[_ Old Earth _] A number reasons why I find Evolution impossible to believe!

[Barbarian]

Barbarian observes:
No. Laws are weaker things than theories.

Ok, we are just going to have to agree to disagree there.

It's not arguable. It's a matter of fact. As you see, laws predict things. Theories predict and explain things. Hence, they are more useful and stronger statements of fact.

Barbarian observes:
And molecular biologists have shown that the visual pigments were preceded by simpler substances that were also light-sensitive.

That is simply not true.

Demonstrably so. For example, the most primitive rhodopsin known, turns out to be a means for bacteria to do phosphorylation (critical to all cells for energy).

The observation is just not true, Barbarian.

I showed you the research documenting it.

ALL visual pigments consist of an opsin combined with the chromophore 11-cis-retinal.

Since proteorhodopsin can function as a light-detecting agent, show us that it is combined with 11-cis-retinal. I don't know the answer, but evolutionary theory would suggest that a slightly different molecule would be involved.

Since they all use 11-cis-retianal, there are no predecessors.

We'll wait until you show us on that one.

Other rhodopsins use isomers of retinal, but there is no "simpler substance" relevant to visual pigments.

So a different molecule, as I anticipated.

Also, the bacteria rhodopsin is not a visual pigment, it uses an isomer of 11-cis-retinal, and there is no relation between eukaryote rhodopsins and prokaryote rhodopsins.

Well, let's take a look...

However, an important preliminary consideration is that it is obvious from our results (Fig. 2) that rhodopsin sequences provide reasonable phylogenetic
information only for relatively closely related species. Several data can be used to determine the age of the splits that separated organisms that appear in supported groups in our trees. It turns out that they are separated by a few hundreds of millions of years of independent evolution. Thus, estimates of divergence time among archaea allowed the origin of all species containing archaeal type 1 rhodopsins to be traced back in time to about 700 million years ago (Ihara et al. 1999).

Quote Originally Posted by Barbarian View Post
The simplest light-sensitive substance, BTW, is silver nitrate. The simplest organic substance that is sensitive to light... (Barbarian checks)

Indole-3-acetic acid

It's an auxin, a substance sensitive to light, that is responsible for plants growing toward the Sun.

Pretty simple, no?

Yes, nice to know that's the simplest. Not that it matters but it's an inorganic compound.

Auxins:
Any of a group of organic compounds which, when applied in low concentration, are able to promote elongation growth of plant shoots excised from a growing region of a young seedling. The ability to increase the rate of shoot elongation is a key to the designation of a synthetic or naturally occurring compound as an auxin. However, auxins, and the other plant hormones, influence a variety of plant processes during various stages of plant development.
McGraw-Hill Science and Technology Encyclopedia

The IUPAC Blue Book on organic nomenclature specifically mentions urea[3] and oxalic acid.[4] Other compounds lacking C-H bonds that are also traditionally considered to be organic include benzenehexol, mesoxalic acid, and carbon tetrachloride. Mellitic acid, which contains no C-H bonds, is considered to be a possible organic substance in Martian soil. All do, however, contain C-C bonds.[5]
http://en.wikipedia.org/wiki/Organic_compound

IUPAC is generally accepted by chemists as the definitive source for organic compounds.

Molecules can be simple like water or extremely complex like ATP synthase, depending on their atomic size and structure. They can have different forms and functions, but I don't get using the term evolve to describe chemical reactions.

The shape of the enzyme gradually changed. Here's how it works:

A molecule is effectively inactive with a specific substrate.
A random mutation, affecting the amino acid sequence changes the shape of the molecule, making it more effective at catalyzing the reaction.
Other mutations that don't make it so effective are lost, as the bacteria having them are unable to compete with the more effective ones.
This more effective group form the new gene pool, and the process repeats.
Eventually, the molecule evolves into a very efficient form.

My comment was about using the term evolve to describe chemical reactions.

Not chemical reactions. Molecules. Molecules evolve as any other property of organisms can evolve.

I can't make any sense from that reply, it begins with a molecule then switches to mutated gene sequence. Evolution applies to species, not chemical reactions.

Evolution applied to populations. And just as anatomical changes can evolve, so can biochemical changes.

It demonstrated critical parts and photoreceptive properties of 11-cis-retinal were present in a rhodopsin of a microbe. Even though they're isotopes 11-cis-retinal works better than 13-cis-retinal.

And yes, it is a huge jump from a light pump to a light sensor.

Barbarian:
Not a light pump. An energy pump. And as you see, one of the most primitive of the rhodopsins, proteorhodopsin can do both.

I meant light-driven pump. Proteorhodopsin doesn't do both.

Apparently, it does:
http://classes.biology.ucsd.edu/bisp194-2.SP10/Downloads/Wk3P2_Proteorhodopsins-Science00.pdf

Even if it did, both systems are irreducibly complex.

As you see, irreducibly complex systems can evolve. Even Behe has now admitted that they can.

There are several changes that would have to be made at the same time to change a pump into a sensor.

Nope. Notice that the evolution of an irreducibly complex enzyme system did not require multiple simultaneous mutations.

 

[Vaccine]

Behe was being disingenuous by redefining what he meant by a multipart system being knocked out.

