If common ancestry is true, we would expect the evolutionary tree of life (TOL) based on animal morphology to line up with the evolutionary TOL based on molecules, but they don’t. In fact, there is no one TOL based on morphology or one TOL based on molecules. There are multiple TOLs.
Interestingly, a comparison of different genes from the same organism can result in different TOLs for that organism. The same is true of morphology. For example, when the TOL is constructed based on germ-cell formation (which is basic to the evolutionary process because it underlies reproduction, and we would expect for all organisms in a branch of the TOL to have the same germ-cell formation) it leads to one TOL, but this TOL differs radically from TOLs constructed based on body-play symmetry, the number of primary tissues, or the mode of development.
Looking at the Cambrian pyla specifically, there is no one TOL showing what the ancestry looked like leading up to the Cambrian.
Convergent evolution is a word to describe how similar morphological features develop in different species, where that feature was not shared by their common ancestor. There are many examples of so-called convergent evolution. But convergent evolution undermines the presupposition underlying the theory of common descent: similar homology indicates similar ancestry. Convergent evolution demonstrates that homological similarities do not necessarily imply a common ancestry. Convergent evolution negates the logic of the argument for common descent from homology.
While the gradualism that Darwin envisioned cannot explain the Cambrian explosion and lack of ancestral fossils in the Precambrian, can the theory of punctuated equilibrium fare any better? Punctuated equilibrium (PE) is the theory developed by Niles Eldridge and Stephen Jay Gould. As paleontologists, they were acutely aware of the lack of transitional forms in the fossil record. They recognized that new animal forms appear abruptly, persist relatively unchanged for millions of years, and often disappear from the fossil record just as abruptly as they appeared – only to be replaced by new animal forms. While they were willing to jettison the gradualism that Darwin proposed, they were still committed to the notion of evolutionary change and common descent. They postulated that evolutionary change occurs in short bursts over very short periods of time, so that the breaks and gaps we see in the fossil record are real – not the result of missing fossil evidence. The question they had to answer is how evolutionary change could happen so rapidly that transitional forms are not captured in the fossil record.
In order for mutations to change a population, they first have to become fixed within a population (rather than just appearing in a few isolated members of the population). In large populations this is very difficult to achieve, but in smaller populations mutations can become fixed more quickly and easily. Eldridge and Gould suggested that what drives rapid evolutionary change is the fragmenting of a population into smaller, geographically isolated groups, where mutations can become fixed more easily because they have to spread to fewer organisms (what they called “allopatric speciation”). Then, natural selection works to select those groups of the species that are better adapted for their new environment (“species selection”). The struggle for survival will eliminate most of the groups, leaving only those who are more fit to survive. PE requires large populations to generate the number of mutations necessary for macroevolution, but also small enough populations to fix those mutations into the population (where they can provide a functional advantage to the species that nature can select).
While PE made better sense of the fossil record as we have it, it has problems of its own, and is no better at explaining the Cambrian explosion than Darwin’s gradualism.
- Both Darwin’s gradualism and Eldridge’s/Gould’s PE assume the truth of common descent. This means we should expect for the number of phyla to be small at the base of the tree of life and increase at the upper levels of the tree. Instead, we see the exact opposite. The base of the tree begins with a large diversity of phyla. Some disappear over time, and only a few have appeared since the Cambrian.
- PE works by species selection, but the Pre-Cambrian does not document a large and diverse number of species on which species selection could work its magic.
- Since PE relies on large populations to generate the number of mutations necessary for biological novelty, it undercuts itself as a viable explanation for why there are no transitional forms in the fossil record. Populations large enough to generate all those mutations should be preserved in the fossil record somewhere. They aren’t. Instead, it only preserved the organisms from the smaller populations in which the mutations became fixed. That’s counterintuitive.
- Allopatric speciation and species selection only explain the fixation of traits, not the generation of traits. Species selection only eliminates the unfit, it does not create new fitness. To generate new traits you need large populations, and the primary mechanism for generating those traits is natural selection acting on random genetic mutations. That means PE is subject to the same criticisms as neo-Darwinism.
While neo-Darwinism provides a mechanism for biological novelty, it operates too slowly to account for the diversity of life on Earth and the abrupt appearance of organisms in the fossil record. PE explains how diversification could be sped up and why we see the abrupt appearance of organisms in the fossil record, but it does not provide its own unique mechanism for generating biological novelty, and, while faster, it is still too slow to account for all of the biological change we witness in the fossil record.
One way of measuring complexity is by looking at the number of cell types an organism has. Single-cell organisms only have one cell type. Humans have ~210. Precambrian sponges required ~10 cell types, while trilobites required 50 or more. Since new cell types require new proteins to build them, and new proteins require new information in the DNA, one has to question where this new information came from. How did it originate? How did single-celled organisms get the additional genetic information to create a second cell type? Where did the all the information come from to build the trilobite?
Darwinism does not seem capable of explaining the origin of the new genetic information required to build new and more complex organisms. Darwin’s own theory of how complexity arises was blended inheritance: The variation in two organisms will blend together during reproduction to form additional variation that blends the two. The problem with this theory is that as the number of combination events increases, the degree of differentiation between organisms within the population decreases. Blended inheritance limits or eliminates diversity rather than generating it. The less variation there is, the less natural selection has to work on.
While it’s easy to see why Darwin’s theory was wrong conceptually, Gregory Mendel’s pea experiments proved empirically that Darwin’s theory of blended inheritance was wrong. He showed that variation was preserved from generation to generation, even if that variation was not being expressed in organisms. Sexual reproduction, then, would not create new variations for natural selection to act on, but just different combinations of existing variation. It was not until the discovery of mutations in the early 20th century and gene theory in the mid-20th century that Darwin’s theory of evolution found the variation-generator it needed to produce the kind of biological novelties natural selection needed to work its design-mimicking magic.
But is natural selection working on random variations produced by genetic mutations sufficient to produce new biological information? Some will say it does, but that’s because they are using a very unhelpful definition of information called “shannon information,” named after MIT engineer Claude Shannon. Shannon pioneered information theory in the 1940s. He noted that information and uncertainty are inversely related, so that information increases as uncertainty is eliminated. The amount of information conveyed is inversely proportional to the probability of the sequence. The greater the probabilities, the more improbable it is that any one event or string of symbols is actualized, and thus that event or string of symbols, if it occurs, will convey more information. Furthermore, probabilities are multiplied as more symbols are added to the mix, so long sequences will always bear more information than shorter sequences. According to Shannon’s definition of information, “nenen ytawoi jll sn mekhdx nnx” has the same information capacity as “Four score and seven years ago” because both strings of symbols contain the same number of symbols, and are equally improbable.
While we do see shannon information in the cell, and while the Darwinian mechanism is able to create new shannon information, there is a deeper level of information exhibited in the cell that Darwinian mechanisms are not able to generate: functional information. Functional information doesn’t just specify an improbable sequence, but an improbable sequence that produces a specific, improbable effect. Shannon’s definition only measures the amount of information-carrying capacity contained in a particular sequence based on the improbability of the sequence, but it does not distinguish between improbable sequences whose arrangements are specified to perform a function from improbable sequences that are not specified to perform a function. There is a difference, then, between information and meaning. What distinguishes the latter from the former is the specificity of the arrangement to perform a function. Only functional information is capable of building new genes.
They saw natural selection working on the species-level rather than the organism-level.