Manganese Nodules: Young or Old?

[sentientsynth]

If you removed your face from Bob's buttocks long enough to read his OP you would clearly see who has the preconceived notions.

I don't have a problem with Bob's preconceived notions. They also happen to be mine.

Preconceived notions are A-OK when they are correct.

But... ferromanganese nodules forming rapidly.....that's something to think about. How in the world do we date these things? On an aluminum can......Strange.

SS

 

[sentientsynth]

Whoa Johnny. This article is pretty intense. I may have to read it more than once, as my Bio 101 course did not sufficiently prepare me for this level of literature. It seems really interesting though. Here's a couple of neat quotes.

The mechanism of gene duplication, however is inherently self- limiting in that a new protein arising by this mechanism invariably retains substantial amino acid sequence homology and, therefore, functional relatedness with its immediate ancestor. Thus, one wonders if this mechansism alone sufficed at the very beginning of life when a large variety of polypeptide chains with divergent functions had to be created almost simultaneously.

He said it so much better than I ever could.

The swiftness with which these two enzymes have evolved is truly remarkable, for several decades are but a flash in the evolutionary time scale.

You mean some things can evolve quickly rather than slowly? Interesting.

Here's the link to this neato-b-zeato paper.

Peace.

SS

 

[sentientsynth]

Bob,

Is there any way you could upload just a segment of that movie into this forum? I'm really itching to hear it from the horse's mouth, y'know.

SS

 

[Johnny]

He said it so much better than I ever could.

Indeed, but note that he is actually proposing one mechanism by which large polypeptide chains with divergent functions could arise very rapidly. Then he describes a case study in which a functional, novel polypeptide arose in a less than 50 years, which is next to nothing on the evolutionary time scale.

 

[Bob Enyart]

Johnny is "unsure" if evidence columns are valid

Johnny is "unsure" if evidence columns are valid

Johnny, when you quote others, you know who you’re quoting, but we don’t necessarily. It would help if you could identify who you’re quoting. Now:

Johnny quoted my examples of non-expert common sense in the three disciplines he used as examples, oncology, law, and economics, and then he complained:

There is no comparison here to assessing the validity of a scientific theory. Perhaps you could elaborate on the connection.

No. You brought up those disciplines, not me.
…
I’ll ignore the niggle.
…
Then, Johnny digs in deeper, and again rejects my:
“general rule: the credibility of a claim increases when it does not reinforce the position of the side making it, and extremely so when it refutes some of their previous strong evidence.”
He dug thusly:

You cannot evaluate the strength of a claim by anything other than its evidence.(emphasis added)

But Johnny, you just contradicted your position on “bias.” For you wrote how important it is to identify bias, because:

…it tells you about the process with which the conclusion was arrived at. It also tells you how likely it is that the conclusion is the correct conclusion.(emphasis added)

Thanks for the concession.

But, have you decided? Are you conceding on my definition of bias? Or on my general rule of credibility?

And going deeper still on this, you wrote:

“I used to be a creationist. Then I admitted evolution took place. Is my credibility increased?”

No. Because: you switched sides while applying the rule! We must obey the rules! And switching sides during application is a no-no for this rule (and many others)! Example: When creationists admit that some of their arguments were wrong, there is increased credibility to that claim. Now Johnny, I imagine in a moment of weakness, you’ll want to agree with that, but remember, it cuts both ways.

: 1) …did you not shift the burden of proof on me?...

You’re the one who is distrusting the World Almanac and their Marine Geologist Yates. The burden of proof is on you. I’ll stand by that source, and my general observations of knee-jerk old-age claims.

Now, this last quote from Johnny is a good one to end with. As the reader will recall, at Johnny's request, I clarified a question that needed no clarification. His answer is a true crack up (and it validates my earlier use of the word "fear"):

To answer your question:
"BEQ1b-J: Two views exist regarding the age of the earth: young earth, and old earth. Also, human beings make careful observations of the world, and those observations will be interpreted differently by adherents of the opposing views of YE and OE. Do you agree that those who hold either view on the age of the earth can sort that evidence into Evidence Columns, one of which is titled Young Earth Evidence, and the other of which is titled Old Earth Evidence. Of course, either side may wrongly categorize evidence. But I’m asking you: is this paradigm valid for evaluating evidence for the age of the earth?"

To be honest I am unsure whether or not this is a valid method. Someone more versed in the philosophy of science may correct me down the line, but I will say "Yes" for now.

Oh brother.

