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Does The E. Coli Long-term Evolution Experiment Evolution


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#81 jason777

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Posted 28 March 2010 - 04:09 PM

In experiments such as Joshua Lederberg’s studies antibiotic resistance has been observed to emerge after time in populations bred from one non-resistant individual. If gene silencing or pre-existing epigenetics were the source of resistance then early generations of the populations would have the resistance. They do not, it emerges though the spread of an adaptive mutation.


Mutation and Adaptation are completely different things. A mutation is random and non-guided and is almost always nuetral and sometimes deleterious. And adaptation is part of the mechanisms' pre-existing ability to produce different proteins.

Do we know antibiotic resistance is the result of a protein change? Yes we do. It has been analyzed by Mass Spectrometry.

Mutations in several ribosomal proteins are known to be related to antibiotic resistance. For several strains of Escherichia coli, the mutated protein is known but the amino acid actually altered has not been documented. Characterization of these determinants for antibiotic resistance in proteins will further the understanding of the precise mechanism of the antibiotic action as well as provide markers for resistance. Mass spectrometry can be used as a valuable tool to rapidly locate and characterize mutant proteins by using a small amount of material. We have used electrospray and matrix-assisted laser desorption ionization–time of flight (MALDI–TOF) mass spectrometry to map out all 56 ribosomal proteins in E. coli based on intact molecular masses. We used this fingerprinting approach to locate variants of ribosomal proteins displaying a change in mass. In particular we have studied proteins responsible for streptomycin, erythromycin, and spectinomycin resistance in three strains of E. coli, and then we characterized each mutation responsible for resistance by analyzing tryptic peptides of these proteins by using MALDI-TOF and nanoelectrospray tandem mass spectrometry. The results provided markers for antibiotic resistance and demonstrated that mass spectrometry can be used to rapidly investigate changes in individual proteins from a complex with picomole amounts of protein.



http://www.ncbi.nlm.nih.gov › ... › v.45(11); Nov 2001


The only thing that remains unanswered is if the protein was replaced by a different one (pre-existing) or is it a random deformity of the protein ( still pre-existing).

#82 jason777

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Posted 28 March 2010 - 05:55 PM

BTW, This exact type of adaptation has been empirically observed in nylon eating bacteria.

Which is conclusive that microevolution (adaptation by protein substitution) could never accumulate into macroevolution which needs genetic mutation to produce new genetic information. I think we now have a clear dividing line between the two.


6-Aminohexanoate-dimer hydrolase (EII), responsible for the degradation of nylon-6 industry by-products, and its analogous enzyme (EII′) that has only ∼0.5% of the specific activity toward the 6-aminohexanoate-linear dimer, are encoded on plasmid pOAD2 of Arthrobacter sp. (formerly Flavobacterium sp.) KI72. Here, we report the three-dimensional structure of Hyb-24 (a hybrid between the EII and EII′ proteins; EII′-level activity) by x-ray crystallography at 1.8 Ã… resolution and refined to an R-factor and R-free of 18.5 and 20.3%, respectively. The fold adopted by the 392-amino acid polypeptide generated a two-domain structure that is similar to the folds of the penicillin-recognizing family of serine-reactive hydrolases, especially to those of d-alanyl-d-alanine-carboxypeptidase from Streptomyces and carboxylesterase from Burkholderia. Enzyme assay using purified enzymes revealed that EII and Hyb-24 possess hydrolytic activity for carboxyl esters with short acyl chains but no detectable activity for d-alanyl-d-alanine. In addition, on the basis of the spatial location and role of amino acid residues constituting the active sites of the nylon oligomer hydrolase, carboxylesterase, d-alanyl-d-alanine-peptidase, and β-lactamases, we conclude that the nylon oligomer hydrolase utilizes nucleophilic Ser112 as a common active site both for nylon oligomer-hydrolytic and esterolytic activities. However, it requires at least two additional amino acid residues (Asp181 and Asn266) specific for nylon oligomer-hydrolytic activity. Here, we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the β-lactamase fold resulted in the evolution of the nylon oligomer hydrolase.



http://www.jbc.org/c.../39644.abstract





Enjoy.

#83 Bex

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Posted 28 March 2010 - 07:24 PM

“According to Christ the majority can't even see truth”... “unregenerate men”... “agnostic and atheistic brethren”...  The scales hath fallen from mine eyes.  This place is a gathering of fundamentalist religious dogmatists resistant to critical thinking and post-enlightenment objectivity.  I’m getting out of here.

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Leaving quietly and simply discontinuing involvement would have been alot more dignified than pulling this stunt. You shouldn't presume such gullibility on behalf of the readership. Anybody honest with a functioning scroll bar can see for themselves the content of the arguments posed here.

