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

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It appears then null hypothesis has less than a 5% probability, which effectively rules it out.
I agree Barbarian, so it means the whole simulation experiment proving that gymnosperms can by random processes obtain the same DNA sequences as angiosperms is false. And when you look into the whole PAML program to begin with, the assumptions behind the program algorithms are also artificial. Wouldn't it be easier to simply say that DNA code is in fact a code, and cannot be processed by random changes into anything meaningfully functional...Being a programmer myself, the programming nature of code is highly technical and precise.

I remember listening to the video of a scientist (linked in previous posts) that the DNA sequence has some 3D arrangements where additional or deleted Amino acids does not matter, obviously He thinks to allow for mutations to NOT affect overall function as desired, but in other protein structures a single Amino Acid in the wrong place completely spoils the functional nature of the protein. He is a genetic scientist, studying bacterial flagella for 15 years, and says the structure is just too complex as a design to be simply the result of gradualism. He cites the Secretory type III intermediate to flagella, and pulls making holes in this as an argument for gradualism. While his reasons are complex to write in simple terms, listen to his video and his experience.

I find the notion of bacteria tumble and run, run and tumble, is a random walk, is used to dumb down the motion of these creatures, but if you were blind, your walk down the street is also random until you sense something, and than follow the gradient. We need to remember how remarkable these bacteria are in seeking food out, and with sensors that include short term memory.

Shalom
 
Yep.
http://www.ncbi.nlm.nih.gov/pubmed/20547844

Even more impressive, the evolution of organelles like mitochondria and chlorplasts (which are essentially endosymbiotic bacteria with their own, bacterial DNA) has been directly observed:
The large, free-living amoebae are inherently phagocytic. They capture, ingest and digest microbes within their phagolysosomes, including those that survive in other cells. One exception is an unidentified strain of Gram-negative, rod-shaped bacteria that spontaneously infected the D strain of Amoeba proteus and came to survive inside them. These bacteria established a stable symbiotic relationship with amoebae that has resulted in phenotypic modulation of the host and mutual dependence for survival.
http://www.sciencedirect.com/science/article/pii/S0962892400889667

The video is a bit out of date. It is now known that there isn't just one sort of prokaryotic flagellum. There are two basic types, and variations in those. Irreducible complexity fell apart as an argument, when it became obvious that the Type III apparatus didn't have all the components of the flagellum, but still had a function.
Cavalier-Smith T (1987). "The origin of eukaryotic and archaebacterial cells". Ann. N. Y. Acad. Sci. 503 (1): 17–54.

So, some simpler versions:
2195833_JEM992288.f1.png


Even more to the point, the evidence shows that the flagellins are evolved from cell dynens.
"Molecular analysis of archael flagellins: similarity to the type IV pilin-transport superfamily widespread in bacteria". Canadian Journal of Microbiology 40 (1): 67–71

Behe has recently agreed that irreducible complexity can evolve naturally. Would you like to see some ways it could?

These are a few reasons why molecular biologists have rejected ID.
I will check out the videos and get back to you....thanks for the links...much appreciated....
 
It appears then null hypothesis has less than a 5% probability, which effectively rules it out.
I agree Barbarian, so it means the whole simulation experiment proving that gymnosperms can by random processes obtain the same DNA sequences as angiosperms is false.

Technically, it can't prove that this happened randomly, but it can show that it's 95% unlikely, thereby establishing that they have a common ancestor.

And when you look into the whole PAML program to begin with, the assumptions behind the program algorithms are also artificial. Wouldn't it be easier to simply say that DNA code is in fact a code, and cannot be processed by random changes into anything meaningfully functional...

Only with random variation and natural selection, have we seen functional changes in the genome. Simple random change would not work.

Being a programmer myself, the programming nature of code is highly technical and precise.

DNA is a lot sloppier than most coding. But not all coding:

"GO!" barks the researcher into the microphone. The oscilloscope in front of him displays a steady green line across the top of its screen. "Stop!" he says and the line immediately drops to the bottom.

Between the microphone and the oscilloscope is an electronic circuit that discriminates between the two words. It puts out 5 volts when it hears "go" and cuts off the signal when it hears "stop".

It is unremarkable that a microprocessor can perform such a task—except in this case. Even though the circuit consists of only a small number of basic components, the researcher, Adrian Thompson, does not know how it works. He can't ask the designer because there wasn't one. Instead, the circuit evolved from a "primordial soup" of silicon components guided by the principles of genetic variation and survival of the fittest. So how did evolution do it--and without a clock? When he looked at the final circuit, Thompson found the input signal routed through a complex assortment of feedback loops. He believes that these probably create modified and time-delayed versions of the signal that interfere with the original signal in a way that enables the circuit to discriminate between the two tones. "But really, I don't have the faintest idea how it works," he says.

One thing is certain: the FPGA is working in an analogue manner. ...

That repertoire turns out to be more intriguing than Thompson could have imagined. Although the configuration program specified tasks for all 100 cells, it transpired that only 32 were essential to the circuit's operation. Thompson could bypass the other cells without affecting it. A further five cells appeared to serve no logical purpose at all--there was no route of connections by which they could influence the output. And yet if he disconnected them, the circuit stopped working.

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.

http://www.newscientist.com/article...obody-understands-clive-davidson-reports.html

I remember listening to the video of a scientist (linked in previous posts) that the DNA sequence has some 3D arrangements where additional or deleted Amino acids does not matter,

DNA contains no amino acids. Perhaps you're thinking of the proteins coded by DNA. And yes, most mutations don't do much of anything. A few are harmful and a very few are beneficial. This is why you'd see no increase in fitness without natural selection.

He is a genetic scientist, studying bacterial flagella for 15 years, and says the structure is just too complex as a design to be simply the result of gradualism

Most scientists disagree with him, partially because there are different sorts of bacterial flagellae, and also because the subunits are very similar to simpler parts of cells, like microtubules, and kinesiens and dyniens.