1 part, the rest of the system was there. Halls own words:
"..thus re-acquisition of lactose utilization requires only the evolution of a new ß-galactosidase function. (Hall 1999)

in the laboratory as a model for the way biochemical pathways might evolve so that they are appropriately organized with respect to both the cell and its environment. It is reasonable to ask whether this model might have any relationship to the real world outside the laboratory. If it is assumed that the selection is strictly for lactose utilization, then a growth advantage exists only when all three mutations are present simultaneously. (Hall 1982a)

There were three steps to get from the deleted gene, to a functional one and the scientists choose every step.

Wrong again. Hall says random mutations, and he didn't pick any of them.

Halls own words:
"The mutations described above have been deliberately selected..."

"Neither the constitutive nor the inducible evolved strains grew on lactose in the absence of IPTG. (Hall 1982b)"
IPTG is an agent which stimulates ß-galactosidase production. In other words if they didn't add the stimulant, all the bacteria died. They kept the e.coli alive with a stimulant and choose every step. In their defense, they acknowledged there wasn't any relation to the real world.

In other environments, it would have done something different. The IPTG issue is just a bunny trail to cover what Hall discovered.

In other environments the ecoli didn't grow. Hall mentioned that.
Halls own words:
Neither the constitutive nor the inducible evolved strains grew on lactose in the absence of IPTG.

 

[Vaccine]

Since proteorhodopsin can function as a light-detecting agent, show us that it is combined with 11-cis-retinal. I don't know the answer, but evolutionary theory would suggest that a slightly different molecule would be involved.

It is only believed to function as a sensor, it binds to all-trans-retinal, 7-cis,9-cis,11-cis,13-cis are all isomers of the retinal molecule.
http://en.wikipedia.org/wiki/Proteorhodopsin

Since they all use 11-cis-retianal, there are no predecessors.

We'll wait until you show us on that one.

"Moreover, of all the possible isomers, only 11-cis-retinal can be the chromophore part of a visual pigment molecule."
http://encyclopedia2.thefreedictionary.com/photoreception

The whole point of bringing this up was life can't be broken down any further than the molecular level. What scientists are finding is there are machines, pumps, motors, generators, sensors, and information storage all exist on a molecular level. There are no pecursors to moleules, nothing for nature to select. Darwins theory is incapable to explain this lilliputian world full of machines and complexity.

The simplest light-sensitive substance, BTW, is silver nitrate.......

Yes, nice to know that's the simplest. Not that it matters but it's an inorganic compound.

Auxins:....

I was referring to silver nitrate, not auxins.

Not chemical reactions. Molecules. Molecules evolve as any other property of organisms can evolve.

Molecules "are a group of atoms bonded together, representing the smallest fundamental unit of a chemical compound that can take part in a chemical reaction".
H2O is a water molecule, C10H16N5O13P3 is an ATP molecule.
View attachment 3469

Molecules themselves don't evolve. ATP didn't evolve, organisms build molecules like that to make energy.

And yes, it is a huge jump from a light pump to a light sensor.

Barbarian:
Not a light pump. An energy pump. And as you see, one of the most primitive of the rhodopsins, proteorhodopsin can do both.

I meant light-driven pump. Proteorhodopsin doesn't do both.

Apparently, it does:
http://classes.biology.ucsd.edu/bisp194-2.SP10/Downloads/Wk3P2_Proteorhodopsins-Science00.pdf

That article you linked to said nothing whatever about proteorhodopsin. It was the other link that mentioned "it is believed" they operate as sensors.

As you see, irreducibly complex systems can evolve. Even Behe has now admitted that they can.

That's a pretty bold claim, got a quote for that?

 

[Barbarian]

Barbarian observes:
Behe was being disingenuous by redefining what he meant by a multipart system being knocked out.

1 part, the rest of the system was there.

Behe says that Hall did not wipe out a "multipart system" as I claimed; he deleted just one gene. Well, that's what I wrote, too. My description clearly and correctly states that Hall started his experiments "by deleting the structural gene for galactosidase," a single gene. However, I did indeed write that this deletion had knocked out a "multipart system." Why? Because once the gene was deleted, three components had to evolve to replace its function: First, a new galactosidase enzyme, second, a new lactose-sensitive control region, and third, a new way to switch on the lac permease gene. And, just as Futuyma and I pointed out, that's exactly what happened - all three parts eventually evolved. Kenneth Miller.

Behe just changed the goal posts and accused Miller of saying something that he did not.

Quote Originally Posted by Barbarian View Post
There were three steps to get from the deleted gene, to a functional one and the scientists choose every step.

Wrong again. Hall says random mutations, and he didn't pick any of them.

Halls own words:
"The mutations described above have been deliberately selected..."

When there are ellipses in quote-mining, it usually means someone is distributing taffy. Show us what it actually says, with a checkable source.

IPTG is an agent which stimulates ß-galactosidase production. In other words if they didn't add the stimulant, all the bacteria died. They kept the e.coli alive with a stimulant and choose every step.

Explain how producing an environment in which the bacteria could live, means that the evolution of those new molecule didn't happen.

