely classical dynamics applied.

It's pretty cool watching the RNA spew out from the enzyme at
such a rate.

It is diffusion limited but a little bit of quantum tunnelling may
well help the right component to find its mark. I expect they are
right about the speed it runs. I found the DNA copy process
animation fascinating.

My concern is simply the rate at which the bases arrive at the
reaction site. In general chemical reactions there are N of one
reactant and M of another reactant bouncing around and periodically
bump into one another in a way that results in the reaction. DNA
replication requires the bases to bump into a relatively few reaction
sites for the enzymes to attach them to the newly forming strand.
Much less likely and so a lower rate.

DNA replicase enzymes work remarkably well.

--
Regards,
Martin Brown

 

[Martin Brown]

On 09/05/2019 17:00, Tim Williams wrote:

"John Larkin" <jjlarkin@highlandtechnology.com> wrote in message
news:hfi8ded0igs8l5e2ipidus433l19ra5mr4@4ax.com...
Most evolutionary algorithms seek a pre-defined goal, and have metrics
for measuring progress along the way. This is intelligent design for
sure.

Critters don't quite work that way.

In the absence of a pre-defined goal, the implicit goal is survival.

Survival and reproduction. Unless the individual with the novel feature
survives to reproduce then the trait is lost to subsequent generations.

This has been reproduced time and time again, even with extremely simple
computational models (cellular automata where each cell runs its code,
interacts with its neighbors, and reproduces under natural selection
conditions).  After thousands of generations, some "species" seems to
take over; then after a while with no change, random mutations
accumulate to cause another tipping point and speciation occurs.

It's really quite obvious.  If a thing ceases to exist, it ceases to
exist. It can only continue to persist if it persists.  In the presence
of competition, we call this natural selection.

What was stunning was how quickly even relatively trivial genomes would
converge on the right solution for their environment (or they all died).
I did program one or two such simulations used in teaching genetics long
before virtual fruit fly. Hercules graphics card which dates it.

Start with random genomes. Starve them for a while and they evolve to
sweep maximum area for food then add a Garden of Eden where the living
is easy and some quickly evolve to loop around inside it.

Zap the garden of Eden again and they either adapt or expire.

You get boom and bust behaviour and catastrophic losses when they
overwhelm the capacity of the Garden of Eden to provide for them too.

It was astonishing how such a simple model had such complex behaviour.

--
Regards,
Martin Brown

 

[Tom Gardner]

On 09/05/19 16:29, Martin Brown wrote:

On 09/05/2019 14:09, Mike Coon wrote:
In article <qb1064$1fg8$1@gioia.aioe.org>,
'''newspam'''@nezumi.demon.co.uk says...
Gas phase chemistry is lousy and
slow.

Statements like that remind me of a demo of oxy-acetylene welding at
school. Teacher: "And finally, you have to remember to turn off the
gasses in the right order."... BANG... "Oh, perhaps it was the other
order...".

Most of it is lousy and slow.
There are as ever a few exceptions that prove the rule.

I have known several lecturers do the oxy-acetylene mix into washup water to
make explosive foam. It quite literally raised the roof in one or two places
with displaced ceiling tiles raining down on the audience.

I was at the Royal Institution as a sixth former,
and the demo was detonating stoichometric mixtures
of gases and oxygen.

The finale was a (glass) 1 pint milk bottle of
acetylene and oxygen. There was a deafening explosion,
two of the surrounding safety shields (reinforced glass
and a lab stool!) were broken, and the glass bottle
was reduced to glass /dust/.

Chemistry was fun, back then.

 

[Tom Gardner]

On 09/05/19 15:28, John Larkin wrote:

On Thu, 9 May 2019 09:04:46 +0100, Tom Gardner
spamjunk@blueyonder.co.uk> wrote:

On 09/05/19 00:41, John Larkin wrote:
On Wed, 8 May 2019 23:32:28 +0100, Tom Gardner
spamjunk@blueyonder.co.uk> wrote:

On 08/05/19 21:21, John Larkin wrote:
On Wed, 8 May 2019 20:48:56 +0100, Tom Gardner
spamjunk@blueyonder.co.uk> wrote:

On 08/05/19 18:28, Tom Del Rosso wrote:
Tim Williams wrote:
"Bill Sloman" <bill.sloman@ieee.org> wrote in message
news:dfa3d2c1-ef88-43c5-abac-c583a2e83bcf@googlegroups.com...