I find the notion of bacteria tumble and run, run and tumble, is a random walk, is used to dumb down the motion of these creatures, but if you were blind, your walk down the street is also random until you sense something, and than follow the gradient.

One of my degrees is in bacteriology. This was figured out a long time, ago, but the mechanism was worked out recently. Changes in gradient of nutrients or noxious materials allow a change in direction by a sort of Euler buckling of the hook of the flagella rotor, changing the orientation, and thus the direction.

It's very mechanistic, and no memory required. One of the things that people do, is mistake prokaryotes for primitive organisms. In fact, they've been evolving as long as humans have. Instead of getting more complex, they've specialized in refining what they have.
 
Technically, it can't prove that this happened randomly, but it can show that it's 95% unlikely, thereby establishing that they have a common ancestor.



Only with random variation and natural selection, have we seen functional changes in the genome. Simple random change would not work.



DNA is a lot sloppier than most coding. But not all coding:

"GO!" barks the researcher into the microphone. The oscilloscope in front of him displays a steady green line across the top of its screen. "Stop!" he says and the line immediately drops to the bottom.

Between the microphone and the oscilloscope is an electronic circuit that discriminates between the two words. It puts out 5 volts when it hears "go" and cuts off the signal when it hears "stop".

It is unremarkable that a microprocessor can perform such a task—except in this case. Even though the circuit consists of only a small number of basic components, the researcher, Adrian Thompson, does not know how it works. He can't ask the designer because there wasn't one. Instead, the circuit evolved from a "primordial soup" of silicon components guided by the principles of genetic variation and survival of the fittest. So how did evolution do it--and without a clock? When he looked at the final circuit, Thompson found the input signal routed through a complex assortment of feedback loops. He believes that these probably create modified and time-delayed versions of the signal that interfere with the original signal in a way that enables the circuit to discriminate between the two tones. "But really, I don't have the faintest idea how it works," he says.

One thing is certain: the FPGA is working in an analogue manner. ...

That repertoire turns out to be more intriguing than Thompson could have imagined. Although the configuration program specified tasks for all 100 cells, it transpired that only 32 were essential to the circuit's operation. Thompson could bypass the other cells without affecting it. A further five cells appeared to serve no logical purpose at all--there was no route of connections by which they could influence the output. And yet if he disconnected them, the circuit stopped working.

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.

http://www.newscientist.com/article...obody-understands-clive-davidson-reports.html



DNA contains no amino acids. Perhaps you're thinking of the proteins coded by DNA. And yes, most mutations don't do much of anything. A few are harmful and a very few are beneficial. This is why you'd see no increase in fitness without natural selection.



Most scientists disagree with him, partially because there are different sorts of bacterial flagellae, and also because the subunits are very similar to simpler parts of cells, like microtubules, and kinesiens and dyniens.



One of my degrees is in bacteriology. This was figured out a long time, ago, but the mechanism was worked out recently. Changes in gradient of nutrients or noxious materials allow a change in direction by a sort of Euler buckling of the hook of the flagella rotor, changing the orientation, and thus the direction.

It's very mechanistic, and no memory required. One of the things that people do, is mistake prokaryotes for primitive organisms. In fact, they've been evolving as long as humans have. Instead of getting more complex, they've specialized in refining what they have.

Thanks for the cordial reply Barbarian, you write well...can I ask you to supply me some video links as to why you think the DNA is a sloppier sort of code, and some scientists who say bacteria flagella is not irreducibly complex....I am finding it difficult to find such videos of evolution experts on this matter...

Your comment about mechanistic is not really a good one because if your programming living machines at nano-scale technology (meaning the same as Binary programming) everything has to be very mechanical in the code, because your dealing with molecules that have to be controlled, not wander around in some chemical way in a beaker for example. And this nano-scale control involves structural mechanical feedback mechanisms that only add to the complexity of a living machine.

You very lucky to access New Scientist, I have to subscribe it seems...

QUOTE "DNA is a lot sloppier than most coding

I am not aware any program done by man that is functional can be sloppy, all code must have zero syntax errors, and of course can tolerate logical errors. but really be 100% perfect to run as designed.

Bill Gates observes, "Human DNA is like a computer program but far, far more advanced than any software we've ever created."21 Craig Venter says that "life is a DNA software system,"22 containing "digital information" or "digital code," and the cell is a "biological machine" full of "protein robots."23 Richard Dawkins has written that "[t]he machine code of the genes is uncannily computer-like."24 Francis Collins notes, "DNA is something like the hard drive on your computer," containing "programming."25

Reference:
21 B. Gates, N. Myhrvold, and P. Rinearson, The Road Ahead: Completely Revised and Up-To-Date (New York: Penguin Books, 1996), 228.
22 J. Craig Venter, "The Big Idea: Craig Venter On the Future of Life," The Daily Beast (October 25, 2013), accessed October 25, 2013, www.thedailybeast.com/articles/2013/10/25/the-big-idea-craig-venter-the-future-of-life.html.
23 See C. Luskin, "Craig Venter in Seattle: ‘Life Is a DNA Software System’," (October 24, 2013), www.evolutionnews.org/2013/10/craig_venter_in078301.html
24 R. Dawkins, River Out of Eden: A Darwinian View of Life (New York: Basic Books, 1995), 17.
25 F. Collins, The Language of God: A Scientist Presents Evidence for Belief (New York: Free Press, 2006), 91.


http://www.evolutionnews.org/backtoschoolguide.pdf

A very interesting brief succinct summary for ID.....that argues against gradualism. In just 36 pages...for university students alike....enjoy !!
Shalom
 
Having studied systems and information theory in graduate school, I know the idea of DNA as coding, but it has a much different way of working than any digital computer. And very few computer languages can reprogram themselves. That's the key to understanding Thompson's machine. Unlike most other computers, it does evolve. And under natural selection, random errors can lead to useful properties.

