In creation-evolution debates, "evolution" isn't mere 'change in gene frequencies.' Unless context indicates otherwise, it refers, ultimately, to naturalistic molecules-to-man transformation - anything less involves creation. Evolutionists/naturalists claim bio-transformation and bio-genesis are separate/unrelated problems. "Macroevolution" makes the large-scale transformation fully explicit.

Message theory states that life was reasonably designed:
1. for survival,
2. to look like the product of one designer (not multiple-independent designers), and
3. to resist all other explanations (including Darwin's, Lamarck's, Gould's, Syvanen's, Hoyle's,)


It has nothing to do with hypotheses that states that: "We dont know how it is/was done therefore God did it." How things operate and pursuit of explanation is central to the theory.
Message Theory disallows encoded/encrypted bio-messages (say, English text) as counterproductive. They engender language barriers. They don't serve survival. Mutation causes their meaning to be altered, lost, or mistaken for products of multiple-independent designers. Rather, life's message uses biocomplexity and the simple universal language of 'similarity and difference' - largely visible even to low-tech observers.
Message theory requires neither universal acknowledgment of the message, nor perfection, nor falsification of all alternatives.

I) Evolutionary explanations.
Lets look at evolutionary explanations:

1) Common descent.. Includes Nrs: 2-5 in this list.
2) Anagenesis. Transformation within single lineage.
3) Cladogenesis. Splitting a lineage.
4) Loss. Traits are lost.
5) Replacement.Traits are replaced.
6) "Convergence". Complex similarities that cannot be explained by 1-14 and is called "Independent origin of similar traits"
7) Lamarckism . Inherited use-and-disuse of parts
8) Atavism - genetic throwbacks. Masked ancient traits unmasked into distant descendants - transposes traits across time. (Can theoretically mimic transposition (9))
9) Transposition. Ancient notion. Moves traits between distant lineages - lateral DNA transfer, plasmids, "endosymbiosis," "leghemoglobin"
10) Recapitulation. Peculiar embryological mechanisms - "terminal addition" & "telescoping acceleration"
11) Multiple biogenesis. Many life origins
12) Incompleteness. "The data is too incomplete"
13) Exobiology. "It came from Space!" Mars rocks, Directed panspermia, SETI, Extraterrestrials, Ancient astronauts
14) "Concerted evolution". Molecular drive

Most if not all evolutionary experts embrace 1-6, 8-9, 10 (in some form) and 14. Lamarckism is still sought by some evolutionists [1]. Woese,[2] Dyson,[3] and others embrace nr. 11. Classical Darwinists appeal to the incompleteness of the fossil record and other evidence. Hoyle, Sagan and many others adhere to nr. 13 too. Syvanen et al. [4] put nr. 9 at the center of evolutionary theory.
These explanations (except nr. 9 among microorganisms, and nr. 4) were never experimentally demonstrated over large-scales - instead, their existence, rate, power, and extent are inferred from the data-patterns themselves. As used by evolutionists, these explanations are pattern-based, not demonstration-based. Evolutionary theory is a mix and match of 'Natural' explanations, and evolutionists 'select' those that seem to match the data-patterns. (Natural selection )

These evolutionary explanations do not - and never did - predict a hierarchy pattern. The data-patterns lend shape to an otherwise structureless evolutionary theory - then this congruence is given as "evidence for evolution" - as used by evolutionists, it's circular reasoning. Evolutionists will claim evolution predicts hierarchy. Evolutionists arrive at that falsity because pattern drives evolutionary theory. They observe life's substantial hierarchy pattern, so they then ignore, de-emphasize, or set-aside mechanisms that prevent hierarchy - such as Transposition, Atavism, Convergence, Multiple-origins, Exobiology, and most other mechanisms identified in nrs 1-14. Evolutionists largely ignored these issues. Macro-evolutionary theory doesn't predict hierarchy - it's a structureless smorgasbord, not science.

