# Stuff and Things > HISTORY, veterans & science >  Darwin and the Titanic

## UKSmartypants

When the Titanic sunk, its dragged down to the bottom of the sea, to 3800 metres depth, and whole gamut of bacteria to what was an other wise sterile envirnoment.


Years later , after the Titanic wreck had been located, it was observed to  be developing icicle like structures but made of rust, called 'rusticles'.  The rusticle are slowly dissolving the ship.


It would seem the rusticle are not a chemical process but a biological one. One of the bacteria that was dragged down into this new, sterile environment has evolved to consume the steel of the ship as a method of generating energy. This bacteria is unique to the Titanic, and called Halomonas titanicae.  There was no bacteria on the sea floor.  Halomonas titanicae, which has 27 different strains, must have evolved from a surface bacteria in response to being plunged into a new ecological niche, an environment with zero light, zero oxygen and 2.5 tonnes PSI water pressure

Its a perfect demonstration of Natural Selection and Darwinian Evolution.

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Conservative Libertarian (12-04-2021),dinosaur (12-04-2021),Foghorn (12-04-2021),LadyMoonlight (12-04-2021),MisterVeritis (12-04-2021),Neo (12-05-2021),nonsqtr (12-05-2021),Quark (12-04-2021)

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## Authentic

Natural selection, but not Evolution.

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Conservative Libertarian (12-04-2021),Freewill (12-04-2021),Physics Hunter (12-05-2021)

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## UKSmartypants

> Natural selection, but not Evolution.



Its Evolution. it's a new species of bacteria from a previous species that adapted and evolved.


Natural selection selects out the weakest members of a species.
Evolution takes a species and turns it into  a new species better adapted to exploit  a new ecological niche.

Natural selection is a continuous process, Evolution  is prompted by the appearance of new ecological niches.

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LadyMoonlight (12-04-2021),MisterVeritis (12-04-2021),Neo (12-05-2021),Quark (12-04-2021)

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## Authentic

> Its Evolution. it's a new species of bacteria from a previous species that adapted and evolved.
> 
> 
> Natural selection selects out the weakest members of a species.
> Evolution takes a species and turns it into  a new species better adapted to exploit  a new ecological niche.
> 
> Natural selection is a continuous process, Evolution  is prompted by the appearance of new ecological niches.


It's still bacteria. Richard Lenski has tried to prove that new species could be made from E Coli bacteria He did get mutations, but at the end of the day they are still E Coli.

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Freewill (12-04-2021)

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## Foghorn

Nature will find a way.



f1739488c2bc009a93329a209237910e.jpg

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Conservative Libertarian (12-04-2021),Quark (12-04-2021)

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## UKSmartypants

> It's still bacteria. Richard Lenski has tried to prove that new species could be made from E Coli bacteria He did get mutations, but at the end of the day they are still E Coli.



Ofc its a bacterium, what was you expecting to get, a new species of hominid? Its a new species of bacteria, thats evolution. Its not the same species altered to do something different, its a complete  new species that exists nowhere on earth and wasnt there before.  It has therefore evolved, which is the step beyond Natural Selection. A species that undergoes natural selection remains the same species, just better adapted for the existing niche. What we have here is new niche, and demonstrably new species - nothing existed there before.

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MisterVeritis (12-04-2021),Neo (12-05-2021),Quark (12-04-2021)

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## Authentic

> Ofc its a bacterium, what was you expecting to get, a new species of hominid? Its a new species of bacteria, thats evolution. Its not the same species altered to do something different, its a complete  new species that exists nowhere on earth and wasnt there before.  It has therefore evolved, which is the step beyond Natural Selection. A species that undergoes natural selection remains the same species, just better adapted for the existing niche. What we have here is new niche, and demonstrably new species - nothing existed there before.


Cool. So we have micro-evolution, not macro-evolution.

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## Frankenvoter

> Ofc its a bacterium, what was you expecting to get, a new species of hominid? Its a new species of bacteria, thats evolution. Its not the same species altered to do something different, its a complete  new species that exists nowhere on earth and wasnt there before.  It has therefore evolved, which is the step beyond Natural Selection. A species that undergoes natural selection remains the same species, just better adapted for the existing niche. What we have here is new niche, and demonstrably new species - nothing existed there before.


I'm curious, was there any "we think" or "it's likely" or "would appear to be" or other "not so sure" statements in their term paper regarding thier "finding"? 

If there was a single one, then they're admitting they're "not 100% sure about".

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Captain Kirk! (12-09-2021)

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## dinosaur

:Thinking:  So ... Have really smart scientists brought this bacteria back up to the surface, and studied the effects?  Does it revert to its original form, a completely new and different form, or just up and die?

Do the scientists have any theories on the original bacterium that evolved into this new specie?  If not, how do they know it evolved from some organism from the ship, and not the sea floor, that acquired a new environment in the form of a steel ship?

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## UKSmartypants

> So ... Have really smart scientists brought this bacteria back up to the surface, and studied the effects?  Does it revert to its original form, a completely new and different form, or just up and die?
> 
> Do the scientists have any theories on the original bacterium that evolved into this new specie?  If not, how do they know it evolved from some organism from the ship, and not the sea floor, that acquired a new environment in the form of a steel ship?



