[_ Old Earth _] How well do you actually know The Theory of Evolution?

[rthom7]

I am not most creationists Barbarian, and am happy to respect evolution theory as long as it makes sense....so I have another look at my link regarding Dr Thompson's strange circuit, and yes it seems would be evolutions praise the circuits because it does things very strangely indeed. But from an electronics point of view, the device still required training, and that means it evolved because an Intelligent Designer forced it to achieve a desirable output he wanted to achieve....

Dr. Thompson dabbled with computer circuits in order to determine whether survival-of-the-fittest principles might provide hints for improved microchip designs. As a test bed, he procured a special type of chip called a Field-Programmable Gate Array (FPGA) whose internal logic can be completely rewritten as opposed to the fixed design of normal chips "
Alan Bellows .2014. On the Origin of Circuits
http://www.damninteresting.com/on-the-origin-of-circuits/

I admit would be evolutionists can put spin on their research anyway they like, as all scientists love to propagate their own bias...But I fail to see how electronic circuitry is anything like biological natural selection...

If this kind of experiment, is so revolutionary, Barbarian do you have a good link yourself about it in today's modern science...I can't find any follow up research with Thompson's idea....

I also decided to have a second look at the other article you linked...afterward you make serious claims for evolution...

HALL, B. 1981. EVOLUTION OF A REGULATED OPERON IN THE LABORATORY
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1201865/pdf/335.pdf
To observe evolution in a dynamic state we can ask, "How do simple cells evolve new metabolic functions?"

I can' t find the context you speak about Barbarian...

No. "Lac operon" is not what you think it is. And the bacteria can still do all the other functions, apparently because there were duplicate genes.

.please post the sentences of his paper that back up your claims please. I can't find it.
View attachment 5908
He starts with a strain of bacteria mutant with failure to make lactose as a food,
and over generations observes some strains digesting lactose....how do we know the strains evolved ? He does not show the DNA sequence that changed...we assume his word for it? How do we know the bacteria didn't use other mechanism with existing genes to digest lactose ?

The paper is old, did he read all the DNA sequences, and show the DNA sequence changed ? Sorry not very convincing...though I would like to see a convincing case....

NEWS update: I was also looking for how the TYPE III secretory system evolved into the flagella system...and rather than find a paper for this, I found instead a paper arguing AGAINST this...
Abby S, and Rocha E. 2012. The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems Reference Source link http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002983
They looked at hundreds of bacteria species for a model and cross referenced the genes across each species...They assert the bacteria evolved the flagella first, and the secretory type III system evolved later through mutational destruction of an existing complex organelle. Barbarian do you have a link showing TYPE III evolving into flagella 2012- 2015 please, or do we now assume such intermediates are not longer parts of an evolutionary answer?


Shalom

 

[Rick W]

I develop a circuit that doesn't perform it's intended purpose all that well. Through diagnostics I find a flaw and reroute a signal to make the circuit do better. I made decisions based on the variables I got from measurements or other data collection processes.

Mathematical calculations were once done on paper. I come up with a formula to do a certain task based on the variables I plug into it. Doing those calculations over and over with various variables was time consuming but using the formula I get the set of data I was looking for.

The computer is nothing more than a faster method of making decisions and doing calculations. A circuit doesn't evolve simply because I determined to change something. But that determination took time. Through trial and error I'd hit upon a solution but doing so took time. A computer however can do what I do but much faster.

The FPGA is nothing new but I suppose there's a certain amount of "wow factor" for the layman upon initial introduction. It didn't come about all of a sudden and it's predecessors were cumbersome, slow and not very complex. As technology advanced in the field of semiconductors such things as microcontrollers, microprocessors, programmable logic devices, eproms, srams along with FPGAs and the like were developed smaller and with added functionality.

I've also written code that would work in one processor but not in another of the same part. I got the functionality from the first circuit I wanted but building a second circuit exactly the same wouldn't work. The design/circuit was "tweaky" and not very stable. Again through diagnostics I might find I'm running it too fast, overloading an output, forgetting to tie an input to gnd or to a supply rail (floating).

AI... Artificial Intelligence, (also used extensively in computer games that go back to "computerized chess") coupled with the appropriate hardware can be used to run diagnostics much faster than I can do much the same as a pocket calculator can do calculations much faster than I can do them on paper. SPICE simulators have come a long way in that area to not only mimic a proposed design but also to output recommended solutions based on libraries of previously stored data from past circuit solutions. More often than not more than one solution is needed to overcome a circuit problem. Once found then that solution is stored in the library.

What works with one chip or circuit may not with another. Intermittent functionality. It's the bane of the electronics industry.

FPGAs have the capability to perform "anything one can imagine" (do be careful with the hype) but only within the available functions within it.
It can't add another CLB (Configurable Logic Block) but it can disable or not utilize a function that already exists. And of course it can implement an existing function previously unused.