And of course, Hall didn't "choose every step." He doesn't even know how to induce specfic mutations.

In their defense, they acknowledged there wasn't any relation to the real world.

And of course that, not true. Hall pointed out that the evolution of a new system through random mutations and natural selection is what happens in the real world.

In other environments, it would have done something different. The IPTG issue is just a bunny trail to cover what Hall discovered.

In other environments the ecoli didn't grow. Hall mentioned that.

Some. But in other environments, it would. Depending on what the food happened to be. The issue is whether or not a substance that allowed the substrate into the cell, means that the subsequent evolution didn't happen. And no, that's not what it means.

Behe is changing his own rules, to find a way to explain away what happened.

 

[Sparkey]

Halls own words:

"The mutations described above have been deliberately selected..."

When there are ellipses in quote-mining, it usually means someone is distributing taffy. Show us what it actually says, with a checkable source.

Here's a source that I've found (so we may read without ellipses)

The mutations described above have been deliberately selected in the laboratory as a model for the way biochemical pathways might evolve so that they are appropriately organized with respect to both the cell and its environment. It is reasonable to ask whether this model might have any relationship to the real world outside the laboratory. If it is assumed that the selection is strictly for lactose utilization, then a growth advantage exists only when all three mutations are present simultaneously. (Hall 1982a)

QuoteLink = "A TRUE ACID TEST": RESPONSE TO KEN MILLER
By: Michael J. Behe, Discovery Institute, July 31, 2000

I took the quote from paragraph #5 found under section title, "V. Caveats Unmentioned"

I do notice that it was Behe who quotes Hall but haven't yet found the original quote that is mentioned. The original source is described in the footnote as: Hall, B. G. (1982a). Evolution of a regulated operon in the laboratory. Genetics 101, 335-344.

Hope this helps?

********************

The original source (for the Hall quote) may be found here (and yes, the quote from page 343 that Behe mentioned is accurate).
EVOLUTION OF A REGULATED OPERON IN THE LABORATORY
BARRY G. HALL, Microbiology Section, U-44, University of Connecticut, Storm, CT. 06268

*********************

It should be noted that the Behe article was written in response to a book (in print) by Kenneth Miller, "Finding Darwin's God (Harper Collins, 1999)". It is in response to Miller's assertions (especially the "Acid Test") that brings Behe to quote Hall.

 

[Barbarian]

Since that statement seems so completely at odds with Hall's position on the issue, I took a closer look. In the preceding paragraph, Hall specifically identifies them as spontaneous mutations.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1201865/pdf/335.pdf

By "chosen", he means "used as an example", not "planned" or "selected for the experiment."

I am not claiming vaccine did this. It's clear that the culprit is whoever did the original rather ingenious quote-mining of this passage.

 

[Vaccine]

Hope this helps?

Yes, it does. Thanks for taking the time to find it.

@Barbarian "I am not claiming vaccine did this." No problem, I assume there's no accusations by asking for a source.

It wasn't my intention to represent Hall as anti-evolution, I really don't know. It seemed to me he thought this particular experiment of his wasn't all that useful outside the lab.

 

[Barbarian]

@Barbarian "I am not claiming vaccine did this." No problem, I assume there's no accusations by asking for a source.

What I meant, is that I know you weren't the one who quote-mined that statement that was edited to make it look as though Hall meant the opposite of what he actually said. A little research shows that Behe or someone from the Discovery Institute was the culprit. As you see, far from selecting the mutations, Hall says that they were spontaneous, and not selected at all by any person.

It wasn't my intention to represent Hall as anti-evolution, I really don't know.

Welll, now you know. It was the usual. A dishonest person saw an opportunity to edit a quote to make it appear that he meant the opposite of what was actually said. This is why you should be extraordinarily cautious of such "quotes" offered by creationists.

It seemed to me he thought this particular experiment of his wasn't all that useful outside the lab.

As you see, that's not what he said. This is a particularly hard bit of evidence for Behe, because it shows that irreducible complexity can evolve rather easily. This follows on the revelation that the examples of "irreducible complexity" touted by Behe aren't irreducibly complex at all. Simpler forms of bacterial flagella, and clotting systems exist even today.

And perhaps most difficult for him was his testimony in the Dover creationism trial, where he admitted under oath that ID is science in the same sense that astrology is science.

Outside of the narrowing circle of ID believers, Behe has little influence.

 

[Vaccine]

It seemed to me he thought this particular experiment of his wasn't all that useful outside the lab.

As you see, that's not what he said.

Ok Barbarian, what did Hall say in his summary?

 

[Barbarian]

Ok Barbarian, what did Hall say in his summary?

(Barbarian checks)

We can fairly conclude that evolution of a well organized, integrated bio-chemical pathway can involve several mutations, not all of which must be individually advantageous. Likewise,
this study provides a concrete example of a way in which neutral mutations can contribute not only to the genetic diversity of populations, but can also contribute to the adaptive potential
of organisms.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1201865/pdf/335.pdf

The point, of course, is that some person quote-mined Hall, to fool people into thinking that the mutations were not spontaneous, but rather chosen by Hall. As you see, that wasn't the case, and Hall said so.

