Evolution Icon Evolution
Intelligent Design Icon Intelligent Design

The Fossils Speak, but Hardly with One Voice

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Editor’s note: We are delighted to inaugurate a new series, “Talk to the Fossils,” by our friend and colleague Denyse O’Leary. See here for her Introduction.

Talk to the Fossils 3.jpgUniversity of Chicago biochemist James Shapiro, not a design theorist, offers in one of his lectures four kinds of rapid, evolutionary change that Darwin “could not have imagined”: horizontal DNA transfer, symbiogenesis, genome doubling, and built-in mechanisms of genome restructuring. His approach is in sharp contrast to the “defend Darwin” strategy usually championed in the academy. So it is no surprise that he is a controversial figure. But is he right in saying that many possible mechanisms of evolution owe little or nothing to Darwin’s theory, the only concept of evolution most of us hear about?

It is reasonably estimated that there are 8.7 million species today (excluding bacteria), but that only about 14 percent have been identified — and only 9 percent of ocean life forms. Our picture of Earth’s life forms might change radically if we had more information about all the others. For example, an entire kingdom of life, the Archaea, was only identified in the 1970s.

How did all these life forms get to be where they are? As we examine some evidence-based mechanisms, we should keep in mind a critical question: How does a given mechanism fit our current picture of evolution? And how much change can it account for?

The welter of data coming back from paleontology, genome mapping, and other studies presents a challenging picture. With so much new information, the history of life begins increasingly to resemble the history of human civilizations. There is peril in that, principally to older ideas that depended on less information and more overarching theory.

Overarching theories often falter when evidence replaces speculation. Darwinian evolution is, despite legislative protection, certainly one of the victims. By contrast, discarded and ridiculed theories like Lamarck’s (inheritance of characteristics acquired in life by the parents) may turn out to have some basis in epigenetics.

So, to start this series, instead of contemplating yet another picture derived from grand theories, let us assemble, under eight headings, some of what we have learned in past decades that we did not expect. That might help us evaluate theories, new and old.

1. First, how reliable is the fossil record? It’s really a question of what we don’t know that would make a difference. Some sense of the difficulty may be gleaned from a comment offered by University of Bristol’s Michael Benton:

Paleontologists are right to be cautious about the quality of the fossil record, but perhaps some have been too cautious. The sequence of fossils in the rocks more or less tells us the story of the history of life, and we have sensible ways of dealing with uncertainty. Some recent work on “correcting” the fossil record by using formation counts may produce nonsense results.

But which results are nonsense? How will we know?

2. Are there patterns in evolution? Yes, probably, at least two: Larger size and growing complexity (partly a function of multicellular body plans). Over the last 542 million years, marine animals’ mean size has increased by 150 times. As it happens, the largest animal that has ever lived, so far as we know, is today’s blue whale.

That said, patterns we assume to exist may not hold up. A classic evolutionary doctrine, “Dollo’s law,” claims that traits once lost can never be regained. But bone worms, for one example, seem to break this law, in that the males are roughly the same size as the females, instead of being the usual thousands of times smaller for their type of worm. Frogs, snapdragons, and snakes, among other life forms, apparently also break the law with impunity. From The Smithsonian, we learn that evolution is indeed reversible:

Some mites have returned to their free-roaming ways after countless millennia living on animal hosts. And a tree frog from South America lost its lower teeth only to re-evolve them after 200 million years.

We don’t actually know how rare reversal is. And we can’t fill in large chunks of time with patterns when there are no verified patterns. Some say Dollo’s law is due for retirement. But others aver, using computer models, that evolution is both irreversible and unpredictable. If evolution is indeed unpredictable, there is no pattern.

Some, like science writer Philip Ball, claim nonetheless that there is a “strange inevitability of evolution.” At Nautilus, he reports:

“Darwin’s theory surely is the most important intellectual achievement of his time, perhaps of all time,” says evolutionary biologist Andreas Wagner of the University of Zurich. “But the biggest mystery about evolution eluded his theory. And he couldn’t even get close to solving it.

But wait! If the biggest mystery in evolution eluded Darwin’s theory, why his theory “the most important intellectual achievement of his time, perhaps of all time”? How are we supposed to get anywhere if we are expected to venerate such a non-explanatory grand theory?

In reality, patterns in life forms are often wrongly interpreted when Darwinism is used as a frame. For example, current evolutionary theory provides no clear basis for interpreting a relationship between longevity and fertility. Thus, some researchers claimed that women undergo menopause but chimpanzees do not, that “menopause is not a part of the life cycle of living apes but has been uniquely derived in the human lineage.”

Darwinian explanations for that are, of course, on offer. For example, men triggered menopause (by preferring younger women). Or women’s selfish genes cause them to forego future breeding in order to invest in the survival of their existing selfish genes (children), sometimes called the grandmother hypothesis. That thesis assumes, of course, that older women are an asset to a group. Sometimes they are, sometimes not.

Despite all such claims, chimpanzees do undergo menopause, as a carefully researched 2012 paper on captive chimpanzees notes. But she-chimps do not typically live long after menopause. A recent article in Nature summarizes the fact that current evolution theory provides no basis for interpretation of the relationship between longevity and fertility in life forms.