I’m glad I’m flying to Florida tomorrow with my family (to give a presentation at Coral Ridge, a seminar in Vero Beach, and then relax with my family). Johnny, if you can't figure out if this is valid or not, you best take yourself out of any threads requiring scientific thought. This post, which follows your final, timid equivocating comment, marks a good place for me to end my participation in this thread.

Thanks to all (except for Fool, because of his crude remark), -Bob

 

[sentientsynth]

Johnny,

Well, it turns out that the novel capabilities of these bacteria are due to something rather than nucleotide insertion, deletion, or replacement.. Rather, these bacteria posses organelles called plastids which allow it to adapt to stressful conditions.

About the bacteria in question, Flavobacterium sp. K172 and Pseudomonas sp. NK87, it's been found that the recombined DNA exists not on the chromosomes, but on the plastids exclusively.

There are five transposable elements on the pOAD2 plasmid. When activated, transposase enzymes coded therein cause genetic recombination. Externally imposed stress such as high temperature, exposure to a poison, or starvation can activate transposases. The presence of the transposases in such numbers on the plasmid suggests that the plasmid is designed to adapt when the bacterium is under stress.(emphasis mine)

AiG gives an example of a similar case to the one given in the Ohno paper.. And forget 50 years. How about 9 days!!

...Japanese researchers demonstrated that nylon degrading ability can be obtained de novo in laboratory cultures of Pseudomonas aeruginosa [strain] POA, which initially had no enzymes capable of degrading nylon oligomers. This was achieved in a mere nine days! The rapidity of this adaptation suggests a special mechanism for such adaptation, not something as haphazard as random mutations and selection.

It would appear that certain bacteria possess incredible adaptation mechanisms. Don Batton goes on to say

This mechanism might be analogous to the way that vertebrates rapidly generate novel effective antibodies with hypermutation in B-cell maturation, which does not lend credibility to the grand scheme of neo-Darwinian evolution. Further research will, I expect, show that there is a sophisticated, irreducibly complex, molecular system involved in plasmid-based adaptation—the evidence strongly suggests that such a system exists. This system will once again, as the black box becomes illuminated, speak of intelligent creation, not chance. Understanding this adaptation system could well lead to a breakthrough in disease control, because specific inhibitors of the adaptation machinery could protect antibiotics from the development of plasmid-based resistance in the target pathogenic microbes.

So much for birthing a novel, functional enzyme by the random mix-up of a nucleotide.

What's that? Humpty Dumpty had a great fall?
Source

 

[sentientsynth]

Read that last quote carefully, y'all.

Understanding this adaptation system could well lead to a breakthrough in disease control, because specific inhibitors of the adaptation machinery could protect antibiotics from the development of plasmid-based resistance in the target pathogenic microbes.

Wouldn't this be a clear case of the intelligent design scientific model producing promising abstracts for research toward the improvement of technology? ID is called a science-stopper by the lame-brains. Rather, the platform of design allows scientific inquiry a strong, practical base not to be found in other models.

Peace

SS

 

[Johnny]

About the bacteria in question, Flavobacterium sp. K172 and Pseudomonas sp. NK87, it's been found that the recombined DNA exists not on the chromosomes, but on the plastids exclusively.

I'm in the middle of responding to Bob, but I have to chuckle at your arrogance. You clearly have no idea what you're talking about.

First, I think you meant "plasmid", not "plastid". http://en.wikipedia.org/wiki/Plasmid. If you would have read your own source definition of plastid, the first paragraph reads "Plastids are major organelles found only in plants and algae." We're dealing with bacteria here.

Second, you are right that the gene is found only on the plasmid. So what? The bacteria also contains 3 other plasmids involved with the metabolism of synthetic compounds. "Sequence analysis of a cryptic plasmid from Flavobacterium sp. KP1, a psychrophilic bacterium," Makoto Ashiuchi, Mia Md. Zakaria, Yuriko Sakaguchi, Toshiharu Yagi, FEMS Microbiology Letters 170 (1999), 243-249

AiG argues from incredulity. Good for them. By their own admission, the enzyme did not exist in the first culture. Yet in just 9 days a mutation had emerged that allowed the bacteria to grow on a nylon polymer. It took 3 months before a mutation allowed the bacteria to handle more complex variations of the polymer. It is important to note that this is typical of natural selection. The first mutation allows survival, subsequent natural selection refines efficiency. So what has AiG to say about all this? "But, but, it was too fast!" Unfortunately, they have no other respons but to assert that it just couldn't have been a simple case of the mutations. Yet analysis shows that it was just a frameshift mutation.

Third, "Well, it turns out that the novel capabilities of these bacteria are due to something rather than nucleotide insertion, deletion, or replacement". Good call. The title said frameshift mutation.