 

[Vaccine]

Read this again, you only addressed one path. Hall mentioned an alternative.

"The mutations described above have been deliberately selected in the laboratory as a model for the way biochemical pathways might evolve so that they are appropriately organized with respect to both the cell and its environment. It is reasonable to ask whether this model might have any relationship to the real world outside the laboratory. If it is assumed that the selection is strictly for lactose utilization, then a growth advantage exists only when all three mutations are present simultaneously. Any one of the mutations alone could well be neutral (it is unlikely that any would be disadvantageous); but neutral mutations do enter populations by random chance events, and are fixed by a chance process termed genetic drift. In the background of a neutral ebgA or ebgR mutation,

a second mutation in the alternative gene increases the fitness slightly

by increasing the survival of the double mutant in the presence of lactose. Selection could thus increase the frequency of double mutants in the population. The third mutation, occurring in the background of the double mutant, is clearly strongly advantageous.
An alternative evolutionary route could involve intragenic recombination. We have previously shown that Class IV ebgA alleles can arise via recombination between Class I and Class I1 alleles (HALLa nd ZUZEL1 980a). A cross between two neutral mutants could result in a slightly advantageous double mutant; similarly a cross between a neutral single mutant and a double mutant

could result in the strongly advantageous triple mutant. We can fairly conclude that evolution of a well organized, integrated biochemical pathway can involve several mutations, not all of which must be individually advantageous. Likewise, this study provides a concrete example of a way in which neutral mutations can contribute not only to the genetic diversity of populations, but can also contribute to the adaptive potential of organisms."


I think there are two factors here, the mutations and the selection. The mutations were spontaneous, Hall deliberately selected them to show how if all 3 happened at the same time and nature selected them it would happen.

"An alternative evolutionary route could involve intragenic recombination."
Barbara McClintlock won a nobel prize for discovering recombination, where when a gene is deleted the genome can replace the lost gene just by examining the rest of the genome. ENCODE discovered 80% of recombinations are intentional. Dr Perez discovered a global checksum.
IMHO Halls' alternative route of recombination is the more reasonable path.

 

[Barbarian]

Hall actually mentions three modes of Darwinian evolution that could produce this result. But the fact is, someone tried to make it appear that Hall said the mutations were chosen beforehand. As you learned, he said they were spontaneous.

The different modes by which evolution can produce an irreducibly complex new system are well-known. Exaption and scaffolding are two of them.

 

[Sparkey]

It seemed to me he thought this particular experiment of his wasn't all that useful outside the lab.

As you see, that's not what he said.

Ok Barbarian, what did Hall say in his summary?

IPTG is an agent which stimulates ß-galactosidase production. In other words if they didn't add the stimulant, all the bacteria died. They kept the e.coli alive with a stimulant and choose every step.

Explain how producing an environment in which the bacteria could live, means that the evolution of those new molecule didn't happen.

It seems that these two questions that you've asked, Barb, may be related. Here's what I found while looking at the Behe rebuttal to Miller (previously cited) titled, "A True Acid Test"

When two or more components were deleted, or when the bacterium was cultured in the absence of an artificial chemical (called IPTG), no viable bacteria could be recovered.

He then goes on to give his thoughts about the "multi-part system" including what we find in section III, Adaptive Mutation, "Thus, contrary to Miller's own criterion for "a true acid test," a multipart system was not "wiped out"--only one component of a multipart system was deleted," before he continues in regard to the IPTG (isopropylthiogalactoside) requirement you've asked about. I'll skip to the "juicy parts" (meaning, the parts that were clear enough for a novice like myself to understand).

V. Caveats Unmentioned

A critical caveat not mentioned by Kenneth Miller is that the mutants that were initially isolated would be unable to use lactose in the wild--they required the artificial inducer IPTG to be present in the growth medium.

Behe suggests here that the 'artificial' component 'IPTG' would not be expected to have been found 'in the wild,' but given Hall's estimate of the time they were looking at being approximately [supposedly] 12 million years ago, I don't know how to figure that one out. Pardon my interjection of the word supposedly - it's sometimes difficult for me to keep my opinion out of stuff.

Behe continues in the attempt at being persuasive and quotes Hall again:

Hall decided to include the artificial inducer in all media up to this point so that the cells could grow. Thus the system was being artificially supported by intelligent intervention. Hall clearly wrote:

At this point it is important to discuss the use of IPTG in these studies. Unless otherwise indicated, IPTG is always included in media containing lactose or other B-galactoside sugars. The sole function of the IPTG is to induce synthesis of the lactose permease, and thus to deliver lactose to the inside of the cell. Neither the constitutive nor the inducible evolved strains grew on lactose in the absence of IPTG. (Hall 1982b)

Behe is in conclusion mode as he reiterates his position, "that the system was carried through nonviable states by inclusion of IPTG, and that the system [would] not function without pre-existing components."

Explain how producing an environment in which the bacteria could live, means that the evolution of those new molecule didn't happen.

They didn't happen [in the wild] if the bacteria needed them to continue to live and thus reproduce. Or in other words, and as mentioned before, the test environment was artificially enhanced so that the experiment could be carried out.