Evolutionary theory is not very conducive to falsification. Take the example of cytochrome c of humans and chimps. If human's cytochrome-c were completely different from chimps wouldn't it be a blow to evolution theory? Not so, as it can be explained by 2-6, 8-9 and 13-14. And in the case where the lamprey's cytochrome c gene appears closer to humans than does that of tuna fish, all these "explanations" come into full swing to save the theory. Evolutionary theory really is enormously amorphous. What can naturalism not explain? What patterns would help resist all naturalistic explanations? Life contains substantial hierarchical pattern, and virtually all macroevolutionary evidences hinge crucially upon it. However, it isn't evidence for evolution, since evolution didn't/doesn't predict it, but can be explained by the sundry of evolutionary explanations at will without demonstration-based explanations.

The sudden appearance and lack of substantial gradual change (lack of clear-cut ancestors and lineages) of most species in the geologic record, from their initial appearance until their extinction, has long been noted and substantially refutes common-descent. Subsequent theories to explain this has arisen. Punctuated equilibrium (essentially unfalsifiable) with the help of transposistions tries to come to the rescue. Claims of fossil 'incompleteness' can't be taken seriously as stated by Gould. Transpositions (nr. 9) is an exceedingly powerful evolutionary explanation and could potentially explain-away the twofold absences of gradualism and clear-cut ancestors/lineages.

Therefore transposition patterns, if sufficiently sturdy, would nullify the fossil record's testimony against common descent. Message Theory predicts life's design avoids transposition patterns and this would serve to falsify Message theory. Some evolutionists de-emphasize Transposition because life systematically lacks this key pattern. Other evolutionists (Syvanen et al.) emphasize Transposition because they see it would explain-away profound evolutionary difficulties (4):
1. Absence of gradualism
2. Absence of clear-cut ancestors
3. Abundance of "convergence"

II) Vital Properties for Message Theory:
a) The substantial absence of Transposition patterns from macroorganisms (at morphological, embryological, and biomolecular levels). This will resists Transposition explanations (nr. 9), exobiology (nr. 13) and will shows life's designer is unordinary.
B ) Life's hierarchy patterns (cladistic and phenetic):
i) Biodiversity is designed for ecological stability and simultaneously to thwart evolutionary interpretations. Supplies biodiversity for above-named purposes - while leaving "ancestors" out!(nr. 1)
ii) Unifies all life together, as product of one designer
iii) Resists Transposition explanations(nr. 9)
iv) Provides background, against which, "convergences"(nr.6) are 'seen.'
v) Allows deep (rather than superficial) embedding of bio-message; making it: resistant to mutation, and inseparable from survival
vi) Resists incompleteness (nr. 12). The above properties retain perceptibility even when lifeforms are severely unavailable.

The traits evolutionists call "convergences", favour Message Theory - which explains their abundance. {Similar arguments apply to biomolecular patterns called "concerted evolution."(nr. 14)} These complex designs are: sufficiently similar (to demand special explanation), yet sufficiently non-identical (to negate Atavism (nr. 8) and/or Transposition (nr. 9) explanations), and systematically-placed (to negate explanation by common descent). Evolutionists are left with their least plausible explanation - independent origin of similar complex designs - such as your eyes and octopus eyes. Morphological "convergences" cannot be explained with biomolecular Transpositions by the absence of clear-cut Transposition patterns at the biomolecular level. Transposition theories are resisted by life's patterns.
Convergences are abundant (at morphological, embryological, and biomolecular levels)[5]) because they:
" Help link diverse life-groups together, as products of one designer
" Help thwart attempts to 'impose' ancestors and lineages onto life's pattern[6]
" Demand explanation, while resisting naturalistic explanations

The hierarchies (morphological, embryological, and biomolecular) - proudly displayed by evolutionists - never were predicted by evolution. But Message Theory requires such patterns testifying, Designed! Systematic unity, lacking ancestors, gradualism, atavism, Lamarckism, and Transpositions!"" And fossils confirm it. "
Message theory depends on fossils. The logic changes somewhat for lifeforms lacking fossilizable morphology - microorganisms. Here it matters less whether lateral DNA transfer occurs, because there exist no fossils sufficient for carrying the argument forward to completion. Also, Message Theory shifts emphasis for microorganisms - toward resisting biogenesis.