It's even crazier that some people think it happened at random.

Nothing crazy about it. That's what random variation plus selection
can manage.

The crazies are the intelligent design fans, who think that an
intelligent designer would have gone to all that trouble then not
put in any error detection and correction coding.

There are math analyses of that, and they involve a lot of zeroes.

So what? Three billion base pairs is already quite a few zeros.


There's only one force in the universe powerful enough to construct
something that complex: evolution. One must either believe that, or
believe that there is something impossibly wrong with all known laws
of physics*.
(*And I don't just mean the stuff we don't know at the bottom, or the
subtle details between things we do. I mean the things that are
settled and proven.)

I'm always incredulous at the lack of thinking ability when people say
complexity requires a designer, but it doesn't occur to them that a
designer must also be complex.

Yup, and they certainly can't get the "its
turtles all the way down" joke concept.

You assume that the only thing that could design our form of life is
our form of life. Maybe it's not all turtles.

No, I don't.

But when I was 7yo I worked out that "doubting" Thomas
was right to insist on feeling the stigmata before
believing Christ had risen from the dead.

So, yes, I demand evidence rather than unsupported fantasies.

This is a design group. Design involves considering possibilities.
Adherence to orthodoxy and reflexive rejection of possibilities is
poison to design.

Quite right.

I always consider that gremlins are the cause of my
circuits' maloperation.


Besides, the random mutation and selection concept of the origin of
life is just another fantasy, and not a very good one. There's no
evidence for it either.

Strawman argument.

Darwinian evolution describes how species evolve, not the
origin of DNA.

Yes. They are very different issues. Darwinian evolution probably
doesn't apply to the origins issue.

As you intimate, it may apply - but we don't know how (yet).

The origin of DNA is, as yet, unclear and a fascinating question.

It's a beautiful system and a beautiful problem. If it doesn't all
work, none of it works. And the only thing that can manufacture a
living cell is a living cell.

That's too simplistic. "Living" is a very fuzzy concept and
has very fuzzy and changing definitions.

I've seen no evidence that flying spaghetti monsters,
earth-divers, protogenoi, and other deities have anything
to do with it.

If you have evidence, let's hear it.

I'm not a biologist, but I can speculate as well as most of them can.
Maybe better.

I doubt that! Speculations are cheap and easy - and
therefore ultimately boring.

For example David Icke (ex footballer and sports
announcer) speculates. His speculations are that an
inter-dimensional race of shape-shifting reptilians
have hijacked the earth.

Any time that the biological origin of life is freely considered, some
people will start to scream about religion to shut off possibilities
that they don't approve of.

No. If evidence is provided, they will listen. It may
take the usual 50 years until all the old fogies have died,
but evidence will be sufficient in the end.

It may take a lot longer than 50 years. We may never know how the
universe, or life, started.

I meant 50 years after there is decent evidence has
been provided. Einstein not wanting to believe quantum
theory, and all that.

 

[John Larkin]

On Thu, 9 May 2019 16:28:43 +0100, Martin Brown
<'''newspam'''@nezumi.demon.co.uk> wrote:

On 09/05/2019 15:37, John Larkin wrote:
On Thu, 9 May 2019 09:07:01 +0100, Martin Brown
'''newspam'''@nezumi.demon.co.uk> wrote:

On 08/05/2019 17:53, John Larkin wrote:

[snip]

I wonder how that could evolve by random processes.

You start out with a spot that is light sensitive and gradually evolve
under competitive pressure. Every tiny incremental improvement makes
survival of the owner more likely (all other things being equal),
neutral things make no difference and defects tend to get you killed.

People seem to forget that incremental improvements stack up
exponentially so that 100 1% improvements gets you to 270%.

Why would incremental evolution go through a large number of
iterations to produce a "terrible design" human eye? Each step would

It isn't terrible but it is nothing like well designed. It is just about
good enough for the purpose of keeping a hominid omnivore alive.

Not every change is for the better either but the ones that are get to
survive and reproduce combining in different ways with each successive
generation. How hard is that to understand?

Humans have done it to domestic dogs and livestock pretty much since we
stopped being hunter gatherers. Playing god with the traits we
considered most desirable in them and selective breeding. The selection
pressure being what we consider useful/pretty rather than predation.

make it worse, and the final, immensely complex, result would be a
competitive disadvantage.

https://www.ncbi.nlm.nih.gov/books/NBK482309/figure/retinal_degeneration.F18/

Oh wow! A pretty picture taken out of context. How interesting!