Barbarian? A question for you. A little while ago you said:

As you see, irreducibly complex systems can evolve. Even Behe has now admitted that they can.

I didn't catch that admission and assume you are citing a source that I am not familiar with - I've tried to stay current (somewhat) and have read a couple Wiki articles on the subject but haven't found the reference. Help me, pls?

 

[Asyncritus]

So your argument is that only complex vertebrate eyes, with eyelids can have "sight?" What about all those other, simpler eyes? Don't they see?

You again misunderstand.

You can produce a series of 'eyes' starting with a photochemical cell, and going right up to the most complex eyes on the planet, and then claim as you have done - look,that's how the eye evolved.

Complete nonsense of course - because your series hasn't touched, or even begun to touch the real question which is being asked. What is 'sight'? At whatever level you care to choose, light rays somehow have to be turned into a comprehensible level - comprehensible, that is, to the organism being dicussed.

The organism must 'see': and the only thing that begins to address that question is that 'sight' is another of those instinctive phenomena, those immaterial and absolutely vital phenomena which evolution cannot account for.

We agree that the messages, in whatever form, reach the 'brain' , again of whatever form, where it is interpreted as an object or whatever the organism is 'looking at'.

It is at this point that all the physico-chemical phenomena which science has exposed, fail , and fail utterly, as far as evolution is concerned.

The organism 'sees': which means that it somehow understands, comprehends and acts on what is 'seen'. How does it do this? It utilises an information processing system - which may or may not be physico-chemical - but there is a distinctly immaterial, instinctive, evolutionarily untouchable element to all this.

Analogies fail at some point, every time. But the computer is an excellent one.

You are talking about the hardware, the wiring, the physics of computing.

But behind and above that is the user of the computer. The mind, if you like of the computing process. This has not evolved along with the hardware - it is totally independent of it.

And just so, in the natural world, the photochemical cell up to the magnificent vertebrate eyes are like the computer. They started off simply (relatively) and have become the unbelievably complex machines we know today.

But without the user, and his unique abilities and powers - all immaterial and unevolvable - the machine is merely a pile of metal and plastic ans whatever else.


So too, without the instinct, the unevolvable and immaterial instinct, the organs of 'sight' are useless.

You know this, and still continue to foolishly present the computer box and its constituents as the answer to the question: 'What is sight'?

Sight is based on those processes and substances. So if you want to understand how sight came to be, you have to know about the way it actually works.

This is the classic silliness of the position you adopt. You are talking about physics and chemistry. Important as they are, they are not the real answer, and on the basis of evolution theory, there IS no answer you can give.

Instinct is immaterial, unevolvable, and not subject to evolution. It has to be perfecr for the organism, or it would perish. It therefore had to be implanted in the organism in perfection, or extinction would have been the price.

Go figure.

 

[Barbarian]

He then goes on to give his thoughts about the "multi-part system" including what we find in section III, Adaptive Mutation, "Thus, contrary to Miller's own criterion for "a true acid test," a multipart system was not "wiped out"--only one component of a multipart system was deleted," before he continues in regard to the IPTG (isopropylthiogalactoside) requirement you've asked about. I'll skip to the "juicy parts" (meaning, the parts that were clear enough for a novice like myself to understand).

He completely misrepresented what Miller wrote, and rather cynically, since Miller was using Behe's own standard there. According to Behe, a single deletion in such a system should make it completely inoperative. Wiped out. And it does.

V. Caveats Unmentioned

A critical caveat not mentioned by Kenneth Miller is that the mutants that were initially isolated would be unable to use lactose in the wild--they required the artificial inducer IPTG to be present in the growth medium.

I don't see how that means the new system didn't evolve. It means it wouldn't have evolved in the wild, because the permease wouldn't be there to even offer the possibility of using lactose.

Understand that neither Hall nor Miller are saying that this particular evolutionary strain would happen in the wild. I think Behe understands this, but he's hoping his readers don't.

Behe continues:
Hall decided to include the artificial inducer in all media up to this point so that the cells could grow. Thus the system was being artificially supported by intelligent intervention. Hall clearly wrote:

At this point it is important to discuss the use of IPTG in these studies. Unless otherwise indicated, IPTG is always included in media containing lactose or other B-galactoside sugars. The sole function of the IPTG is to induce synthesis of the lactose permease, and thus to deliver lactose to the inside of the cell. Neither the constitutive nor the inducible evolved strains grew on lactose in the absence of IPTG. (Hall 1982b)

This merely tells us why this particular system could only evolve in a lab. All evolutionary events depend on the environment. Of course, all we can check in a rigorous way, is events that happen in labs, because "intelligent intervention" is required for any experiment. Again, Behe is blowing smoke.

Behe is in conclusion mode as he reiterates his position, "that the system was carried through nonviable states by inclusion of IPTG, and that the system [would] not function without pre-existing components."

In other words, fitness applies only in terms of the environment. No surprise there. The fact that Behe doesn't tell us how he thinks this negates the evolution of the system, tells me that he is aware of the fact.

Explain how producing an environment in which the bacteria could live, means that the evolution of those new molecule didn't happen.

They didn't happen [in the wild] if the bacteria needed them to continue to live and thus reproduce.