FPGA functionality is nothing more than the hardware version of a set of program subroutines called in sequence to perform a certain task. Been doing that for years. The advent of "small" within the semiconductor industry has allowed the hardware version to be contained on a small, compact wafer like the introduction of the first pocket calculator.


One can substitute terms like "cell", "genome" or "DNA" for circuit function, subroutine, register, multiplexer and various logic gates all one likes to make it appear "evolutionary" but at the end of the day the FPGA can only do what's it's specifically designed to do. That's probably why there are various FPGAs on the market. And that only with specified hardware. In reality the FPGA is much more comparable to Intelligent Design than evolution.

 

[rthom7]

The computer is nothing more than a faster method of making decisions and doing calculations. A circuit doesn't evolve simply because I determined to change something. But that determination took time. Through trial and error I'd hit upon a solution but doing so took time. A computer however can do what I do but much faster.

Correct Rick, glad to hear another programmer like me agrees too.

The FPGA is nothing new but I suppose there's a certain amount of "wow factor" for the layman upon initial introduction. It didn't come about all of a sudden and it's predecessors were cumbersome, slow and not very complex. As technology advanced in the field of semiconductors such things as microcontrollers, microprocessors, programmable logic devices, eproms, srams along with FPGAs and the like were developed smaller and with added functionality.

Correct FPGA circuits are ID designed circuits, and required ID training and programming to set up. Once setup, such circuits can change over time to suit the training done by the ID....thus this is experimental evidence how the various kinds of organisms with their own FPGA simulations changed according to Creationism.....it's proof of how Genesis works....nothing to do with evolution at all...Sadly Darwin stole Creationism models of selection, to suggest small changes are evidence of evolution...its not.. small changes is evidence of God's ID since the Genesis creation.

I've also written code that would work in one processor but not in another of the same part. I got the functionality from the first circuit I wanted but building a second circuit exactly the same wouldn't work. The design/circuit was "tweaky" and not very stable. Again through diagnostics I might find I'm running it too fast, overloading an output, forgetting to tie an input to gnd or to a supply rail (floating).

Exactly Thompson's experiment required an ID to train his experiment, Himself! and changes to his hardware....He did not sit back and do nothing, allowing nature (electronics) to do all things themselves....in other words his experiment was brought about be a cause, and the cause had a mind....bingo ! We call that purposed experiments of intelligence.

AI... Artificial Intelligence, (also used extensively in computer games that go back to "computerized chess") coupled with the appropriate hardware can be used to run diagnostics much faster than I can do much the same as a pocket calculator can do calculations much faster than I can do them on paper.

Yes I have done many neural network programs myself. I have never seen a program able to sense its own input with purpose self interest in changing in a meaningful way... Like the move matrix suggests, machines becoming alive for a purpose for themselves....Can we write a neural network program able to train itself ? No that would be evolution without a Designer...indeed proof evolution can work by itself....although ID was required to start the process rolling....


FPGAs have the capability to perform "anything one can imagine" (do be careful with the hype) but only within the available functions within it.

Correct...though others see it doing "evolutionary things" inside....as if the word evolution simply means "to change" which it does not. The word "evolution" means to "change something into something else entirely brand new, which some call speciation today, the ability to make massive changes from nothing"

FPGA functionality is nothing more than the hardware version of a set of program subroutines called in sequence to perform a certain task. Been doing that for years.

Correct...like the EPROM, the field circuits can be changed to hold new logic gates but only if an ID trains the circuits.

Did Dr Thompson train his experiment to detect audible sound waves correctly ? He most certainly did....So this is evidence of ID at work.


One can substitute terms like "cell", "genome" or "DNA" for circuit function, subroutine, register, multiplexer and various logic gates all one likes to make it appear "evolutionary" but at the end of the day the FPGA can only do what's it's specifically designed to do.

It amazes me that scientists reverse engineer God's ID, and then afterwards try to put evolutionary words around the Design to demystify the evidence of GOD's Design ....much the same way people in other religion destroy God's Word with fancy notions of humanism....we love to add humanism to Creationism...as if we are the bigger strong authority here...

In reality the FPGA is much more comparable to Intelligent Design than evolution.

Absolutely correct....I wish others would see this. FPGA circuits have to be trained by ID to work....and set up by ID to begin with. They were even designed by ID as electronic circuits. ID is everywhere, molecules by themselves do not have mind, they simply do what programs tell them to do....
that's the beauty of DNA....its a program.... great post brother Rick thanks for your support....Shalom

 

[Rick W]

http://cs.nyu.edu/courses/fall12/CSCI-GA.2965-001/geneticalgex

"It appears that evolution made use of some physical property of these
cells--possibly a capacitive effect or electromagnetic inductance--to
influence a signal passing nearby. Somehow, it seized on this subtle
effect and incorporated it into the solution."

