Saturday, January 27, 2018

Early Complexity: A Case Study of Evolutionary Theory

No Matter How Perplexing

Nature does not make jumps. That old canon of natural history, as Darwin called it, goes back centuries and was heartily endorsed and adopted by evolutionary theory. Here are representative quotes from Origin, 1st edition, explaining important this doctrine was to Darwin:

I have been astonished how rarely an organ can be named, towards which no transitional grade is known to lead. The truth of this remark is indeed shown by that old canon in natural history of "Natura non facit saltum." We meet with this admission in the writings of almost every experienced naturalist; or, as Milne Edwards has well expressed it, nature is prodigal in variety, but niggard in innovation. Why, on the theory of Creation, should this be so? [194]

On the theory of natural selection we can clearly understand the full meaning of that old canon in natural history, "Natura non facit saltum." This canon, if we look only to the present inhabitants of the world, is not strictly correct, but if we include all those of past times, it must by my theory be strictly true. [206]

The canon of "Natura non facit saltum" applies with almost equal force to instincts as to bodily organs. [210]

the canon in natural history, of "natura non facit saltum" is applicable to instincts as well as to corporeal structure, and is plainly explicable on the foregoing views, but is otherwise inexplicable,—all tend to corroborate the theory of natural selection. [243]

As natural selection acts solely by accumulating slight, successive, favourable variations, it can produce no great or sudden modification; it can act only by very short and slow steps. Hence the canon of "Natura non facit saltum," which every fresh addition to our knowledge tends to make more strictly correct, is on this theory simply intelligible. We can plainly see why nature is prodigal in variety, though niggard in innovation. But why this should be a law of nature if each species has been independently created, no man can explain. [471]

In these and other passages Darwin explained the fundamental evolutionary view and prediction that evolution and natural selection produce gradual change with no sudden changes or jumps.

At this point, more than a century and a half later, that fundamental prediction of evolution has been falsified so many times by the empirical evidence it is a wonder there is anyone left believing in the theory.

One way that this prediction has been falsified, among many, is in the finding of early complexity. Evolutionists of course expected that the history of life would reveal a gradual increase in complexity. But as I have discussed many times here, life does not fit this evolutionary expectation. Instead the very earliest life forms reveal high complexity.

For example, as science writer (and evolutionist) Amy Maxmen explains, Amoebas contain hundreds of times more DNA than humans, and this “just didn’t make sense.”

amoebas date back farther in time than humans, and simplicity is considered an attribute of primitive beings. It just didn’t make sense.

The amoeba versus human comparison was just one example of how genome size contradicts evolutionary theory. What about the number of genes? Here again, evolution makes a clear prediction, as Maxmen explains:

Simple, early organisms would have fewer genes than complex ones, they [evolutionists] predicted

And here again, the evolution prediction was demolished by the science. For example, evolutionists were surprised to find sea anemones have more genes than insects, in spite of arising earlier. That, admits Maxmen, “meant animals might have been genetically complex from the start.”

These sorts of findings also contradict the evolutionary tree. Your high school biology book said that the new genetic data perfectly corroborated the traditional morphological data. Evolutionists have triumphantly celebrated the confirmation that the molecular sequence data provided to pre-existing evolutionary trees.

But that celebration was premature. In fact, study after study have found there is no such corroboration. In fact, as I have documented many times, morphological data across the species contradict the evolutionary tree (i.e., they do not fall into an evolutionary common descent pattern), and the new molecular data simply continued that trend.

Then molecular analyses did something else. They rearranged the order of branches on evolutionary trees. Biologists pushed aside trees based on how similar organisms looked to one another, and made new ones based on similarities in DNA and protein sequences. The results suggested that complex body parts evolved multiple times and had also been lost.

In other words, the scientific data contradict the theory. The result is that evolutionists have had to concoct increasingly complex and bizarre epicycles to try to explain the data. This includes complex structures evolving, then disappearing, then re-evolving, all in the same lineage, as well as independently evolving in a separate lineage. As Maxmen explains:

Furthermore, the idea that complex parts like a brain and nervous system—including nerve cells, synapses, and neurotransmitter molecules—could evolve separately multiple times perplexes evolutionary biologists because parts are gained one at a time. The chance of the same progression happening twice in separate lineages seems unlikely—or so biologists thought.