3. Life forms sometimes survive in ways we did not imagine, let alone predict. Some bacteria eat electrons, demonstrating “the almost miraculous tenacity of life.” If some life forms live on pure energy, one wonders, will we one day discover life forms that live on pure information? Don’t count it out.

And some life forms defy classification: The ancient (chancelloriid) “balloon animal” from over 500 mya doesn’t seem to fit in with anything living today. And in a Chinese fossil trove from 570 mya, it is hard to decide whether the fossils are animals or bacteria. To quote a researcher, “What isn’t widely appreciated is that the Doushantuo rock formation contains billions of microfossils, many of which have no traits that are diagnostic of any living group and contain features that are not of biological origin.”

Another mysterious giant fossil that “seems to defy all known groups of organisms” is 450 million years old. Similarly, a billion-year-old microorganism is not apparently a fungus, alga, parasite, plant, or animal, so classifiers just called it “protozoa” (first life). Not that we know it was the first life, as the name implies.

Even when life forms can be classified, they may still present conundrums rather than gaps filled. For example, when a 60-million-year-old shrew-like mammal fossil turned up, a researcher noted, “The new dryolestoid, Cronopio, is without a doubt one of the most unusual mammals that I have seen, extinct or living.”

Might there be life forms out there that are permanently unclassifiable using our present system? Maybe using a genetic code we don’t understand? From Motherboard, we learn, “There’s already some evidence that something weird and undiscovered exists out there. Highly novel (and large) viruses, with weird strings of DNA (for a virus) have been discovered that seem to have strings of DNA from seemingly archaeal and eukaryotic genomes.” If we take the ID approach seriously — that DNA is a language — the DNA might use different elements to form the instructional words, as long as they are functional in a given context.

Even when we can classify life forms, we are always finding forms that don’t fit. Consider a recently discovered vegetarian relative of T. rex, an “evolutionary muddle of a beast,” the size of a small horse, whose numbers dominated Patagonia 145 million years ago.” We are promised “plenty of headaches for paleontologists hoping to place the animal in the dinosaur family tree.” Also dubbed the platypus dinosaur, it mainly demonstrates that evolution studies don’t feature much predictive power.

One could say the same of a huge, recently discovered North American dinosaur that could terrorize early tyrannosaurs 100 mya. “Contemporary tyrannosaurs would have been no more than a nuisance to Siats, like jackals at a lion kill.”

So a whole narrative of late Cretaceous ecology got started entirely in ignorance of this top predator? That is like trying to understand the northern wilderness without knowing about the existence of bears. Or wolf packs. Similarly, the DNA of some ocean bacteria crucial to ecosystem health defies explanation, and “contradicts nearly all accounts of free-living microbial genome architectures to date.”

Even when life forms do fit our beliefs, they don’t always do what we say they must: A theory of animal origin, that complex life evolved because atmospheric oxygen levels began to rise about 630-635 million years ago, was challenged recently by the discovery that some early animals, including common sea sponges, need almost no oxygen.

Other life forms do things we assumed they could not: A living wasp has an ovipositor partially metal-plated with zinc. Why? “It must be hard but flexible so that the female wasp can curve and bore it through the fig. And the wasp must be able to use it repeatedly and efficiently without it wearing down or fracturing.”

4. Beyond this, we keep discovering new life forms that we did not expect or predict. A newly discovered Pacific Northwest spider, announced in 2012, represents a hitherto unknown family, according to conventional classification, not just a new genus or species. Recently discovered mushroom-shaped sea creatures turn out to be neither jellyfish nor comb jelly, and could be related to groups thought to be extinct for over half a billion years. Or possibly a newly discovered branch on the tree of life.

We also keep finding new life forms that change the picture. A mystery mammal’s tracks, found alongside those of dinosaurs, belong to a raccoon-size animal at a time (118 mya) when most mammals are thought to have been no bigger than a rat. Similarly, a new fossil find from 130 mya in China features “not a parade of galumphing giants, but an assemblage of quirky little creatures like feathered dinosaurs, pterosaurs with advanced heads on primitive bodies, and the Mesozoic equivalent of a flying squirrel.”

Yet despite all this, so far as our research can tell, non-life never exploits any strategy to become life. So one thing is still true: Pasteur’s dictum, “Omne vivum ex vivo” (“All life comes [only] from life”).

5. Far too much attention may be given to genes and DNA. So much current evolution thinking, including questionable fields like evolutionary psychology, depends on the alleged power of the gene. Does anyone remember that fellow who said in the early 90s that a CD of your genome is “you”?

Not even close. From the New Statesman: “According to a growing number of researchers, the standard story of the influence of genes is overblown. So many other factors influence how we turn out as individuals and how we evolve as a species that the fundamentals of biology need a rewrite.” “This is no storm in an academic tearoom,” a group of biologists wrote in the journal Nature recently: “It is a struggle for the very soul of the discipline.”

The gene isn’t even necessarily what we think. Diverse genomes can exist in a single person: Mothers’ cells may remain in their children and children’s cells in their mothers decades after childbirth. So that CD of your genome is both you and your mom?

