The adaptation of bacteria to feeding on nylon waste
by Don Batten
In 1975, Japanese scientists discovered bacteria that could live on the waste products
of nylon manufacture as their only source of carbon and nitrogen.1 Two species, Flavobacterium sp. K172 and Pseudomonas
sp. NK87, were identified that degrade nylon compounds.
Much research has flowed from this discovery to elucidate the mechanism for the
apparently novel ability of these bacteria.2
Three enzymes are involved in Flavobacterium K172: F-EI, F-EII and F-EIII,
and two in Pseudomonas NK87: P-EI and P-EII. None of these have been found
to have any catalytic activity towards naturally occurring amide compounds, suggesting
that the enzymes are completely new, not just modified existing enzymes. Indeed
no homology has been found with known enzymes. The genes for these enzymes are located
on plasmids:3 plasmid pOAD2 in Flavobacterium
and on two plasmids, pNAD2 and pNAD6, in Pseudomonas.
Apologists for materialism latched onto these findings as an example of evolution
of new information by random mutations and natural selection, for example, Thwaites
in 1985.4 Thwaites’ claims have
been repeated by many, without updating or critical evaluation, since.
Is the evidence consistent with random mutations generating the new genes?
Thwaites claimed that the new enzyme arose through a frame shift mutation. He based
this on a research paper published the previous year where this was suggested.5 If this were the case, the production
of an enzyme would indeed be a fortuitous result, attributable to ‘pure chance’.
However, there are good reasons to doubt the claim that this is an example of random
mutations and natural selection generating new enzymes, quite aside from the extreme
improbability of such coming about by chance.6
Evidence against the evolutionary explanation includes:
-
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.
-
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.
-
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 genes—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.
-
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).
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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.
-
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.8
P. aeruginosa is renowned for its ability to adapt to unusual food sources—such
as toluene, naphthalene, camphor, salicylates and alkanes. These abilities reside
on plasmids known as TOL, NAH, CAM, SAL and OCT respectively.2
Significantly, they do not reside on the chromosome (many examples of antibiotic
resistance also reside on plasmids).
The chromosome of P. aeruginosa has 6.3 million base pairs, which makes
it one of the largest bacterial genomes sequenced. Being a large genome means that
only a relatively low mutation rate can be tolerated within the actual chromosome,
otherwise error catastrophe would result. There is no way that normal mutations
in the chromosome could generate a new enzyme in nine days and hypermutation of
the chromosome itself would result in non-viable bacteria. Plasmids seem to be adaptive
elements designed to make bacteria capable of adaptation to new situations while
maintaining the integrity of the main chromosome.
Stasis in bacteria
P. aeruginosa was first named by Schroeter in 1872.10 It still has the same features that identify it as
such. So, in spite of being so ubiquitous, so prolific and so rapidly adaptable,
this bacterium has not evolved into a different type of bacterium. Note that the
number of bacterial generations possible in over 130 years is huge—equivalent
to tens of millions of years of human generations, encompassing the origin of the
putative common ancestor of ape and man, according to the evolutionary story, indeed
perhaps even all primates. And yet the bacterium shows no evidence of directional
change—stasis rules, not progressive evolution. This alone should cast doubt
on the evolutionary paradigm. Flavobacterium was first named in 1889 and
it likewise still has the same characteristics as originally described.
It seems clear that plasmids are designed features of bacteria that enable adaptation
to new food sources or the degradation of toxins. The details of just how they do
this remains to be elucidated. The results so far clearly suggest that these adaptations
did not come about by chance mutations, but by some designed mechanism. 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.11
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.
References
- Kinoshita, S., Kageyama, S., Iba, K., Yamada, Y. and Okada, H.,
Utilization of a cyclic dimer and linear oligomers of ε-aminocapronoic
acid by Achromobacter guttatus K172, Agric. Biol. Chem. 39(6):1219–1223,
1975. Note: A. guttatus K172 syn. Flavobacterium sp. K172.
Return to text.
- Negoro, S., Biodegradation of nylon oligomers [review], Applied
Microbiology and Biotechnology 54:461–466, 2000.
Return to text.
- A plasmid is an extra-chromosomal loop of DNA in a bacterium. Such
loops of DNA, unlike the chromosomal DNA, can be swapped between different species
of bacteria. An individual bacterium can have several types of plasmid, and multiple
copies of each. Return to text.
- Thwaites, W.M., New proteins without God’s help, Creation/Evolution
5(2):1–3 (issue XVI), 1985. Return to text.
- Ohno, S., Birth of a unique enzyme from an alternative reading
frame of the preexisted, internally repetitious coding sequence, Proceedings of
the National Academy of Sciences USA 81:2421–2425,
1984. Return to text.
- Truman, R., Protein mutational context dependence:
a challenge to neo-Darwinism theory: part 1, Journal of Creation 17(1):117–127;
Truman, R. and Heisig, M.,
Protein families: chance or design? Journal of Creation 15(3):115–127.
Return to text.
- As of the date of writing, no Flavobacterium sp. genome
has been sequenced. Return to text.
- Yomo, T., Urabe, I. and Okada, H., No stop codons in the antisense
strands of the genes for nylon oligomer degradation, Proceedings of the National
Academy of Sciences USA 89:3780–3784, 1992.
Return to text.
- Prijambada, I.D., Negoro, S., Yomo, T. and Urabe, I., Emergence
of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through
experimental evolution, Applied and Environmental Microbiology 61(5):2020–2022,
1995. Return to text.
- Bacterial Nomenclature Up-to-date, Deutsche Sammlung von Mikroorganismen
und Zellkulturen GmbH, Braunschweig, Germany. <www.dsmz.de/bactnom/bactname.htm>,
18 September 2003. Return to text.
- Truman, R., The unsuitability
of B-cell maturation as an analogy for neo-Darwinian Theory, March 2002; <www.trueorigin.org/b_cell_maturation.asp>,
22 August 2003. Return to text.
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