Umm, a floating input will do this. Especially a high impedance input. Just putting your finger near an open input/circuit will induce enough signal to make it change states. Or oscillate.
Building circuits that rely on such instabilities to work isn't what I call prudent design.

To solve this mystery, Thompson needs to measure the input and output
values of each cell when the circuit is operating. But the FPGA
allows only digital access to these points, so he can't measure the
analogue values. Thompson's colleague, Paul Layzell, is building a
circuit board that will allow all the components to be measured with
analogue instruments."

Mystery? Well, yes. He has to do the diagnostics to find the instability. I can guarantee it won't take long once he touches an open input with a scope probe.


"Paul Layzell, is building a
circuit board that will allow all the components to be measured with
analogue instruments."

What? You're kidding right? I'm using that stuff now every single day. Build one? Why not just buy one.

We do diagnostics using what's called a "bed of nails". It's a bunch of sprung probes that contact selected or all the nets (traces) on a board. In this way each component can be tested. Within the test fixture that has the bed of nails multiplexers are used to select which probes are routed to a voltmeter, freq counter, capacitance/inductance meter or any other test equipment you care to name.
At the same time I can output signals to a board, "false inputs" to check items on a component level or test selected function blocks on the board. All this is controlled by program to perform tests to assure all is working and within spec. A board having 300 or more components can be tested within a couple minutes. It's diagnostics on steroids. Why in the world would "Layzell" want to reinvent the wheel? It makes no sense.

Automated testing is far from new. My goodness, I was using a CoCo computer back in the 80's hooked up to a few PIAs to test boards at a manufacturing facility in Maiden NC. They were testing boards by throwing certain switches, measuring this or that, move a rotary switch, do the measurement, watch some LEDs.... All I did was automate the process. Test engineering 101.



Genrad, Teredyne just to name a couple of the big hitters in the automated test industry. We're also using "Labview" from National Instruments.
From the company:
" We use hardware and software from National Instruments to deliver a complete solution. Our services include LabVIEW and TestStand Programming Data Acquisition Systems Hardware in the Loop Simulation Product Validation Machine Vision and Real Time Systems LabVIEW Training"

Heck, I'll loan Mr Layzell a CoCo setup including harddrives, toss in an I/O board (PIAs) if he needs one and show him how to hook it up. (Would you believe I still have those things? ) Or he can just spend a few bucks on a standalone desktop test unit.


unbelievable.


And the public soaks up this hype like it's some kind of guru hocus pocus nobody's ever done before.

 

[Barbarian]

I am not most creationists Barbarian, and am happy to respect evolution theory as long as it makes sense....so I have another look at my link regarding Dr Thompson's strange circuit, and yes it seems would be evolutions praise the circuits because it does things very strangely indeed. But from an electronics point of view, the device still required training, and that means it evolved because an Intelligent Designer forced it to achieve a desirable output he wanted to achieve....

Dr. Thompson dabbled with computer circuits in order to determine whether survival-of-the-fittest principles might provide hints for improved microchip designs. As a test bed, he procured a special type of chip called a Field-Programmable Gate Array (FPGA) whose internal logic can be completely rewritten as opposed to the fixed design of normal chips "

Thought you knew. Neural networks don't depend on hardware, but are software or firmware.

But I fail to see how electronic circuitry is anything like biological natural selection...

Usually, that takes some experience in both cybernetics and biology to understand.

If this kind of experiment, is so revolutionary, Barbarian do you have a good link yourself about it in today's modern science...I can't find any follow up research with Thompson's idea....

It's pretty much general practice in engineering now. Here's about 80 examples of the way computers can apply evolutionary processes for practical applications.
http://en.wikipedia.org/wiki/List_of_genetic_algorithm_applications

I also decided to have a second look at the other article you linked...afterward you make serious claims for evolution...

HALL, B. 1981. EVOLUTION OF A REGULATED OPERON IN THE LABORATORY
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1201865/pdf/335.pdf
To observe evolution in a dynamic state we can ask, "How do simple cells evolve new metabolic functions?"

I can' t find the context you speak about Barbarian...

No. "Lac operon" is not what you think it is. And the bacteria can still do all the other functions, apparently because there were duplicate genes.

.please post the sentences of his paper that back up your claims please. I can't find it.

There are an unbelievable number of function necessary for bacteria. Rather than have me show you that none of them are compromised by the evolution of the new system, how about telling me which function you think no longer works?

He starts with a strain of bacteria mutant with failure to make lactose as a food,
and over generations observes some strains digesting lactose....how do we know the strains evolved ?

New genes. And it's not just natural selection, since all of them are descended from a single bacterium lacking these genes. Also, the gene in question was observed to change in several steps over the experiment, becoming more efficient. The initial gene was known, and quite unlike the final gene, which produced a different enzyme for a different substrate.