Now, you can obviously layer this on top of a computer program, and get something of the same thing. I actually got it done on a programmable desktop calculator in the 1970s, but much better things are done today. Engineers are using genetic algorithms to solve problems that are too complicated by design, using Darwinian evolution. They start with an inefficient initial solution, allow random variation of that solution, and then pare away all but them most efficient of the new solutions. The process repeats. As in living populations, the fitness of the solutions rises until it fluctuates around an optimum. It's like that bacterial flagellum in which the hook buckles under force; a failure of the structure was adapted to serve a useful function.

For highly complex things, like living things, this beats design every time. It seems God chose the most elegant solution, which is what we always see in nature. If a theory is conceptually ugly, it almost always turns out to be wrong.
 
Having studied systems and information theory in graduate school, I know the idea of DNA as coding, but it has a much different way of working than any digital computer. And very few computer languages can reprogram themselves. That's the key to understanding Thompson's machine. Unlike most other computers, it does evolve. And under natural selection, random errors can lead to useful properties.

Now, you can obviously layer this on top of a computer program, and get something of the same thing. I actually got it done on a programmable desktop calculator in the 1970s, but much better things are done today. Engineers are using genetic algorithms to solve problems that are too complicated by design, using Darwinian evolution. They start with an inefficient initial solution, allow random variation of that solution, and then pare away all but them most efficient of the new solutions. The process repeats. As in living populations, the fitness of the solutions rises until it fluctuates around an optimum. It's like that bacterial flagellum in which the hook buckles under force; a failure of the structure was adapted to serve a useful function.

For highly complex things, like living things, this beats design every time. It seems God chose the most elegant solution, which is what we always see in nature. If a theory is conceptually ugly, it almost always turns out to be wrong.
Wow Barbarian you write some interesting stuff here....can you give me some links to where I can learn more of what your saying.... (not those I have to subscribe to ... )

(1) This Thompson machine for example...are you saying an artificial program code can make brand new code all by itself ? I know of neural network code, but while these are trained, they do not write brand new code by themselves....show me some links to such programs....

(2) Secondly show me some scientists on video perhaps who talk about what your saying in expert detail...
The video I posted before is an expert microbial geneticist for 15 years on bacterial flagellum, where as Michael Behe is a biochemist with a different view of things. Show me any evolutionist talking about the hook structure buckling under pressure....I would certainly love to hear these expert opinions on video and on image...I would also love to hear some expert speak of the type III secretory system, how it can evolve to flagella system and how similar are both systems ?

(3)" Engineers are using genetic algorithms to solve problems that are too complicated by design" When you speak of algorithm's, I assume your speaking of functional mathematical calculations used to solve problems, not write new code...eg using a function to calculate square roots, the more you loop the program the more accurate the solution becomes. What are you actually trying to say? Can you speak in more application terms and less riddle please, I am not following you ..

(4) "Unlike most other computers, it does evolve." What do you mean by this ? Write new code ? Remember new neural network training all by itself automatically? Please detail and start writing application terms...I would love to see this computer program that evolves ....

The only computer program that I know of that switches for changes within limits of the program code is DNA, it does not evolve (whatever that term means) but the DNA program does allow switching of parameters for reactions to environmental stimuli for survival reasons within the limits of the programming code. And this is a part of the Creation for all living kinds. But there is no evidence of DNA writing new DNA code...mutations spoil the gene code, most mutations make deletions of DNA letters , maybe add some DNA letters ?? or cause missing letters or foul up the switching processes...

(5) "Having studied systems and information theory in graduate school, I know the idea of DNA as coding, but it has a much different way of working than any digital computer. And very few computer languages can reprogram themselves" Glad to be speaking to an expert, now please detail what you mean by this statement.....Thanks...

Shalom
 
Barbarian have you considered the video of Roman Catholic by Bro. Peter Dimond O.S.B. from Most Holy Family Monastery,

He advocates Intelligent Design, and he does it well....I wonder why you consider DNA a poor sloppy sequence of chemical arrangements of ACTG....I find that conclusion surprising...Do you have any video supporting your hypothesis ?

Shalom
 
1) This Thompson machine for example...are you saying an artificial program code can make brand new code all by itself ?

It alters connections in the circuit. There is no code as such. If there was, the researcher could learn how it works. But he doesn't know; the circuit is more efficient than we know how to program, because it apparently uses some unrecognized effect to get things done.

(2) Secondly show me some scientists on video perhaps who talk about what your saying in expert detail...

In science, they write papers. No videos for the technical side. I don't view videos much for science. I make them for flipped classrooms, but never made one on evolutionary processes. I'll see if I can find you a source for he Thompson experiment. It's rather aged by now, and AI people have been implementing the process in all sorts of ways.

The video I posted before is an expert microbial geneticist for 15 years on bacterial flagellum, where as Michael Behe is a biochemist with a different view of things.

There are a few scientists who, for religious reasons, reject some part of science or another. But Behe, for example, has been shown to be wrong about his claims in various ways. Would you like to see about that?

Show me any evolutionist talking about the hook structure buckling under pressure....

Bacteria can exploit a flagellar buckling instability to change direction
http://www.nature.com/nphys/journal/v9/n8/full/nphys2676.html

Much of evolution works that way. Nature can exploit a flaw to make it a useful thing. I'm not aware of any engineers who have as yet exploited this evolutionary development, but I can see where Euler buckling could be used in machines. It's found in things like seaweed and in sea anemones in a much larger context, of course.

I would certainly love to hear these expert opinions on video and on image...I would also love to hear some expert speak of the type III secretory system, how it can evolve to flagella system and how similar are both systems ?

The great irony of the flagellum's increasing acceptance as an icon of anti-evolution is that fact that research had demolished its status as an example of irreducible complexity almost at the very moment it was first proclaimed. The purpose of this article is to explore the arguments by which the flagellum's notoriety has been achieved, and to review the research developments that have now undermined they very foundations of those arguments.