So evolution of irreducible complexity can evolve so long as the organism is capable of living in the environment in the first place. Yes. Again, I don't see how that's an objection.

Or in other words, and as mentioned before, the test environment was artificially enhanced so that the experiment could be carried out.

And that's an all-purpose objection, since every scientific experiment involves "artificial enhancement" and "intelligent intervention." So Behe is arguing that the act of doing an experiment destroys any scientific validity for it.

Barbarian? A question for you. A little while ago you said:

Barbarian observes:
As you see, irreducibly complex systems can evolve. Even Behe has now admitted that they can.

I didn't catch that admission and assume you are citing a source that I am not familiar with - I've tried to stay current (somewhat) and have read a couple Wiki articles on the subject but haven't found the reference. Help me, pls?

Sure. I don't have a copy of "Darwin's Black Box", but I'll see what I can do.
My notes say he acknowledged that exaption could produce irreducible complexity on page 40. Ah, here's Behe's admission in his testimony in Kitzmiller vs. Dover:

He then goes on to give his thoughts about the "multi-part system" including what we find in section III, Adaptive Mutation, "Thus, contrary to Miller's own criterion for "a true acid test," a multipart system was not "wiped out"--only one component of a multipart system was deleted," before he continues in regard to the IPTG (isopropylthiogalactoside) requirement you've asked about. I'll skip to the "juicy parts" (meaning, the parts that were clear enough for a novice like myself to understand).

He completely misrepresented what Miller wrote, and rather cynically, since Miller was using Behe's own standard there. According to Behe, a single deletion in such a system should make it completely inoperative. Wiped out. And it does.

V. Caveats Unmentioned

A critical caveat not mentioned by Kenneth Miller is that the mutants that were initially isolated would be unable to use lactose in the wild--they required the artificial inducer IPTG to be present in the growth medium.

I don't see how that means the new system didn't evolve. It means it wouldn't have evolved in the wild, because the permease wouldn't be there to even offer the possibility of using lactose.

Understand that neither Hall nor Miller are saying that this particular evolutionary strain would happen in the wild. I think Behe understands this, but he's hoping his readers don't.

Behe continues:
Hall decided to include the artificial inducer in all media up to this point so that the cells could grow. Thus the system was being artificially supported by intelligent intervention. Hall clearly wrote:

At this point it is important to discuss the use of IPTG in these studies. Unless otherwise indicated, IPTG is always included in media containing lactose or other B-galactoside sugars. The sole function of the IPTG is to induce synthesis of the lactose permease, and thus to deliver lactose to the inside of the cell. Neither the constitutive nor the inducible evolved strains grew on lactose in the absence of IPTG. (Hall 1982b)

This merely tells us why this particular system could only evolve in a lab. All evolutionary events depend on the environment. Of course, all we can check in a rigorous way, is events that happen in labs, because "intelligent intervention" is required for any experiment. Again, Behe is blowing smoke.

Behe is in conclusion mode as he reiterates his position, "that the system was carried through nonviable states by inclusion of IPTG, and that the system [would] not function without pre-existing components."

In other words, fitness applies only in terms of the environment. No surprise there. The fact that Behe doesn't tell us how he thinks this negates the evolution of the system, tells me that he is aware of the fact.

Explain how producing an environment in which the bacteria could live, means that the evolution of those new molecule didn't happen.

They didn't happen [in the wild] if the bacteria needed them to continue to live and thus reproduce.

So evolution of irreducible complexity can evolve so long as the organism is capable of living in the environment in the first place. Yes. Again, I don't see how that's an objection.

Or in other words, and as mentioned before, the test environment was artificially enhanced so that the experiment could be carried out.

And that's an all-purpose objection, since every scientific experiment involves "artificial enhancement" and "intelligent intervention." So Behe is arguing that the act of doing an experiment destroys any scientific validity for it.

Barbarian? A question for you. A little while ago you said:

Barbarian observes:
As you see, irreducibly complex systems can evolve. Even Behe has now admitted that they can.

I didn't catch that admission and assume you are citing a source that I am not familiar with - I've tried to stay current (somewhat) and have read a couple Wiki articles on the subject but haven't found the reference. Help me, pls?

Sure. I don't have a copy of "Darwin's Black Box", but I'll see what I can do.
My notes say he acknowledged that exaption could produce irreducible complexity on page 40. Ah, here's Behe's admission in his testimony in Kitzmiller vs. Dover:

Q: You say, Even if a system is irreducibly complex and thus could not have been produced directly, however, one cannot definitively rule out the possibility of an indirect, circuitous route, right?

Behe: Yes.

Q: And by indirect, you mean evolution from a pre-cursor with a different function than the system being studied?

Behe: Yes, different function, perhaps different number of parts, and so on.

Q: And one example of that is what's discussed in, among evolutionary biologists, as the concept of exaptation, correct?

Behe: Yeah -- well, before I say, yes, I'd just like to say, the word exaptation is oftentimes used in loose sense, but, yes, that's generally correct.

Q: And that is a concept that people in the field of evolutionary biology consider to be a valid concept, a valid description of the way more and more complex systems get developed?