This is a tautology. Whatever we observe, evolution somehow created it, no matter how ridiculous the narrative becomes. An unfair criticism? Consider Maxmen’s conclusion:

When new data suggests a rearrangement, it must be considered no matter how perplexing the conclusion seems.

In other words, the plausibility of evolution is not a consideration. No matter “how perplexing” are the data, we must find a way to force fit it into the theory.

Religion drives science, and it matters.

Tuesday, January 23, 2018

Embryonic Development Reveals Staggering Complexity

Oh My

I recently cited a paper on the evolution of embryonic development and how the evidence contradicts evolutionary theory and common descent. Even the evolutionists, though in understated terms, admitted there were problems. Evolutionary analyses are “reaching their limits,” it is difficult to “conclude anything about evolutionary origins,” genetic similarities “do not necessarily imply common ancestry,” and “conserved regulatory networks can become unrecognizably divergent.” In other words, like all other disciplines within the life sciences, embryonic development is not working. The science contradicts the theory.

But there is much more to the paper, and as a reader noticed, the authors give a rather blunt admission of the magnitude of the problem, not often seen in the literature:

One of the main reasons for Duboule’s pessimism about the return of the EvoDevo comet is the staggering complexity and diversity of cellular and developmental regulatory processes. The configuration space for realistic models of such systems is vast, high dimensional, and potentially infinitely complex.

Staggering complexity? Staggering diversity? The configuration space is vast and high-dimensional?

And it is potentially infinitely complex?

And we are to believe this is the product of random mutations?

Religion drives science, and it matters.

Sunday, January 21, 2018

About That RNA World Hypothesis

It Just Doesn’t Make Sense

Given its widespread popularity and acceptance you might not have realized that the so-called RNA-World hypothesis suffers from some dramatic problems. At the top of the list is the rather awkward fact that there is, err, no evidence for it. While skeptics have pointed this out for years, we now see evolutionists coming clean on this inconvenient truth as well. To wit, here is how Peter Wills and Charles Carter open their recent BioSystems paper:

The RNA World is a widely-embraced hypothetical stage of molecular evolution, devoid of protein enzymes, in which all functional catalysts were ribozymes. Only one fact concerning the RNA World can be established by direct observation: if it ever existed, it ended without leaving any unambiguous trace of itself.

Even this is a bit of an understatement. Because without the prior assumption of evolution, which can and has underwritten a wide range of speculation, there is precisely zero reason to believe this wild hypothesis. No organisms have ever been discovered that demonstrate the RNA World hypothesis in action. Nor have scientists ever constructed any such organisms in their laboratories. This is not too surprising because no one has even produced anything remotely close to a detailed design of how such organisms could function.

Wills and Carter also point out negative evidences such as catalysis (RNA enzymes lack the ability to function over a wide range of temperatures) and the “impossible obstacles” to the hypothetical yet necessary transition from the RNA World to something resembling today’s extant cells. As Carter explains:

Such a rise from RNA to cell-based life would have required an out-of-the-blue appearance of an aaRS [aminoacyl-tRNA synthetase]-like protein that worked even better than its adapted RNA counterpart. That extremely unlikely event would have needed to happen not just once but multiple times—once for every amino acid in the existing gene-protein code. It just doesn’t make sense.

Indeed, it just doesn’t make sense. And yet in spite of these obvious problems, the RNA World has been a textbook staple, presented as a plausible and likely example of how early life evolved.

Religion drives science, and it matters.

Friday, January 19, 2018

How Embryonic Development Bears on Evolution

Follow the Theory

In order for evolution to have occurred, the intricate embryonic development stages of species must have evolved. Indeed, the developmental pathways of the species would be crucial in such a process. If we are to believe the evolutionary claim that the species spontaneously arose, then untold embryonic development pathways must have somehow undergone massive change. But while evolutionists expected the study of such evolution of development to yield great insight into the evolutionary process and history, it has underwhelmed. This shortcoming is well known, as exemplified in this 2015 paper:

First, traditional comparative approaches to the evolution of development—whether focused on the morphological or on the molecular/genetic level—are reaching their limits in terms of explanatory power.

