DNA animation

[Piotr Wyderski]

bloggs.fredbloggs.fred@gmail.com wrote:

> Only an unimaginative fool would believe living organisms evolved at random.

No organism ever evolve, what evolves is just the recipe for the next
one. In most cases a minor failure, rarely a fatal one, very rarely a
successful mutation.

Best regards, Piotr

 

[Rick C]

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."

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.

--

Rick C.

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

 

[John Larkin]

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.

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.

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.

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.


--

John Larkin Highland Technology, Inc

lunatic fringe electronics

 

[John Larkin]

On Thu, 9 May 2019 14:09:42 +0100, Mike Coon <gravity@mjcoon.plus.com>
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...".

Mike.

Rocket engines must burn wood pellets or something.

The Sprint missile went from launch to 7500 MPH in five seconds, but
that was solid fuel.


--

John Larkin Highland Technology, Inc

lunatic fringe electronics

 

[John Larkin]

On Thu, 9 May 2019 11:42:12 +0100, Martin Brown
<'''newspam'''@nezumi.demon.co.uk> wrote:

On 08/05/2019 21:10, John Larkin wrote:
On Wed, 8 May 2019 15:55:18 -0400, "Tom Del Rosso"
fizzbintuesday@that-google-mail-domain.com> wrote:

John Larkin wrote:
On Wed, 8 May 2019 13:03:36 -0500, "Tim Williams"
tiwill@seventransistorlabs.com> wrote:

"Tom Del Rosso" <fizzbintuesday@that-google-mail-domain.com> wrote in
message news:qav3jo$v1g$1@dont-email.me...
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.


Indeed, and not just complex, but _more_ complex.

And what if -- it's designers all the way down? Well, it
*certainly* can't be that. Any sufficiently advanced being would
contain so much information it would collapse into a black hole! To
assume that such a "god" exists, contradicts the laws of
physics-as-we-know-them.

They can be conveniently placed outside the universe as we know it.

Well, duh, anything that you don't know now is "outside the universe
as we know it." Your opportunities for discovery, or amazement, are
small.

"Light inaccessible hid from our eyes" is a bit tricky in the
electromagnetic spectrum now that we have sensors for just about
everything from ultra low frequencies to hard gamma rays.

There are lots of reasonable paths to building our biology other than
random mutation and selection, but too many people refuse to even
think about them, but prefer to use their limited imaginations to
manufacture insults.

Well I didn't intend to insult you, and it isn't apparent that you are a
creationist. I interpreted the original post as amazement rather than
skepticism.

I'm not a bit religious and I don't know exactly what your definition
of "creationist" is.

Someone who refuses to accept that evolution driven by natural selection
is quite capable of generating the diversity of life we see around us.

I suppose it's fundamental that people who never have ideas are
usually hostile to ideas.


--

John Larkin Highland Technology, Inc

lunatic fringe electronics

 

[John Larkin]

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.

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

It is if it's faked.


--

John Larkin Highland Technology, Inc

lunatic fringe electronics

 

[Rick C]

On Thursday, May 9, 2019 at 3:15:06 AM UTC-4, whit3rd wrote:

On Wednesday, May 8, 2019 at 8:26:21 AM UTC-7, John Larkin wrote:

The great mysteries are the origin of the universe, the origin of
life, and consciousness. So far we are clueless about all three.

Huh?
Every object IN the universe, and their dispositions as we can see them,
are clues.

Life is well enough understood to custom-build some...
https://www.technologyreview.com/s/419359/how-to-make-an-artificial-cell/

Consciousness is possible to mimic with mechanisms, because
we've collected enough clues for that one, too.

If you don't see clues, see your eye doctor.

So that's your argument... if you can't see the validity of my claim, you must be blind? Way to go. No evidence required!

--

Rick C.

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

 

[Martin Brown]

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.

LOX on cotton wool was another favourite explosive demo.

--
Regards,
Martin Brown

 

[Martin Brown]

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.

Our eye is just about good enough to keep us from getting killed by
things that can see better - nothing special in terms of resolution with
raptors 3-5x better or sensitivity with night predators 2-3x better.

--
Regards,
Martin Brown

 

[John Larkin]

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) ?

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?


--

John Larkin Highland Technology, Inc

lunatic fringe electronics

 

[Rick C]

On Thursday, May 9, 2019 at 5:26:39 AM UTC-4, Tim Williams 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.

I thought it was an FPGA, but that seemed a bit odd for the resulting circuit features.

The result was very fragile too, AFAIK.

Fragility seems very normal with evolutionary systems, including with neural
networks, and life itself.

