Evolution, the genetic code, and ‘message theory’: A response to Walter Remine

Good article, as always.

However, I wish to point out something that I find relevant. In your article, you write “Enzymes are always made of protein (or are based on protein)”. This is true most of the time, although some RNA molecules (Ribozymes for instance) are known to have enzyme properties.
http://en.wikipedia.org/wiki/Ribozyme

Also, autocatalytic chemical reactions are known to exist in nature.
http://en.wikipedia.org/wiki/Autocatalysis

Keep up the good work, you just might get a buck from me someday.

I don’t understand this codon thing. I thought codons were just three letters in a dna strand, and they are the code for amino acids. And that all mutations involve codon letters changing. But I keep hearing about this change that can’t take place with codons. Does this have to do with certain essential proteins which can’t be folded wrong or you get extinction? Do I have a wrong definition for codon or something?

Here’s the study I was mentioning:

“Penn biologists discover how ’silent’ mutations influence protein production”
http://esciencenews.com/articles/2009/04/09/penn.biologists.discover.how.silent.mutations.influence.protein.production

Thanks Olivier, This is the paragraph I’m confused about:

“Why should this be? Well, if a change occurred so that a codon (the three letters of an amino acid’s genetic code) was suddenly “reassigned” and began coding as some other amino acid, it would very likely change every protein that an organism had, and such a radical change would almost certainly mean that the organism would be far less fit than other other members of the species (if such a change was not fatal). So any radical changes to the genetic code (such as these) are essentially impossible.”

There is something to what he’s saying as I’ve seen something like what he’s saying elsewhere, but I don’t understand it. Because ALL mutations involve these codon changes from what I know.

Codon’s code for amino acids, I know that. But isn’t coding for amino acids what every single mutation is doing? Or are regular mutations simply changing which amino acids are used in a protein, and not the amino acid’s properties itself? This is a basic biology question, but there’s no easy reference for this question that I’ve seen.

I saw the link and understand the new found purpose for what were thought of as neutral, or silent mutations.

Walter:

Feel free to point to us how message theory is readily testable, seeing you’re so enclined to say evolution isn’t. Elaborate a way to test message theory’s claim that “Life looks like the product of one designer”. Until you or your peers does so you’re pretty much bound to not be taken seriously anywhere. And no, saying that convergence equals God doesn’t count.

Olivier

BIOLOGIC UNIVERSALS —

—— “What I meant to say was that the first living thing would not have been missing many (if any) biological universals.”

I challenge you to find any leading origin-of-life researcher who even remotely agrees with your assertion.

—— “if all organisms are descended from the same original organism, they should have inherited the genetic code of this organism. All organisms should have the same genetic code (with a possibility of a rare variation here and there).”

There are potent objections to your argument. First, you (and Francis Crick, and others) already identified a means whereby the genetic code can drift without limit, and therefore evolutionists have no scientific reason why, for example, yeast and elephants should share the same genetic code.

Second, evolutionists discovered that our genetic code itself shows substantial design, and is not a randomly “frozen accident” of happenstance as had previously been thought. From these evolutionists’ point of view, it is highly improbable the first genetic code on Earth was much like ours. Instead, these evolutionists suggest many genetic codes existed, and evolved, on this planet. Once again, evolutionary theory does not make your prediction.

—— “What I was doing was giving a plausible explanation of why other forms of life did not exist. Even if you reject it as unscientific…” (italics added)

Yes, I reject your explanation as untestable, and therefore unscientific (under the same criteria evolutionists use in all their court cases). Walter ReMine claims evolutionary theory is a structureless smorgasbord of storytelling and able to “explain” virtually anything and its opposite — macro-evolutionary theory is untestable, and therefore unscientific.

—— “the genetic code provides a way for us to test assertions about which animals are related,”

That is misleading. If each of the animal phyla had a different genetic code, then evolutionary theory could effortlessly accommodate that observation. “These genetic changes,” evolutionists would say, “happened way back before the Cambrian Explosion, lost in the mists of time” and blah, blah, blah, you can figure the rest. Evolutionists could explain it as many separate origins of life, for example. Evolutionary theory never predicted a unified genetic code. You are wrong to pretend it does.

As ReMine notes: If evolutionary theory has anything clear to say about the biochemical unity of life, it predicts this unity should not exist. On this issue, evolutionary theory is either false, or unfalsifiable — and either way it is unscientific.

The biochemical unity of life also falsifies any notions that life came from multiple designers acting independently, such as ancient astronauts or extraterrestrial civilizations. Rather, all life must have come from one source — a single designer — precisely as predicted by Message Theory. This is a testable (potentially falsifiable) prediction, straight from the core of Message Theory.

Concerning the biochemical unity of life, Message Theory is testable science; and evolutionary theory is not.

ATAVISM, TRANSPOSITION, AND “CONVERGENCE” —

—— “How could the genetic material from the tail of a fish have survived over 200 million years, still in usable form, without having been altered at all?”

In Stephen Jay Gould’s book, Hen’s Teeth and Horse’s Toes, the “Hen’s Teeth” from the title was allegedly an example of an Atavism (genetic throwback) from 80 million years ago. Evolutionists “explained” its maintenance in the genome as the result of pleiotropy and selection. This demonstrates that modern evolutionists are quite willing to invoke Atavisms crossing long periods of time. Darwin and the early Darwinists’ invoked Atavism, and so do modern evolutionists.

Evolutionists were never seriously limited by their inability to experimentally demonstrate their macro-evolutionary explanations. They have not remotely demonstrated the transformation of, say, a horse into something as different as, say, a pig. Or a dog into a cat. Yet these would be exceedingly minor transformations compared to the evolutionists’ claims. Also, evolutionists have not experimentally demonstrated any great convergence transformation, such as your example: the so-called whale-tail / fish-tail convergence. Instead, evolutionists are moved by pattern: When evolutionists see a pattern, they “explain” it by selecting a story from their vast structureless smorgasbord of naturalistic explanations. Evolutionists are driven by pattern. Throughout history, evolutionists invoked (and sometimes later renounced) their explanations due solely to their perception of pattern — this is a nearly universal phenomenon. To evolutionists, pattern is king. Therefore, the designer of life wisely designed life’s patterns to resist macro-evolutionary explanations.