Except that this is an overstatement. To say that comparative approaches “are reaching their limits in terms of explanatory power” is to suggest that there was, at one time, some significant level of explanatory power provided. That would be a very optimistic interpretation of the data.

The paper continues:

The more we learn about the evolution of pattern-forming gene networks, or the ontogeny of complex morphological traits, the more it becomes clear that it is less than straightforward to conclude anything about evolutionary origins or dynamics based on such comparisons alone.

“Less than straightforward”? Let’s be clear—a more accurate descriptor would be “impossible.” In fact, the evidence does not reveal an evolutionary history, but rather is supported by the theory. Evolutionary theory does not follow the data, as Huxley prescribed, but rather the data follow the theory.

The paper continues:

On the one hand, homoplasy or convergent evolution abounds at all levels of investigation. One of the most lauded major insights of EvoDevo is that a common toolkit of genes and signaling pathways is reused over and over again to create a large diversity of different body plans, shapes, and organs.

Most lauded major insights? That would be the mother of all euphemisms. Evolutionists are always rationalizing devastating contradictions as teachable moments, and here we have yet another example. To cast the nonsensical finding of a “common toolkit” as a “major insight” is laughable.

This becomes clear as the paper continues:

Because of this, similarities in gene expression patterns or morphological structure often do not necessarily imply common ancestry, since they may as well reflect the frequent reuse of the same regulatory or morphogenetic modules.

Profound similarities “do not necessarily imply common ancestry.” We have now entered a Lewis Carroll world, as Sober would put it. The whole point of evolution was that such similarities revealed and mandated common descent. But now, we have the exact opposite, as similarities cannot be due to common descent, but must have arisen independently. And this is an “insight”? A fundamental prediction is demolished and evolutionists do not skip a beat. This is not science.

But it gets worse:

On the other hand, developmental system drift allows conserved networks to change considerably in terms of their component genes and regulatory interactions without changing the phenotypic outcomes such systems produce. This means that even functionally conserved regulatory networks can become unrecognizably divergent at the molecular and genetic level, especially across large evolutionary time spans.

We have now reached the height of absurdity. First, profound developmental similarities were found which could not be ascribed to common descent. Now we find that those developmental pathways which can (theoretically) be ascribed to common descent are profoundly different.

When will this bad dream end? The science contradicts the theory. Over. And over. And over. And over.

It never ends. Religion drives science, and it matters.

[h/t: El Hombre]

Wednesday, January 17, 2018

Allmon and Ross Demolish Evolution

It Gets Worse

Last time we saw, in a new paper, evolutionists Warren Allmon and Robert Ross reformulate the argument for evolution from homologous structures. The paper makes several mistakes, but is important because it is a rare case of evolutionists (i) recognizing the religion in evolutionary thinking, and (ii) trying to do something about it. In this case the religion is in the claim that God would not have created non optimal homologies (such as vestigial structures). Allmon and Ross attempt to remove the religion by restating the claim as: God did not have to create such homologies. It is good that evolutionists are finally recognizing the religion, after having been in denial for so many years. But Allmon and Ross’ solution fails on several counts.

The first failure of Allmon and Ross’ solution is that it strips the power of the argument. The traditional religious arguments (i.e., God would not create those structures) at least had the virtue of providing a strong argument for evolution. Granted it was a religious argument, and granted one had to agree with that particular religion. And granted it ignored the problems of process and pattern (more below on that). And granted it turned evolution into, as Elliott Sober hinted, a “Lewis Carroll world in which down is up,” because the argument required evidence that is unlikely on evolution. The more unlikely, the better. Such is the logic of evolution’s religion. But after all those caveats, at least it provided a strong argument for evolution.

With design refuted, evolution had to be true, no matter how many problems it had. But with Allmon and Ross’ reformulation, design is not refuted. Now the advantage for evolution is not that the alternative is false or even highly unlikely, but that the alternative does not specify what we observe whereas evolution does. Allmon and Ross triumphantly conclude their new formulation is a powerful argument for evolution. They apparently think their reformulation is merely a minor tweak, and that their new argument is just as strong as the traditional argument. It isn’t. There is no free lunch. What Allmon and Ross fail to understand is that this is a much weaker argument.