He does not show the DNA sequence that changed...we assume his word for it?

That's what gene is. Thought you knew.

How do we know the bacteria didn't use other mechanism with existing genes to digest lactose ?

Because he knows how the new gene works. It's why biololgists find it so convincing.

NEWS update: I was also looking for how the TYPE III secretory system evolved into the flagella system...and rather than find a paper for this, I found instead a paper arguing AGAINST this...

Biologists have, for some time realized that the Type III secretory system likely evolved from one type of bacterial flagellum. All the basic parts are there, so a change in microtubules and dynens would be all that would be required.

Here's a diagram of the flagellum normally shown by IDers and the less evolved form from Gram-positive bacteria. As you see, the more primitive form is rather like the Type III pilus. This is, of course, a macroevolutinary change in both definitions; a change in taxa, and a major reworking of a homologous feature to a new use.

The evolution of the complex flagellum is indicated by the change from the simpler Gram positive flagellum. And that?

The connection can still be seen, first in the various early-branching single-celled eukaryotes that have a microtubule basal body, where microtubules on one end form a spindle-like cone around the nucleus, while microtubules on the other end point away from the cell and form the cilium. A further connection is that the centriole, involved in the formation of the mitotic spindle in many (but not all) eukaryotes, is homologous to the cilium, and in many cases is the basal body from which the cilium grows.
An apparent intermediate stage between spindle and cilium would be a non-swimming appendage made of microtubules with a selectable function like increasing surface area, helping the protozoan to remain suspended in water, increasing the chances of bumping into bacteria to eat, or serving as a stalk attaching the cell to a solid substrate.


Regarding the origin of the individual protein components, an interesting paper on the evolution of dyneins[2][3] shows that the more complex protein family of ciliary dynein has an apparent ancestor in a simpler cytoplasmic dynein (which itself has evolved from the AAA protein family that occurs widely in all archea, bacteria and eukaryotes). Long-standing suspicions that tubulin was homologous to FtsZ (based on very weak sequence similarity and some behavioral similarities) were confirmed in 1998 by the independent resolution of the 3-dimensional structures of the two proteins.
http://en.wikipedia.org/wiki/Evolution_of_flagella

 

[Barbarian]

Umm, a floating input will do this. Especially a high impedance input. Just putting your finger near an open input/circuit will induce enough signal to make it change states. Or oscillate.
Building circuits that rely on such instabilities to work isn't what I call prudent design.

Wasn't design at all. And yet it worked more efficiently than anything engineers could design. Does that suggest why genetic algorithms are now so often used for complex problems? Evolutionary processes work better than design in those cases.

 

[Rick W]

Wasn't design at all. And yet it worked more efficiently than anything engineers could design.

Engineers did design it. All of it.
Let's see.

The FPGAs were designed.
The PCB the FPGA was mounted on was designed.
The hardware was designed.
The electronics that ran the program for the FPGA was designed.
The program itself was designed for a particular task.
And of course the experiment was designed as a whole.

But it wasn't design at all.
I don't think it would be a stretch to imagine why I disagree.

 

[Rick W]

Thought you knew. Neural networks don't depend on hardware, but are software or firmware.

http://en.wikipedia.org/wiki/Artificial_neural_network

To implement large and effective software neural networks, considerable processing and storage resources need to be committed. While the brain has hardware tailored to the task of processing signals through a graph of neurons, simulating even a most simplified form on Von Neumann technology may compel a neural network designer to fill many millions of database rows for its connections – which can consume vast amounts of computer memory and hard disk space.

 

[Barbarian]

One problem for computer simulations of neural networks, is that computers use discrete digital components, while neurons have multiple connections and operate on an analog basis with inputs from several other neurons determining the state of that neuron.

 

[Barbarian]

Engineers did design it. All of it.

Nope. The guy who started the process, doesn't even know how the solution works. Because it evolved by steps that he doesn't quite understand.

Let's see.

The FPGAs were designed.
The PCB the FPGA was mounted on was designed.
The hardware was designed.
The electronics that ran the program for the FPGA was designed.
The program itself was designed for a particular task.
And of course the experiment was designed as a whole.

But the solution was obtained by random variation and natural selection. Evolved, not designed. No one designed it.

But it wasn't design at all.

Right. The hardware meant nothing at all. It could have been run by a person totally ignorant of the goal, following an algorithm of rolling dice and making changes as indicated. Would have taken an unbelievable amount of time, and complicated rules, but it would still work.

I don't think it would be a stretch to imagine why I disagree.

Pretty much the same reason most creationists disagree.

 

[Rick W]

One problem for computer simulations of neural networks, is that computers use discrete digital components, while neurons have multiple connections and operate on an analog basis with inputs from several other neurons determining the state of that neuron.

http://en.wikipedia.org/wiki/Analog_computer

Analog computers are not unknown Barbarian.