For example, had the whale-tail and fish-tail been identical, then the ancient Greeks, and the early Darwinians, (as well as modern evolutionists too), would have had little restraint in claiming it was due to Atavism or Transposition. Life’s-designer wisely resisted those explanations by omitting Atavism and Transposition patterns. Evolutionists are left with their least plausible explanation: The independent origin and “convergence” of complex designs that cannot be explained by common descent. This pattern is abundant in nature, as predicted by Message Theory.

—— “Evolutionists would expect that the two tails originated differently, and since we know that there are often many solutions to a problem, we would expect the two lineages to have ‘hit on’ different solutions.”

In every respect, that statement is false or misleading. Evolutionists, from the ancient Greeks, to the early Darwinians, to modern evolutionists, invoked Atavism-Transposition explanations, therefore it is false to claim evolutionary theory “expects” those to be absent. There is one, and only one, over-riding reason why these explanations are seldom given: These patterns are substantially absent. And that is predicted by Message Theory.

As ReMine points out, if convergences were identical, they would no longer be “convergences”: instead evolutionists would explain them as Transpositions or Atavisms.

—— “No, convergent evolution is the only thing that explains why the two are different.”

Again you focus on “explanation”, as though that were scientifically sufficient. Your whale-tail convergence explanation cannot remotely be demonstrated experimentally, nor is it testable; therefore it is unscientific. It is an unscientific story, given with religious fervor.

ODDS AND ENDS —

—— “So when creatures are different its not evidence against your theory, but when they’re created similarly, its evidence for your theory? Who’s being unscientific now?”

You are being reckless. You are already aware (from Walter ReMine’s essay) that the existence of even one natural living being, sufficiently different or dis-united from our system of life, would falsify Message Theory. Message Theory makes testable scientific predictions about the things we should see, and should not see.

—— “your definition of evolution which includes the origin of life (which is not the standard)”

You are being needlessly (without legitimate purpose) evasive over the definition of “evolution”. In the origins debate, “evolution” (and evolutionary theory) refers to naturalistic transformation all the way from rocks (if not before) to people, and anything less is creation. This point is neither controversial, nor unfair. As Walter ReMine points out, the evolutionists’ insistence on keeping the origin-of-life as a “separate issue” had the effect of concealing/obscuring the evolutionists’ self-contradictions — for example, the contradictions between Dobzhansky and the origin-of-life theorists.

—— [Walter wrote:] “For example, the up-down tail of whales (versus the side-to-side tail of fish) cannot be explained by common descent, nor by Atavism (or genetic throwback),”

—— [Your response:] “Bullshit. I have already explained how whales move their bodies in a way similar to that of land mammals when they swim. It’s a modification of the same muscles. Do you have a problem reading or something?”

The evolutionary relationship between whale-tail and fish-tail (which is the issue you raised) is not explained by common descent, but instead by independent origin and so-called “convergence”. But you knew that already …so why are you making stink?

—— “Life is defined as being able to reproduce, evolve, and have metabolism. Therefore it must have had some of the biological universals.”

You gave a non sequitur, that is, your conclusion does not follow logically from your starting premise. Reproduction and metabolism are broad abstract processes, not specific implementations — whereas life’s biologic universals (as listed by Dobzhansky and other evolutionists) are specific physical implementations. Your argument is like saying, “Houses are defined as stable buildings, therefore all houses must have been held together with staples.”

—— “The scenario I presented requires that a codon be rendered very rare (or nonexistent) in an organism’s genome and then be reassigned to code for another amino acid. A codon being rendered rare or nonexistent in the genome is not something that would happen in many lineages, nor would such a thing happen very often. So the code cannot change without limit.”

You mistakenly think ‘not very often’ means ‘limited change’. Your argument is about frequency or probability, and your argument identifies a process whereby, over time, the genetic code can drift endlessly and accumulate change without limit — all it needs is time. [Note: Neutral drift would occur because (as implicit in your presentation) one genetic code is as good as any other, and therefore stabilizing selection would not prevent the drift.]

—— “The fact that all life on earth has the same genetic code is explained by postulating a common ancestor which possessed that code.” (italics added)

You continue to emphasize the ability of evolutionary theory to “explain,” which is not the issue since evolutionary theory can “explain” virtually anything and its opposite. The issue is that evolutionary theory predicts neither a unified biochemistry nor a unified genetic code: on the contrary, if evolutionary theory predicts anything clearly on the matter it predicts the opposite of what we observe.

I repeat, in order to salvage evolutionary theory from falsification, origin-of-life researchers now claim countless other biochemistries and genetic codes must have existed on this planet.

—— “Fine. I don’t owe you any explanation as to why any other lifeforms went extinct, nor is that relevant to the subject.”

You’re trying to dodge the issue. Here it is again: Origin-of-life specialists now acknowledge that known lifeforms are far too complex to have originated by known processes aided by chance and the available time. That would falsify the evolutionists’ worldview, so to salvage it they assume the first Earthly lifeforms were vastly simpler, and contained essentially none of the known biologic universals. The absence of those lifeforms is yet another falsification of the evolutionists’ views. In another attempt to salvage the evolutionists’ views from falsification, you were “explaining” why those other lifeforms are absent, and I responded that your explanation is untestable and therefore unscientific. In summary, the evolutionists’ position is either false, or unfalsifiable, and either way it is unscientific.

You are trying to dodge this by walking away from it, saying you “don’t owe” anything. On the contrary, evolutionists owe on their promise of a scientific explanation, and they don’t have it.