Behe: Let me say --

Q: I'm not asking you to agree with it. I'm asking you, is that what an evolutionary biologist proposes?

Behe: Again, let me make clear what we're talking about here. Some evolutionary biologists certainly think that exaptation is real and that it's important and so on. But simply saying that this part over here was exapted from that part over here does not give an explanation of how random mutation and natural selection could have gotten it from one state to the other.

(Michael Behe, Kitzmiller v. Dover testimony, Day 12 AM session, pp. 66-67.)
- See more at: http://www.evolutionnews.org/2012/08/did_michael_beh063271.html#sthash.pDggkyUR.dpuf

Exaption is well-documented, of course. The enzyme system that evolved in Hall's bacteria, was based on a protein already existing, but not effective as a lactose. It was exapted to a new function.

 

[Sparkey]

I don't see how that means the new system didn't evolve. It means it wouldn't have evolved in the wild, because the permease wouldn't be there to even offer the possibility of using lactose.

That's what I understood too. I tend to stand apart from conclusions and don't believe that evolution isn't possible. Personally, and as you know, I would challenge the whole single ancestor thought, not the changes that can readily be observed. But this thread isn't about my opinion.

 

[Barbarian]

Barbarian asks:
So your argument is that only complex vertebrate eyes, with eyelids can have "sight?" What about all those other, simpler eyes? Don't they see?

You again misunderstand.

It seems more likely that you haven't considered the implications of your previous position.

You can produce a series of 'eyes' starting with a photochemical cell, and going right up to the most complex eyes on the planet, and then claim as you have done - look,that's how the eye evolved.

First, you've failed to see that there isn't one way. As I pointed out, the existing transitionals in several phyla show that it happened in different ways.

Complete nonsense of course - because your series hasn't touched, or even begun to touch the real question which is being asked. What is 'sight'?

We have been using "detection of electromagnetic waves" for that purpose, which is the definition used by most scientists studying perception. If you'd care to submit your own, we can discuss it.

At whatever level you care to choose, light rays somehow have to be turned into a comprehensible level - comprehensible, that is, to the organism being dicussed.

You think bacteria comprehend things? How so?

The organism must 'see': and the only thing that begins to address that question is that 'sight' is another of those instinctive phenomena, those immaterial and absolutely vital phenomena which evolution cannot account for.

You went down this path before. You confirmed to me that the sun-seeking behavior of plants is "instinct", but I showed you it was a purely chemical phenomenon, under the influence of light. So, not so immaterial. Show me that bacterial "comprehend."

We agree that the messages, in whatever form, reach the 'brain' , again of whatever form, where it is interpreted as an object or whatever the organism is 'looking at'.

So your argument is that it must have a brain to use vision?

It is at this point that all the physico-chemical phenomena which science has exposed, fail , and fail utterly, as far as evolution is concerned.

Here, you assume what you had proposed to prove.

The organism 'sees': which means that it somehow understands, comprehends and acts on what is 'seen'. How does it do this?

In plants, the photosensitive molecule results in differential growth toward light. I don't see any comprehension in plants, and plants are a lot more sophisticated than bacteria.

It utilises an information processing system - which may or may not be physico-chemical - but there is a distinctly immaterial, instinctive, evolutionarily untouchable element to all this.

If so, you've yet to find it.

Analogies fail at some point, every time.

So let's stick to reality, this time.

And just so, in the natural world, the photochemical cell up to the magnificent vertebrate eyes are like the computer. They started off simply (relatively) and have become the unbelievably complex machines we know today.

So the evidence (such as in the mollusks) shows.

So too, without the instinct, the unevolvable and immaterial instinct, the organs of 'sight' are useless.

As in those plants that you said had "instinct?" Turns out we can describe the process without any instinct at all. "Instinct", as we discussed earlier, means "we don't know why it does that."

You know this, and still continue to foolishly present the computer box and its constituents as the answer to the question: 'What is sight'?

Sight is based on those processes and substances. So if you want to understand how sight came to be, you have to know about the way it actually works.

What would you like to know?

You are talking about physics and chemistry.

Yep. As you learned, that's what causes the "instinct" that impressed you in plants.

Turns out, vision is mediated by chemistry. Even in the brain, the functioning of neurons is a matter of physics and chemistry.

Instinct is immaterial, unevolvable, and not subject to evolution.

It sounds as though you have decided to use "instinct" as a synonym for "magic." In fact, it is quite evolvable, as any wired-in behavior can be. The auxins, for example, are evolved molecules.

It has to be perfecr for the organism, or it would perish.

If so, all organisms would be dead, since no "instinct" is perfect

It therefore had to be implanted in the organism in perfection, or extinction would have been the price.

Let's see... so a bowerbird "instictively" build a bower to woo a mate. If it doesn't do so perfectly, it won't get a mate?

This is clearly wrong, since different species of bowerbirds build bowers of different complexities, including some that are little more than a few sticks. One species normally doesn't even build that. So much for "perfection."

Go figure.

Yep.

 

[Sparkey]

Q: You say, Even if a system is irreducibly complex and thus could not have been produced directly, however, one cannot definitively rule out the possibility of an indirect, circuitous route, right?

Behe: Yes.