Analog computers were widely used in scientific and industrial applications where digital computers of the time lacked sufficient performance. Analog computers can have a very wide range of complexity. Slide rules and nomographs are the simplest, while naval gunfire control computers and large hybrid digital/analog computers were among the most complicated.[1] Systems for process control and protective relays used analog computation to perform control and protective functions.

The advent of digital computing and its success made analog computers largely obsolete in 1950s and 1960s, though they remain in use in some specific applications, like the flight computers in aircraft, and for teaching control systems in universities.




As far as the digital based computers are concerned the same function can be done with DACs (Digital to Analog Converter) or ADCs (Analog to Digital Converter) coupled with analog multiplexers. A CMOS 4051, 4052, 4053 are old chip analog multiplexers and I'm thinking engineers know how to use them by now.

 

[Rick W]

Leads to an interesting question:
What came first... the hardware or the program?

Nope. The guy who started the process, doesn't even know how the solution works. Because it evolved by steps that he doesn't quite understand.

I don't understand the process of manufacturing a chip or how it works inside but I use them anyway.


"I don't know how it works but it does" is not an uncommon phrase among engineers.

 

[Rick W]

But the solution was obtained by random variation and natural selection. Evolved, not designed. No one designed it.

So what's good is retained and the next variation is tested.
A safecracker does pretty much the same thing.

Evolved? Not quite. Simply a fast and efficient means of using computers to find out what didn't work and never tried again. Randomness flies out the window as soon as something that doesn't work is checked off a list as "negative". And that's what Thomson and his computers were doing... "That didn't work so don't do it again". That's not random. That's a process of elimination storing what didn't work so it's not repeated.



You ever use a PCB autorouter?
You place the components on the board where you want them to be. Input the DRC (design rules check) and initiate. Watching it work is fascinating. You'll see traces being drawn, vias being placed and watch random variations erased if a connection wasn't made. Sometimes entire sections will be erased and the process continues again in that area. Once all the connections are made it outputs the solution as "gerber files". Those files are sent to the PCB fabricator who uses them to make the board. I suppose I could say I didn't design the board because technically speaking I didn't. The program came up with the solution. A PCB that works. All I did was get it going, sat back and it came up with a fully functional board.

Using those buzz words like evolve, natural selection, random variation and the like doesn't mean it's evolution. All that's doing is making it sound like it is. If his experiments were presented in the common language of engineering it would sound like yet another artificial intelligence research project.

When I read what Mr.Layzell was doing, "building a circuit board that will allow all the components to be measured with analogue instruments.", I knew then that whoever was reporting this stuff was the same kind of guy that is awestruck reporting on free energy and perpetual motion machines. I was doing that as a test technician who got bored with the monotony of throwing switches and watching LEDs back in '85.

 

[rthom7]

(1)

Well Barbarian your reply makes me laugh, because your not helping us have a good conversation....in Australia I would stay, "stop beating around the bush"...

Thought you knew. Neural networks don't depend on hardware, but are software or firmware.

Pedantic...not much difference between hardware and firmware...and besides FPGA circuits require hardware, software and firmware to work, and they can be used in Neural Networks too....


Here's about 80 examples of the way computers can apply evolutionary processes for practical applications.
http://en.wikipedia.org/wiki/List_of_genetic_algorithm_applications

Can you provide proper peer review links, not wiki summaries...proper science papers to back up your claims....please..

Like I have done here :-

HALL, B. 1981. EVOLUTION OF A REGULATED OPERON IN THE LABORATORY
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1201865/pdf/335.pdf



There are an unbelievable number of function necessary for bacteria. Rather than have me show you that none of them are compromised by the evolution of the new system, how about telling me which function you think no longer works?
Your not answering my question....if you make a statement off the top of your head, and I ask you to show me the context where you got your claims from, please stop beating around the bush....your being dishonest....and unfair....

If you make a claim from a science paper, and somebody asks you to show where the claims came from, why can't you show them the sentences?

When you talk from your head, people will ask where's your research papers to back up your claims....that's fair isn't it ?

You said and I quote " "Lac operon" is not what you think it is. And the bacteria can still do all the other functions, apparently because there were duplicate genes."

And I asked you where did this claim come from....

HALL, B. 1981. EVOLUTION OF A REGULATED OPERON IN THE LABORATORY
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1201865/pdf/335.pdf

Here's the paper, show me the sentences please....no mention of duplicate genes....


New genes. And it's not just natural selection, since all of them are descended from a single bacterium lacking these genes. Also, the gene in question was observed to change in several steps over the experiment, becoming more efficient. The initial gene was known, and quite unlike the final gene, which produced a different enzyme for a different substrate.