I wrote:

If each of the animal phyla had a different genetic code, then evolutionary theory could effortlessly accommodate that observation. “These genetic changes,” evolutionists would say, “happened way back before the Cambrian Explosion, lost in the mists of time” and blah, blah, blah, you can figure the rest. Evolutionists could explain it as many separate origins of life, for example. Evolutionary theory never predicted a unified genetic code.

—— “you ignore my fourth reference, which quotes an article published in 1963 predicting the universality of the genetic code.”

Astrologers make many “predictions,” and some of those predictions actually come to pass, which is not surprising. The issue is whether the prediction is actually spoken by a coherent theory, and in the case at hand it is not. Evolutionary theory does not predict a universality of the genetic code. If anything, it predicts the opposite, because evolutionary specialists now claim countless other genetic codes must have existed on this planet.

By 1963, scientists had already sampled the genetic codes of numerous diverse organisms; enough to conjecture that further sampling would detect ‘more of the same.’ You don’t even need evolutionary theory to make that prediction: you just predict ‘more of the same’. (This prediction method typically works for many things, such as for predicting tomorrow’s weather; you just predict ‘more of the same’.) Again, evolutionary theory never predicted a universality of the genetic code, instead evolutionists adapted their stories to that observation.

—— “the instance with the tail of the fish is different: For one thing, you would think that the genes controlling its development would not have simply been shutoff, like the bird’s teeth, but transformed into something else.”

Evolutionists have countless stories in their vast structureless smorgasbord of “explanations”, and you are overly impressed by your ability to pick one that meets your fancy. Modern evolutionists now claim evolution occurs mostly by gene duplication, where one set of genes is preserved while a duplicate set is transformed — but your story contradicts that. Don’t worry, you still have lots of other smorgasbord to choose from, so you’ll just find another “explanation” that satisfies you.

The evolutionists’ expansive abilities — to “explain” virtually everything and its opposite — blinds them to the fact that life is very well-designed (perhaps even optimally designed) to resist their explanations while still looking like the product of one designer.

—— “You have not demonstrated your claim that convergent evolution is implausible.”

You mis-read my claim. First, I claimed your “convergence” stories are experimentally undemonstrated and untestable — and therefore unscientific. [Note: Untestability and unfalsifiability is my most persistent objection to macro-evolutionary theory. If you missed that, then you haven't been paying attention.]

Second, I said so-called “convergences” cannot be explained by common descent, nor by Transposition, nor by Atavism (those are three different versions of inheritance), so evolutionists are left with their least plausible (emphasis added there) explanation: The independent origin of similar complex traits. In short, so-called “convergences” are well-designed to resist macro-evolutionary explanations, and to serve the goals of the biotic message.

—— “If the designer wanted to design things as similarly as possible, as you suggest, why didn’t he design the above examples the same way?”

It is not the goal “to design things as similarly as possible”. You are misrepresenting Message Theory. (see below)

—— “If living things had a designer who intended to leave all his creations with his imprint, why would he design the two tails differently?”

You are again mis-stating Message Theory. Message Theory claims all life was designed: (1) to look like the product of one designer (and unlike multiple designers acting independently); and simultaneously (2) to resist all macro-evolutionary explanations.

Point #1 is successfully accomplished, because no one — not even you — claims life is compatible with multiple designers acting independently. So the designer had the latitude (indeed the intent, according to Message Theory) to also design life toward point #2, which is where the answer to your question resides: The whale-tail and fish-tail are designed sufficiently differently that they cannot be “explained” by Transposition, nor by Atavism, nor can the similarity between the two tails be explained by common descent. Evolutionists are left with their least plausible “explanation”, the independent origin of complex traits that “converged” toward a similar design solution.

The pattern known as “convergences” are designed to demand special explanation, yet they are sufficiently different that they cannot be explained by Transposition, nor by Atavism, and they are systematically placed so their relationship cannot be explained by common descent. Concerning any two “convergent” traits, evolutionists are prevented from claiming the complex design was merely “inherited” from one to the other (via any of these three processes). As just described, this pattern requires precisely balanced design and is fundamentally anti-evolutionary in thrust: yet this pattern is abundant in life, as predicted by Message Theory.

—— “We know that there are often many solutions to the same problem, so when some adaptation has arisen in independent evolutionary lineages, we will often expect to see that they have “hit on” different solutions.”

Your story is commonplace among evolutionists. It silently assumes-away Transposition and Atavism, when these cannot be assumed away, since they are part of modern evolutionary theory. As I said before, evolutionists have countless contradictory stories to tell; they just choose the ones that match the pattern they want to explain (and then silently ignore the rest). If the whale-tail and fish-tail had been identical, then evolutionists would “explain” it as Transposition or Atavism — as mere inheritance.

The substantial absence of Atavism and Transposition patterns from the fossil-bearing organisms is a prediction of Message Theory.

—— “No, I addressed the point head on, by allowing the definition of common descent to be bent…”

You’re trying to change the issue there. The issue (quoted in my post, but excised in your latest) was explicitly your complaints about the definition of “evolution” (not the definition of common descent).

—— “It is explained by the theory of common descent, although the explanation … is not that their design stems from a common ancestor.”

You are contradicting yourself. Write your essay more carefully next time… ;)

UPDATE: I now feel that the following statements I made in my last comment have no relevance to the debate. After all, Walt could claim that all organisms were created with the same genetic code and that the ones that reproduced more quickly had more generations for genetic drift and codon reassignment to occur:

Yet I can say one thing: Since bacteria (and mitochondria) reproduce more often than multicellular organisms, there have surely been more generations of them than of multicellular animals. More generations means more chance for genetic drift to occur. And more genetic drift means a higher chance of the genetic code changing. Therefore, organisms which reproduce quickly (like bacteria and mitochondria) ought to show more genetic code variation than plant and animals. Indeed they do! See:
RD Knight, SJ Freeland, LF Landweber, “Rewiring the Keyboard: The
Evolvability of the Genetic Code” Nature Reviews: Genetics, 2, 49-58 (2001).