"An irreducibly complex system cannot be produced directly by numerous, successive, slight modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. .... Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on." (Behe 1996b)

At first glance, the existence of the TTSS, a nasty little device that allows bacteria to inject these toxins through the cell membranes of its unsuspecting hosts, would seem to have little to do with the flagellum. However, molecular studies of proteins in the TTSS have revealed a surprising fact – the proteins of the TTSS are directly homologous to the proteins in the basal portion of the bacterial flagellum. As figure 2 (Heuck 1998) shows, these homologies extend to a cluster of closely-associated proteins found in both of these molecular "machines." On the basis of these homologies, McNab (McNab 1999) has argued that the flagellum itself should be regarded as a type III secretory system. Extending such studies with a detailed comparison of the proteins associated with both systems, Aizawa has seconded this suggestion, noting that the two systems "consist of homologous component proteins with common physico-chemical properties" (Aizawa 2001, 163). It is now clear, therefore, that a smaller subset of the full complement of proteins in the flagellum makes up the functional transmembrane portion of the TTSS.


So the irreducible complexity argument has crashed and burned by a counterexample.

(3)" Engineers are using genetic algorithms to solve problems that are too complicated by design" When you speak of algorithm's, I assume your speaking of functional mathematical calculations used to solve problems, not write new code...eg using a function to calculate square roots, the more you loop the program the more accurate the solution becomes. What are you actually trying to say? Can you speak in more application terms and less riddle please, I am not following you ..

It's more natural in the way it works. You start with a feasible, but inefficient solution. Then the algorithm generates a number of "offspring" with random changes. The algorithm then examines them and determines which of them is more fit (more efficient than the previous generation) and retains only those most fit. Then the process repeats, always keeping the best, and removing the less efficient. The process converges on one or more optimal solutions.

I could give you a some feel for the way it works, with an exercise using dice and graph paper, if you like.

(4) "Unlike most other computers, it does evolve." What do you mean by this ? Write new code ?

It changes the connections in the circuits. This probably seems less weird to those of use who remember when you reprogrammed a machine using jumpers.

I'll see if I can find some examples for you. Years ago, someone did this with virtual circuits using LISP. But maybe you could write Thompson himself. I believe he's still in an office at the university as teacher and chair emeritus.

The only computer program that I know of that switches for changes within limits of the program code is DNA

Seems like a bad fit, trying to map the concept "program" onto DNA. More sensible to try to map hardware onto the molecule, although there are difficulties with that also. You see, DNA is not the information; it is merely the "hardware" onto which the information is "programmed" by changes in the sequence of bases. This would again be more apparent to one used to more primitive computers than to modern digital computers.

it does not evolve

Actually, it does. The code is not quite universal. It varies among different kinds of living things, and not surprisingly, according to evolutionary phylogenies worked out using other evidence. This had been predicted early on, based on evolutionary theory, but was not verified until the late 70s or early 80s.
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c

(whatever that term means)

Change in allele frequency in a population over time.

but the DNA program does allow switching of parameters for reactions to environmental stimuli for survival reasons within the limits of the programming code.

It's called "natural selection", and both recombinations from mating of sexual organisms and random mutations found in all organisms provide the necessary variation on which natural selection acts. New alleles appear in all organisms. You have a fair number of mutations that were not present in either of your parents. Most don't do much, a few are harmful, and a very few are useful. That's what natural selection does. Amazing that God was able to create such a world, but then He is God.

And this is a part of the Creation for all living kinds. But there is no evidence of DNA writing new DNA code

The Milano mutation, for example, which gives very good resistance to arteriosclerosis, made a slight change in the code for a certain lipoprotein. (the old one still exists, via a gene duplication) We know, from genetic tracing, the name of the individual in which this mutation took place, hundreds of years ago.

Bacteriologist Barry Hall observed the evolution of a new, irreducibly complex enzyme system in bacteria. The code was "written" by a series of mutations that produced a new, regulated system.

mutations spoil the gene code

Normally, they do very little. Proteins are quite large, and a change of one amino acid usually has no consquences.

most mutations make deletions of DNA letters , maybe add some DNA letters ?? or cause missing letters or foul up the switching processes...

It's more interesting than you think it is. Lots of different mechanisms and kinds of mutations. Start a new thread and we'll talk about it.

Glad to be speaking to an expert,

No expert, but I had to learn about it. You can simulate DNA functioning on a digital computer, but it is an analog process. Not surprisingly analog computers were first used to simulate it. One of the remarkable things about DNA is that some organisms will increase their mutation rate when envirionmentally stressed. Some prokaryotes will mutate at a higher rate if placed in media for which they are unfit. Without the benefit of sexual reproduction, their best bet is to do as much variation as possible, with an increased likelihood that one of the variants will survive.

Understand that there's no adaptive response in terms of the mutations arising in response to need. They are all still random. It's just that more mutations mean more chances of an adaptive mutation.
 
Thank you very much Barbarian for a really interesting and detailed reply...I am learning so much and it's interesting...

(1) Thompson's experiments. This apparently is a common style of programming similar to neural network programming, in which a black box of millions of logic gates, blah blah,

View attachment 5885

is surrounded with hardwired computer programs to train the Field-Programmable Gate Array (FPGA) to do the kind of output processing you want to achieve.

So by programming and re-programming the hardware over and over, as Thompson did until 4,0000 test trials occur, you eventually reach the desire output signals when a input signal is processed.

I have played around with neural network programs as a computer teacher, and its a simple elementary model for the FPGA concept.

Here I found an article on Thompson's work
http://www.damninteresting.com/on-the-origin-of-circuits/

The informatics researcher began his experiment by selecting a straightforward task for the chip to complete: he decided that it must reliably differentiate between two particular audio tones. A traditional sound processor with its hundreds of thousands of pre-programmed logic blocks would have no trouble filling such a request, but Thompson wanted to ensure that his hardware evolved a novel solution. To that end, he employed a chip only ten cells wide and ten cells across-- a mere 100 logic gates. He also strayed from convention by omitting the system clock, thereby stripping the chip of its ability to synchronize its digital resources in the traditional way.

