Charles Darwin gave science a major step forward in intellectual progress, many assume. He replaced what he considered “miracles” of design by natural processes. His goal seemed noble to many: unifying the disparate organisms of the earth into a unified picture of descent with modification, united by a law of nature he called natural selection. Science was thus rid of miracles. So he thought.

Darwin’s law of nature, however, amounted to little more than historical contingency. Variations appear randomly in his view — without direction or purpose — at the basis of life which evolutionists today usually locate in the genes. From the “bottom up” view, to avoid looking miraculous, variations had to be small and gradual, barely making a difference to the organism except for some slight increment in a nebulous quality he called “fitness.” From the “top down” view, however (the tree of life), many disparate organisms needed to be united by lines of common descent with huge gaps between them. Bringing the bottom-up and top-down pictures together has not been easy. Two recent articles show how modern evolutionists do it by employing miracles — stretching credibility beyond the breaking point to bring the two pictures together.

In Current Biology, Thibaut Brunet and Detlev Arendt appear excited about the possibility of solving the “hard problem of cartilage origins.” Their title, a play on the “hard problem of consciousness” described by David Chalmers, refers here to the origin of hard parts in animal bodies. Can all the disparate animal body plans be united by a common ancestor?

Skeletons are misunderstood. Because of their resistance to decay, bones have become symbols of death; yet, they are intensely alive tissues, undergoing lifelong active remodeling. To the evolutionary biologist, the hard parts of animals are similarly double-faced: their endurance makes them the prime candidates for fossilization and provides paleontologists with a wealth of information on the skeleton of extinct animals. From the paleontologist’s view, animal evolution is thus mainly the evolution of hard parts (plus what can be deduced from them). But for the same reason, the origin of the first animal skeletons, and the ancestral structures that gave rise to them in soft-bodied animals, remains mysterious; preservation of soft tissue is too rare to provide a clear-cut solution. For more than a century, morphologists have been debating, with precious little evidence, the hard questions of skeleton origins: When did animal skeletons first evolve? Did they appear once or several times independently? Which ancestral soft tissues first became rigid, and by what molecular mechanisms? A recent study by Tarazona and co-authors, comparing skeleton formation between invertebrates and vertebrates at the molecular level, sheds new light on these questions. [Emphasis added.]

As is common in evolutionary literature, Brunet and Arendt do not ask whether hard parts evolved, but only how they evolved. According to the “rules of science,” questioning naturalism is forbidden. By limiting one’s explanatory toolkit to unguided natural processes, however, difficulties arise. There’s nothing like an appeal to miracles to get around a difficulty. As Finagle advised, “Do not believe in miracles. Rely on them.”

The authors admit that “Historical attempts to compare vertebrate and invertebrate skeletons have not fared well.” That’s why Tarazona’s solution appeals to them. That paper found similarities in cartilage formation between a cuttlefish and a horseshoe crab — very distant creatures in Darwin’s ancestral tree, belonging to different phyla. In their thinking, therefore, the common ancestor of both these animals must have had the ability to manufacture cartilage. Brunet and Arendt masterfully illustrate possible evolutionary links between those animals and annelids (earthworms), brachiopods, arthropods, and vertebrates by pointing out similarities between the general organization of their collagen expression sites and the developmental genes that regulate the expression of collagen. Like a magic trick, it looks simple until you probe the details. Consider:

1. They give no explanation for the emergence of 3 sets of genes that code for collagen. “The ancestral soxD+ soxE+ colA+ ventral mesentery is assumed to have given rise to both the chordate sclerotome and the chelicerate endosternite,” they say, ‘assuming’ that six transcription factor genes and the collagenase gene conspired to create the first hard parts. Either the genes were co-opted from some other function, or emerged on their own. Is that magic? Luck? What else in naturalistic evolution could “give rise” to the improbable?

2. Collagen is a complex protein, using all 20 amino acids except tryptophan. Wikipedia lists 7 steps in its manufacture inside cells, including the formation of precursors (like “pre-pro-peptide to pro-collagen”) followed by extensive post-translational modifications.

3. The formation of cartilage involves additional complex steps, including a balance between the signal proteins Hedgehog and Wnt. You can’t just assume the innovation of collagen is going to automatically lead to cartilage or bone. As for bone, specialized cells (osteoblasts and osteoclasts) build and dissolve bone in a delicate balance of processes.

4. Hard parts do not appear randomly in cells or on animal body plans, but are specifically arranged for function. Look at the elaborate armor on Cambrian comb jellies (Science Advances), assumed by some evolutionists to be one of the earliest animal phyla. It’s not enough to create collagen building blocks. The materials have to be delivered to specific locations during development.