MESSAGE THEORY –

He wrote:
—- “In fact, since [the designer] wants to make everything look as if it is the product of one designer, why not simply do it like that?”

For the fourth time, he is misrepresenting Message Theory, despite having been repeatedly told of his misrepresentations. (That behavior now seems universal among Internet evolutionists.) He repeatedly omits the key point that answers his challenge: Message Theory claims life was also designed to resist evolutionary explanations. (see previous posts)

******

EVOLUTIONARY THEORY AND THE GENETIC CODE —

—- “… I predict that if someone did the calculations they would find …. Note here that I am making a falsifiable, scientific prediction. However, I have not done these calculations.”

It is of little concern that he makes a personal prediction. The issue is that evolutionary theory, itself, never predicted a universal genetic code. Instead, evolutionists retroactively mold their amorphous theory to the observations.

If we found a natural living thing (even a micro-organism; terrestrial or extraterrestrial) distinctly unlike the known lifeforms, then: (1) it would instantly falsify Message Theory; and (2) evolutionists would hail it as yet another “confirmation” of evolutionary theory (because evolutionists now claim such organisms must have lived on this planet — contrary to our observations).

—- “for the genetic codes present in all living things to have changed beyond recognition would surely require lots of time.” …. “More generations means more chance for genetic drift to occur. And more genetic drift means a higher chance of the genetic code changing.”

Evolutionists have lots of time, and lots of generations. Prokaryotes and eukaryotes allegedly diverged about a billion years ago, which allows a billion years for genetic change to accrue in parallel, in each separate lineage. For example, if from one billion years ago there were a thousand separate lineages, that would allow a thousand billion years for genetic divergence to accrue. And the vast majority of those generations would have extremely short generation times.

******

INTELLIGENT DESIGN AND THE GENETIC CODE —

In the following quote, he gives a rather good idea how intelligent design can explain the observed few dozen minor variations in the genetic code.

—- “[An intelligent design proponent] could claim that all organisms were created with the same genetic code and that the ones that reproduced more quickly had more generations for genetic drift and codon reassignment to occur” …. “Since bacteria (and mitochondria) reproduce more often than multicellular organisms, there have surely been more generations of them than of multicellular animals. More generations means more chance for genetic drift to occur. And more genetic drift means a higher chance of the genetic code changing. Therefore, organisms which reproduce quickly (like bacteria and mitochondria) ought to show more genetic code variation than plant and animals. Indeed they do! See: RD Knight, SJ Freeland, LF Landweber, “Rewiring the Keyboard: The Evolvability of the Genetic Code” Nature Reviews: Genetics, 2, 49-58 (2001).” [Walter notes: Mitochondria are organelles, not organisms.]

******

CONVERGENCE —

—- “What I meant was that evolutionary reasoning (under the paradigm of common descent) would lead one to the conclusion of convergent evolution.

That is a contradiction. By definition, convergences cannot be explained by common descent. Convergence is the independent origin of similar complex features.

Evolutionary theory (as practiced by its modern proponents) does not “lead one” to any conclusions. Instead, evolutionary theory is a structureless smorgasbord that can “explain” virtually anything and its opposite. Because of this, (macro)evolutionary theory is untestable, and therefore unscientific.

Here is how the “evolutionary reasoning” actually operates in the case at hand. When evolutionists want to explain the similarities between lifeforms, they have four options, and three of those options are merely different versions of inheritance. These are: (1) common descent, (2) Transposition (such as lateral DNA transfer), and (3) Atavism (also known a genetic throwback). When those simpler explanations fail, evolutionists resort to their last option, which is the least plausible of all: so-called “convergence”. Evolutionists have no prediction or test taking place. They merely choose from among the options available on their smorgasbord.

Message Theory predicts that so-called “convergence” patterns are abundant in life because these optimally resist evolutionary explanation.

—- “Convergent evolution predicts different designs will often emerge”

False. “Convergent evolution” is a story, and a story does not predict itself.

More precisely, evolutionary theory does not “predict convergence will often emerge” — it makes no such prediction; rather it is an untestable story, conveniently chosen to “explain” observations.

******

SILENT MUTATIONS —

—- “UPDATE: I’d like to once again call attention to the study cited previously showing that “silent mutations” affect protein production”

That study shows so-called “silent mutations” are not silent, rather they have serious affect on the organism’s survival and reproduction. That finding substantially damages the neutral theory of evolution (and the “molecular clock” too), since these theories relied on the silence of the “silent mutations.” Much of evolutionary genetic theory (and its arguments concerning macro-evolution) will now have to be jettisoned, reworked, re-examined.

******

BIOLOGIC UNIVERSALS —

—- “My argument is:
1. Living things by definition can metabolize and reproduce.
2. By definition they must have structures to perform these tasks.
3. Since the amount of variation which can take place is limited, if all living things today share a common ancestor then they should have inherited the structures for reproducing and metabolizing.”

Notice, in this, his latest version of his argument, he drops all prediction of (or even mention of) biologic universals. Instead he backed away into ambiguity, with his vague reference to “the structures”. His conclusion — that “all living things … should have inherited the structures for reproducing and metabolizing” — is compatible with every species having completely different structures for reproducing and metabolizing. His conclusion is that vague. His conclusion does not claim “the structures” should be the same ones used throughout life.

>ATAVISM, TRANSPOSITION, AND “CONVERGENCE” —

>—— “How could the genetic material from the tail of a fish have survived over >200 million years, still in usable form, without having been altered at all?”