Again I have read the paper, show me where he discusses getting new genes...and where he maps the ACTG of this to show us the new genes did evolve from the new bacteria strain.

That's what gene is. Thought you knew.

I am asking you to help me read his paper.....not very smart in reading complex stuff, so a little copy and paste with your comments would be nice....

(2)

Biologists have, for some time realized that the Type III secretory system likely evolved from one type of bacterial flagellum. All the basic parts are there, so a change in microtubules and dynens would be all that would be required.

Really before 2012.... I presume? Again Barbarian you mixing the wrong categories of bacterial evolution, your link is about the presumed evolution of multiple celled organisms, whereas I want to know how the bacteria flagella of single celled organisms come about.

Here's a diagram of the flagellum normally shown by IDers and the less evolved form from Gram-positive bacteria. As you see, the more primitive form is rather like the Type III pilus. This is, of course, a macroevolutinary change in both definitions; a change in taxa, and a major reworking of a homologous feature to a new use.

Pardon my ignorance what's the difference between the Type III pilus and the type III secretory system?

The evolution of the complex flagellum is indicated by the change from the simpler Gram positive flagellum. And that?

Can I have a peer review paper supporting this claim please? I didn't know gram + flagellum is less primitive than gram - flagellum. So I would love a peer review paper explaining the evolution of the single cell bacteria flagella please.

Hope we continue useful dialogue....I would like to know more about evolution... Barbarian I note your a Christian, why do you support evolution, rather than ID ?

Shalom

 

[Barbarian]

Barbarian observes:
One problem for computer simulations of neural networks, is that computers use discrete digital components, while neurons have multiple connections and operate on an analog basis with inputs from several other neurons determining the state of that neuron.

Analog computers are not unknown Barbarian.

No kidding. Remember, I was in college in the 60s. There was still some thought that analog might be better.

Essentially, neural networks have to be set as analog processes, if they are to properly model real neuron networks.

 

[Barbarian]

Well Barbarian your reply makes me laugh, because your not helping us have a good conversation....in Australia I would stay, "stop beating around the bush"...

I'm not trying to irritate you. Often, when someone annoys me on the net, I go get an iced tea, play with the dog a bit, and go back to the conversation in a better frame of mind.

Barbarian observes:
Thought you knew. Neural networks don't depend on hardware, but are software or firmware.

Pedantic...not much difference between hardware and firmware...

My old Pentax *st DS seemed to think so. It matters a lot if your goal is to actually model biological processes.

Barbarian offers:
Here's about 80 examples of the way computers can apply evolutionary processes for practical applications.
http://en.wikipedia.org/wiki/List_of_genetic_algorithm_applications

Can you provide proper peer review links, not wiki summaries

At the bottom of the page are the cites, many of which are in the literature. Is it your argument that such applications don't exist? Would you like me to directly link you to the cites on the page?

(Barbarian asked to support his claim that the bacterium which evolved a new enzyme system, didn't lose any essential genetic information)
There are an unbelievable number of function necessary for bacteria. Rather than have me show you that none of them are compromised by the evolution of the new system, how about telling me which function you think no longer works?

Your not answering my question....

No, I guess a few tens of thousands of genes might be hard to put in one post. Again, do you have any specific loss of essential function in mind? If not, I guess I have to admit I can't list every one of them here. And that I've become the victim of a truly unique form of the Gish Gallop.

You said and I quote " "Lac operon" is not what you think it is. And the bacteria can still do all the other functions, apparently because there were duplicate genes."

Yep. Duplicate genes are numerous in bacteria, and are the most common reason that a gene can assume a new function without losing the old one.

New genes. And it's not just natural selection, since all of them are descended from a single bacterium lacking these genes. Also, the gene in question was observed to change in several steps over the experiment, becoming more efficient. The initial gene was known, and quite unlike the final gene, which produced a different enzyme for a different substrate.

gain I have read the paper, show me where he discusses getting new genes...and where he maps the ACTG of this to show us the new genes did evolve from the new bacteria strain.

The Abstract:
The evolution of new metabolic functions is being studied in the laboratory using the EBG system of E. coli as a model system. It is demonstrated that the evolution of lactose utilization by lacZ deletion strains requires a series of structural and regulatory gene mutations. Two structural gene mutations act to increase the activity of ebg enzyme toward lactose, and to permit ebg enzyme to convert lactose into allolactose, an inducer of the lac operon. A regulatory mutation increases the sensitivity of the ebg repressor to lactose, and permits sufficient ebg enzyme activity for growth. The resulting fully evolved ebg operon regulates its own expression, and also regulates the synthesis of the lactose permease.

Notice that Hall identified the gene that evolved the new function. So there it is.

That's what gene is. Thought you knew.

I am asking you to help me read his paper.....not very smart in reading complex stuff, so a little copy and paste with your comments would be nice....