Why would a designer equip us with such a botched design having already
got it right in cephalopods? We have a blind spot where the nerve bundle
enters the eye. They do not. Ours is a considerably worse design.

https://en.wikipedia.org/wiki/Cephalopod_eye


It is pretty much the difference between a bog standard cheap and nasty
webcam design and a thinned rear window astronomical CCD camera.

Why would variation and selection result in an extraordinally complex
and optically inferior eye, when squid had a better one already?


--

John Larkin Highland Technology, Inc
picosecond timing precision measurement

jlarkin att highlandtechnology dott com
http://www.highlandtechnology.com

 

[Martin Brown]

On 09/05/2019 15:28, John Larkin wrote:

On Thu, 9 May 2019 09:04:46 +0100, Tom Gardner
spamjunk@blueyonder.co.uk> wrote:

Darwinian evolution describes how species evolve, not the
origin of DNA.

Yes. They are very different issues. Darwinian evolution probably
doesn't apply to the origins issue.

We don't know that. Evolution as a result of imperfect copying and the
early TNA or RNA strands were probably very unstable would have to
converge on a dual purpose autocatalyst that can replicate. Quite
probably as a pair with it's own antisense self.

The origin of DNA is, as yet, unclear and a fascinating question.

It's a beautiful system and a beautiful problem. If it doesn't all
work, none of it works. And the only thing that can manufacture a
living cell is a living cell.

Parts of a modern eukaryote like the mitochondria and chloroplasts were
almost certainly free living organisms once upon a time. Somehow they
managed to get inside another cell without being lysed and the rest is
history. The modern cell was able to thrive and take over.

Just because a modern mammalian eukaryote living cell needs all of its
complexity to work doesn't mean that earlier simpler ones did. There are
still plenty of simpler prokaryotes like bacteria for us to study.

https://www.diffen.com/difference/Eukaryotic_Cell_vs_Prokaryotic_Cell

The search is on for the simplest possible canonical cell DNA.

I've seen no evidence that flying spaghetti monsters,
earth-divers, protogenoi, and other deities have anything
to do with it.

If you have evidence, let's hear it.

I'm not a biologist, but I can speculate as well as most of them can.
Maybe better.

And modest too.

Any time that the biological origin of life is freely considered, some
people will start to scream about religion to shut off possibilities
that they don't approve of.

No. If evidence is provided, they will listen. It may
take the usual 50 years until all the old fogies have died,
but evidence will be sufficient in the end.

It may take a lot longer than 50 years. We may never know how the
universe, or life, started.

I expect us to get close enough to a workable solution within a few
decades now and possibly the same for simulating consciousness.

--
Regards,
Martin Brown

 

[Tom Gardner]

On 09/05/19 19:14, John Larkin wrote:

On Thu, 9 May 2019 16:28:43 +0100, Martin Brown
'''newspam'''@nezumi.demon.co.uk> wrote:

On 09/05/2019 15:37, John Larkin wrote:
On Thu, 9 May 2019 09:07:01 +0100, Martin Brown
'''newspam'''@nezumi.demon.co.uk> wrote:

On 08/05/2019 17:53, John Larkin wrote:

[snip]

I wonder how that could evolve by random processes.

You start out with a spot that is light sensitive and gradually evolve
under competitive pressure. Every tiny incremental improvement makes
survival of the owner more likely (all other things being equal),
neutral things make no difference and defects tend to get you killed.

People seem to forget that incremental improvements stack up
exponentially so that 100 1% improvements gets you to 270%.

Why would incremental evolution go through a large number of
iterations to produce a "terrible design" human eye? Each step would

It isn't terrible but it is nothing like well designed. It is just about
good enough for the purpose of keeping a hominid omnivore alive.

Not every change is for the better either but the ones that are get to
survive and reproduce combining in different ways with each successive
generation. How hard is that to understand?

Humans have done it to domestic dogs and livestock pretty much since we
stopped being hunter gatherers. Playing god with the traits we
considered most desirable in them and selective breeding. The selection
pressure being what we consider useful/pretty rather than predation.

make it worse, and the final, immensely complex, result would be a
competitive disadvantage.

https://www.ncbi.nlm.nih.gov/books/NBK482309/figure/retinal_degeneration.F18/

Oh wow! A pretty picture taken out of context. How interesting!