A mention of Christ or the word of God, has not blurred or removed the points made in challenge/opposition to yours. Just because you don't like them, and have your own bias' (as we all do) shouldn't mean resorting to this as your reason in abandoning the argument/forum.

#84 AFJ

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Posted 28 March 2010 - 08:03 PM

AFJ--
You believe this and that's it.  You gave me no data based on deductive observation.  Your so-called data is based on the assumptions of unregenerate men who study each the other's "facts."

For instance, you give me a mutation rate per generation, yet you have no earthly idea how many generations there have been and of what. This is wishful fantasy cloaked by math notation, not science.

It's also based on assuming introns, highly and moderate repetitive sequences, pseudogenes, selfish DNA and and other non coding squences are all a result of slow gradual mutation through 'genetic' time.  You have absolutley no shred of evidence for this and a self admission of any honest microbiologist is that there are many things we don't know.  So to state this mutation rate as an actual scientific measurement is invalid.

Most of the rest of these doctrines you gave me were born as a 'suggested' hypothesis by some respected scientist in a paper somewhere and given a hearty amen by their agnostic and atheistic brethren, followed by a few liberal theologians.  Majority consensus doesn't produce truth.  According to Christ the majority can't even see truth.

*
“According to Christ the majority can't even see truth”... “unregenerate men”... “agnostic and atheistic brethren”... The scales hath fallen from mine eyes. This place is a gathering of fundamentalist religious dogmatists resistant to critical thinking and post-enlightenment objectivity. I’m getting out of here.

Note to Ron or Ikester: please cancel my log-in.

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Suit yourself Tommy. You didn't answer my charge that your given mutation rate is not based on true science. What's the matter? You guys come in here not aware of your indoctrination and obvious assumptions, spouting them off as though they are facts. When you are confronted with the FACT that they are assumptions you can't take it.

You registered as agnostic, and you are debating creationists who believe in God. We admit our conviction that God exists. But you can't admit your philosophical worldview of metaphysical naturalism!

Finally, I answered what little science you gave with science, and you want to accuse me of being some kind of religious fanatic. The truth is you're running because you can't take the fact that you can't prove your theory. Just because it's written in 5th grade textbooks over the entire world doesn't make it a fact. At one time the entire world believed the earth was the center of the universe.

#85 ikester7579

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Posted 28 March 2010 - 08:13 PM

“According to Christ the majority can't even see truth”... “unregenerate men”... “agnostic and atheistic brethren”...  The scales hath fallen from mine eyes.  This place is a gathering of fundamentalist religious dogmatists resistant to critical thinking and post-enlightenment objectivity.  I’m getting out of here.

Note to Ron or Ikester: please cancel my log-in.

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When people break rules, equivocate, use deception, etc.. They get suspended or banned. If your peers cannot follow rules not my problem. If you decide to leave with them, not our problem.

#86 jason777

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Posted 28 March 2010 - 10:32 PM

The sad part is, he is going to go somewhere else and claim that evolution is a fact because creation is a religion. What a bunch of cretards we are. :rolleyes:

If that were true, then how did I formulate a quantifiable and empirical theory of microevolution in post#82? Oh well, I guess they can change the theory to "common descent by means of protein replacement".

#87 Hawkins

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Posted 28 March 2010 - 11:34 PM

I think that there are serveral points needed to be clarified here.

1. adaptation vs evolution
I try to view this from the designer's point of view (just trying as i am by no means anywhere near His mind). It is quite possible that the low end organisms such as bectira can adapt in a way viewed by the evolutionists as 'evolution'. That is for simple organisms, millions of random mutations can lead to one beneficial mutation and when this change is subject to natural selection, a 'evolution' is thus resulted. Yet this perhaps is just one of the many ways how a simple organisms adapt themselves into the environment.

Other possible way is that these organisms might have already built-in mechanism to accelarate genetic re-organization when certain environmental extremes are met. To simply put, God may have designed such a built-in process for organisms to adapt the extreme conditions more easily and smoothly, random mutation is just not good enough.

So the question here is, other than random mutation is there any other cases are studied to rule out the possibility that other adaptation mechanism exists in these simple becteria? That is, are you sure that the becteria can only subject themselves to the 'mutation followed by natural selection' process. Have you tested other extreme cases which might (or might not) possibly trigger the becteria's adaptation process instead of the 'evolution' process?