Really is it necessary to bring religious bias into the work of electronic experiments "his hardware evolved a novel solution. "

He cooked up a batch of primordial data-soup by generating fifty random blobs of ones and zeros. One by one his computer loaded these digital genomes into the FPGA chip, played the two distinct audio tones, and rated each genome's fitness according to how closely its output satisfied pre-set criteria. Unsurprisingly, none of the initial randomized configuration programs came anywhere close. Even the top performers were so profoundly inadequate that the computer had to choose its favorites based on tiny nuances. The genetic algorithm eliminated the worst of the bunch, and the best were allowed to mingle their virtual DNA by swapping fragments of source code with their partners. Occasional mutations were introduced into the fruit of their digital loins when the control program randomly changed a one or a zero here and there.

Notice the strange relating this back to biological systems? "mingle their virtual DNA by swapping fragments of source code with their partners" Really did the electronic program swap DNA code with its internal FPGA circuitry ? Why the biased intent of the author ?

"Occasional mutations" Now I have written many a neural network programme, its obviously similar to the FPGA circuitry programming, and I wonder how in just 200 training rules a connect four game simulator is already 60% smart in making clever moves, but I would never say the internal circuitry is making "Occasional mutations" .


OK I am satisfied that the Thompson machine did not achieve anything special electronic experts are already using neural network with FPGA circuit in lots of application around the world. It is not an example of evolution.

Now if you could write a program capable of sensing by itself and making intelligence by itself you would have something, true AI.


(2) Genetic codes. This is really interesting and research ongoing.

So do we have the codons of life ? or still learning?

Barbarian do you have any videos showing DNA sequences changing with new information...
letter swapping is nice, but not really complex model.

(3) My own research do far. Please critique. http://spiritualsprings.org/ss-1120.htm

Is my assessment of general theory of evolution OK ?

http://spiritualsprings.org/ss-1123.htm

Is my concept of ID as a science OK ?

View attachment 5886
What about this idea for ED and ID?

http://spiritualsprings.org/ss-1124.htm
Here I show from Scripture source of Designers

I also show type III systems fairly,
but note they are not really close to flagella
62% similar proteins for example.

http://spiritualsprings.org/ss-1125.htm
Here is the real good part
Can DNA macro-evolve naturally?

It's unfinished because man cannot even do DNA sequenced complex information changes yet...

Shalom
 
So by programming and re-programming the hardware over and over, as Thompson did until 4,0000 test trials occur, you eventually reach the desire output signals when a input signal is processed.

Except Thompson didn't do the programming. He doesn't even know how the program works. He merely set the parameters for fitness, and the machine did the rest.

What you're describing is the way evolution works. The machine was left to randomly change and to keep the most efficient changes. That's what evolution does. Engineers use it regularly now, for very complex problems.

Combining Neural Networks and Genetic Algorithms to Predict and Reduce Diesel Engine Emissions
Alonso, J.M. ; High Performance Networking & Comput. Group, Univ. Politecnica de Valencia
Diesel engines are fuel efficient which benefits the reduction of CO2 released to the atmosphere compared with gasoline engines, but still result in negative environmental impact related to their emissions. As new degrees of freedom are created, due to advances in technology, the complicated processes of emission formation are difficult to assess. This paper studies the feasibility of using artificial neural networks (ANNs) in combination with genetic algorithms (GAs) to optimize the diesel engine settings. The objective of the optimization was to find settings that complied with the increasingly stringent emission regulations while also maintaining, or even reducing the fuel consumption. A large database of stationary engine tests, covering a wide range of experimental conditions was used for this analysis. The ANNs were used as a simulation tool, receiving as inputs the engine operating parameters, and producing as outputs the resulting emission levels and fuel consumption. The ANN outputs were then used to evaluate the objective function of the optimization process, which was performed with a GA approach. The combination of ANN and GA for the optimization of two different engine operating conditions was analyzed and important reductions in emissions and fuel consumption were reached, while also keeping the computational times low

The Dover Trial ended with the finding that ID is a religious doctrine. Among the evidence and testimony that convinced the court was Behe's admission that ID was science in the same sense that astrology is science, and the evidence showing that the "ID text book" Of Pandas and People was actually a creationist book with references to God replaced by the term "designer." One typo actually showed the incomplete removal of God from the text.

In your blog, the most notable error is in the assertion that science doesn't allow irreducible complexity. There are many ways that irreducible complexity can evolve.
 
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Except Thompson didn't do the programming. He doesn't even know how the program works. He merely set the parameters for fitness, and the machine did the rest.

What you're describing is the way evolution works. The machine was left to randomly change and to keep the most efficient changes. That's what evolution does. Engineers use it regularly now, for very complex problems.

Combining Neural Networks and Genetic Algorithms to Predict and Reduce Diesel Engine Emissions
Alonso, J.M. ; High Performance Networking & Comput. Group, Univ. Politecnica de Valencia
Diesel engines are fuel efficient which benefits the reduction of CO2 released to the atmosphere compared with gasoline engines, but still result in negative environmental impact related to their emissions. As new degrees of freedom are created, due to advances in technology, the complicated processes of emission formation are difficult to assess. This paper studies the feasibility of using artificial neural networks (ANNs) in combination with genetic algorithms (GAs) to optimize the diesel engine settings. The objective of the optimization was to find settings that complied with the increasingly stringent emission regulations while also maintaining, or even reducing the fuel consumption. A large database of stationary engine tests, covering a wide range of experimental conditions was used for this analysis. The ANNs were used as a simulation tool, receiving as inputs the engine operating parameters, and producing as outputs the resulting emission levels and fuel consumption. The ANN outputs were then used to evaluate the objective function of the optimization process, which was performed with a GA approach. The combination of ANN and GA for the optimization of two different engine operating conditions was analyzed and important reductions in emissions and fuel consumption were reached, while also keeping the computational times low

The Dover Trial ended with the finding that ID is a religious doctrine. Among the evidence and testimony that convinced the court was Behe's admission that ID was science in the same sense that astrology is science, and the evidence showing that the "ID text book" Of Pandas and People was actually a creationist book with references to God replaced by the term "designer." One typo actually showed the incomplete removal of God from the text.