So Behe, under cross examination admits (as you have said) yet, to be fair, it might be noted that he was treated there as a hostile witness and even though he did give that testimony under cross, he was all the while asserting that there is still a problem with plausibility.

Oh, and I found the review of Behe's book (by Miller) - you've probably already seen this, but it is clearly written and easy to follow so: Darwin's Black Box Reviewed by Kenneth R. Miller
(as published in Creation / Evolution Volume 16: pp, 36-40 [1996])

 

[Barbarian]

So Behe, under cross examination admits (as you have said) yet, to be fair, it might be noted that he was treated there as a hostile witness and even though he did give that testimony under cross, he was all the while asserting that there is still a problem with plausibility.

The question was relating to the admission he made in his first book. In that book, he admitted that exaption could produce irreducible complexity. (It does).

 

[Asyncritus]

So your argument is that only complex vertebrate eyes, with eyelids can have "sight?" What about all those other, simpler eyes? Don't they see?

Sight is based on those processes and substances. So if you want to understand how sight came to be, you have to know about the way it actually works.

This is again pure misunderstanding of the case you have to answer. I don't know how I can get this across to you.

We understand the MECHANICS of vision fairly well.

That is like saying I understand HOW a car engine works.

But the organism uses the mechanics to 'see'. As you should know, we don't see with our eyes. Yes, the eyes are instrumental in vision - but we do not see with them. The information collected by the organs of vision undergoes 4 processes:

1 The collection of the information (by the 'eyes' or whatever organ the organism uses)

2 The transmission of the info to the central processing unit (ie the brain in our case, simpler structures in the lower animals)

3 The interpretation of that information

4 The utilisation of that information by the organism.

Maybe there's a 5th step in there: the decision how to utilise the information.

Science is excellent at stages 1 and 2 - which is the very limited area to which you are forced to rectrict yourself. That is also the area in which evolution is constrained to produce fallacious and fictitious accounts.

But 3, 4 and 5 are untouchable by evolution, because they are immaterial. Interpretation and utilisation of information is unevolvable.

You read these words: and the physico-chemical equipment is in use - but once that information reaches your brain, it immediately steps out of the physico-chemical. There is no p-c mechanism involved in your thought processes.

So all of your decisions to accept or reject the fully valid information I have continually placed on this board are above and beyond the p-c.

That is the unevolvable area at which evolution is utterly futile and dis-empowered. It is helpless to account for any such thing.

That is because there is a SELF IN US, AND IN EVERY LIVING THING, which makes the decisions and thinks, sees, feels hears and all the other processes of life.

That is what I choose to call 'instinct'. It is not an entirely satisfactory description, but is the best science has been able to produce so far - because it fears and cannot account for its existence anywhere and in any organism.

However, it does absolutely exist.

You keep repeating the statement that we know HOW a plant responds thigmotropically, phototropically and geotropically, and that is a big plank in your argument.

However, you cannot account for WHY those responses exist. And that is the truly vital question: and one that evolution cannot answer, because evolution's main premise is that things happen randomly and for no reason.

Because the moment you accept that things have a reason for their existence, your theory has collapsed completely.

There is no directing intelligence in evolution, no matter how much you may protest that things happen non-randomly.

The evidence shows that it evolved. So no problem for science. As in all sciences, there are still many things for us to yet discover. But the evolution of vision is very well-established.

I regret to have to inform you that that is not the case.

As shown above, evolution cannot account for the most important instincts involved in vision - just as it cannot account for the instincts involved in ANY of the living processes.

I asked you how a reptile could ever learn to fly - even if it has feathers, something that is becoming increasingly doubtful, given the recognised skill of the Chinese fossil-fakers.

Your answer, completely contrary to the tenets of evolution, is that the instincts were already there, waiting to be used.

But if they were there, and of no use to a non-flying reptile, then 'natural selection' - whose existence and value is now under considerable fire, as I showed you - should have wiped them out.

At every step of the way, you have been shown that evolution is helpless to explain the existence of instinct: that inborn, inherited, immaterial information store - which no amount of your fudging can gainsay or dilute.

How does anything see?

Light-sensitive substances can transform electromagnetic energy into chemical energy, which makes neurons fire.

That, as I have shown, is a totally inadequate answer.

We understand HOW the car engine works - but it is the driver, for whose existence we are seeking an account.

And how does it know what it's 'seeing'?

I don't think a scallop "knows" anything. But it can see a predator and take action accordingly.

And there's your problem again. If it 'takes action accordingly', then it SEES the predator, REALISES that it is a predator, and DECIDES to run in the opposite direction.

Those are examples of some kind of BEING in the scallop, making those decisions. That immaterial BEING governing the scallop's behaviour is the thing evolution cannot account for.

I'm afraid you are in an endless loop here.

1 You believe in evolution and generate all sorts of inadequate 'explanations'

2 You can see, I'm sure, that the reasons for the behaviours we have extensively discussed are inexplicable in evolutionary terms

3 So you generate further and wilder 'explanations' for the inexplicable.

That's your real problem.

As you see, it's not a problem for science; the way that complex eyes evolved is quite clear.

See above for the refutation of this specious piece of 'reasoning'.