>In Stephen Jay Gould’s book, Hen’s Teeth and Horse’s Toes, the “Hen’s Teeth” >from the title was allegedly an example of an Atavism (genetic throwback) from >80 million years ago. Evolutionists “explained” its maintenance in the genome as >the result of pleiotropy and selection. This demonstrates that modern >evolutionists are quite willing to invoke Atavisms crossing long periods of time. >Darwin and the early Darwinists’ invoked Atavism, and so do modern >evolutionists.

I have Stephen Jay Gould’s book. The case of the ‘Hen’s Teeth’ is where epithelial tissue of a 5 day old chicken embryo was grafted with mouse mesenchyme tissue and then transplanted into the eye tissue of a mouse embryo. The epithelial tissue was able to induce the mouse mesenchyme to produce dentine. The explanation is that the genes for producing epithelial tissue have other functions not just inducing dentine production when in contact with mesenchyme. This is the pleiotropy Walter mentions. By just mentioning the term without explanation Walter wants us to think it’s some scientific cop out answer. It is not, it is a perfectly reasonable explanation. In any case this is very far from the case of the whale tail vs the fish tail. In this case such a vast set of changes would have to take place that atavisms are out of the question and nobody proposes this as an explanation.
The nice thing is that in support of evolution we can see mammals today where the process of conversion of limbs to swimming tails is still not complete. This is the case of seals and walruses for example. The descent of whales from land mammals explains very well the up-down motion of the whale tail.
Walter, why are the tails different then? I’ve not heard a good explanation. They have similarities mostly in shape but the differences are vast. Same for the human and octopus eye or the bird’s and bat’s wings. And if you go to the genetic level the differences are huge. Your point #2 is just hand waving. Pretty much structures will be the same because they come from the same designer unless they are not the same in which case we just wave our hands and say the designer must have wanted them different and you make up some arbitrary criteria, “to resist all macro-evolutionary explanations.”
The convergent evolution explanation is so much better. The same solution is arrived from different paths because it is the best solution. This is not difficult when we just look at shape. The differences (which I reiterate are huge) are explained by the different evolutionary paths taken. When you see the path taken by the bird’s wing you can see why it has feathers and not hairs like the bat’s for example. Why not give feathers to the bat? It could not be explained by transpositions or atavisms either. No macro-evolutionary explanation would be possible. Why not make the tail of the whale and fish the same? That would be even harder to explain by transpositions and atavisms.
And there are hosts of other questions which evolution explains nicely. Why do whales still need to breathe air? Why not give them gills. That would make them better adapted to life at sea. They would not have that window of vulnerability when they need to go to the surface and breathe air. I guess you will say the designer wanted to amuse us with the spectacle given by blow holes or some other pulled by the hairs explanation like your point number 2.

Some Final Thoughts on this thread:

First of all, Walt claims that Evolutionary theory could explain everything and its opposite because it is theoretically possible that there might have been enough time for new genetic codes to evolve. Point taken. But he misses the fact that even if a designer created organisms to be unified at the biochemical level, it is also theoretically possible that they may have evolved new genetic codes since the original creation. So Evolution doesn’t predict a universal genetic code and neither does Message “Theory”. And if Message “Theory” does predict a universal code, then Mr. Remine needs to explain why we find organisms with slightly different codes. Is that a falsification of his theory?

Second, Remine has missed some crucial points: Atavisms (from ancestors millions of generations ago) are only plausible if the genetic material in question has other functions through which it might be preserved, as is the case with hen’s teeth. An atavism would not be plausible in the case of whales, because the genetic material which makes the body of the whale would have been radically changed over the course of evolution into amphibians, then reptiles, mammals, etc. Nor is “transposition” (Which I think is his term for lateral gene transfer) a plausible explanation, because lateral gene transfer in higher organisms works with small amounts of genetic material, certainly not enough material to make a tail. The only explanation that makes sense is convergent evolution of fish and whales (adapting to the same environment separately). And convergent evolution makes sense, because whales swim in a manner very similar to the way other mammals swim (by beating their tails up and down). On the other hand, there’s no reason a designer couldn’t have designed whales to swim the same way as fish. Indeed, if he’s so fond of uniting organisms on the biochemical level (for some reason) then the same reason that caused him to design animals alike on the molecular level ought to cause him to design animals as similarly as is reasonably possible on the macro-level. What flaw is there in that reasoning, Walter?

In conclusion, I think my argument that Common Descent predicts a universal code was wrong. I don’t think any theory “predicts” a universal code, including Walt’s “theory” for reasons I outlined above. I think we need to focus on explaining the code. One possible explanation is that there was a single designer (or team of designers, acting in unison) that made the code. After all, Apple and Microsoft design computers to read computer code in the same way. That explanation is possible as long as one does not hypothesize that the designer created all living things (just the first living things). And the reason you can’t hypothesize that the same designer created all living things is for the difficulties I outlined earlier.

Another possible explanation is that the code was inherited from a common ancestor and hasn’t changed much because of difficulties in its evolving and lack of time for it to diverge.  

> … Walt claims that Evolutionary theory could
> explain everything and its opposite because it
> is theoretically possible that there might have
> been enough time for new genetic codes to evolve.

I did not say that. Those are two separate issues that he mistakenly joined with the word “because”.

Moreover, I did not say “it is theoretically possible”; my wording was stronger than that. Rather, I said leading evolutionists today ACTUALLY CLAIM that numerous other genetic codes and countless lifeforms completely unlike anything known [i]must have existed on this planet.[/i] They make this grand unfalsifiable assertion in order to rescue evolutionary theory from falsification. Why? Because leading evolutionists now acknowledge that a single step from non-life to the simplest known self-reproducing lifeform (containing the known genetic code and the known biologic universals) is vastly too implausible. This would falsify evolutionists on the origin-of-life, so they retreat into unfalsifiability by claiming that other lifeforms — containing essentially none of the known biologic universals — [i]must have existed on this planet.[/i] Evolutionists are now on the horns of a dilemma. On this issue, evolutionary theory is either false, or unfalsifiable — and either way it is unscientific.