But it gets worse.

The second failure of Allmon and Ross’ solution is that it never did get rid of the religion as they had hoped. Allmon and Ross naively assume that the claim God may or may not create these homologies is merely an obvious point of fact. This is a deep subject into which Allmon and Ross have rushed in, but suffice it to say that it is not at all clear that God can go with either world. Leibniz undoubtedly would disagree. The Lutheran polymath would argue that because of His perfection and other attributes, God cannot just create any old world. The bottom line, and one which Allmon and Ross are blissfully na├»ve of, is that like it or not, claims about God are religious.

But it gets worse. Much worse.

Not only did Allmon and Ross utterly misapprehend and expose the homology argument, they have, in fact, altogether demolished evolutionary theory. Remember, with their reformulation it becomes utterly crucial that evolution predicts what we observe. In other words, evolution must predict the pattern of similarities and differences we observe across the species. This is because their new formulation was that while design can explain a common descent pattern or other patterns, evolution is narrowly restricted to the common descent pattern.

With that the two Harvard trained Epicureans just inadvertently blew up evolution. This is because what we actually observe is not the common descent pattern.

The actual comparisons between the species have contradicted the common descent pattern over and over. It is, as we have documented here so many times, not even close.

If evolution predicts the common descent pattern, then by modus tollens, evolution is false.

Religion drives science, and it matters.

Monday, January 15, 2018

Warren Allmon on the Argument from Homology

An Enormous Concession

I once debated two evolutionists on the campus of Cornell University. In that debate I raised several fundamental problems with evolutionary theory. The problems that I pointed out fell into two broad categories: process and pattern. In the latter category, I pointed out that the keystone argument for evolution from homology had badly failed. Unfortunately, that failure was waved off and went unaddressed by the evolution professors. That may not have been the case had Warren Allmon been able to participate. Allmon, Director of the Cornell University-affiliated Paleontological Research Institution (PRI), has thought more deeply about the homology argument than most evolutionists. Now in 2018, he has published, along with adjunct professor Robert Ross, a new paper containing a very important concession.

As is typical, the new Allmon/Ross paper makes several serious scientific errors, either through ignorance, denial, confirmation bias, or whatever. The paper also relies heavily religious claims and arguments, which again is typical.

I have covered this religiously-driven phony science here many times. And in future posts I will address the specifics in the Allmon/Ross paper.

But most importantly, the paper does accomplish something new. The paper takes several turns, but in the end Allmon and Ross do recognize, at least somewhat, the presence of religion in evolutionary thought. To remedy this, they downsize the argument from homology.

In its canonical form, this keystone argument proves evolution by the process of elimination. That is, it refutes design and independent creation, leaving naturalistic evolution, in one form or another, as the only solution. God wouldn’t have created these lousy designs, according to evolutionists, so the designs must have arisen naturalistically. As usual, it is the religion that provides the certainty.

This isn’t science.

Rather than deny this obvious fact (see here for examples of such denial), Allmon and Ross ultimately admit to it (after appealing to it repeatedly), and seek to reformulate the argument from homology without the religion. They do this as follows.

Rather than claiming God would not have created non optimal homologies (such as vestigial structures), Allmon and Ross walk back the claim to say merely that God did not have to create such homologies. Under independent, divine, creation, God could have done it differently. Allmon and Ross then contrast this with descent with modification which, they say, necessarily would have resulted in such homologies.

So you have Theory A (design) which can accommodate Observation X or ~X (not X). And you have Theory B (evolution) which requires Observation X, and cannot accommodate ~X. Our observation of X, therefore, makes Theory B more probable.

Readers here will know there are enormous problems with this argument. It fails badly, right out of the gate. And I will discuss these failures in the future. But before we get to that, it is important to understand the implications of the argument, even without its problems.

In their attempt to save the theory, what Allmon and Ross have done is to provide an enormous concession. What traditionally has been an iron-clad, unquestionable, textbook proof of evolution, now becomes a minor Bayesian term, slightly improving the probability of evolution.

This is a monumental concession, neutering the keystone argument for evolution. Why should anyone believe in the heroic claim that the biological world arose by itself if the strongest argument merely increases its probability by some unspecified amount?