In your blog, the most notable error is in the assertion that science doesn't allow irreducible complexity. There are many ways that irreducible complexity can evolve.

You didn't agree with the way the article described Thompson's work, Barbarian... he was designing a way to recognize sound waves, yet talks about evolving this and that, and speaks of mutations, as I posted before...what a physics programming exercise has to do with biology I never know...

Glad you posted a FPGA program is similar to neural networks...but you are not acknowledging my points with that also...FPGA programs, like Neural Network programs are NOT examples of evolution, nor never will be....

They have to be trained by "god" like Intelligent Designers, before they even begin to work properly as the ID Designer wants it to work, so its not an example of evolution at all, more like an example of ID programming if anything....

I take it you didn't look at my work, or wish to make constructive comments?
http://spiritualsprings.org/ss-1125.htm

In this webpage, I was hoping for a discussion at least in how similar is the intermediate function type III system to a flagella organelle...

Perhaps you might like to tell me how DNA sequence code comes about in bacteria changing the DNA strand with additional switches and gene code please?
 
You didn't agree with the way the article described Thompson's work, Barbarian... he was designing a way to recognize sound waves, yet talks about evolving this and that, and speaks of mutations, as I posted before...what a physics programming exercise has to do with biology I never know...

He set it up to work the way evolution does. Random variation, keep anything that works better, delete anything that doesn't. Over many interations, fitness increases.


They have to be trained by "god" like Intelligent Designers, before they even begin to work properly as the ID Designer wants it to work,

Not in these cases. Often, as in Thompson's case, he doesn't even know how it works. Certainly, he didn't design it.

its not an example of evolution at all,

That's the way evolution works. Many people don't really get it, and suppose some kind or orthogenesis. It's not like that at all.

I take it you didn't look at my work, or wish to make constructive comments?

Mentioned one, above.

[homology]In this webpage, I was hoping for a discussion at least in how similar is the intermediate function type III system to a flagella organelle...[/quote]

Homology. Mostly the same parts, different use. The eubacterial and archaeal flagella are analogous. Different parts, same function.

Perhaps you might like to tell me how DNA sequence code comes about in bacteria changing the DNA strand with additional switches and gene code please?

Random mutation and natural selection. Here's an example:

Genetics. Jul 1982; 101(3-4): 335–344.

Evolution of a Regulated Operon in the Laboratory
Barry G. Hall
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.

 
I will ignore your comments regarding Thompson's experiments, Barbarian, perhaps you have not done any Neural Network programming or FPGA programming before, and do not understand that electronic logic gate switching and making new field affects is not really the same as evolution, for to achieve the output the circuit pathways are already defined within the black box, but for biological evolution to achieve a beneficial output a new DNA sequence is required, not just changing additional circuitry but adding whole circuits and hardware switches as well....so you model you propose is nothing like macroevolution, microevolution maybe...but I never want to discuss microevolution, its already a part of ID as well as evolution theory for minor changes within existing DNA programming.

Now as for your example of DNA changing to a new sequence of code, this again is a mutation of affecting an existing operon or gene or switch on the Ecoli DNA strand, and so making a slight benefit to a new Lac operon ....again this this microevolution...
you have lost the lactose gene in favour of another operon gene....now retain the original lactose gene to eat lactose and build the precursor of a brand new gene such as for the Lac operon , and you might have a major break through for macro-evolution....love to see a link to something like that....

Shalom
 
Electronics engineering, design, testing, quality control are a few hats I've worn during my career.
Any circuit board or firmware programmed is designed to function as the engineer's creativity allows.

I continue to follow ongoing technology at home. I use a CAD program to design the circuitry (schematics) design surface mount PC boards again through CAD, send the gerber files to a fabricator (OSH PARK), assemble/prototype using a Vision Mantis binocular overhead microscope, program, test and revise the board/s and circuitry as needed.
I use microprocessors and various types of memory extensively. I write my own code/firmware favoring machine language (direct manipulation of a processor's registers)
Circuits/programs don't "evolve". They perform their prescribed tasks.

Bottom line:
It's intelligent design. Not evolution.
 
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Electronics engineering, design, testing, quality control are a few hats I've worn during my career.
Any circuit board or firmware programmed is designed to function as the engineer's creativity allows.

I continue to follow ongoing technology at home. I use a CAD program to design the circuitry (schematics) design surface mount PC boards again through CAD, send the gerber files to a fabricator (OSH PARK), assemble/prototype using a Vision Mantis binocular overhead microscope, program, test and revise the board/s and circuitry as needed.
I use microprocessors and various types of memory extensively. I write my own code/firmware favoring machine language (direct manipulation of a processor's registers)
Circuits/programs don't "evolve". They perform their prescribed tasks.

Bottom line:
It's intelligent design. Not evolution.

Well said brother Rick, I have had only the privilege of doing a CAD design of circuits for PCB of surface mount technology only once, as part of my electronics engineering degree, we also did many different types of programming with several computer hardware types, so I can tell you what the interior logic gates of field affect circuits are fixed, they do have the ability to make new pathways inside, in a electronic way that is difficult to understand....I admire science to designing such intelligent circuits...I wonder if GOD didn't also design such circuits in some of the genome for the DNA for animals too. Such a design would allow under extreme conditions of bad envirnoments previously unknown to God's orginal design of how they should live to change to suit the conditions...some might call this evolution as some do....but really its a Intelligent Design on the part of the programmer to make circuits capable of changing themselves within the limits of the hardware....And it's these limits of change within the confines of hardware and software programming that makes Intelligent Design what it is. I thinks its rather clever of GOD to deign species variability and change in a kind of animals. Its saves having to design an organism for every unique circumstance and every environmental change it may likely come up against. Seeing God foreknew the impact of mutations, we would predict to see within the DNA system machine numerous molecular motors for removing the damage caused by mutations. We would also see lots of redundancy built into the genome to counter mutation so the vital ingredients of living can continue even if whole genes are damaged, others can take their place. Indeed the DNA programme is so complex that the error fixing and editorial repair of the DNA molecule is mind boggling and complex. It is even capable of fixing double break of the DNA strand within seconds....there are electrical conduits and passive insulators in the DNA strand so enzyme's can rapidly test for mistakes rapidly using processes similar to how engineers local fault kilometres along underground wire systems. And my predictions science will discover the life in the cell will become more and more complex over time.