2. Becteria vs more complicated organisms (such as apes?!)
Now if you can draw your conclusion here that evolution exists in becterias, how can you say that it also exists in other living beings. Please notice that 'because evolution exists in becteria, it must exist in, say, apes', this statement is a fallacy. What can be observed in becteria may or may not (you need to prove) give any hint on more complicated organisms, unless you discovered a set of common natural rules which is applicable to all organisms alike. For instance, if you discovered that under -20 celcius degree, 80% humidity, all living cells will change from one state to another, then and only then you can extend your conclusion to other species than the becteria. Before that, if you find that evolution occurs in becteria, then it occurs only to becteria, no less no more.

Moreover, it is possble that a working mechanism already exists in high end creatures that extreme environment may trigger the adaptation process instead of the evolution process to allow animals to finish their adaptation within several generations.

3. Now vs history
Now if you discovered the required set of scientific rules which allows you to conclude that more complicated species are also subject themselves to 'evolution', you need to find a way to prove that history DOES evolves this way. Now you may need to figure out what evolves to what, that is, what and under what temperature and humidity and how long it takes to evolve to what. Say, wolves under -20 degree celcius and 80% humidity and after 100 million years, they evolves to dogs...and so on.

This is what science is about. ToE at the moment is a joke. :rolleyes:

#88 Ron

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Posted 01 April 2010 - 03:41 PM

“According to Christ the majority can't even see truth”... “unregenerate men”... “agnostic and atheistic brethren”...  The scales hath fallen from mine eyes.  This place is a gathering of fundamentalist religious dogmatists resistant to critical thinking and post-enlightenment objectivity.  I’m getting out of here.

Note to Ron or Ikester: please cancel my log-in.

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I have yet to see a fundamentalistic dogmatism of greater ferocity than you've displayed here Tommy. And you have every right to your theistic beliefs as everyone else here. Just as you have every right to leave.

But, I must say, I haven't seen any critical thinking or objectivity in the post-enlightenment movement (your case not withstanding).

#89 Ron

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Posted 01 April 2010 - 03:43 PM

The sad part is, he is going to go somewhere else and claim that evolution is a fact because creation is a religion.

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That's because he refuses to see the religiosity built into the evolution doctrine.

#90 AFJ

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Posted 03 April 2010 - 06:11 AM

I think that there are serveral points needed to be clarified here.

1. adaptation vs evolution
I try to view this from the designer's point of view (just trying as i am by no means anywhere near His mind). It is quite possible that the low end organisms such as bectira can adapt in a way viewed by the evolutionists as 'evolution'....

Other possible way is that these organisms might have already built-in mechanism to accelarate genetic re-organization when certain environmental extremes are met. To simply put, God may have designed such a built-in process for organisms to adapt the extreme conditions more easily and smoothly, random mutation is just not good enough.

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Hawkins, the observable built in mechanisms are exactly what happens in some cases. Take the s@x pilus, a feature that makes a bacteria a 'male.' It holds a 'female' in place so that bacterial conjugation can take place. After conjugation, the 'female' becomes a 'male' and has encoding DNA which makes a s@x pilus.

This particular conjugation involves an F-plasmid passing from the male to the female. The plasmid contains the information which incorporates into the female's genes, making in a male.

1. Unlike the idea of Dawkins' Mount Improbable, the s@x pilus is not a precursor or transitional. It is encoded fully functional for the task.

2. The female has no restricting enzymes for these passing genes, but accepts them. Restricting enzymes will many times eat destructive phage DNA, demonstrating a chemical program which is able to discern harmful and friendly DNA.

3. The pilus is like a 'grappling hook' designed to hold the female secure, so that conjugation can take place. There is no implication of purpose here, but rather a demonstration of purpose.

4. The DNAs of the plasmid and the female match up with the express purpose of an insertion which codes for a s@x pilus.

5. The bacteria show knowledge and will to conjugate. This is purpose and intention within a one cell organism. What accounts for this?

At this point, the system involved, which is not isolated, shows design. Design defined as an integrated system with interlocking, and inter working parts, which can not work without the function of each part.

-----------------
In many cases of bacterial resistance of antibiotics the actual mechanism of cause is not known. Only the results of the mechanism are known.

If plasmids (and perhaps by association--phages) are involved in known cases they may be also involved in some of these cases.

-----------------
Hypothetical mechanism in some cases may be. A bacterium in a colony may receive DNA from plasmid x in a given environment, which gives it a deleterious trait, causing eventual death. The trait is therefore not conferred to the population.

Now comes the antibiotic environment. A bacterium again receives the same DNA from plasmid x which causes resistance. The colony dies and the bacterium lives to produce a resistant colony.