1.  It must have evolved as a separate species from some other member of _Halomonas_, some of which are found in saline river estuaries .


2. yes, it was identified from samples brought up from the Titanic. The sea floor at the location is sterile, as is a lot of the deep ocean, due to the lack of oxygen, light and anything to eat.


3.  A bacteriologist called Henrietta Mann is now the worlds foremost living expert on the bacteria.....


https://www.bbc.com/news/science-environment-11926932

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dinosaur (12-05-2021),Neo (12-05-2021)

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## nonsqtr

> Cool. So we have micro-evolution, not macro-evolution.


lol

There's no difference.

Let me state bluntly: you're not qualified to make any statements about biological evolution until you understand the basics of embryology.

Life is biophysics. Period. 

For instance - it's not enough to know that a cell membrane is a phospholipid bilayer. One must also be aware that the phosphates are negatively charged, and therefore water molecules in the vicinity (which are electrically polarized) will align themselves with the + side towards the - of the phosphate, thereby forming a large "cloud" of negative charge around the outside of each phosphate. So, ions, like sodium and calcium which are positively charged, will be attracted to these negative clouds. Which is why, around the outside of most cells, you'll find an accumulation of ions, they tend to "stick to" the cell membrane.

Why does this matter?

Because we're talking about a single celled organism in salt water.

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Neo (12-05-2021)

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## Authentic

> lol
> 
> There's no difference.
> 
> Let me state bluntly: you're not qualified to make any statements about biological evolution until you understand the basics of embryology.
> 
> Life is biophysics. Period. 
> 
> For instance - it's not enough to know that a cell membrane is a phospholipid bilayer. One must also be aware that the phosphates are negatively charged, and therefore water molecules in the vicinity (which are electrically polarized) will align themselves with the + side towards the - of the phosphate, thereby forming a large "cloud" of negative charge around the outside of each phosphate. So, ions, like sodium and calcium which are positively charged, will be attracted to these negative clouds. Which is why, around the outside of most cells, you'll find an accumulation of ions, they tend to "stick to" the cell membrane.
> ...


I understand ions.

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## Authentic

What is life? Is it the physical aspect of a living cell?

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## Authentic

Is it possible for order to arise from disorder?

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## Authentic

> I understand ions.


And icons, like the Catholics use.

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## nonsqtr

> Is it possible for order to arise from disorder?


Of course.

It happens all the time.

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MisterVeritis (12-05-2021)

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## nonsqtr

> I understand ions.


Do you understand species?

Smarty is quite correct, species are defined by the niche.

But to understand how a species comes to be, one must understand embryology. The very first cell of a new organism, immediately after fertilization, already knows which end is the head and which end is the tail. This is accomplished with chemical gradients inside the cell. One must understand where the gradients come from.

Disruption of these gradients, by ANYTHING, will do one of three things, in decreasing order of likelihood: either kill the organism, which is most likely - or create a monster (a three headed frog, or something) - or create a new species. It's not the ONLY way to create a new species, there are others.

Chakrabarty created the first synthetic species in 1976 (or was it 1972? I forget).

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## Physics Hunter

Source: BBC.  If they reported any other result it would be more shocking than (the space type, not the invader type) aliens landing in the yard.

Assertions are not proof.

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## UKSmartypants

> Source: BBC.  If they reported any other result it would be more shocking than (the space type, not the invader type) aliens landing in the yard.
> 
> Assertions are not proof.



Oh theres other sources, i can find the original peer reviewed paper, but since your the only one making a fuss I cant be arsed. Everyone else gets it.


*edit*

Oh go on then, ill take pity on you.....

The most closely related type strains were Halomonas neptunia (98.6 % 16S rRNA sequence similarity), Halomonas variabilis (98.4 %), Halomonas boliviensis (98.3 %) and Halomonas sulfidaeris (97.5 %).

So it probably mutated from _neptunia_


_Overall, our results show clearly that strain BH1T is phylogenetically related to other species of the genus Halomonas; however, there are important differences in its phenotypic and chemotaxonomic features and the DNA–DNA hybridization studies confirmed its distinct species status_


Halomonas titanicae sp. nov., a halophilic bacterium isolated from the RMS Titanic | Microbiology Society

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Neo (12-05-2021)

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## Physics Hunter

> Oh theres other sources, i can find the original peer reviewed paper, but since your the only one making a fuss I cant be arsed. Everyone else gets it.
> 
> 
> *edit*
> 
> Oh go on then, ill take pity on you.....
> 
> The most closely related type strains were Halomonas neptunia (98.6 % 16S rRNA sequence similarity), Halomonas variabilis (98.4 %), Halomonas boliviensis (98.3 %) and Halomonas sulfidaeris (97.5 %).
> 
> ...


Our?

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## Physics Hunter

> Is it possible for order to arise from disorder?