Sorry. Seemed obvious to me. More detail here:
Genetica. 2003 Jul;118(2-3):143-56.
The EBG system of E. coli: origin and evolution of a novel beta-galactosidase for the metabolism of lactose.

Biologists have, for some time realized that the Type III secretory system likely evolved from one type of bacterial flagellum. All the basic parts are there, so a change in microtubules and dynens would be all that would be required.
Continued

 

[Barbarian]

Really before 2012.... I presume? Again Barbarian you mixing the wrong categories of bacterial evolution, your link is about the presumed evolution of multiple celled organisms, whereas I want to know how the bacteria flagella of single celled organisms come about.

I'll go back and check.

Here's a diagram of the flagellum normally shown by IDers and the less evolved form from Gram-positive bacteria. As you see, the more primitive form is rather like the Type III pilus. This is, of course, a macroevolutinary change in both definitions; a change in taxa, and a major reworking of a homologous feature to a new use.

Pardon my ignorance what's the difference between the Type III pilus and the type III secretory system?

Pili are things sticking out of bacteria. The pilus is the structural pare of the system.

So I would love a peer review paper explaining the evolution of the single cell bacteria flagella please.

Some helpful papers:
Annu Rev Genet. 2014;48:319-40.
The structure and regulation of flagella in Bacillus subtilis.
Abstract
Bacterial flagellar motility is among the most extensively studied physiological systems in biology, but most research has been restricted to using the highly similar Gram-negative species Escherichia coli and Salmonella enterica. Here, we review the recent advances in the study of flagellar structure and regulation of the distantly related and genetically tractable Gram-positive bacterium Bacillus subtilis. B. subtilis has a thicker layer of peptidoglycan and lacks the outer membrane of the Gram-negative bacteria; thus, not only phylogenetic separation but also differences in fundamental cell architecture contribute to deviations in flagellar structure and regulation. We speculate that a large number of flagella and the absence of a periplasm make B. subtilis a premier organism for the study of the earliest events in flagellar morphogenesis and the type III secretion system. Furthermore, B. subtilis has been instrumental in the study of heterogeneous gene transcription in subpopulations and of flagellar regulation at the translational and functional level.
........
Biotechnol Genet Eng Rev. 2014;30:49-64.
From molecular evolution to biobricks and synthetic modules: a lesson by the bacterial flagellum.
'.............
Mol Syst Biol. 2007; 3: 128.

The protein network of bacterial motility
Abstract
Motility is achieved in most bacterial species by the flagellar apparatus. It consists of dozens of different proteins with thousands of individual subunits. The published literature about bacterial chemotaxis and flagella documented 51 protein–protein interactions (PPIs) so far. We have screened whole genome two-hybrid arrays of Treponema pallidum and Campylobacter jejuni for PPIs involving known flagellar proteins and recovered 176 and 140 high-confidence interactions involving 110 and 133 proteins, respectively. To explore the biological relevance of these interactions, we tested an Escherichia coli gene deletion array for motility defects (using swarming assays) and found 159 gene deletion strains to have reduced or no motility. Comparing our interaction data with motility phenotypes from E. coli, Bacillus subtilis, and Helicobacter pylori, we found 23 hitherto uncharacterized proteins involved in motility. Integration of phylogenetic information with our interaction and phenotyping data reveals a conserved core of motility proteins, which appear to have recruited many additional species-specific components over time. Our interaction data also predict 18 110 interactions for 64 flagellated bacteria.

Hope we continue useful dialogue....I would like to know more about evolution... Barbarian I note your a Christian, why do you support evolution, rather than ID ?

I don't agree with IDers who say that the "designer" might be a "space alien." You should know that many IDers who are biologists acknowledge the fact of creation. Michael Behe, for example, is an evolutionist. He just thinks God has to step in now and then to keep things working. And Michael Denton writes:

t is important to emphasize at the outset that the argument presented here is entirely consistent with the basic naturalistic assumption of modern science--that the cosmos is a seamless unity which can be comprehended in its entirety by human reason and in which all phenomena, including life and evolution and the origin of man, are ultimately explicable in terms of natural processes. This is an assumption which is entirely opposed to that of the so-called "special creationist school." According to special creationism, living organisms are not natural forms, whose origin and design were built into the laws of nature from the beginning, but rather contingent forms analogous in essence to human artifacts, the result of a series of supernatural acts, involving God's direct intervention in the course of nature, each of which involved the suspension of natural law. Contrary to the creationist position, the whole argument presented here is critically dependent on the presumption of the unbroken continuity of the organic world--that is, on the reality of organic evolution and on the presumption that all living organisms on earth are natural forms in the profoundest sense of the word, no less natural than salt crystals, atoms, waterfalls, or galaxies.