> ReMine has missed some crucial points: Atavisms
> (from ancestors millions of generations ago) are
> only plausible if the genetic material in question
> has other functions through which it might be
> preserved, as is the case with hen’s teeth.

Ryan claims Atavism is only plausible if a strong case for genetic pleiotropy can be made. He is thoroughly mistaken. The early Darwinians roundly embraced Atavism [i]even though they had no notion whatever of pleiotropy or genetics.[/i] Moreover, even [i]modern[/i] evolutionists frequently construct claims for pleiotropy out of thin air — they claim the genetic material in question has [i]“other functions”[/i] through which it might be selectively preserved, while scarcely pausing to identify those “other functions” — as in the case of hen’s teeth. 

Ryan is also mistaken about evolutionary thinking. To evolutionists, pattern is king. Evolutionists invoke Atavism whenever the data [i]pattern[/i] suggests Atavism — regardless of the presence or absence of suitable mechanisms or suitable experimental demonstrations. That is, evolutionists invoke Atavism whenever a trait occurs in an organism that is NOT visible in its nearest ancestors, but which is alleged to occur in its more distant ancestors. Since evolutionists easily embrace Atavism based solely on [i]pattern[/i], life’s designer went great lengths to AVOID creating patterns that could be interpreted as Atavism.  This is why, for example, the whale-tail and the fish-tail were given substantially different designs. AND IT SUCCEEDED. No evolutionists (not even the early Darwinians, who were unconstrained by notions of pleiotropy) claim these are the result of Atavism.

[NOTE: According to recent papers by evolutionary geneticists, the typical gene affects 7.5 traits, and some genes affect over 30 traits, which means there is an abundance of pleiotropy in nature. This abundance of pleiotropy is an aid to Atavistic "explanations," but it is a serious problem for the evolutionary origin of new complex traits. Evolutionary stories tend to be of the form "one-gene makes one-trait" because that assumption makes evolutionary stories seem more plausible. When in actual fact the relationship is NOT one-to-one, but many-to-many. A trait (such as a feather) tends to be comprised of many genes (this is called polygeny), and each gene tends to affect many traits (this is called pleiotropy).  This is the evolutionists' polygeny-pleiotropy problem that ReMine has brought up. In general, evolutionists embrace pleiotropy when they want to (as when discussing Atavism), and they [i]ignore[/i] pleiotropy when they want to (as when discussing the origin of new complex traits). As ReMine has said, evolutionary theory is a structureless smorgasbord, from which evolutionists [i]select[/i] whatever [i]Natural[/i] explanations they need — This is ‘Natural’ selection in action.]

> Indeed, if [life's designer is] so fond of
> uniting organisms on the biochemical level
> (for some reason) then the same reason that
> caused him to design animals alike on the
> molecular level ought to cause him to design
> animals as similarly as is reasonably possible
> on the macro-level. What flaw is there in that
> reasoning, Walter?

Again, Ryan is misrepresenting Message Theory. Designing lifeforms “as similarly as is reasonably possible” is NOT the goal claimed in Message Theory. Re-read the claims of Message Theory.

> And the reason you can’t hypothesize that
> the same designer created all living things
> is for the difficulties I outlined earlier.

He is talking nonsense. Life is utterly incompatible with life being created by multiple designers acting independently — the idea of life being created by ONE designer (or group of designers acting together as ONE) is driven by the data.

> An atavism would not be plausible in the case
> of whales [i.e., whale-tails versus fish-tails],
> …. Nor is “transposition” …

He agrees with me that the similarity between whale-tails and fish-tails cannot be explained by Atavism, or by Transposition, or by common descent. This is by design — as predicted by Message Theory.

> if [the designer is] so fond of uniting organisms
> on the biochemical level (for some reason) then
> the same reason that caused him to design animals
> alike on the molecular level ought to cause him to
> design animals as similarly as is reasonably
> possible on the macro-level. What flaw is there
> in that reasoning, Walter?

First, unity at the [i]biochemical[/i] level is the only suitable way to unify any two organisms as the work of one designer — organisms as different as yeast and elephants. (Putting tusks on yeast doesn’t work.)

Second, unity at the [i]biochemical[/i] resists evolutionary explanations (particularly their explanations on the origin-of-life. In other words, biochemical unity neatly advances all the goals of Message Theory.

Third, he again MISREPRESENTS Message Theory. It is NOT the goal “to design animals as similarly as reasonably possible on the macro-level.”

> In conclusion, I think my argument that Common
> Descent predicts a universal code was wrong.

Thank you for that acknowledgement.

> Walter conflates “Evolution” with “all possible
> natural explanations” which is incorrect. ….
> For instance, he conflates common descent with
> multiple origins of life.

Ryan is continuing the evolutionists’ mischief of trying to SEPARATE the origin-of-life from evolution — as though the two problems are unrelated. This is how they traditionally obscured (i.e., concealed) their self-contradictions over the biochemical unity of life. Dobzhansky’s famous paper — titled “Nothing in biology makes sense except in the light of evolution” — used biologic universals (such as the genetic code) as powerful evidence for evolution. Ryan now acknowledges that was wrong, but nonetheless he continues the evolutionist attempt to obscure the issue by separating the origin-of-life from evolution.

Many evolutionists today propose [i]multiple[/i] origins of life. I have not misrepresented that.  

In conclusion, Ryan repeatedly misrepresents Message Theory; he should first straighten that out. If he then thinks he has an argument against Message Theory, he ought publish it in a suitable journal. So far, no one has. I predict he won’t even try. 