OH KNOW YOU DIDN'T!   :Smiley ROFLMAO:

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## Physics Hunter

> lol
> 
> There's no difference.
> 
> Let me state bluntly: *you're not qualified to make any statements about biological evolution until you understand the basics of embryology.*
> 
> Life is biophysics. Period. 
> 
> For instance - it's not enough to know that a cell membrane is a phospholipid bilayer. One must also be aware that the phosphates are negatively charged, and therefore water molecules in the vicinity (which are electrically polarized) will align themselves with the + side towards the - of the phosphate, thereby forming a large "cloud" of negative charge around the outside of each phosphate. So, ions, like sodium and calcium which are positively charged, will be attracted to these negative clouds. Which is why, around the outside of most cells, you'll find an accumulation of ions, they tend to "stick to" the cell membrane.
> ...


Step backwards for a moment and reread your post.  You are using the same BS arguments that the AGW crowd and Fauchi backers use?

Do you really want to live there?

Really?

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## nonsqtr

> Step backwards for a moment and reread your post.  You are using the same BS arguments that the AGW crowd and Fauchi backers use?
> 
> Do you really want to live there?
> 
> Really?


I stand by my statement.

Anyone can be an armchair scientist, but if you try that with evolution, a) you'll have no idea what you''re reading, and b) you can pretend to understand but you won't.

Evolution is THE most sophisticated topic in biology. If you haven't studied embryology, you don't qualify - and not only that, you'll probably make stupid nonsensical statements about stuff being "impossible" and the like.

You need to understand morphogenesis, if you want to be a credible participant in a discussion about evolution.

I really really DON'T want to hear any more of the macroscopic-microscopic bullshit. It represents profound ignorance - which would be ALLEVIATED if you'd crack an embryology book instead of the NYT and start doing a little independent study.

STUDY morphogenesis. Then come back and talk to me. Otherwise it's the same old tired bullshit in these threads. Anyone who does NOT understand keeps saying stuff is impossible and there some kinda magic difference between the small and the large.

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## Authentic

Biology is a soft science.

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## nonsqtr

> Biology is a soft science.


Yeah. It's wet too.

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## Authentic

> Yeah. It's wet too.


Primordial soup.

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## Authentic

Learning evolutionary embryology is a von Baer of a task.

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## Authentic

Why do human arms resemble Chinese batwing soup?

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## nonsqtr

> Why do human arms resemble Chinese batwing soup?


Study character rigging for animation.

You'll have all the answers.

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Authentic (12-05-2021)

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## nonsqtr

> Primordial soup.


There's nothing primordial about it.

Cell membranes are composed mainly of phospholipids, which are polarized. The phosphate part is charged and likes water, the lipid part is fatty/oily and doesn't like water.

Phosphate is paramagnetic, like water. There is phosphate MRI, except instead of taking pictures of the water in your body it takes picture of the cell membranes.

When ATP (the cell's energy currency) is spent it's converted to cAMP or some other form of monophosphate, and a pyrophosphate. The cell tightly regulates phosphate concentrations.

Phosphatidic acid actually curves the cell membrane, physically. It is important for membrane fusion and endocytosis.

Pyrophosphate, can tunnel with it's neighbors, at the quantum level. Pyrophosphates are hydrolyzed enzymatically to create two molecules of phosphate, and when that happens, the nuclear spins are entangled in a singlet state. That means, a measurement in one will dictate the results of a measurement on the other. The entanglement does NOT depend on distance, it is long range and non-local. It is exactly equivalent to Einstein's "spooky action at a distance".

Neurons and leukocytes make use of the entanglement for signalling. For example, when phosphatidic acid binds to a membrane it can be immediately destroyed and a signal sent to neighboring molecules that says, "okay, I'm bound".

The SAME phenomenon occurs with DNA, where there is tunneling among neighboring nucleotides.

Quantum tunneling is related to membrane curvature in the single cell. Obviously, small vesicles are more curved than either the cell membrane or the nuclear membrane. The cell has to compartmentalize the phosphate concentrations for proper operation.

So here you have a perfect model system, with which to study morphogenesis as it relates to evolution. Membrane curvature is "shape", and when there's a new tree branch or a new budding limb that's shape too.

Mandelbrot showed that growing trees obey a fractal growth equation. Ask yourself, based on what I just told you, "how does this happen".

A single mutation in plant DNA can result in a change from a large 3-blafed leaf structure to a small dense branching pattern like a fern.

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## nonsqtr

Electron tunneling is vital for photosynthesis and respiration.

You can actually SEE electron tunneling now, with QBET spectroscopy.

This is important because cell membranes organize extracellular ions (like, the sodium in seawater).

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## Physics Hunter

> I stand by my statement.
> 
> Anyone can be an armchair scientist, but if you try that with evolution, a) you'll have no idea what you''re reading, and b) you can pretend to understand but you won't.
> 
> Evolution is THE most sophisticated topic in biology. If you haven't studied embryology, you don't qualify - and not only that, you'll probably make stupid nonsensical statements about stuff being "impossible" and the like.
> 
> You need to understand morphogenesis, if you want to be a credible participant in a discussion about evolution.
> 
> I really really DON'T want to hear any more of the macroscopic-microscopic bullshit. It represents profound ignorance - which would be ALLEVIATED if you'd crack an embryology book instead of the NYT and start doing a little independent study.
> ...


Not stopping.  My instinct (and my personal spreadsheet on this topic) says that Lucy (pig tooth) turning into me in 2M years just ain't possible, on the basis of probability.