Why would a designer equip us with such a botched design having already
got it right in cephalopods? We have a blind spot where the nerve bundle
enters the eye. They do not. Ours is a considerably worse design.

https://en.wikipedia.org/wiki/Cephalopod_eye


It is pretty much the difference between a bog standard cheap and nasty
webcam design and a thinned rear window astronomical CCD camera.

Why would variation and selection result in an extraordinally complex
and optically inferior eye, when squid had a better one already?

Oh, come on John: /think/ before you post! Speculate a little

The answer to that really isn't difficult.

 

[Tom Gardner]

On 09/05/19 16:24, John Larkin wrote:

On Wed, 08 May 2019 21:49:14 -0400, Joseph Gwinn
joegwinn@comcast.net> wrote:

On May 8, 2019, John Larkin wrote
(in article<cto5depv30g3gh1dd4i6vm40e1m5cq5kta@4ax.com&gt:

On Wed, 08 May 2019 09:44:21 -0400, Joseph Gwinn
joegwinn@comcast.net> wrote:

On May 8, 2019, John Larkin wrote
(in article<k9m4de93eokbg9gh91ekedg0vsu06kg34q@4ax.com&gt:


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

This is insane. This is impossible.

Yes, but that is how it works. It took some billions of years for all that
organized complexity to evolve, one trick at a time.

But it couldn't evolve one bit at a time. If it doesn't all work, none
of it works. And it builds every bit of itself.

Sure it can. Very slowly, with lots of mistakes made and then erased. Not an
efficient process at all. But it does not need to be.

But each incremental step must be an improvement or it won't be
selected.

Not quite.

Incremental steps that are worse become deselected.

Not the same thing at all.

DNA is useless without a complex machinery to support and use and copy
it; see the video. But DNA is programmed to build all those support
things. How could that happen? Where did the programming come from?

DNA is not "programmed"; there is no "programmer".

All that counts is the survival of the selfish gene,
and humans (both individually and as a species) are
one of many mechanisms ensuring that survival.

 

[Rick C]

On Thursday, May 9, 2019 at 12:42:26 PM UTC-4, Martin Brown wrote:

On 09/05/2019 15:42, Rick C wrote:
On Thursday, May 9, 2019 at 12:31:11 AM UTC-4, Jasen Betts wrote:
On 2019-05-08, John Larkin <jjlarkin@highland_snip_technology.com> wrote:
On Wed, 8 May 2019 16:54:08 +0100, Martin Brown
'''newspam'''@nezumi.demon.co.uk> wrote:


There is still a lot of hand waving. As in

"it is fruitful to consider the alternative possibility that RNA was
preceded by some other replicating, evolving molecule, just as DNA and
proteins were preceded by RNA."

Its entirely reasonable to try and find the simplest possible canonical
thing that can be said to meet the minimum requirements for "life".

Is that a fact? In modern life, DNA builds RNA.

Reverse transcriptase does the opposite.

but the RNA for that is found in retroviruses so it could be argued that
it's not "life", weasel words that pomoters of that claim may cling
to.

Really? There are people who claim viruses are not life? I don't know what they think viruses are then.

They can only reproduce by hijacking the cellular apparatus of a
suitable host. They sit in the DMZ between life and non-life.

DMZ is your term, not science. Every organism that consumes other organisms has the same sort of requirement on other life forms. The fact that the virus does it from the inside doesn't mean it isn't alive.

Viroids specific to plants are even smaller and still less like life.
They are in essence small loops of RNA that catalyse making copies of
themselves once they find the right host.

https://www.sciencedirect.com/topics/neuroscience/viroids

Shortest are under 500 base pairs and they are infectious agents for the
very specific plant that they target. Transposons are even more curious.

https://www.sciencedirect.com/topics/medicine-and-dentistry/transposon

They are very much a double edged sword.

Virons are not well understood. It's a bit early to say much about their classification. Viruses are much better understood. That's why we say they are life.

--

Rick C.