So much for birthing a novel, functional enzyme by the random mix-up of a nucleotide.

A frameshift mutation is not a random mixup. Are you sure you took Bio 101?

 

[Johnny]

Rather, the platform of design allows scientific inquiry a strong, practical base not to be found in other models.

Are you serious? Just stop posting now. You're embarassing yourself.

 

[fool]

Thanks to all (except for Fool, because of his crude remark), -Bob

Which ones?

 

[sentientsynth]

Well, Johnny, it's apparent that don't understand that this wans't some random process that all bacteria go through. It's something that the bacteria are designed to do when encountered with a stressful environment. Under normal conditions, there is no recombination of the plasmid sequence. The recombination is a reaction to the environment, not at all a random event in the course of speciation, as you would presume.

 

[sentientsynth]

Are you serious? Just stop posting now. You're embarassing yourself.

What embarasses me is you, Johnny: a fellow Christian who prides himself in undermining the authority of God's word.

 

[sentientsynth]

YO!!

Here's some more information about our nylon-eating friends.

Exerpt from AiG editorial response.

... Finally, Mr Cerutti is out of date about this new nylon digesting ability allegedly from a frame shift. New evidence shows that the ability was due to plasmids [e.g. K. Kato, et al., ‘A plasmid encoding enzymes for nylon oligomer degradation: Nucleotide sequence analysis of pOAD2’, Microbiology (Reading) 141(10):2585–2590, 1995.] In fact, more than one species of bacteria have the ability, residing on plasmids. This suggests that the information probably already existed, and was just passed between different types of bacteria.All that would be needed to enable an enzyme to digest nylon is a mutation causing loss of specificity in a proteolytic (protein-degrading) enzyme. This may seem surprising—how would a loss of information create a new ability? Answer: enzymes are usually tuned very precisely to only one type of molecule (the substrate). Loss of information would reduce the effectiveness of its primary function, but would enable it to degrade other substrates, too. Since both nylon and proteins are broken down by breaking amide linkages, a change in a proteolytic enzyme could also allow it to work on nylon. If this process were continued, the result would be a general enzyme with a weakly catalytic effect on the hydrolysis of too many chemicals to be useful where much selectivity is required. To put it into perspective, acids and alkalis also catalyze many hydrolysis reactions, but they also lack specificity. Indeed, an inhibitor of a protein degrading enzyme also inhibits the action of the nylon degrading enzyme.

The principle is explained (for a different example) in the book Not By Chance by Israeli biophysicist Dr Lee Spetner. Yet another example of a ‘defect’ being an advantage, but totally irrelevant to evolution. Dr Spetner explains enzyme information in more mathematical detail in his response to the sceptic Dr Edward Max.

[Ed. note, 9 April 2004: Research has shown that the correct explanation for the nylon-eating enzyme produced on the plasmids is somewhat different from the previous two paragraphs. It also confirms that the frameshift idea is totally wrong. Rather, there seems to be a special mechanism that recombines parts of the genes in the plasmids in a way that is non-random. This is shown by the absence of stop codons, which would be generated if the variation were random....

Well, Johnny, since my Bio 101 level of education won't allow me to fully comprehend all that, I though I'd let you read the sad news for yourself.

But, to be honest, there may be some room for evolution. but perhaps that's not what you had in mind, JohnnyFive.

Peace

SS

 

[Vaquero45]

What embarasses me is you, Johnny: a fellow Christian who prides himself in undermining the authority of God's word.

After reading many of Johnny's posts, I'd love to hear how he reconciles calling himself "Christian" with the fact that Jesus believed the Old Testament and he doesn't. Either Jesus is a fool or you are Johnny.

 

[sentientsynth]

After reading many of Johnny's posts, I'd love to hear how he reconciles calling himself "Christian" with the fact that Jesus believed the Old Testament and he doesn't. Either Jesus is a fool or you are Johnny.

Not to mention that ridiculous signature.

 

[truthteller86]

Might as well quote one of Johnny's heroes while we're at it... (go ahead and claim context and senility) It was just fun to copy and paste(the 2nd greatest invention of all time) :cheers:

“To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.”

"I am quite conscious that my speculations run quite beyond the bounds of true science."

“For myself, also, I rejoice profoundly; for, thinking of so many cases of men pursuing an illusion for years, often and often a cold shudder has run through me, and I have asked myself whether I may not have devoted my life to a phantasy.”

“Long before the reader has arrived at this part of my work, a crowd of difficulties will have occurred to him. Some of them are so serious that to this day I can hardly reflect on them without being in some degree staggered”

“First, why, if species have descended from other species by fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion, instead of the species being, as we see them, well defined?”