And I don't apologize, it's not a cellular scale topic.

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## nonsqtr

> Not stopping.  My instinct (and my personal spreadsheet on this topic) says that Lucy (pig tooth) turning into me in 2M years just ain't possible, on the basis of probability.
> 
> And I don't apologize, it's not a cellular scale topic.


Yes, it is. You should learn some math

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## Authentic

> Yes, it is. You should learn some math


You're telling a physics guy to learn math?

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## nonsqtr

> You're telling a physics guy to learn math?


No, I'm telling YOU!  :Grin: 

Go do what I said - study embryology.

You don't even know what math MEANS until you know what you're describing.

If I had a nickel for every fool that said things were impossible I'd be filthy rich.

Biochemical evolution is not equivalent to chemical bonds forming randomly in water.

A SINGLE MUTATION can result in a brand new species. One, that's all that's required.

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## nonsqtr

> Not stopping.  My instinct (and my personal spreadsheet on this topic) says that Lucy (pig tooth) turning into me in 2M years just ain't possible, on the basis of probability.
> 
> And I don't apologize, it's not a cellular scale topic.


See, this is exactly what we get from you clowns.

When you think about the distance from Lucy to you, you think of thousands upon thousands of mutations, basically one per trait 

And that is NOT what happens! Such a thought process is completely unrealistic and ignorant.

You have to understand how the system works first, before you can tell me something is possible or impossible.

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## nonsqtr

Here, start here:

Complete genome sequence of Halomonas sp. R5-57

The task is to understand HOW these 4670 genes form a complete organism.

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## Authentic

> Here, start here:
> 
> Complete genome sequence of Halomonas sp. R5-57
> 
> The task is to understand HOW these 4670 genes form a complete organism.


Do I need to apply LaPlace transforms?

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## nonsqtr

> Do I need to apply LaPlace transforms?


No. You need to count.




> A pairwise comparison using the nucleotide sequences of these two genomes and visualization in ACT [26] identified eight regions which differ between the two genomes: two of these appear to be translocations and correspond to parts of the Halomonas sp. R5-57 which are not found in H. elongata, H. campaniensis, or H. boliviensis, five others are insertions which are unique to Halomonas sp. R5-57 and one is an insertion in Halomonassp. TG39a Fig. 3b.


Here you have a species difference consisting of 8 mutations.

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## Authentic

Learning about lysogeny broth now.

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## Authentic

Cool. I got the salt and yeast. How do I get hold of tryptone?

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## nonsqtr

> Learning about lysogeny broth now.


This the nature of things today:




> complete genome sequencing and the de novo assembly were carried out using Illumina sequencing and SPAdes genome assembler (ver 3.11.1)


Genome analysis of a halophilic bacterium Halomonas malpeensis YU-PRIM-29T reveals its exopolysaccharide and pigment producing capabilities | Scientific Reports

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## nonsqtr

> Cool. I got the salt and yeast. How do I get hold of tryptone?


If mutations are so rare, then how come there are at least SEVEN types of DNA repair mechanisms?

There are a trillion cells in the human body. If the chances of a mutation are one in a million over a lifetime, that means every individual gets a million mutations.

One million mutations, per person, per lifetime.

Most of them are dumb little things like skin taps, you pick em off and they're gone. Some of them are cancers. Many are deadly, but some mutations are actually desirable.

Our bodies KEEP TRACK of how many mutations there are and where they are. Cells signal each other when they're undergoing repair. Cells will even commit suicide if mutations can't be fixed.

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## nonsqtr

Halomonas as a chassis | Essays in Biochemistry | Portland Press

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## nonsqtr

> Not stopping.  My instinct (and my personal spreadsheet on this topic) says that Lucy (pig tooth) turning into me in 2M years just ain't possible, on the basis of probability.
> 
> And I don't apologize, it's not a cellular scale topic.


Your instinct is not science.

This is why we do experiments, so we don't have to rely on instinct.

I'm sorry, but if you refuse to stop with the garbage assertions then I will mercilessly beat you back.

There is no place for personal belief in science. Science is BY DEFINITION a social activity. My opinions matter exactly as much as yours: ZERO.

The evolutionary landscape IS cellular biophysics, and nothing else. DNA expression and replication is accomplished by enzymes, and enzymes make mistakes. Therefore cells have excision repair, mismatch repair, homologous and non-homologous end joining... direct chemical reversal, crosslink repair... there must be a few more I've forgotten about.

With 1 million mutations, everyone should die of cancer. But we don't. We repair ourselves, and keep going.

Of the 4 trillion cells in the body, only a few thousand are germ cells. Mutations anywhere else don't really matter, they only affect the individual. If one of those 1 million mutations happens to be in a germ cell though, it'll get passed on.

EVERY gene has multiple functions at multiple times. In Halomonas, there are 4.8 million base pairs and a few thousand genes. 13 of them are for cross-membrane transport of ions, with and without an exchange. See if you can find out how many of them DON'T have an identified purpose (the answer is: not many).

Halomonas Salt Lake #7 is a well studied variant, and a precedent for sustainable mutation in salt water.

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## Physics Hunter

> No. You need to count.
> 
> 
> 
> Here you have a species difference consisting of 8 mutations.