In large measure, therefore, the teleological argument presented here and the special creationist worldview are mutually exclusive accounts of the world. In the last analysis, evidence for one is evidence against the other. Put simply, the more convincing is the evidence for believing that the world is prefabricated to the end of life, that the design is built into the laws of nature, the less credible becomes the special creationist worldview.
Michael Denton, Nature's Destiny

 

[rthom7]

Really good reply Barbarian.... let's see if we can discuss this paper together in some detail...

Hall B 1982 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1201865/pdf/335.pdf

OK you just highlighted the abstract...I have already read the abstract many times Barbarian but it makes no sense to me...lots of jargon...

If evolution of a fully integrated new
enzyme system requires several mutations, then some of those mutations may

not be selectively advantageous in the genetic background in which they arise,

but may confer a selective advantage only in the presence of a second mutation.

Such mutations would be initially neutral, but would have adaptive potential.

In this paper it is demonstrated that such mutations can and do arise in the

laboratory.
He is saying some mutations are neutral, but some how are still replicated by the cell....?

He cites his own older papers over 15 times making it hard to prove his work or understand what he is talking about..

Selection of the fully euolued strain: A spontaneous galactosyl-arabinose utilizing

mutant was selected by plating strain 5A103 onto galactosyl-arabinose

minimal medium containing 0.2 mM IPTG. Colonies that arose were purified

by restreaking them onto MACCONKEgYa lactosyl-arabinose indicator plates containing

0.2 mM IPTG. One of these galactosyl-arabinose positive isolates was

designated strain 5A1032. Strain 5A1032 was positive on MACCONKEiYnd icator

plates containing either lactose + IPTG or lactulose + IPTG. As expected,
strain 5A1032 was positive on R/ZAcCoNKEY-~actosep lates without IPTG, indicating

that it was converting lactose into an inducer of the lac operon.

What is he doing here ...?

Strain 5A1032 was mated with

the tolC rpsL ebgAo ebgR+ strain SJ7, and rpsL tolC+ recombinants

Why is he mating strains of bacteria?

We began with a lacZ deletion strain, DS4680A, that could not grow on lactose

because (a) it lacked an enzyme
So he begins with DS4680A(lactose missing genes) strain

The first evolutionary step was a mutation in the ebgA gene that allowed ebg

enzyme to hydrolyze lactose effectively. The resulting strain, 5A1, was isolated

by chance during selection for lactose utilization.
Ok how does this new strain emerge from DS4680A(lactose missing genes) to the new strain 5A1 (presumably with lactose genes)? He does not explain how....

That would be a great start Barbarian if you could explain this to me so far....

Thanks for your help...
Shalom

 

[rthom7]

Your second post of help Barbarian is terrible....If you really believe in Evolution as you claim, then why is it so difficult for you to show me really good papers...?
http://www.ncbi.nlm.nih.gov/pubmed/25251856 Your first example is just an abstract, no details, nothing unless your a paid subscriber...so please check your links, and give me the http:// links, not the title only...stop being unscientific and show me really good papers...

Your second paper is better, but again you do not have the http: so I have to find it for you.....is that a good science expert ?

Rajagopala, S, et al 2007. The protein network of bacterial motility
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1943423/

Here I have referenced it correctly for you, talking the time to do it properly...and now I have to read your paper, I assume its your best evidence ?

Quoting the paper in brown

Many features of the bacterial flagellum have changed over the course of evolution. This is reflected in the surprisingly different composition and protein interaction patterns in the flagella of different species, which may reflect adaptations to species-specific motility needs

Just because DNA can change to suit environs and this micro-evolve does not prove macroevolution...or speciation....

A major goal of this study was to find novel flagellar components among the many proteins of still unknown function.

The paper is not about evolution of bacteria flagella at all, Barbarian.

Given the amazing complexity of the bacterial motility system, we wondered whether our interaction data and phenotypes can contribute to the understanding of its evolution. As a first step into that direction, we first constructed a phylogenetic supertree of 30 species based on 35 flagellar protein families (Supplementary Figure 4).
View attachment 5917
12 pages of charts...complex and not well explained.

This shows that the flagellar system evolved together with other cellular systems and not independently
How can people write this sentence straight after a pile of charts is beyond me...explained what? nothing I can understand...jargon charts....


Whereas it is generally believed that the motility machinery evolved from an ancient type III secretion system, the detailed steps leading to current structures have yet to be defined
Barbarian you have to do better than this...my paper posted here in 2012 shows that type III came after flagella and you yourself acknowledge this, so why are you showing me an old paper?

Again my question, do you have a really good peer review paper showing the evolution of the bacteria flagella ? as a http: link please ? and written after 2012...

Shalom

 

[Barbarian]

I'm thinking that a basic text in bact. and one in genetics would be invaluable to you. You ask detailed questions, and that leads me to think you know more about it than you do.

I'll back off on the next post (I'm a little busy tonight) and see if I can't make it clearer.