Consider how many stupid edge-cases there are in terms of environment (oh,
you got slightly too hot and died), chemistry (oh, you ate the wrong thing
and died), adversarial evolution (oh, you contracted the wrong virus and
died), even just stimuli (oh, you watched the wrong video and it triggered
PTSD symptoms).

The Fever Monument - Poem by Richard Brautigan

I walked across the park to the fever monument.
It was in the center of a glass square surrounded
by red flowers and fountains. The monument
was in the shape of a sea horse and the plaque read
We got hot and died.

--

Rick C.

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

 

[Bill Sloman]

On Friday, May 10, 2019 at 12:42:11 AM UTC+10, John Larkin wrote:

On Thu, 9 May 2019 10:01:22 +0100, Martin Brown
'''newspam'''@nezumi.demon.co.uk> wrote:

On 08/05/2019 20:58, Tom Del Rosso wrote:
John Larkin wrote:
"Junk DNA" was dogma for decades. A lot of the stuff between the
obvious genes turns out to have functions.

Some junk DNA is recognisable as stuff that retroviruses have inserted.
So long as it doesn't cause harm it replicates along with the good stuff.

It sounds like hypothesis rather than dogma, but it seems clear that if
there is junk it would replicate.

And it does tend to accumulate in the nucleus.

A human genome has about 30 billion base pairs. *BUT*

The largest known plant genome as of 2010 is Paris Japonica which so
shocked the researchers that they had to double check its sequencing.
150 bn base pairs 50x that of a human and for a plant that is fragile
slow and difficult to grow. There might even be a bigger one by now.

150e9/30e9 = 5

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

150e9/3e9 = 50

The human genome contains three billion base pairs, not thirty billion.

--
Bill Sloman, Sydney

 

[Bill Sloman]

On Friday, May 10, 2019 at 12:37:09 AM UTC+10, 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:
On Wed, 8 May 2019 17:35:25 +0100, Tom Gardner
spamjunk@blueyonder.co.uk> wrote:

On 08/05/19 15:31, Bill Sloman wrote:
On Thursday, May 9, 2019 at 12:11:14 AM UTC+10, John Larkin wrote:
On Wed, 8 May 2019 01:04:50 -0500, "Tim Williams"
tiwill@seventransistorlabs.com> wrote:

Hardly. There's a lot of room at the bottom. A phrase still as true
today as it was half a century ago!

What's insane is people still think this stuff was created in the snap
of some magic finger.

Tim

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.

Plus give us humans clearly "suboptimal" designs when
there are better designs available, e.g. the "wiring"
between our retina and our brains.

I read one book that suggests that our retinas aren't designed wrong.
The light has to make its way through a maze of nerves and blood
vessels to hit the sensitive stuff on the back of the retina, which
sounds bad, but the light is conveyed through the maze on fiber
optics.

Our eyes are a terrible design compared to either top preditors or deep
sea cephalopods. They are just good enough for a hominid omnivore. We
have the advantageous feature of colour vision for seeing ripe fruit. A
few people have various forms of colour blindness and much rarer are
people who can distinguish living and dead plant pigments by eye.

Raptor livers are another complete disaster area. Somewhat dodgy
compromises for being able to fly fast and take severe impact stresses.

If a God designed them then he was having an off day when he did so.

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
make it worse,

Why would you think that? At every stage, the eye has to be better than the ones the competitors are using, otherwise it's the competitors - and their eyes - who survive to represent the next step in the process

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

John Larkin claims to believe in evolution, but obviously doesn't understand how it works.

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

Retinal degeneration is problem that shows up at ages when childbearing and child raising is long past. Darwinian evolution doesn't have a lot of leverage then.

--
Bill Sloman, Sydney

 

[Rick C]

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.

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?

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.

--

Rick C.

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

 

[Bill Sloman]

On Friday, May 10, 2019 at 12:28:39 AM UTC+10, 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.

Once you've got a string of atoms that can reproduce itself with variation, you've got something that can exploit Darwinian evolution.

That puts the origin right back at random noise in a chemically active system.

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

There are lots of other closely related chemicals that aren't "living". It's clear enough where DNA came from.

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.

Now. In today's world a seething mass of incipient life becomes some living cell's lunch before it can evolve into anything.

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.

Actually, a whole lot worse, because you don't know what you are talking about.

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.

But we'll probably work out some much more plausible and detailed hypotheses that the twaddle you peddle.

--
Bill Sloman, Sydney

 

[Bill Sloman]

On Friday, May 10, 2019 at 12:12:53 AM UTC+10, 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.

Not exactly. If people are doing enough experiments, 5% of them are going to look significant the 5% level. The people doing the experiment and reporting it are reporting what they saw. The 95% of them who didn't get a significant effect don't publish, so the few who got lucky don't - initially - realise that they'd got lucky.