Why? Because leading evolutionists now acknowledge that a single step from non-life to the simplest known self-reproducing lifeform (containing the known genetic code and the known biologic universals) is vastly too implausible. This would falsify evolutionists on the origin-of-life, so they retreat into unfalsifiability by claiming that other lifeforms — containing essentially none of the known biologic universals — [i]must have existed on this planet.[/i]
But the origin of life is separate from the theory of evolution, as repeatedly stated.
“No evolutionists (not even the early Darwinians, who were unconstrained by notions of pleiotropy) claim these are the result of Atavism.”
Yeah, because the tails of whales and fish are not even remotely alike.
“Again, Ryan is misrepresenting Message Theory. Designing lifeforms “as similarly as is reasonably possible” is NOT the goal claimed in Message Theory. Re-read the claims of Message Theory”
NOPE. You claimed that the designer wanted to make life look like the product of ONE designer. What does it mean for life to look like the product of one designer? What does it mean for life to look UNLIKE the product of a single designer? You never gave any criterion for this, so I stated that the only way I knew to make sense of this was to interpret it the way I did.
“He is talking nonsense. Life is utterly incompatible with life being created by multiple designers acting independently — the idea of life being created by ONE designer (or group of designers acting together as ONE) is driven by the data.”
Why is it nonsense? What criteria do you have for deciding whether something was designed by one designer, ten, or none?
“He agrees with me that the similarity between whale-tails and fish-tails cannot be explained by Atavism, or by Transposition, or by common descent. This is by design — as predicted by Message Theory.”
Are you mentally deficient?!? Convergent evolution explains this. Whales and fish acquired their adaptations to water in separate lineages, and that is why they are the way they are. Message theory predicts nothing about this.
“First, unity at the [i]biochemical[/i] level is the only suitable way to unify any two organisms as the work of one designer — organisms as different as yeast and elephants. (Putting tusks on yeast doesn’t work.) ”
I never asked you to show me a yeast with tusks. No one thinks that the designer should have unified organisms in implausible ways like that. What I asked for was completely plausible: The designer could have designed whales to swim like fish.
“Third, he again MISREPRESENTS Message Theory. It is NOT the goal ‘to design animals as similarly as reasonably possible on the macro-level.’”
I did not say it was. I asked you a question, which you quoted:

 if [the designer is] so fond of uniting organisms
> on the biochemical level (for some reason) then
> the same reason that caused him to design animals
> alike on the molecular level ought to cause him to
> design animals as similarly as is reasonably
> possible on the macro-level. What flaw is there
> in that reasoning, Walter?

“Ryan is continuing the evolutionists’ mischief of trying to SEPARATE the origin-of-life from evolution — as though the two problems are unrelated. This is how they traditionally obscured (i.e., concealed) their self-contradictions over the biochemical unity of life.”
No, the theory that all living things had a living common ancestor is not the same as the hypothesis that the first living thing (which, by the way, is not necessarily identical to the common ancestor of all life) ultimately came from inanimate matter. Anyone who can understand simple logic can understand that. A is not equal to non-A. The common ancestry of all living things is not the same as the hypothesis that the first life came from inanimate matter.

> [Ryan wrote] But the origin of life is separate from
> the theory of evolution, as repeatedly stated.

He is quite correct that evolutionists have “repeatedly stated” the origin-of-life is separate from the theory of evolution. Yes, they have REPEATEDLY said so. But as ReMine points out, that is how evolutionists obscured from view their self-contradictions. For example, that is how Dobzhansky — in his famous paper, “Nothing in biology makes sense except in the light of evolution” — was able to use biologic universals as one of his major evidences for evolution. When the opposite is the case: If evolution predicts anything on the matter, it predicts biologic universals ought not exist.

Evolution is either all-the-way from rocks to rockstars, including the origin-of-life — or else it is creation. That is the simple fact of the matter, and it does no unfairness to evolutionists in saying so.

The origin-of-life issue is now scientifically owned by creationists, and evolutionists are vainly trying to disown the origin-of-life. Ryan is an example of it.

> [Walter wrote] “No evolutionists (not even the
> early Darwinians, who were unconstrained by
> notions of pleiotropy) claim these are the
> result of Atavism.”[END QUOTE]
>
> [Ryan answered] Yeah, because the tails of
> whales and fish are not even remotely alike.

Ryan is agreeing with me. He asked why whale-tails and fish-tails were designed differently. And I answered: to resist being interpreted as Atavisms. He now agrees that is the reason they were not interpreted as Atavisms.

> I never asked you to show me a yeast with
> tusks. No one thinks that the designer should
> have unified organisms in implausible ways
> like that.

Once again, he is agreeing with me.

He asked why the difference between the profoundly unifying similarities at the BIOCHEMICAL level versus the differences at the MORPHOLOGICAL level (as in the whale-tail / fish-tail example). I explained both legs of that issue, and he agrees with both (see above).

> [Walter wrote] “Again, Ryan is misrepresenting
> Message Theory. Designing lifeforms “as similarly
> as is reasonably possible” is NOT the goal claimed
> in Message Theory. Re-read the claims of Message Theory”
>
> [Ryan answered] NOPE. You claimed that the designer
> wanted to make life look like the product of ONE
> designer. What does it mean for life to look like
> the product of one designer? What does it mean for
> life to look UNLIKE the product of a single designer?
> You never gave any criterion for this, so I stated
> that the only way I knew to make sense of this was
> to interpret it the way I did.

I gave a clear statement of Message Theory early in this thread. Ryan continues to misrepresent it, though he has been repeatedly warned of it. All the necessary evidences for his misrepresentations are contained in this thread.

> [Walter wrote] “He is talking nonsense. Life is
> utterly incompatible with life being created by
> multiple designers acting independently — the
> idea of life being created by ONE designer (or
> group of designers acting together as ONE) is
> driven by the data.”
>
> [Ryan answered] Why is it nonsense? What criteria
> do you have for deciding whether something was
> designed by one designer, ten, or none?

Ryan is still advancing nonsense. NO ONE claims life was created by multiple designers acting independently. The staggering unity of life (especially at the biochemical level) falsifies that idea. It is a dead idea. Yet Ryan is trying to breath life into that idea, in order to sow confusion, where there is no confusion.