III) Biologic Universals and biomolecular unity
These include:
1) DNA>RNA>protein, tri-nucleotide genetic-code, left-handed amino-acids, bi-layered phosphatide cell-membrane.
2) alpha-bonded amino-acids, ribosomes, limited 20 amino-acid subset from thousands of other possibilities.
3) Ubiquitin
4) ATP, biotin, riboflavin, hemes, pyridoxin, folic acid, vitamins B12 and K.

These are believed to be powerful, central evidence for evolution, but Nobel-laureate Francis Crick contradicts: "Such an astonishing degree of [biochemical] uniformity was hardly suspected as little as forty years ago"[7].
Evolution never predicted biomolecular unity. Evolutionists claim many lifeforms completely lacking the known biologic universals must have existed on Earth [8,9]. Origin-of-life theorists (to make naturalistic origins more probable) claim there's countless other workable life-arrangements unlike known-life. Some evolutionists claim multiple-origins of distinct lifeforms must have occurred,[ 2,3] or came from Space! Given such latitude in workable molecules/arrangements, this is another reason why biomolecular unity is unexpected from evolution, if anything it predicts the opposite.
Moreover, considering macroevolution's many mechanisms (nrs 1-14), there's no reason yeast and elephants should share any similarities. Message Theory claims lifeforms are designed to look like products of one designer - and only biomolecular unity can broadly accomplish that. Moreover, biomolecular unity simultaneously contradicts evolution. If there exists even one endemic living species dis-associated from our life-system, then Message Theory would be refuted - Message Theory is testable - macroevolution isn't.

IV) Cellulose and multi-gene families as evidence:
A) Plants make cellulose and fungi and microorganisms digest it with complex forms of "cellulase" enzyme-systems.
Generally, multicellular-animals don't have cellulase, so cannot digest cellulose. Instead, herbivores prolong digestion long enough for microorganism symbionts to digest the cellulose - then the animal digests the symbionts.
Consider the consequences if most higher-animals could efficiently convert forests into progeny (use cellulose as energy source and increase reproductive success). It would be catastrophic for the system. Therefore, a designer should protect plants from limitless overgrazing. Multicellular animals' inability to efficiently digest cellulose is one-facet of ecological balance for the system.
This simultaneously resists evolutionary explanation - (another goal of Message Theory) - because natural selection cannot look-ahead to benefit the system. Cellulose is Earth's most abundant food compound, so cellulase would evolutionarily benefit practically any individual, and selection cannot coherently discriminate against such individuals. So why are these enzymes not nearly universal in multicellular-animals? Evolutionists glibly explain origins of hearts, brains, and hemoglobin; so what deterred evolution from Earth's most abundant food-source?![10] This shows evolutionary theory has no coherent structure.
Relatively few multicellular-animals have cellulase, and even fewer have all components of a complete efficient cellulase system - so complete freedom from reliance on symbionts is exceptional. These various uncommon cellulase components are dispersed among extremely variegated taxonomic groups,[9] where they pose further problems for evolutionists to explain their repeated origins and loss!

B ) Multi-gene-families display peculiar patterns unexplainable by ordinary evolution. The genes allegedly evolve "in concert," making similar changes to different genes - as though choreographed together. Evolutionists embrace this peculiar macroevolutionary explanation - called "concerted evolution" - based on patterns in living organisms. It isn't demonstrated over macroevolutionary-scales.
The alleged mechanism involves repeated, highly-fortuitous occurrences of gene conversion and/or unequal crossing-over (at precise locations!), followed by successful substitution. These improbable events wouldn't likely produce the observed patterns. However, these same mechanisms would: confound biomolecular clocks; aggravate error catastrophe; and be yet another reason why evolution doesn't predict hierarchy.
The so-called "concerted" pattern is unified and 'choreographed' - as from one designer - and simultaneously problematic for evolutionists - thus supporting Message Theory.