How many tries to get that combo of 8 mutations, and what macro effect in the macro organism?

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## Physics Hunter

> Your instinct is not science.
> 
> This is why we do experiments, so we don't have to rely on instinct.
> 
> I'm sorry, but if you refuse to stop with the garbage assertions then I will mercilessly beat you back.
> 
> There is no place for personal belief in science. Science is BY DEFINITION a social activity. My opinions matter exactly as much as yours: ZERO.
> 
> The evolutionary landscape IS cellular biophysics, and nothing else. DNA expression and replication is accomplished by enzymes, and enzymes make mistakes. Therefore cells have excision repair, mismatch repair, homologous and non-homologous end joining... direct chemical reversal, crosslink repair... there must be a few more I've forgotten about.
> ...


If you have not done an experiment based at the core level on an instinct, then you have not ever made a leap of science.

And mercilessly?   :Smiley ROFLMAO:

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## nonsqtr

> How many tries to get that combo of 8 mutations, and what macro effect in the macro organism?


You see the new Covid with 30 mutations, don't you?

That took, what, a year?

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## nonsqtr

> If you have not done an experiment based at the core level on an instinct, then you have not ever made a leap of science.
> 
> And mercilessly?


Now you're saying something different though.

Now it's instinct => experiment.

Before it was instinct => impossible.

Backpedal much?  :Grin:

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## Physics Hunter

> You see the new Covid with 30 mutations, don't you?
> 
> That took, what, a year?


Come out and play in the big world of opposable thumbs...

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## Physics Hunter

> Now you're saying something different though.
> 
> Now it's instinct => experiment.
> 
> Before it was instinct => impossible.
> 
> Backpedal much?


Hell no, I am pushing.  I walk without fear.
Newton may not have been hit on the head with an apple, but he had an insight, instinct, an epiphany.
And Einstein.
And Galileo.
Hell, Columbus...

You like accidents, I like insight.  Think deeply on that.

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## nonsqtr

> Come out and play in the big world of opposable thumbs...


I could rub it in... but boredom is usually an admission of defeat.

DON'T tell me anything's impossible, I'll slap you if you do. That's right up there with PC, I fight back.  :Grin: 

I've spent a WHOLE CAREER doing the impossible for people who don't appreciate it. I finally stopped working, cause someone wanted to put a man behind the curtain and call it engineering.

Well, there is NO man behind the curtain on this one.

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## Physics Hunter

> You're telling a physics guy to learn math?



Except for a probability class, I cleaned the math catalog out in my undergrad.  He ain't got shit.

He refuses to come out into the big world.

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Authentic (12-06-2021)

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## nonsqtr

> Hell no, I am pushing.  I walk without fear.
> Newton may not have been hit on the head with an apple, but he had an insight, instinct, an epiphany.
> And Einstein.
> And Galileo.
> Hell, Columbus...
> 
> You like accidents, I like insight.  Think deeply on that.


I make more progress than you do, and more quickly. The odds are in my favor.

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## nonsqtr

> Except for a probability class, I cleaned the math catalog out in my undergrad.  He ain't got shit.
> 
> He refuses to come out into the big world.


Yeah yeah. And still doesn't understand basic probability.

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## nonsqtr

> Except for a probability class, I cleaned the math catalog out in my undergrad.  He ain't got shit.
> 
> He refuses to come out into the big world.


The word you're looking for is "chiral".

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## nonsqtr

> Except for a probability class, I cleaned the math catalog out in my undergrad.  He ain't got shit.
> 
> He refuses to come out into the big world.


You need to start simple.

You're a LONG way from thumbs.

Start here: Research shows human cells assembling into fractal-like clusters | Brown University

How does a thumb become a thumb?

Here's your answer.

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## nonsqtr

Three behaviors are required to instantiate a fractal. Do you know what they are?

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## nonsqtr

Dendritic gold:



Dendritic copper:



Dendritic manganese oxide on limestone:

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## Physics Hunter

> I could rub it in... but boredom is usually an admission of defeat.
> 
> DON'T tell me anything's impossible, I'll slap you if you do. That's right up there with PC, I fight back. 
> 
> I've spent a WHOLE CAREER doing the impossible for people who don't appreciate it. I finally stopped working, cause someone wanted to put a man behind the curtain and call it engineering.
> 
> Well, there is NO man behind the curtain on this one.


I've spent a WHOLE CAREER doing the amazing for people who don't appreciate it, TOO.  So take that lone ranger shit off the table, you are not the only one!

NP complete problems are impossible.
Free range autonomous high performance and safe driving is impossible.
Accurate language translation is probably impossible.
Charging the entire American POV and Commercial vehicle fleet on renewables is impossible in our lifetimes.

There is a man behind the curtain and he want's to sniff someone's daughter's hair...

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## Physics Hunter

> You need to start simple.
> 
> You're a LONG way from thumbs.
> 
> Start here: Research shows human cells assembling into fractal-like clusters | Brown University
> 
> How does a thumb become a thumb?
> 
> Here's your answer.


No, I have two thumbs, they work great.

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## Physics Hunter

Done for this eve.

But please do rant on...