One thing Science does not realize if human engineer's before us before the great flood were also fiddling with genetic changes....one such obviously creation is malaria, a genetic engineering of a protozoan and bacteria in some ancient lab. Some also do not realize is Satan and his angels have changed the genome to suit their world, where does evidence of dysfunctional evolution comes from? Not God...His design was very good.

What does amalgamation mean in the Bible, and is there any evidence?

Ps 7:14 Behold, he travaileth with iniquity "aven", and hath conceived mischief, and brought forth "yalad" falsehood.

The above Bible verse is profound and a key text. It describes the evil one making born "aven", which we will discover leads to Evolution, and the corruption of all life forms designed by GOD perfectly during Creation.

aven.bmp
Strong's 205 "aven"
The Ancient Hebrew reads "The Strong secure Seed"
or
"The Strong secure Seed over the nations"

Comes in positive form I and negative form II

Jeff Benner translates these two forms as action words, vigor and vanity (its opposite).

The Bible has two meanings for the “strong fixed seed” Hebrew “Aven” :-
  • (1) The power within the gene pool for functional work or
  • (2) The power within the gene pool for dysfunctional work.

In a positive sense through Jesus our gene pool can have vigor as it receives divine strength from GOD.
In a negative sense through Satan our gene pool can express propensities of vanity that make us do wickedness in the sight of GOD.

The gene pool is inherited from Adam through successive generations; the expression of that gene pool depends upon how the cognitive mind is nurtured.

Isa 59:4 None calleth for justice, nor any pleadeth for truth: they trust in vanity, and speak lies; they conceive mischief, and bring forth "talad" (born) iniquity "aven" "genetic propensities".
  • 5 They hatch cockatrice' eggs, and weave the spider's web: he that eateth of their eggs dieth, and that which is crushed breaketh out into a viper.

The Bible records here poetry symbols of genetic amalgamations gone wrong

Now let us explore the Hebrew word "aven" and see applications for this word.
Job 15:35 They conceive mischief, and bring forth "yalad" (born) vanity (propensities of vanity), and their belly prepareth deceit. (KJV)
Propensities are like our epi-genetics that sit over our "good" genetic expressions of potential and rule over us instead of our "good" genes. Such epi-genetices is born or passed on by parents or other adults making dysfunction through the process of conception.

Ps 6:8 ¶ Depart from me, all ye workers of iniquity(propensities of vanity), for the LORD hath heard the voice of my weeping.

How sad that peer group pressure is the greatest threat to the development of our own "Strong secure Seeds" either for vigor (good) or propensities for vanity (bad)?

Ps 7:14 Behold, he travaileth with iniquity(propensities of vanity), and hath conceived mischief, and brought forth (born) falsehood.

Satan can influence our "Strong secure Seeds" awaking genes into propensities of vanity, which come ready to give birth to mischief.

Ps 10:7 His mouth is full of cursing and deceit and fraud: under his tongue is mischief and iniquity(propensities of vanity).

Zones of influence (foul language, and immoral acts) impact upon our epi-genetics, thus we pass on our propensities for vanity, to our children through the conception process.

Ps 59:2 Deliver me from the workers of iniquity(propensities of vanity) , and save me from bloody men.

Violence is the ultimate climax of Satanic propensities unleashed.

Ps 66:18 If I regard iniquity(propensities of vanity) in my heart, the Lord will not hear me.

This verse explains why so many so called Christians are powerless with Jesus, because they are not overcoming all known and ignorant propensities in their lives.
This is not a reference to sinning even, wilful or ignorant. This is a reference to the epi-genetic potential in your to sinning, you must pray for the Holy Spirit to remove.

1Jo 3:6 Whosoever abideth in him sinneth not: whosoever sinneth hath not seen him, neither known him.

This verse is written correctly with power. If we are not overcoming every propensity in our lives, we are powerless before Jesus, and He does not hear us. Pray, fast and meditate in Him, ask Jesus to cut your away your flesh and give you His flesh, the creative task of quickening which only the Holy Spirit can do in you, to Jesus glory. Be clean, and be found with no guile in your mouth.

Pr 6:18 An heart that deviseth vain (wicked)(propensities of vanity) imaginations, feet that be swift in running to mischief,

Propensities begin in the mind with our thoughts and imaginations. These thoughts awaken certain gene expressions, causing a cognitive habit of the mind leading to some dysfunctional sin.

Pr 12:21 ¶ There shall no evil(propensities of vanity) happen to the just: but the wicked shall be filled with mischief.

The righteous do not evil propensities, only the wicked do.

Pr 22:8 ¶ He that soweth iniquity shall reap vanity:sadpropensities of vanity) and the rod of his anger shall fail.

We reap what we sow. If our minds think dysfunctional thoughts we will awaken genes to produce evil propensities. If we produce children these propensities are inherited by our children in their epi-genetics.

So in summary there is a Hebrew word for "genes" in Scripture. Shalom
 
Thanks Rick, I wish others would read and appreciate how evolution does NOT work as well. I was doing some reading this afternoon looking for examples of simple bacteria with even simpler examples of flagellum.

I found none...