V) Evolution and molecular clocks fallacy:
1) "Clarification of the phylogenetic relationships of the major animal phyla has been an elusive problem, with analyses based on different genes and even different analyses based on the same genes yielding a diversity of phylogenetic trees."[11]
2) "Congruence between molecular phylogenies...is as elusive as it is in morphology"[12]
3) Parallelism "is rampant at both the morphological and the chemical level."[13]
4) Discordance often occurs between levels. "In our opinion cases where there is severe incongruence between chemical and morphological data do exist and such cases do pose both fundamental and practical problems for taxonomists."[14]
5. There's no inherent reason macroevolution should produce clock-like results, and many reasons it's unexpected.
6. Evolutionists use fossil-ages to "calibrate" the molecular clock - thereby guaranteeing a "match" between the two.
7. Even so, the pattern isn't so simple, and doesn't square with uniform molecular-clock-rates (for all genes jointly, nor even for most genes singly). So evolutionists ignore some genes and include others - to increase the match. Evolutionists also allow fluctuating molecular-clock-rates (between separate genes, and for a given gene) - which are "calibrated" with multiple references to fossil-ages - again increasing the match. This method allows evolutionists to further eliminate (ignore or "calibrate"-away) discrepancies between molecular and fossil data.
8. Evolutionists easily explain-away further discrepancies between 'molecular-age' and fossil-age. Large radiometric/sedimentary dating inaccuracies; over-thrusts, re-mixing, and "incompleteness," all allegedly alter the 'apparent' fossil-sequence. Most importantly; hierarchies - whether based on molecules or fossil-morphology - don't identify real ancestors, therefore virtually any fossil-sequence is compatible with evolution and molecular data. The evolutionist method artificially constructs unreal ancestors (from molecules, and from fossil-morphologies), and then claims a correspondence between the 'ages' of these unreal entities! These unreal organisms don't exist, so their 'age' and 'order of appearance' are a farce!
9. The molecular clock isn't fundamentally about age. In effect, it claims the correspondence between two types of hierarchy - (based on molecules, and fossil-morphology) - is evidence for macroevolution. It's the classic 'hierarchy' argument in different guise.
10. Many evolutionists vigorously reject the molecular clock:
Considering the strong demands usually applied in experimental biology, it is hard to understand why the [molecular clock] concept survived such a long period at all. It can neither be used as a tool for dating phylogenetic splits nor as reliable supportive evidence for any particular phylogenetic hypothesis. ... . A reliable molecular clock with respect to protein sequences seems not to exist. ... . It is concluded that the protein molecular clock hypothesis should be rejected.[15]

V) “Why the nylon bug” is not an example of macro-evolution. (Combination of Answersingenesis and creationwiki responses)

Natural genetic engineering to put it plainly.

a) 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.
b ) 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.
c) 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, 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.
d) The antisense DNA strand of the four nylon genes investigated in Flavobacterium and Pseudomonas lacks any stop codons [16]. 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 (natural genetic engineering) 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).
e) 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. 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.
f) 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


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.
Antibacterial resistance (although not all), modification of E. coli's frucose pathway to metabolize propanediol, evolution in Klebsiella bacteria of a new metabolic pathway for metabolizing 5-carbon sugars and other are also probaly more examples of Natural genetic engineering.

References

1) Steele, E., et al, 1998, Lamarck’s Signature
2) Woese, C., 2002, “On the evolution of Cells,” PNAS, Vol. 99, Issue 13, 8742-8747
3) Dyson, F., 1985, Origins of Life
4) Syvanen and Kado/editors, 2002, Horizontal Gene Transfer, 2nd Edition
5) Gould, S.J., 1980, The Panda’s Thumb, p 271
6) Cain, A.J., 1982, “On Homology and Convergence,” Problems of Phylogenetic Reconstruction, (Joysey/editor), Systematics Association, p 1
7) Crick, F., 1981, Life Itself, p47
8) Cairns-Smith, A.G., 1985, Seven Clues to the Origin of Life, p91, 100, 107
9) Shapiro, R., 1986, Origins: A Skeptic's Guide, p186, 207, 293
10) Watanabe, H., and Tokuda, G., "Animal cellulases," Cell.Mol Life Sci. 58(2001)1167-1178
11) Lynch, M., 1999, "The Age and Relationships of the Major Animal Phyla," Evolution, 53(1999);319-325, p323
12) Patterson, C., et al, "Homology in Classical and Molecular Biology," Molecular Biology and Evolution 5(1988), pp.603-625
13) Joysey, 1980, "Principles and Practice in Chemosystematics: a Summing Up," in Chemosystematics: Principles and Practice, Bisby et al,(editors), p 420
14) Harris and Bisby, 1980, "Classification from Chemical Data," in Chemosystematics: Principles and Practice, Bisby, F.A, et al,(editors), p308
15) Margulis and Sagan, 1986, Origins of Sex, p119
16) 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