-++- Get a 1,000 miles of free Supercharging
-++- Tesla referral code - https://ts.la/richard11209

 

[John Larkin]

On Thu, 9 May 2019 19:23:47 +0100, Tom Gardner
<spamjunk@blueyonder.co.uk> wrote:

On 09/05/19 16:24, John Larkin wrote:
On Wed, 08 May 2019 21:49:14 -0400, Joseph Gwinn
joegwinn@comcast.net> wrote:

On May 8, 2019, John Larkin wrote
(in article<cto5depv30g3gh1dd4i6vm40e1m5cq5kta@4ax.com&gt:

On Wed, 08 May 2019 09:44:21 -0400, Joseph Gwinn
joegwinn@comcast.net> wrote:

On May 8, 2019, John Larkin wrote
(in article<k9m4de93eokbg9gh91ekedg0vsu06kg34q@4ax.com&gt:


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

This is insane. This is impossible.

Yes, but that is how it works. It took some billions of years for all that
organized complexity to evolve, one trick at a time.

But it couldn't evolve one bit at a time. If it doesn't all work, none
of it works. And it builds every bit of itself.

Sure it can. Very slowly, with lots of mistakes made and then erased. Not an
efficient process at all. But it does not need to be.

But each incremental step must be an improvement or it won't be
selected.

Not quite.

Incremental steps that are worse become deselected.

Not the same thing at all.

Sounds equivalent to me.

So how did we evolve such bad eyes?

DNA is useless without a complex machinery to support and use and copy
it; see the video. But DNA is programmed to build all those support
things. How could that happen? Where did the programming come from?

DNA is not "programmed"; there is no "programmer".

Of course it's programmed. It systhesizes specific proteins and
structures. And viruses.




--

John Larkin Highland Technology, Inc
picosecond timing precision measurement

jlarkin att highlandtechnology dott com
http://www.highlandtechnology.com

 

[whit3rd]

On Thursday, May 9, 2019 at 11:14:27 AM UTC-7, John Larkin wrote:

On Thu, 9 May 2019 16:28:43 +0100, Martin Brown
'''newspam'''@nezumi.demon.co.uk> wrote:

Why would a designer equip us with such a botched design having already
got it right in cephalopods? We have a blind spot where the nerve bundle
enters the eye. They do not. Ours is a considerably worse design.

Why would variation and selection result in an extraordinally complex
and optically inferior eye, when squid had a better one already?

In the absence of a creator, who would communicate the 'better design'
to the distant outposts of life? Squid only communicate their
design to their offspring.

 

[Rick C]

On Thursday, May 9, 2019 at 1:16:56 PM UTC-4, Martin Brown wrote:

On 09/05/2019 16:04, Rick C wrote:

What four way branch does quantum mechanics provide?

I'm struggling to find an explanation that isn't far too mathematical
but this is the best I have been able to find in a quick search.

https://physics.stackexchange.com/questions/164155/what-is-the-difference-between-a-bit-and-a-qubit

I know there is a better one somewhere that showed how well you could do
with anything up to 4 quantum comparison branches nested but its URL
eludes me. It is more than a decade since I last looked at this stuff.

In a handwaving sort of way a qubit can represent 2 conventional bits at
once. This is a little bit more technical without going overboard:

http://www.thphys.nuim.ie/staff/joost/TQM/QvC.html

This seems to be showing that qubits are the same as bits in this regard.

My concern is simply the rate at which the bases arrive at the
reaction site. In general chemical reactions there are N of one
reactant and M of another reactant bouncing around and periodically
bump into one another in a way that results in the reaction. DNA
replication requires the bases to bump into a relatively few reaction
sites for the enzymes to attach them to the newly forming strand.
Much less likely and so a lower rate.

DNA replicase enzymes work remarkably well.

Doesn't matter that it works "well". What matters is how fast diffusion can supply bases.

--

Rick C.

-+++ Get a 1,000 miles of free Supercharging
-+++ Tesla referral code - https://ts.la/richard11209

 

[whit3rd]

On Thursday, May 9, 2019 at 7:12:53 AM UTC-7, John Larkin wrote:

On Thu, 9 May 2019 01:56:25 -0700 (PDT), whit3rd <whit3rd@gmail.com
wrote:

On Wednesday, May 8, 2019 at 8:09:39 PM UTC-7, John Larkin wrote:

Yup, most gene correlation studies are wrong.

Meaning, what?

Statistically invalid. Cherry picked for publication. Not
reproducible. Faked.

Most statistics are valid, but not necessarily easily understood.

Most publishers ARE picky, but a 'wrong' conclusion cannot be
reached on that basis in any meaningful way. The publishers
that are NOT picky, you just have to notice that they're supported
by advertisements for whoopie-cushions and X-ray glasses.