After a while people get to discuss why their experiments didn't work and other peoples did, and you start seeing meta-analyses, but it takes a while.

They weren't aware that they were cherry-picking, and didn't have to fake anything to fall into the trap.

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

It is if it's faked.

They can be wrong without being faked. "Misleading" is a less loaded piece of invective.

In fact John Larkin was commenting on a the link

https://slatestarcodex.com/2019/05/07/5-httlpr-a-pointed-review/

which was confined to gene correlation studies in psychiatry.

Gene correlation studies in other branches of medicine can get by with smaller samples, because often the number of genes involved is small, or the effect dramatic.

https://en.wikipedia.org/wiki/FOXP2

Is a gene correlation study that wasn't wrong. The single gene involved is rarely defective, but when it is the people carrying the defective have lots of problems with fine motor control, and can't do speech well.

Most genes of psychiatric interest have very small effects, and there seem to be a lot of them, so you need large populations to look at, and it helps if each participant in the study has had their genome completely sequenced (which only has to be done once to capture all the genes that the investigators might want to look at).

There haven't been a lot of studies like that done yet but Robert Plomin's "Blueprint" picks up a few.

https://www.theguardian.com/books/2018/oct/24/blueprint-by-robert-plomin-review

--
Bill Sloman, Sydney

 

[Bill Sloman]

On Friday, May 10, 2019 at 12:12:53 AM UTC+10, 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.

Not exactly. If people are doing enough experiments, 5% of them are going to look significant the 5% level. The people doing the experiment and reporting it are reporting what they saw. The 95% of them who didn't get a significant effect don't publish, so the few who got lucky don't - initially - realise that they'd got lucky.

After a while people get to discuss why their experiments didn't work and other peoples did, and you start seeing meta-analyses, but it takes a while.

They weren't aware that they were cherry-picking, and didn't have to fake anything to fall into the trap.

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

It is if it's faked.

They can be wrong without being faked. "Misleading" is a less loaded piece of invective.

In fact John Larkin was commenting on a the link

https://slatestarcodex.com/2019/05/07/5-httlpr-a-pointed-review/

which was confined to gene correlation studies in psychiatry.

Gene correlation studies in other branches of medicine can get by with smaller samples, because often the number of genes involved is small, or the effect dramatic.

https://en.wikipedia.org/wiki/FOXP2

Is a gene correlation study that wasn't wrong. The single gene involved is rarely defective, but when it is the people carrying the defective have lots of problems with fine motor control, and can't do speech well.

Most genes of psychiatric interest have very small effects, and there seem to be a lot of them, so you need large populations to look at, and it helps if each participant in the study has had their genome completely sequenced (which only has to be done once to capture all the genes that the investigators might want to look at).

There haven't been a lot of studies like that done yet but Robert Plomin's "Blueprint" picks up a few.

https://www.theguardian.com/books/2018/oct/24/blueprint-by-robert-plomin-review

--
Bill Sloman, Sydney

 

[Rick C]

On Thursday, May 9, 2019 at 11:47:41 AM UTC-4, John Larkin wrote:

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.

Of course they do. The predefined goal is survival. It's always about survival.

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.

Yep, much like evolution in nature.

--

Rick C.

-+-+ Get a 1,000 miles of free Supercharging
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[Rick C]

On Thursday, May 9, 2019 at 11:24:32 AM UTC-4, 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) ?

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?

How can you not understand this? Every detail of DNA replication is not required for it to work. Or earlier versions of enzymes might have done the job, but not as well. I don't have any specifics, but I recall reading about enzyme evolution that has improved disease resistance among populations. Small changes provide small improvements. Are you one of those people who think the human eye could not have developed through evolution? If you look around you can see the various stages of development in other species. I seem to recall Planaria have "eye spots" which are just photosensitive tissue without other features except for having two of them on opposite sides of their center line and so slanted slightly apart.

It's not hard to imagine how the eye developed in thousands or even millions of tiny steps. the green and blue receptors are thought to be an evolutionary result from a number of very small changes in the genes.

https://en.wikipedia.org/wiki/Evolution_of_human_colour_vision#Evolution_of_Cone_Opsins_and_Human_Colour_Vision

--

Rick C.

-+-- Get a 1,000 miles of free Supercharging
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[Tim Williams]

"John Larkin" <jjlarkin@highlandtechnology.com> wrote in message
news:kbd8detp8up7ba1tf1upvjclhlbds4gjjg@4ax.com...

Someone who refuses to accept that evolution driven by natural selection
is quite capable of generating the diversity of life we see around us.

I suppose it's fundamental that people who never have ideas are
usually hostile to ideas.

The term you're looking for is "self-awarewolves".

Tim

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