Most of the above mentioned material was from a debate between David Thomas and Walter ReMine (Here) and this is just an introduction to the basic concepts and arguments of Message theory. In essence, Message theory proposes that the current status of nature and the fossil record can altogether be better explained by the theory and not by pure naturalism and Message Theory turns the origins debate inside-out.

Also shows evolutionary theory is structureless, and predicts virtually nothing. It adapts to data like fog adapts to landscape.

all right i took the time to read most of the post but what is it your trying to say man. I think nobody knows the answer to the most asked question in the world.

Doh.... double post. Apologies

7 minutes... wow, hope everything made complete sense
Origin debates are fascinating and boils down to which philosophy of life you follow.

They aren't. Both involves evolution. The requirements for something to be subject to evolution are:
Reproduction, which means the property of a structure to increase the probability of formation of similar structures in its presence.
And Mutation, which means that the mechanism of reproduction is imperfect and not stable.

Evolution does not require homeostasis, organisation, metabolism, growth or response to stimuli. Therefore the principles of evolution also apply to certain chemical structures which do not show all characteristics of life. It is thought that the remaining characteristics have developt in a process of evolution.

No. I haven't heard anyone making that claim until now.


Isolation and differing selection pressures lead to speciation. This is because they prevent transposition and convergence. Atavism would not prevent hierarchy.

Considering multiple origins, it is possible that there exists a shadow biosphere. But as long as this is pure speculation, I'd say that the formation of life seems to be so improbable that it happened only once in our galactic neighbourhood.


Am I right to suspect that 'sudden' is used here in terms of geological time scales?

Similar conditions yield similar results. What would be more plausible?


Yet, the observation of horizontal gene transfer in microorganisms is somewhat confusing in the proposed scenario. As some Microorganisms are parasitic it can be hypothised that they provide the mechanism for HGT in the larger organisms who are their hosts. Wouldn't the testimony of the creation be clearer if microorganisms were omitted?


The discovery of DNA has supported the theory of evolution because it was the discovery of the mechanism accounting for the basic observations on which evolution is based.
That DNA is universal to all known life (and even more: that all known DNA spirals in the same direction) and that other molecular components are shared does imply (though not proof) common ancestry. But when was it ever considered "central evidence"?


see above:

QUOTE

Most if not all evolutionary experts embrace 1-6, 8-9, 10 (in some form)

Multiple biogenesis (11) is considered by some, not by most experts. It is not a central assumption nor requirement of evolutionary theory and never was.


Even without 'countless' possibilities it is instantly clear that any life form would also work if we'd build it with all molecules mirror-inverted. But all DNA spirals the same way. So it seems that the formation of life is suffiecently improbable to have occured only once in our galactic neighbourhood and still sufficiently probable to have happend at least once in the whole vast universe.
Yes, evolutionary theory does not predict this. But it does predict common ancestry for large classes of species'. And molecular biology did not falsify that prediction.

No. It would have prevented the system from forming.
This way of reasoning is like violently shaking a box, on opening it ignoring all shards and observing that none of the intact objects inside the box are of fragile nature and thus concluding that the person who filled the box must have expected that you would shake it. Only that in this situation there are no visible 'shards', which makes it's being wrong less obvious.

Digesting cellulose costs much energy. It is not reasonable to develop the ability to feed from cellulose as long as other, less tough food sources are available.

That is pretty interesting. Well, as bacteria have a long history of adapting to different environmental conditions they might have developt some not yet understood mechanism of mutating in a slightly more aimed way than would be expected. Our own nerval system serves the same purpose in a way. It is a mechanism for changeing our behavior in less than one generation. And through education behavioreal adaptions can be inherited. If bacteria turn out to have a mechanism for similar tasks which does change their genetic code, then basic evolutionary principles would not be the sole answer to how life evolved.