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 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...
View attachment 5903
Here is some of their results, they assert the bacteria evolved the flagella first, and the secretory type III system evolved later through mutational destruction of an existing complex organelle. That fits perfectly God's design for bacteria helping mankind with food and DNA fragments for life, and later as a result of sin, Satan changed the design into something for disease...or mutations did...which I doubt...even the disease secretory type III system is too advantaged for mutation changes at random....

I was hoping for a paper to show evolution from type III to flagella....well the paper is dated 2012 ---so much for evolution models before 2012 for intermediate functional designs...they will have to think of something else....

Shalom
 
Genetic propensity...
The sinful nature
And the mix of some truth with a lie as seen in the Garden, working through the pride of man, "propensity to vanity", his greatest weakness, to widen the chasm toward reconciliation with God wrought with an ancient technology man as come to believe was of his own devise in pursuit to be as it were God.

Science is the God-given gift to man that he may stand in ever-increasing awe of God's glory and power.
Science is not an entity of it's own but a means to collect data of God's Creation. It is the mind of man that provides the conclusions.
There can be no excuse.
 
Nice quotes and good research brother Rick...Science is not an entity of it's own but a means to collect data of God's Creation
Well said...

.(1)

The point of my post is to show that scripture has genetic words, indeed Science even if one is willing to read it so...

View attachment 5905
The Hebrew word "aven" Strong's 205 reads as shown. The letters of each ancient pictograph contains a meaning in itself...the first letter is a bull's horns
or ox, and means "strong" the second letter is a tent peg, and means "secure" or "fixed" and the third letter is a sperm travelling, and means "seed" of the next generation, or "across the nations".

So the word reads "the Strong secure seed, ...across the nations"

http://spiritualsprings.org/ss-5.htm Many scholars scoff at the ability to read ancient Hebrew pictograph script....see my study of it....yes it is not much use to read all the time, but as a tool like any tool, it is also useful....I got the idea from
Jeff Benner's research on Hebrew.... http://www.ancient-hebrew.org/ He writes an interesting take on Hebrew language in the Bible....I like him because like me he does not see Hebrew words with multiple meanings, each word has a single basic meaning regardless of its context....as any language does....though some multiply words do exists, it's rare...

Interestingly Jeff Benner list this word with two opposite meanings, the inherent vigor for life and the genetic destruction against life.

.(2)


This video by Robert Carter is very good showing other genetic proof using the Bible....he too is a genetic scientist....

The point is there is a lot of genetics in Scripture verified by Science, if we seek the truth and make predictions from Scripture carefully...

Have a listen, he's a great genetic scientist and knows he's stuff...

He genetically proves the human race coming from 3 or 4 women lines...coming out from Noah's boat...

Shalom
 
I will ignore your comments regarding Thompson's experiments, Barbarian

Most creationists go that way, when they discover that the circuit was not designed, but merely evolved from random changes and natural selection. As you know, engineers are now using that process to solve problems that are too complex for design.

In artificial intelligence, an evolutionary algorithm (EA) is a subset of evolutionary computation, a generic population-based metaheuristic optimization algorithm. An EA uses mechanisms inspired by biological evolution, such as reproduction, mutation, recombination, and selection. Candidate solutions to the optimization problem play the role of individuals in a population, and the fitness function determines the quality of the solutions (see also loss function). Evolution of the population then takes place after the repeated application of the above operators. Artificial evolution (AE) describes a process involving individual evolutionary algorithms; EAs are individual components that participate in an AE.

Evolutionary algorithms often perform well approximating solutions to all types of problems because they ideally do not make any assumption about the underlying fitness landscape; this generality is shown by successes in fields as diverse as engineering, art, biology, economics, marketing, genetics, operations research, robotics, social sciences, physics, politics and chemistry
http://en.wikipedia.org/wiki/Evolutionary_algorithm

I've been out of the field for a few years, and I was pleased to see that two of the concerns we had at USC are being addressed; the macroevolutionary processes in which a feature jumps to an entirely new function, like the clock in Thompson's experiment, and the (in our time) lack of distinction between genotype and phenotype. Those are now the cutting edge of evolutionary computation in genetic algorithms.


perhaps you have not done any Neural Network programming or FPGA programming before

We called them "meat machines." The trick was to somehow mimic the sort of processing going on between neurons, by building analogs in electronics, or to program such a thing ("the computer dreaming of being a robot" as Searle put it) Didn't do much with that, though. Fun to go to the lab and mess with it.

When I started, in the mid-70s, it seemed like an impossible task. But by the late 70s, a considerable amount of progress had been made.

and do not understand that electronic logic gate switching and making new field affects is not really the same as evolution, for to achieve the output the circuit pathways are already defined within the black box

Except for Thompson's timer. It's perfect. Evolution is all about homology, and repurposing things.

but for biological evolution to achieve a beneficial output a new DNA sequence is required

A mutation, in other words. Genetic algorithms do it above the level of switches, in a virtual space.

not just changing additional circuitry but adding whole circuits and hardware switches as well....so you model you propose is nothing like macroevolution, microevolution maybe...but I never want to discuss microevolution, its already a part of ID as well as evolution theory for minor changes within existing DNA programming.

In biology, "microevolution" is variation within a species, and "macroevolution" is evolution that produces new taxa. Speciation, in other words. It's difficult for people to understand that the evolution of a new digestive organ (observed in Italian wall lizards) is microevolution, because it did not make the population reproductively isolated, while a single point mutation can cause reproductive isolation, and thereby cause macroevolution. In the case of ring species, the extinction of one local population can retroactively change microevolution to macroevolution.

Now as for your example of DNA changing to a new sequence of code, this again is a mutation of affecting an existing operon or gene or switch on the Ecoli DNA strand, and so making a slight benefit to a new Lac operon

No. Not only is the new enzyme different than any previous enzymes, a new regulator formed, which shuts off the new enzyme when the substrate is not present. So we have a new, irreducibly complex system, formed by random mutation and natural selection. That information did not exist prior to those mutations.

you have lost the lactose gene in favour of another operon gene...

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.
 
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