“What you hint at generally is very, very true: that my work will be grievously hypothetical, and large parts by no means worthy of being called induction, my commonest error being probably induction from too few facts.”

“Thank you heartily for what you say about my book; but you will be greatly disappointed; it will be grievously too hypothetical. It will very likely be of no other service than collocating some facts; though I myself think I see my way approximately on the origin of species. But, alas, how frequent, how almost universal it is in an author to persuade himself of the truth of his own dogmas.”

 

[Johnny]

Well, Johnny, since my Bio 101 level of education won't allow me to fully comprehend all that, I though I'd let you read the sad news for yourself.

How do you know if they're making a valid argument? Do you care? If you would have read carefully you could have picked out one of the most glaring mistakes that AiG makes: asserting that "This suggests that the information probably already existed, and was just passed between different types of bacteria."

Finally, Mr Cerutti is out of date about this new nylon digesting ability allegedly from a frame shift. New evidence shows that the ability was due to plasmids [e.g. K. Kato, et al., ‘A plasmid encoding enzymes for nylon oligomer degradation: Nucleotide sequence analysis of pOAD2’, Microbiology (Reading) 141(10):2585–2590, 1995.]

So? It's on a plasmid...that doesn't change a thing. Plasmids are replicons. They replicate just like chromosomal DNA. As others have pointed out, the pre-mutation and post-mutation plasmids were carefully studied. Again, the comparison reveals that it was a simple frameshift mutation of a repetitive noncoding region that yielded the new protein. Also, note the portion I have bolded. "New evidence"? As usual, AiG just can't get it right. Scientists knew this occured on a plasmid nearly 8 years prior to AiG's response.

In fact, more than one species of bacteria have the ability, residing on plasmids. This suggests that the information probably already existed, and was just passed between different types of bacteria.

Bad response. You should see this simply based on something else you posted earlier: "Japanese researchers demonstrated that nylon degrading ability can be obtained de novo in laboratory cultures of Pseudomonas aeruginosa [strain] POA, which initially had no enzymes capable of degrading nylon oligomers. This was achieved in a mere nine days! The rapidity of this adaptation suggests a special mechanism for such adaptation, not something as haphazard as random mutations and selection." This indicates that it simply wasn't plasmid trading, as the author suggests.

The principle is explained (for a different example) in the book Not By Chance by Israeli biophysicist Dr Lee Spetner. Yet another example of a ‘defect’ being an advantage, but totally irrelevant to evolution. Dr Spetner explains enzyme information in more mathematical detail in his response to the sceptic Dr Edward Max.

Interesting that AiG would quote Spetner, who contradicts their claim. Spetner admits that it was an increase in information.

AiG sees that this is a big, big problem for them. The only thing they can agree on is that mutations must not be random. And for that, I take you back to 1952 to the Lederberg experiment. http://evolution.berkeley.edu/evosite/evo101/IIIC1bLederberg.shtml. Basic biology. AiG just can't get it.

 

[Johnny]

What embarasses me is you, Johnny: a fellow Christian who prides himself in undermining the authority of God's word.

I am not undermining the authority of God's word. The authority of God's word is not wrapped up in a literal interpretation of Genesis. This false dilemma leads to the demise of many young people's faiths. While the enlightenment brought us many wonderful things, the scientific application of Genesis was not one of them. The Bible is not a science book. It was not intended to be a science book. The whole idea of reading the Bible like a science book is a relatively new phenomenon. I am not going to respond to any comments regarding my salvation or the nylon-degradation enzymes any further. Suffice it to say AiG hasn't got their facts right (as usual). If you'd like to continue this discussion, create a new thread and I will be happy to participate. Otherwise this discussion is over.

 

[Vaquero45]

I am not undermining the authority of God's word. The authority of God's word is not wrapped up in a literal interpretation of Genesis.

Johnny, what if I said the same about Exodus, or Jeremiah, or Romans? Would you bristle and try to correct me? Do you believe in the miracles of the old testament?

Do you believe God parted the Red Sea? Do you believe in the plagues God brought on Egypt? How about Noah's flood? Jonah? Where do you start taking the Bible literally?

Johnny, sorry to jump you like this, but I see you unnecessarily attacking the Bible and claiming to be Christian at the same time. If you really are a Christian I'm trying to help you see the problem you are making for yourself.

I know you said "this discussion is over", and we can start a new thread if you want.

 

[Jukia]

This thread has gotten a bit far from manganese nodules on the ocean floor. Has anyone ever found the Yates guy who made the comment re concretions around beer cans? You know, the comment that Pastor Bob puts so much stock in?