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## nonsqtr

> Except for a probability class, I cleaned the math catalog out in my undergrad.  He ain't got shit.
> 
> He refuses to come out into the big world.


Even though you don't deserve it, I'll take a few moments to educate you.

A FRACTAL is a scale invariant structure. Human beings are fractals, we look the same whether we're big or small.

Fractals are intimately related with SYMMETRY, which you know all about if you're a physicist 

NOETHER'S THEOREM equates invariance (conservation) and symmetry.

The universe is not at equilibrium. It exists as a flow, and as such it self organizes according to the laws of non-equilibrium thermodynamics.

Fractional structures result from dissipative systems. There is no "gene that codes for the shape of the leaf". Such a thing doesn't exist.

What there IS, is a reaction-duffusion system where the coefficients are kept in bounds by genetic regulatory mechanisms.

Fractal structure in nature is generated by CHEMICAL GRADIENTS. It's that simple.

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## nonsqtr

> No, I have two thumbs, they work great.


Now you're moping.

Come on, pick up the ball and get in the game.

The only way you win this game is by knowing more than I do. Which will only take you... forty years.

Or, you could shortcut the process a bit, by listening instead of arguing.  :Smile:

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## nonsqtr

> NP complete problems are impossible.


No, they're not. A quantum computer just solved one in finite time.




> Free range autonomous high performance and safe driving is impossible.


Horseshit. That's what driver's licenses are for 




> Accurate language translation is probably impossible.


lol - you don't believe the diplomats?

Psst... all those sign language types are laughing at you and you don't even know it.




> Charging the entire American POV and Commercial vehicle fleet on renewables is impossible in our lifetimes.


I dunno. Mussolini made the trains run on time. People said that was impossible too.




> There is a man behind the curtain and he want's to sniff someone's daughter's hair...


If I ever spot a man behind the curtain at a trade show, I'll expose the SOB. I don't care if it's Jesus Christ himself, he's going public. I'll yank his power, pepper spray him, whatever I gotta do.

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## nonsqtr

> NP complete problems are impossible.


You're not a very careful physicist, are you?

You say "impossible" even after it's already been done.

Same for evolution - you say impossible after it's already been done.

Here's a solvable problem that's in BQP but not in PH: determine if two random number generators are correlated.

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## CWF

What evolution and the Titanic have in common?  Both of them sank.

As a notable highly educated person of science once stated:  "The Theory has two major
 problems. It makes little sense, and It has little evidence to support it." 

While widely believed in the science community it is disbelieved by nearly everyone else. The response to it is, " You have got to be kidding, right?"

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Authentic (12-06-2021)

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## UKSmartypants

> What evolution and the Titanic have in common?  Both of them sank.
> 
> As a notable highly educated person of science once stated:  "The Theory has two major
>  problems. It makes little sense, and It has little evidence to support it." 
> 
> While widely believed in the science community it is disbelieved by nearly everyone else. The response to it is, " You have got to be kidding, right?"



your response is garbage. Try reading the  entire thread again. The thread is about the evolution of a unique new bacterial species which adapted to consume the steel of the Titanic's Hull.   If you dont understand the science, dont comment. And dont try dragging ang God Bollox into here, this is the Science forum, and God is banned in this subforum.

And making statement like "While widely believed in the science community it is disbelieved by nearly everyone else"  is total nonsense since its not backed by a single iota of evidence or proof. DID you conduct a poll of a substantial part of the planets population to ascertain this? Or was it from the Ministry of Made Up statistics? 

Now eff off.

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## UKSmartypants

> NP complete problems are impossible.



Totally incorrect

The name "NP-complete" is short for "nondeterministic polynomial-time complete". In this name, "nondeterministic" refers to nondeterministic Turing machines, a way of mathematically formalizing the idea of a brute-force search algorithm. Polynomial time refers to an amount of time that is considered "quick" for a deterministic algorithm to check a single solution, or for a nondeterministic Turing machine to perform the whole search. "Complete" refers to the property of being able to simulate everything in the same complexity class. 


In other words, NP-Complete problems are probably solvable only in exponential time.  It is believed that if anyone could *ever* solve an "NP-Complete" problem in "P" time, then *all* "NP-complete" problems could also be solved that way by using the same method, and the whole class of "NP-Complete" would cease to exist.


The classic NP-Complete Problem is The Travelling Salesman problem.


This problem can be stated as- "Given n number of cities and a travelling salesman has to visit each city. Then we have to find the shortest tour so that the travelling salesman can visit each and every city only once." 



The point is as you increase the number of cities ina linear fashion, the solution time increases exponentially. Its always solvable, but when the number of cities gets very large, the computation time gets longer than the age of the universe....

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## Authentic

> your response is garbage. Try reading the  entire thread again. The thread is about the evolution of a unique new bacterial species which adapted to consume the steel of the Titanic's Hull.   If you dont understand the science, dont comment. And dont try dragging ang God Bollox into here, this is the Science forum, and God is banned in this subforum.
> 
> And making statement like "While widely believed in the science community it is disbelieved by nearly everyone else"  is total nonsense since its not backed by a single iota of evidence or proof. DID you conduct a poll of a substantial part of the planets population to ascertain this? Or was it from the Ministry of Made Up statistics? 
> 
> Now eff off.


