The Evolution of Complexity
How did life originate on earth? How do irreducibly complex systems evolve? It’s possible that the answers to both questions are related (from page 627):
As far as we know, life originated only once, as did flowers, vertebrates, terrestrial vertebrates, the amnion, the feather, the mammalian diaphragm, the elephant’s trunk, and countless other examples. A single origin is very close to no origin at all.
The two questions, however, are treated separate and distinct in this book. On the one hand, Futuyma acknowledges our collective ignorance of how life originated (p. 105, 106):
The most difficult problem in accounting for the origin of life is that in known living systems, only nucleic acids replicate, but their replication requires the action of proteins that are encoded by the nucleic acids.
How protein enzymes evolved is perhaps the greatest unsolved problem.
And on the other, he blithely asserts the lack of any difficulty with explaining the evolution of complexity (p. 616):
Neither at the morphological nor the molecular level is the notion of “irreducible complexity” a barrier to evolution.
This is a bold statement (as Vincent Vega might say) not borne out subsequently in the text. While such complexity is obviously not a barrier to evolution (given that such complexity exists), the actual barrier arises in providing a convincing explanation for such complexity, something the text fails to do. For example, consider the following (p. 611):
Alleles with large effects contribute importantly to mimetic phenotypes in butterflies such as Heliconius, in which a species has converged toward the phenotype of another unpalatable species. Were phenotypes to arise that deviated only slightly from one mimetic patter toward another, they would lack protective resemblance to either unpalatable model and presumably would suffer a disadvantage. Thus it is likely that the evolution of one mimetic pattern from another was initiated by a mutation of large enough effect to provide substantial resemblance to a different model species, followed by selection of alleles with smaller effects that “fine-tuned” the phenotype. [my emphsis]
This example was well illustrated in the book, showing how a lesser mutation would provide no value to the butterfly. The change had to be significant enough to provide the mimic the protection that was ultimately gained by the species. How did such a large mutation take place, in this instance? What changes in the genotype were required? How many alleles involved? And if several, how does such a coordinated mutation take place?
One example of a coordinated mutation was provided on page 626:
The course of evolution, moreover, can depend on rare mutations or combinations of interacting mutations: in one of twelve experimental populations of E. coli, the ability to metabolize citrate (based on a combination of two mutations) evolved only after 30,000 generations, during which billions of mutations had occurred.
So in this example, one small coordinated mutation required 30,000 generations and billions of mutations. Apply those numbers to the evolution of the whale, for instance, an animal that underwent tremendous change in a few millions of years (not unlike humans). Given the slow birth rate of whales and the amount of change evident in the fossil record, does the math hold? How many coordinated mutations were required for whales to evolve from land-living mammals into the oceanic behemoths of today? What was the nature of these coordinated mutations? Two, three, four alleles at a time? Or was the rapid evolution of whales due entirely to single mutations, recombination, and/or genetic drift?
The book provides some potential clues to the evolution of complexity. For example, on page 609:
Goldschmidt’s genetic system hypothesis has been completely repudiated, but the possibility of evolution by more modest jumps remains one of the most enduring controversies in evolutionary theory.
So without actual saltation to the level of ‘hopeful monsters’, perhaps more modest jumps explain elements of evolution. This seems to be on the right track. Other examples of possible sources for larger changes can be found on p. 546 and 584:
Alternative splicing appears to be a major mechanism by which metazoans can increase functional diversity with a limited set of genes. For example, over one-third of alternative splicing events in human cells are distinct from those occurring for the same genes in mice, and recent research shows that the pattern of alternative splicing can evolve surprisingly quickly….Additionally, alternative splicing occurs in an environment-and tissue-dependent manner…suggesting a link between alternative splicing and functional diversification.
Protein sequence evolution can also be an important source of regulatory novelty in evolution. Amino acid substitutions in transcription factors, affecting either their interactions with other regulatory proteins or their binding to cis-regulatory elements, represent an important potential source of novelty because these changes can potentially affect the expression of many downstream genes during development….it is clear that even a small number of changes in a regulatory protein can lead to important macroevolutionary novelties.
These are interesting clues, and it would be helpful to see them tied to a specific case where a significant evolutionary step was taken.
Futuyma asks the relevant question when he writes (p. 614):
…we may well ask whether each step, from the slightest initial alteration of a feature to the full complexity of form displayed by later descendants, could have been guided by selection. What functional advantage can there be, skeptics ask, in an incompletely developed eye? And we can ask how complex characters could have evolved if their proper function depends on the mutually adjusted form of each of their many components.
He will later go on to show that many eyes exist in nature of various levels of complexity, indicating that something less than a fully operational eye provides adaptive value. My question would be this: how does one form of eye, one that operates as a coordinated and functional biological mechanism (pick any of them of lesser complexity than a mammalian eye) evolve to the next step, one that is equally coordinated and functional, yet different somehow? It can’t happen with many small steps, because any one small change will disrupt the functioning of the existing eye, and therefore be selected against. Futuyma might respond to this as follows (p. 642):
Complex adaptations are usually based not on single mutations, but on combinations of mutations that jointly or successively increase in frequency as a result of natural selection.