> [Ryan wrote] Are you mentally deficient?!?
> Convergent evolution explains this. Whales and
> fish acquired their adaptations to water in
> separate lineages, and that is why they are
> the way they are. Message theory predicts
> nothing about this.

He is mistaken. Evolutionary theory “explains” virtually anything and its opposite, and on those few occasions when it makes a clear prediction, it predicts the opposite of what we observe.

Biologic universals are a rare example where ’similarity’ is awkward for evolutionists to explain. Other than that example, similarity is usually EASY for evolutionists to “explain”, because nothing is easier than saying the similar complex traits were simply “inherited”, as by common descent, by Transposition, or by Atavism. Those are merely three different versions of inheritance. They are three potent, powerful, potential “explanations,” and that is why life’s designer had to especially resist those.

Message Theory predicts an abundance of pattern that evolutionists interpret as “convergence”. Here is how “convergences” are observed: They are complex traits that are sufficiently similar that it demands an explanation, yet sufficiently different that they cannot be “explained” by Atavism nor by Transposition, and are placed (within the system of life) so that they CANNOT be explained by common descent. This special balance requires design. “Convergences” are substantially anti-evolutionary evidences — that is why they are abundant.

For example, evolutionists claim the origin of sight occurred more than forty separate times. And the origin of a complex eye (with a lens and retina) occurred at least five times — in vertebrates, cephalopods (octopus and squid), annelid worms, jelly-fish, and spiders. Likewise they claim the origin of flight occurred many separate times, and likewise the origin of swimming. And so forth, through countless examples.

Life’s abundance of “convergence” is not predicted by evolution. Neither is it experimentally demonstrated. To evolutionists, the ONLY way to refute convergence is to show that the traits evolved by common descent, by Atavism, or by Transposition. In other words, this evolution can be “refuted” only by providing better evidence FOR evolution. As ReMine has said: Evolutionary theory, as practiced by its modern proponents, is not testable, and therefore unscientific by their own criteria.

“Evolution is either all-the-way from rocks to rockstars, including the origin-of-life — or else it is creation. That is the simple fact of the matter, and it does no unfairness to evolutionists in saying so. ”
No, No, A thousand times No! The first life could have been created by God, or aliens for that matter, and then it could have evolved into everything we see today.
“The origin-of-life issue is now scientifically owned by creationists, and evolutionists are vainly trying to disown the origin-of-life. Ryan is an example of it.”
No, it is not ‘owned’ by creationists. Origin of life studies are a flourishing field. More and more is being discovered about it every year.
“Ryan is agreeing with me. He asked why whale-tails and fish-tails were designed differently. And I answered: to resist being interpreted as Atavisms. He now agrees that is the reason they were not interpreted as Atavisms.”
WRONG! Whale and fish tails could never have been interpreted as atavisms because the genes which create the fish body were transformed in mammals to the point that they could not have reverted back to their original design in the evolution of whales. An evolutionist would expect the two to be different because they are due to convergent evolution. A creationist ought to expect God to have used the same design.
“Once again, he is agreeing with me.
He asked why the difference between the profoundly unifying similarities at the BIOCHEMICAL level versus the differences at the MORPHOLOGICAL level (as in the whale-tail / fish-tail example). I explained both legs of that issue, and he agrees with both (see above).”
WRONG! I said that tusks on a yeast would be a silly and impractical idea. However, I suggested less silly, more practical ways to unify animals on the morphological level. You responded that those would have been interpreted as an atavism. I’ve just argued that, No, they could not have been interpreted that way. Furthermore, why didn’t God create them the same to avoid the interpretation that these were cases of convergent evolution?
“I gave a clear statement of Message Theory early in this thread. Ryan continues to misrepresent it, though he has been repeatedly warned of it. All the necessary evidences for his misrepresentations are contained in this thread.”
You did not answer the following questions: What does it mean for life to look like
> the product of one designer? What does it mean for
> life to look UNLIKE the product of a single designer?
> You never gave any criterion for this, so I stated
> that the only way I knew to make sense of this was
> to interpret it the way I did.
Your eagerness to avoid these issues proves that you have no good answers to them.
“Ryan is still advancing nonsense. NO ONE claims life was created by multiple designers acting independently. The staggering unity of life (especially at the biochemical level) falsifies that idea. It is a dead idea. Yet Ryan is trying to breath life into that idea, in order to sow confusion, where there is no confusion.”
What if one designer borrowed the biochemical design from another?

“For example, evolutionists claim the origin of sight occurred more than forty separate times. And the origin of a complex eye (with a lens and retina) occurred at least five times — in vertebrates, cephalopods (octopus and squid), annelid worms, jelly-fish, and spiders. Likewise they claim the origin of flight occurred many separate times, and likewise the origin of swimming. And so forth, through countless examples. ”
Yes, and in the cases of sight and flight, the eyes and wings are sufficiently different that we could tell that they originated separately. Darwin discussed the eye of the cuttlefish in the Origin, and talked about how the muscles in the eye of the cuttlefish were about as different as they could have been from the vertebrate eye. Bat wings, Bird Wings, and Pterosaur wings are all expected to have evolved separately, and sure enough, they all hit upon different ’solutions’ for making the wing: Birds, Bats and Pterosaurs all use different modifications of the pentadactyl hand to form a wing. They are so different that no biologist would attribute the evolution of these wings to a wing in the common ancestor of pterosaurs, bats, and birds. They would have had to evolve separateley.
“Life’s abundance of “convergence” is not predicted by evolution. Neither is it experimentally demonstrated.”
Wrong! Convergence is predicted by evolution. We know that there are often many ways to build a wing, an eye, or just about any other biological structure. Therefore, when two lineages independently evolve some adaptation, one expects that they evolve the same adaptation in different ways.
I think I’m done here. I’ve explained this stuff to you again and again and again, and yet you’re apparently not able to get a mental grasp on it.