Whether reproducible or not, it has to be published to guilde a
second study, and that's 'essential', not 'wrong'. It's not smart
to believe the first hints of a new phenomenon, but the early reports
aren't wrong because later ones give a clearer picture, or a more complete one.

Study isn't 'wrong' in any sense, on any subject.

It is if it's faked.

Fakery doesn't qualify as study. At least, those are distinctly different words
in my vocabulary, for completely different things.

 

[Tom Gardner]

On 09/05/19 20:36, John Larkin wrote:

On Thu, 9 May 2019 19:23:47 +0100, Tom Gardner
spamjunk@blueyonder.co.uk> wrote:

On 09/05/19 16:24, John Larkin wrote:
On Wed, 08 May 2019 21:49:14 -0400, Joseph Gwinn
joegwinn@comcast.net> wrote:

On May 8, 2019, John Larkin wrote
(in article<cto5depv30g3gh1dd4i6vm40e1m5cq5kta@4ax.com&gt:

On Wed, 08 May 2019 09:44:21 -0400, Joseph Gwinn
joegwinn@comcast.net> wrote:

On May 8, 2019, John Larkin wrote
(in article<k9m4de93eokbg9gh91ekedg0vsu06kg34q@4ax.com&gt:


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

This is insane. This is impossible.

Yes, but that is how it works. It took some billions of years for all that
organized complexity to evolve, one trick at a time.

But it couldn't evolve one bit at a time. If it doesn't all work, none
of it works. And it builds every bit of itself.

Sure it can. Very slowly, with lots of mistakes made and then erased. Not an
efficient process at all. But it does not need to be.

But each incremental step must be an improvement or it won't be
selected.

Not quite.

Incremental steps that are worse become deselected.

Not the same thing at all.

Sounds equivalent to me.

Really? Wow.

I wonder how you interpret and infer what data
sheets /aren't/ saying.

On second thoughts, it is probably best that you
don't write software.

So how did we evolve such bad eyes?




DNA is useless without a complex machinery to support and use and copy
it; see the video. But DNA is programmed to build all those support
things. How could that happen? Where did the programming come from?

DNA is not "programmed"; there is no "programmer".

Of course it's programmed. It systhesizes specific proteins and
structures. And viruses.

So a grain of sand is programmed to form piles with a
half-angle of 35 degrees?

Or maybe you are using the word "programmed" in a way
that is unfamiliar to me.

 

[Tom Gardner]

On 09/05/19 21:31, whit3rd wrote:

On Thursday, May 9, 2019 at 11:14:27 AM UTC-7, John Larkin wrote:
On Thu, 9 May 2019 16:28:43 +0100, Martin Brown
'''newspam'''@nezumi.demon.co.uk> wrote:

Why would a designer equip us with such a botched design having already
got it right in cephalopods? We have a blind spot where the nerve bundle
enters the eye. They do not. Ours is a considerably worse design.

Why would variation and selection result in an extraordinally complex
and optically inferior eye, when squid had a better one already?

In the absence of a creator, who would communicate the 'better design'
to the distant outposts of life? Squid only communicate their
design to their offspring.

Many of John's points and questions indicate he can't
get past the concept that a creator isn't necessary.

Maybe if he read "The Blind Watchmaker", but I doubt it.

 

[John Larkin]

On Thu, 9 May 2019 21:05:23 +0100, Tom Gardner
<spamjunk@blueyonder.co.uk> wrote:

On 09/05/19 20:36, John Larkin wrote:
On Thu, 9 May 2019 19:23:47 +0100, Tom Gardner
spamjunk@blueyonder.co.uk> wrote:

On 09/05/19 16:24, John Larkin wrote:
On Wed, 08 May 2019 21:49:14 -0400, Joseph Gwinn
joegwinn@comcast.net> wrote:

On May 8, 2019, John Larkin wrote
(in article<cto5depv30g3gh1dd4i6vm40e1m5cq5kta@4ax.com&gt:

On Wed, 08 May 2019 09:44:21 -0400, Joseph Gwinn
joegwinn@comcast.net> wrote:

On May 8, 2019, John Larkin wrote
(in article<k9m4de93eokbg9gh91ekedg0vsu06kg34q@4ax.com&gt:


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

This is insane. This is impossible.

Yes, but that is how it works. It took some billions of years for all that
organized complexity to evolve, one trick at a time.

But it couldn't evolve one bit at a time. If it doesn't all work, none
of it works. And it builds every bit of itself.