5. One “miraculous” innovation like collagen would be astonishing, but that’s not enough. Collagen makes a “scattered appearance” on the tree of life. The authors invoke even more miracles to explain this: “If so, this would exemplify an often neglected type of independent evolution called ‘parallel evolution’, in which the same ancestral structure undergoes a similar sequence of modifications in separate lines of descent.” Giving an improbable wonder a name like “parallel evolution” does not make it any less “miraculous.”

6. Hard parts appear suddenly in the fossil record. Wave the magic wand for more miracles! “Also, the fossil record suggests that most phyla evolved skeletons in a rapid and parallel fashion during the Cambrian explosion, fuelled by an arms race between the first elaborate predators and their prey.” Our readers have heard plenty about all the failed explanations for the Cambrian explosion, so we won’t belabor the point here. Suffice it to say that the details do not make belief in “evolutionary innovations” as Darwinians are wont to call them look “natural.”

Good Luck, LUCA

An even greater appeal to miracles is found in evolutionary stories about the origin of life, because until reliable self-replication begins, there can be no natural selection. Consequently, evolutionists cannot avail themselves of their favorite hand-waving rescue device and can only appeal only to laws of chemistry and to chance.

The “last universal common ancestor” (LUCA) “is what scientists call the forerunner of all living things,” Live Science observes. LUCA must mark the point, therefore, at which natural selection begins, because if natural selection had acted on anything prior (such as speculative “RNA World” replicators), it had no bearing on life as we actually observe it. Anything prior left no record; it is outside empirical science.

As much as evolutionists would like to simplify LUCA, there comes a point at which the organism would not have been able to carry on the necessary functions of metabolism, motility, and reproduction to be called alive. LUCA had to be a “cell” of some sort, with a genetic code and protein machines enclosed in a membrane to keep it together. As we learned in March, Craig Venter’s team could not get their synthetic cell simpler than 463 genes. The new study says,

Much about LUCA remains uncertain; while previous research suggested that it was little more than a chemical soup from which evolution gradually built more complex forms, recent work suggested it may have been a sophisticated organism with an intricate structure.

How sophisticated? By comparing millions of prokaryotic genes, researchers at Heinrich Heine University in Düsseldorf, Germany estimated the requirements for LUCA:

The genes the scientists examined were blueprints for proteins. (Some genes are not thought to direct protein-making.) Of the 286,514 protein groups the researchers looked at, only 355 matched the strict criteria that the researchers set for potentially belonging to LUCA. Previous research had uncovered the functions of many of these genes, so they now shed light on LUCA’s habitat and lifestyle.

Their paper, published in Nature Microbiology, expects this “forerunner of all living things” to have been able to metabolize hydrogen, fix nitrogen, use transition metals and coenzymes, and much more. It had genomics and epigenomics: “Its genetic code required nucleoside modifications and S-adenosyl methionine-dependent methylations.” None of these are simple! Furthermore, the researchers believe that LUCA was a thermophile, living in the harsh conditions of hot springs or hydrothermal vents. The thermophiles we see today have sophisticated mechanisms for repairing and preserving their DNA and proteins from destruction by heat.

Did LUCA arise by chance? Jeff Errington, cell biologist at Newcastle University, doesn’t even ask the question. At The Conversation, he speculates about what kind of organism LUCA was, assuming it originated in the high temperatures of hot springs, had enzymes and a genetic code, metabolized hydrogen, and was well equipped for survival. He knows, though, that LUCA had minimum requirements:

Sadly, without a time machine, there is no way to directly verify these results. Nevertheless, this information will now be of great interest, not least to those scientists wishing to use the information to inform their bottom-up experiments in recreating modern forms of primitive life. But it will not be easy, given the requirement for high temperature, nitrogen, carbon dioxide and explosive hydrogen gas.

In Signature in the Cell, building on research by Douglas Axe on protein function, Stephen Meyer calculated the probability of one relatively short protein 150 amino acids in length as being one chance in 10 to the 164th power (10^-164, pp. 210-212). In other words, expecting just one protein by chance exceeds the universal probability bound calculated by William Dembski (10^-150) by 14 orders of magnitude — 100 trillionth the chance! The word “miracle” doesn’t even come close to belief in such an event. Yet these evolutionists want us to believe that somewhere between 355 and 463 genes or protein products, all working in concert, emerged by chance.

It’s time to stop the caricature of ID by evolutionists that the former believe in miracles and the latter do not. It makes better sense to think that the “innovations” we observe were planned for a purpose by an intelligent cause necessary and sufficient to explain them, rather than to trust in sheer dumb luck. Arranging parts for function is not a “miracle” anyway. We do it all the time ourselves against the natural course of things.

Image: Trilobites, by Heinrich Harder (1858-1935) (The Wonderful Paleo Art of Heinrich Harder) [Public domain], via Wikimedia Commons.

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