There are some relatively new genes. There are also “hidden” genes that don’t show in current populations but might later. Some genes are not “junk” but also not strictly necessary either: “In the late 1990s a team of researchers at Stanford University created around 6,000 mutants of brewer’s yeast, each of them lacking a different single gene, and found that many of them thrived just as well as the unmutated yeast did.” No surprise there; successful life forms would feature redundant systems.

Some life forms can edit their genes extensively. Squid can, apparently. A researcher noted, “It was astonishing to find that 60 percent of the squid RNA transcripts were edited.” The iconic fruit fly is thought to edit only 3 percent of its makeup.

Some species can have more than one genetic origin. Polyploidy, which means that the species has two complete sets of chromosomes, has been identified in a mimulus plant in Scotland. We learn that polyploids “are common among plants, as well as among certain groups of fish and amphibians. For instance, some salamanders, frogs, and leeches are polyploids.” and “Mimulus peregrinus is an example of how some branches can come back together again and spawn new species that are in part the combination of their ancestors.”

Basic claims about inheritance principles are also coming under fire. Researchers recently found that Mendel’s “law of segregation” (an equal probability of inheriting each of two copies of each gene from both parents) doesn’t always hold. We now learn, “For years, scientists had evidence that this law was being broken in mammals, but they didn’t know how.” Apparently, female mice pass on one copy of the R2d2 gene more frequently than the other copy. This finding, if it holds, matters because the probability of heritable illness is calculated by doctors assuming Mendel’s Law. But maybe it’s not a law.

Not surprisingly, some respected researchers now question the amount of attention given to the gene as such. A recent Royal Society paper denotes genes as “merely a means of specifying polypeptides.” Whether the researchers are right or wrong, they add to a growing chorus against the vision of evolution that started with Darwin and was revived by Mendelian genetics, as natural selection acting on random mutation of genes to create the world of life we see around us.

6. Some data that garner attention in the pop science media sound counterfactual. For example, we are told by some researchers that evolution favors the collapse of cooperation, according to game theory:

“It’s a somewhat depressing evolutionary outcome, but it makes intuitive sense,” said [Joshua] Plotkin, a professor in Penn’s Department of Biology in the School of Arts & Sciences, who coauthored the study with [Alexander] Stewart, a postdoctoral researcher in his lab. “We had a nice picture of how evolution can promote cooperation even amongst self-interested agents and indeed it sometimes can, but, when we allow mutations that change the nature of the game, there is a runaway evolutionary process, and suddenly defection becomes the more robust outcome.”

Does it make intuitive sense? How is it that many of the most durable species are adept at co-operation, whether we are talking about humans, bees, or Canada geese? And do we know that a high-observed level of co-operation existed back in the Cambrian?

7. Some claims sound either trivial or politically sourced. For example, we are told, “Some species are evolving far more quickly than Darwin ever imagined.” How? “Mosquitoes that colonized the London Underground in 1863 are now so different they can no longer mate with their above-ground relatives. Chinook salmon from Alaska to California needed just a human generation to become smaller and shorter-lived after an increase in commercial fishing in the 1920s. Adaptation is happening right under our noses, in our lifetimes.” But all of this can be accounted for, assuming mere loss of information. It is gain in information that matters in evolution.

Then there is the assertion that human-caused climate change will spur the evolution of new species in an evolutionary surge, and that new species are beginning to emerge already. At last! A claim we can verify. What and where are these species?

More problematic are widely publicized false claims about “throwbacks” to earlier human evolutionary time. Some readers may recall the Turkish family that walks on all fours, as a supposed instance of “backward evolution” (along with human tails that turn out to be Photoshopped). But, contradicting earlier claims, a careful study showed that the family members do not walk in a diagonal pattern like apes or monkeys. They walk on all fours as other humans would, if asked to do so (laterally). Their unusual mobility is a response to an untreated human disorder, Uner Tan Syndrome (UTS). Many distressing conditions only come to attention when a person seeks modern medical diagnosis. Urban legends about “evolution” are an unwelcome distraction in such a case.

8. Evolution is often spoken of as if it were a deliberating intelligence, though the idea is considered a heresy. “Evolution,” we are told by one respected source, has been “experimenting” with different types of early humans, based on the fact that skeletons show more diverse features than expected. That prompts two questions: If all the passengers in a subway car in a large, multicultural city met a mishap and were fossilized, how many “different species” would be identified today, using current methods? Second, is evolution (Evolution?) an intelligent agent? If it is not possible to speak of evolution’s course without resort to the language of agency, is that a defect in human intelligence or an apprehension of fact?

Recently, the Washington Post ran a story about ten fossils that explain life on Earth. They only “explain” life on Earth if you think that ten disconnected headlines constitute an explanation.

Along those lines, we are now told at PBS that we must try thinking harder so that we will come to “believe in” evolution. But what specifically ought we to believe in? And is that really a way to approach science?

Instead, let us take a whirlwind tour of ways evolution is known to occur, as opposed to how grand theories say it occurs, and see what we can find out.

Image: La Brea Tar Pits, Los Angeles, by Charles Robert Knight [Public domain], via Wikimedia Commons.