Here's the situation you presented:
jwu wrote:
As a seperate line of reasoning...what happens to the information content of a string of DNA if a base pair is deleted and whatever was coded in it doesn't fulfil a purpose anymore? Does the information content decrease because of that, or can this not be determined based on the effect of the codex enzyme or protein on the organism?
In this situation, there has been a loss of information, because of message
corruption.
jwu wrote:
And exactly that is why Shannon's information theory is absolutely inapplicable to biology. In it by definition any change of the original message is considered a loss of information, as it's a deviation from the "original intent".
Just because it doesn't make sense in evolutionary terms, doesn't mean it
doesn't make sense. In ID terms, it makes total sense...the message
transmitted is not the intended message.
jwu wrote:
Does the claim that information can only decrease then not imply that no mutation can happen which inserts that particular base pair again then? After all, otherwise that would be an increase of information, as the previously extant information was lost and it is being regained from nothing.
What's occured here is a
net neutral effect on the message...a loss
of meaning, and then by accident, regaining that info. The message is back
to it's original state(albiet accidently). The lost function is regained.
jwu wrote:
SO when an increase of binding specifity is observed, it "was designed to behave like that under stress"? Did God plan to enable it to be able to digest nylon once man made that substance? That makes the claim that no information can be gained unfalsifyable, and hence it loses any meaning.
3, 4, 5 and 6 do not make the observed emergence of a new ability go away either. They look for a-posteriori statistical anomalies in the genome, and then claim that it was designed to behave like that somehow. Note that they did not in any way dispute that an increase of functionality happened, they just say "Goddidit". The emergence of a new ability stands unrefuted, and by AiGs reasoning any new ability can be handwaved away as God guiding the mutation or whatever else mechanism provided it.
The reason scientists conducting the research believe it was designed to
behave accordingly is highlighted:
Quote:
1.
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.
2.
All five transposable elements are identical, with 764 base pairs (bp) each. This comprises over eight percent of the plasmid. How could random mutations produce three new catalytic/degradative genes (coding for EI, EII and EIII) without at least some changes being made to the transposable elements? Negoro speculated that the transposable elements must have been a ‘late addition’ to the plasmids to not have changed. But there is no evidence for this, other than the circular reasoning that supposedly random mutations generated the three enzymes and so they would have changed the transposase genes if they had been in the plasmid all along. Furthermore, the adaptation to nylon digestion does not take very long (see point 5 below), so the addition of the transposable elements afterwards cannot be seriously entertained.
3.
All three types of nylon degrading genes appear on plasmids and only on plasmids. None appear on the main bacterial chromosomes of either Flavobacterium or Pseudomonas. This does not look like some random origin of these genesâ€â€the chance of this happening is low. If the genome of Flavobacterium is about two million bp,7 and the pOAD2 plasmid comprises 45,519 bp, and if there were say 5 pOAD2 plasmids per cell (~10% of the total chromosomal DNA), then the chance of getting all three of the genes on the pOAD2 plasmid would be about 0.0015. If we add the probability of the nylon degrading genes of Pseudomonas also only being on plasmids, the probability falls to 2.3 x 10-6. If the enzymes developed in the independent laboratory-controlled adaptation experiments (see point 5, below) also resulted in enzyme activity on plasmids (almost certainly, but not yet determined), then attributing the development of the adaptive enzymes purely to chance mutations becomes even more implausible.
4.
The antisense DNA strand of the four nylon genes investigated in Flavobacterium and Pseudomonas lacks any stop codons.8 This is most remarkable in a total of 1,535 bases. The probability of this happening by chance in all four antisense sequences is about 1 in 1012.
Furthermore, the EIII gene in Pseudomonas is clearly not phylogenetically related to the EII genes of Flavobacterium, so the lack of stop codons in the antisense strands of all genes cannot be due to any commonality in the genes themselves (or in their ancestry). Also, the wild-type pOAD2 plasmid is not necessary for the normal growth of Flavobacterium, so functionality in the wild-type parent DNA sequences would appear not to be a factor in keeping the reading frames open in the genes themselves, let alone the antisense strands.
Some statements by Yomo et al., express their consternation:
‘These results imply that there may be some unknown mechanism behind the evolution of these genes for nylon oligomer-degrading enzymes.
‘The presence of a long NSF (non-stop frame) in the antisense strand seems to be a rare case, but it may be due to the unusual characteristics of the genes or plasmids for nylon oligomer degradation.
‘Accordingly, the actual existence of these NSFs leads us to speculate that some special mechanism exists in the regions of these genes.’
It looks like recombination of codons (base pair triplets), not single base pairs, has occurred between the start and stop codons for each sequence. This would be about the simplest way that the antisense strand could be protected from stop codon generation. The mechanism for such a recombination is unknown, but it is highly likely that the transposase genes are involved.
Interestingly, Yomo et al. also show that it is highly unlikely that any of these genes arose through a frame shift mutation, because such mutations (forward or reverse) would have generated lots of stop codons. This nullifies the claim of Thwaites that a functional gene arose from a purely random process (an accident).
5.
The 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.9 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.
6.
The researchers have not been able to ascertain any putative ancestral gene to the nylon-degrading genes. They represent a new gene family. This seems to rule out gene duplications as a source of the raw material for the new genes.
http://www.answersingenesis.org/tj/v17/i3/bacteria.asp
jwu wrote:
No, it's because evolution requires no increase of Shannon information.
I did not say "evolution happens, therefore shannon information theory is inapplicable." That'd be circular reasoning.
Again, your making the assumption evolution occurs in your statement.
What if Information Theory applies to biology? Then the 2 theories are at
odds.
You're mixing various flavours of information theory, nominally those which have an established law of conservation (Shannon) with others which actually attempt to measure the function of the genome, not just its transmission integrity as Shannon does. That is not valid.
The different flavors of information theory to which your referring are
different aspects of the theory that have been developed since the inception
of classical information theory (Shannon's). Their complementary, not at
odds with one another.
Charlie wrote:
...violate the rule
of Cause and Effect...
To start with, a cause must be greater than the effect. ToE contradicts this
rule...actually reversing the rule.
jwu wrote:
Earth is an open system.
All systems are open. All real-world change or dynamics follow, or
are motivated, by this law (2nd).
Even so, increased complexity requires outside energy and information or a
code to direct this energy into useful work.
The energy in itself has no organizational properties.
Peace