And is there any wonder why scientists are so distrusted today, when they come across as arrogant and offputting?

Better work on your messaging, _scientist_.

Start taking paying attention to  @nonsqtr. I actually read some of his links.

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## nonsqtr

> Totally incorrect
> 
> The name "NP-complete" is short for "nondeterministic polynomial-time complete". In this name, "nondeterministic" refers to nondeterministic Turing machines, a way of mathematically formalizing the idea of a brute-force search algorithm. Polynomial time refers to an amount of time that is considered "quick" for a deterministic algorithm to check a single solution, or for a nondeterministic Turing machine to perform the whole search. "Complete" refers to the property of being able to simulate everything in the same complexity class. 
> 
> 
> In other words, NP-Complete problems are probably solvable only in exponential time.  It is believed that if anyone could *ever* solve an "NP-Complete" problem in "P" time, then *all* "NP-complete" problems could also be solved that way by using the same method, and the whole class of "NP-Complete" would cease to exist.
> 
> 
> The classic NP-Complete Problem is The Travelling Salesman problem.
> ...


Except if you use a neural network, with as many neurons as you have cities, and an extra associative layer, which will arrive at the optimal solution "most" of the time. "Very quickly", if it's appropriately trained. 

TSP is an interesting example. As the number of cities grows (exponentially), you get a whole class of solutions where basically "one solution is as good as another". The shortest distance is asymptotic in the set of paths, and if there are lots of paths they'll tend to cluster around certain distances. Neural networks happen to excel at finding "one of many" solutions. The downside is they get stuck in local minima sometimes, and that's fixable but most people just run the experiment again.

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## nonsqtr

> And is there any wonder why scientists are so distrusted today, when they come across as arrogant and offputting?
> 
> Better work on your messaging, _scientist_.
> 
> Start taking paying attention to  @nonsqtr. I actually read some of his links.


Excellent, Grasshopper! If you're reading, you're learning.

When I started in biophysics there were no neural networks, no nonlinear thermodynamics, no fancy microscopes beyond the ordinary electron variety.

What attracted me to this part of science, was precisely the opportunity to bridge the gap, between what we can see and what we can't.

The whole idea that the shape of a fern leaf is determined by chemical gradients only came around in maybe late 90's. Before that, all through the 70's and 80's, people were looking for genes that code shape. After 20 years of exhaustive search they finally figured out there's really no such thing. The shape of the human body, for example, is so intricate that 4 million genes wouldn't be enough to code for it.

What happens instead is there are thousands upon thousands of interacting chemical gradients. What is instructive is to look at the type of molecules that are being used. Glycerol, for instance, is a key component of the phospholipids in cell membranes. Some of the byproducts of phospholipid breakdown include molecules that will physically bend the membrane - so this is "shape", of sorts. Then there is also the cytoskeleton, which is like a scaffolding directly underneath the cell membrane. Part of its function is to anchor molecules to the membrane, for example at a synapse the postsynaptic density is what keeps the receptors in place. (Otherwise they would float around, in the membrane - that's the "fluid mosaic" concept). 

So that's another kind of "shape", the cytoskeleton consists mainly of actin and tubulin (microfilaments and microtubules). There are several of these low-level cellular mechanisms for shape, and in each case the question is, how does the cell "compartmentalize" the concentrations of molecules, and how does it create chemical gradients. But generally speaking, none of these mechanisms extend beyond the cell. In development nerve fibers from the spinal cord will climb all the way up into the brain, but they dont know where they're going or what they're going to connect with, they're just following a chemical gradient. Which is why everyone's spinal cord looks just a tad different.

This is why embryology is important. Because it's all about the gradients. In 1976 they showed me I could stick a pin in a frog embryo in just the right place at the right time, and it would grow a third front leg. We should have known "right then" that shape is mechanical and therefore chemical.

So when you look across 'species' your eye sees the differences in shape, yet we share 95+ percent of our DNA with chimpanzees. And it turns out, the SEQUENCE of development is vital, things have to develop in order. A great example is the complex log mapping in the primary visual system, again making use of chemical gradients.

Generally speaking to build a fractal structure like a fern leaf, three operations are needed: copy, move, and divide. Biological systems easily accomplish all three. Then what happens is, you get interaction between neighboring fractal generators, which is were the beautiful dendritic branching patterns in the brain come from.

So, this is why I say, to understand biophysical evolution (which is the level at which it occurs), one must have some dynamics, some embryology,  and a good solid understanding of (bio)chemistry. And math never hurts. You can have with this stuff, it's not all drab. There's a lot of free fractal generators you can use on your computer.

But I digress. Halomonas binds copper and other ions, because it's kind of a salt-water organism. In Halomonas membrane we find bidirectional transporters that shuttle ions in opposite directions. Halomonas proteins often require ionic cofactors, and they stop working in fresh water and in low pH environments. It can withstand severe temperature changes though, which we can't, our internal temperature has to stay pretty much the same.