#91 Guest_Eocene_*

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Posted 19 April 2010 - 04:33 AM

The Topic should be: Does the E. Coli Long Term Evolution Experiment Support Evolution?

What evolutionists and Mr Richard Lenski try and do is prove an assumed mechanism by which evolution is driven. Here's their main problem and why they cherish these bacterial experiments.

If you go back to the dilema they've created in that infamous "Evolution Definition Shell Game" arguement of what is and what it's not, they know full well the it is absolutely impossible to use the "Scientific Method" EVER to demonstrate mud to man philosophy. Or even just one type or KIND of animal turning into another KIND of animal. Hence in their mind, all they need do is observe a small change, then apply their worldview assumption to it using their version of inventive/creative holy terminology and demand that it is a FACT and say this is the proven mechanism of evolution by which mud to man came about without ANY purpose or intent or as Richard Dawkins said, "a lucky chemical accident".

The problem though with the above titled subject of E.coli experiments by Mr Lenski is that in most intellectual circles, they are so wrapped up in intelletualism and looking at thing from complicated angles from which only they themselves have the ability to understand and comprehend and therefore any percieved knowledge must be view through their eyes only, is that they most often fail to graps or ask the absolute simple questions that even a child could grasp. For example, where are most E.coli found , where do they live or what is their function & purpose ???????

For the most part they are the micro-flora of the gut or lower intestines of numerous living warm blooded organisms, but also in cold blooded animals and they help in the processing of waste. I work with mycorrhizal and bacterial applications regarding the roots of plants. These are fungi and bacteria which enable a plant to process and take in nutrients and water efficiently to be able to thrive in the wild. You might say they are the disgestive organisms turned inside out of what we have internally. Most all microbiology in the natural world are the work horses for what happens above that we all see and experience.

The link to Perry Marshall's site is interesting because he has many valid and intelligent points which absolutely infuriate Atheists because they have no answer. Here's an example. Evolutionists say that all life is driven by random mutations, thus this is what Mr Lenski and others try to prove. So they make an assumption of what they see in some new gene as proof of a lucky copying error (random mutation) as proof of the wonders of evolution at work doing it's amazing thing. Unfortunately as Perry and others here have brought out, geneticist such as James Shapiro, and I believe he quotes physicist Huburt Yockey quite a bit, they have shown where randomness is a joke. DNA actually has multiple algorithm genes for purposeful with intent reprogramming if necessary itself to environmental changes. There's no randomness. Again, back to E.coli, with us and other creatures they are constantly being immersed with change, that is depending on what we throw at them. That's why many of those native indigenus cultures of the Amazon can be seen on those documentaries hunting and days later back at camp cooking and feeding on what has been rotting for days but offers no health risk to themselves. The researchers on site were made sick by the mere stench of the food. Now if the researcher and his cameramen were to eat such foods they'd become deathly ill because it is totally foreign to the bacterial flora in their own digestive tract. Perhaps given time and small amounts they could acquire the taste as it's commonly said.

So the E.coli (like other bacteria) are actually designed to adapted to new situations. In fact the entire microflora of this whole entire planet is one big digestive recycling machine. It adapts to whatever situation is forced onto it. Most of the adaptive results have at times resulted in unfortunate diseases and such, but even that had the ultimate human cause, nature cannot be blamed even though many evolutionist celebrate such out breaks of Swine Flu, spanish Infuenza, etc as proof of their god. This adaptational purposeful engineering features however, as Perry Marshall has even brought out, were known as far back as 1948 - 1953 when Barbara McClintock discovered and observed, but not acknowledged until 1973. Why ????????? Because the evolutionary cronies who ran the show back then were so hung up on randomness that their egos wouldn't allow them to think any differently. To this day you will not find much about her in modern evolution biology books because of the embarrassment it causes them.

The interesting thing here is with all these discussions, the subject of DNA, RNA, Ribosomes, Bacteria (E.coli, etc) have been extremely slowed down for us to grasp. But in real life they do what they do at faster than supercomputer speed without traffic jams, accidents, mistakes and with precision efficiency. Randomness and evolution without purpose or intent simply do not nor will they ever give satisfying answers to these functions and their origins. Lenski's experiment was diliberately and intentionally slowed down to observe an outcome and I understand that. But the point is he didn't observe some remarkable lucky mistake. What happened was no different than what was found with the Nylonase bacteria, again yet another resultant adaptation to deal with mankind's stupidty and error in the first place.

My time is short for the moment as I need to attend to a student, but I believe there is a thread subject here from sometime back entitled, "Does DNA contain a Code?" That's where the real discussion should be, then you can move on to other matters, but I guess we all know that will never be laid to rest !!! :rolleyes:




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