Sure it can. Very slowly, with lots of mistakes made and then erased. Not an
efficient process at all. But it does not need to be.

But each incremental step must be an improvement or it won't be
selected.

Not quite.

Incremental steps that are worse become deselected.

Not the same thing at all.

Sounds equivalent to me.

Really? Wow.

I wonder how you interpret and infer what data
sheets /aren't/ saying.

On second thoughts, it is probably best that you
don't write software.

I've maybe done a few hundred K lines of code by now. Lots of realtime
systems, instruments, two compilers, three pre-emptive RTOSs.

I wrote one RTOS while staying with a girlfriend in Juneau. I wrote a
few pages on paper each day and mailed them back to the factory.
People there typed it and assembled it. It had one bug.

I don't program a lot these days; coding is boring. The kids here do a
lot of c and Python and VHDL and I mostly do product ideas and
architectures and hardware design.

This is SED. Electronic design.

So how did we evolve such bad eyes?




DNA is useless without a complex machinery to support and use and copy
it; see the video. But DNA is programmed to build all those support
things. How could that happen? Where did the programming come from?

DNA is not "programmed"; there is no "programmer".

Of course it's programmed. It systhesizes specific proteins and
structures. And viruses.

So a grain of sand is programmed to form piles with a
half-angle of 35 degrees?

Or maybe you are using the word "programmed" in a way
that is unfamiliar to me.

DNA has long sequences of base pairs that direct the synthesis of
complex molecules, and physical structures in people, and then more
DNA itself. I consider those sets of instructions to be programs, with
instruction sets, that are executed by cellular machinery. I don't
know who the authors are, but people are now learning how to edit
those programs.

The program instructions specify the construction of the machines that
execute the programs. That's life, I guess. [1]

I kind of hope that someone left copyright notices.

I guess you object to calling these sequences of base pair
instructions "programs" because you are afraid that might sound like
creationism. I suspect that fear of the c-word prevents all sorts of
things from being discovered. Actually, that effect has been
documented.

[1] Steve Jobs once claimed that he used a Cray computer to design one
of the Apple machines. Seymour Cray replied that he used an Apple
computer to design his Cray machines.


--

John Larkin Highland Technology, Inc
picosecond timing precision measurement

jlarkin att highlandtechnology dott com
http://www.highlandtechnology.com

 

[Martin Brown]

On 09/05/2019 16:24, John Larkin wrote:

On Wed, 08 May 2019 21:49:14 -0400, Joseph Gwinn
joegwinn@comcast.net> wrote:

On May 8, 2019, John Larkin wrote
(in article<cto5depv30g3gh1dd4i6vm40e1m5cq5kta@4ax.com&gt:

On Wed, 08 May 2019 09:44:21 -0400, Joseph Gwinn
joegwinn@comcast.net> wrote:

On May 8, 2019, John Larkin wrote
(in article<k9m4de93eokbg9gh91ekedg0vsu06kg34q@4ax.com&gt:


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

This is insane. This is impossible.

Yes, but that is how it works. It took some billions of years for all that
organized complexity to evolve, one trick at a time.

But it couldn't evolve one bit at a time. If it doesn't all work, none
of it works. And it builds every bit of itself.

Sure it can. Very slowly, with lots of mistakes made and then erased. Not an
efficient process at all. But it does not need to be.

But each incremental step must be an improvement or it won't be
selected. So how can evolution build an immensely complex system,
where all the pieces have to be working before any of it it can work
(and reproduce itself) ?

No. It doesn't. You are putting arbitrary constraints on what evolution
can and cannot do. Evolution has explored many weird dead ends as well.
It basically spans the space of life forms and if there is a niche with
no competition eventually something will evolve to exploit it.

A change that is beneficial, neutral or only slightly detrimental to
individual survival can persist. Sickle cell anaemia is one such example
- not optimum for the individual but it confers some immunity to deadly
malaria not found in those of us with more normal blood cells.

https://www.newscientist.com/article/dn20450-how-sickle-cell-carriers-fend-off-malaria/

The requirement for a novel trait to establish in the population is for
the first person with that novel feature to survive and reproduce (and
for their offspring to be fertile).

DNA is useless without a complex machinery to support and use and copy
it; see the video. But DNA is programmed to build all those support
things. How could that happen? Where did the programming come from?

It must have all been done in SuperBasic ;-)

--
Regards,
Martin Brown