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## Physics Hunter

> Totally incorrect
> 
> The name "NP-complete" is short for "nondeterministic polynomial-time complete". In this name, "nondeterministic" refers to nondeterministic Turing machines, a way of mathematically formalizing the idea of a brute-force search algorithm. Polynomial time refers to an amount of time that is considered "quick" for a deterministic algorithm to check a single solution, or for a nondeterministic Turing machine to perform the whole search. "Complete" refers to the property of being able to simulate everything in the same complexity class. 
> 
> 
> In other words, NP-Complete problems are probably solvable only in exponential time.  It is believed that if anyone could *ever* solve an "NP-Complete" problem in "P" time, then *all* "NP-complete" problems could also be solved that way by using the same method, and the whole class of "NP-Complete" would cease to exist.
> 
> 
> The classic NP-Complete Problem is The Travelling Salesman problem.
> ...


Wellll......

Not totally incorrect:

A: you did not critique the other 4 examples.
B: NP Complete problems are ones that we watch in the computing world, because invariably someone will suggest some cockeyed snakeoil method to slice the Gordian knot...

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## nonsqtr

> Wellll......
> 
> Not totally incorrect:
> 
> A: you did not critique the other 4 examples.
> B: NP Complete problems are ones that we watch in the computing world, because invariably someone will suggest some cockeyed snakeoil method to slice the Gordian knot...


Oh, you mean like Grover's algorithm?  :Grin:

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## nonsqtr

https://en.m.wikipedia.org/wiki/The_..._Morphogenesis

Prigogine got the Nobel Prize for actually doing this.

He was one of the early students of nonlinear thermodynamics.

That work was mostly in the late 60's and early 70's.

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## nonsqtr

Let's talk about evolution.

Let's talk about a specific example.

I said evolution was biophysics, well here's an example.

In a previous post I mentioned that there's a cloud of negative charge around cells, because of the phosphates sticking up out of the membrane.

This charge cloud is interesting, physically. It will attract positive ions (sodium, calcium) electrostatically, but the ions can not go through (across) the membrane, because of the lipids.

And, that's a problem for the cell, because cells need sodium and calcium.

Lipid micelles are easy, they form spontaneously. However they can't get ions because the charge cloud is too dense, hydrogen is a lot smaller than calcium.

The first step in the evolution of a trans-membrane ion channel, is simply the ability for a molecule to stick it's head up out of the membrane. Because that's the only way it's going to get an ion. The binding site must be "taller than" the charge cloud.

So, when we look around in nature, we observe a fair number of reactive molecules that have bound with lipids and phospholipids. Sugars, are ubiquitous. Choline, same way. These molecules are floating around freely in the ocean and they're in every form of life, they're easy to get. (Amino acids are easy to get too, halobacter eats them and uses them to build proteins).

If you have a bunch of lipid and a bunch of sugars floating around in a solution, you'll get some glycolipids. And, primitive life forms eat by invaginating (endocytosis), so they'll just drink up these various molecules.

And, if a dumb cell suddenly gets a glycolipid it can begin shuttling ions. Ion channels are glycolipids, they usually exist as trimers or tetramers.

Right now, there is plenty of experimentation going on, to see how cells handle unknown molecules. Primitive cells just seem to eat them willy-nilly, and getting something useful is the luck of the draw. (However if you're a billion bacteria in a sea of trillions of molecules, the odds are in your favor).

So, how do we get from there, to actually making these molecules from DNA? Well... there's something that comes before that, there is the maintenance of concentrations of a molecule, "without" DNA. Glycerol is a byproduct of glucose metabolism, via the glycolytic pathway, and it's also recycled via lipase enzymes. The cell can still function even without synthesizing glycerol.

The requirement is that molecular concentrations be maintained, for biochemical activity to continue. Cells use a variety of strategies to maintain concentrations, not just synthesis and not just random invagination.

One can begin to understand biophysical evolution by looking at primitive organisms. Cyanobacter makes AEG (amino ethyl glycine), which forms a polymer backbone much like DNA. In this way, the cells can use proteins to encode genetic information. Before DNA there was RNA, and before that there was protein.

The first micelle to be able to channel an ion, will survive.

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## Physics Hunter

> Let's talk about evolution.
> 
> Let's talk about a specific example.
> 
> I said evolution was biophysics, well here's an example.
> 
> In a previous post I mentioned that there's a cloud of negative charge around cells, because of the phosphates sticking up out of the membrane.
> 
> This charge cloud is interesting, physically. It will attract positive ions (sodium, calcium) electrostatically, but the ions can not go through (across) the membrane, because of the lipids.
> ...


I am way too busy talking about opposing Global Godless Communism to trifle with the ground that they smugly assume that they own.

Be well.

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## Oceander

> I am way too busy talking about opposing Global Godless Communism to trifle with the ground that they smugly assume that they own.
> 
> Be well.


Yeah, because some gigantic dude with a long white flowing beard twinkled his fingers and it all magically appeared as-is.

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## nonsqtr

> I am way too busy talking about opposing Global Godless Communism to trifle with the ground that they smugly assume that they own.
> 
> Be well.


The Chinese will kick our butts if we don't understand this stuff.

Their physicists are very good, and there's millions of them.

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## Trinnity

> your response is garbage. [...]Now eff off.


Thread closed.

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nonsqtr (12-09-2021)

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