This may be (perhaps must be) exactly right. But is there a specific example of this? How would it work? How many simultaneous mutations would be required to move from one complex system (say a primitive form of an eye) to a slightly better version?
Or take another example (this one is my own, so perhaps an answer already exists): pit vipers have complex system of subduing their prey:
- sensitivies to heat for tracking and identifying their warm blooded prey
- poison glands that render their prey immobile (and actually begin the process of digestion after being struck)
- long, hollow fangs that deploy when the viper strikes
- ducts that conduct the poison from the glands through the hollow fangs into their victim
How did such a system evolve? What came first? What value are hollow teeth without the poison? What value is poison without the means of delivering it? The list goes on, and examples could be extended endlessly. How many multiple-mutation events would be required to go from the proto-viper to one that exists today?
The text offers conflicting statements on the matter. While Futuyma writes in one place: “Evolution requires genetic variation, which originates by mutation.” (p. 640), on page 643, in response to a question relating ‘chance’ and ‘complex structures,’ the response reads:
This is true [that chance could not produce complex structures], but natural selection is a deterministic, not a random, process. The random processes of evolution—mutation and genetic drift—do not result in the evolution of complexity, as far as we know.
If “evolution requires genetic variation, which originates by mutation,” but the “random processes of evolution—mutation and genetic drift—do not result in the evolution of complexity,” then what does?
To be fair, let’s consider an expanded definition of evolutionary science, given on page 15:
A body of ideas about the causes of evolution, including mutation, recombination, gene flow, isolation, random genetic drift, the many forms of natural selection, and other factors, constitutes our current theory of evolution, or “evolutionary theory.”
Nothing in this brief description, or any subsequent sections, provides a convincing argument, proof or example of the evolution of a complex system.
To be perfectly clear, the principle question might be stated like this: What is the source of variation that leads to the evolution of complex systems? As for the main thrust of evolutionary theory, I agree completely with the following (p. 15):
The main tenets of evolutionary theory—descent with modification from a common ancestor, in part caused by natural selection—are so well supported that almost all biologists confidently accept evolutionary theory as the foundation of the science of life.
I consider this beyond reasonable doubt. What I find confusing is the admittance that not everything is yet well understood:
Like all theories in science, it is a work in progress, for we do not yet know the causes of all of evolution, or of all the biological phenomena that evolutionary biology will have to explain. (p. 15)
…while at the same time claiming that everything can be explained by evolutionary theory (recall the quote from p. 616: ‘Neither at the morphological nor the molecular level is the notion of “irreducible complexity” a barrier to evolution.’)
This goes back, I am certain, to the culture wars mentioned above, and represents one of the insidious consequences. This is made plain on page 633:
[Intelligent Design Theory] proponents generally do not publicly invoke special creation by God. Some of them even accept certain aspects of evolution, such as development of different species from common ancestors. They argue, however, that many biological phenomena are too complicated to have arisen by natural processes and can therefore be explained only by an intelligent designer….The designer they envision, however, is a supernatural rather than a material being.
An intelligent designer isn’t the only explanation, but it remains a possibility. However, instead of ‘intelligent design’ I might look for something closer to ‘coordinated evolution’, perhaps. In any case, once a full explanation is determined, it will undoubtedly be natural processes found responsible. It could also be (and this is what I think most biologists believe) that it will simply be more of the same, in that no new processes or elements will be discovered, simply an extension of the biochemical world already in view.
The book takes an unnecessarily defensive stand against Intelligent Design, unnecessarily defensive in that it remains possible that some form of intentional (or designed, or coordinated) evolution takes place:
Unless the [Intelligent Design] advocate proposes that extraterrestrial creatures are responsible (which would merely shift the problem a step back), this designer must be a supernatural rather than material being. (p. 634)
This statement is mistaken in two ways. First of all, whether alien-caused evolution shifts the problem back would entirely depend on the nature of the aliens. It’s possible that aliens exist in an entirely different way than biological life on Earth, in ways we can’t imagine or comprehend. It’s possible that such creatures have already determined how their life originated, leaving the question fully resolved.
The range of human understanding is potentially quite limited. We perceive and conceptualize very little of what actually exists in the universe. We think we know everything there is to know, or at the very least, we think we are capable of knowing everything there is to know. But this might not be the case.
To understand how this might be so, consider the common guinea pig, and how such a creature perceives and conceptualizes the world. They see, smell, hear the same things we do, in a given instance, yet process the sense data in an entirely different—and in most cases—limited way. Given the limitations of guinea pigs, it would be unreasonable to expect one ever to comprehend Milton, or understand the game of baseball. It’s possible that the hypothetical aliens have the same relationship to humans that humans have to guinea pigs. I call this the Guinea Pig Conundrum.
This assertion of radical human ignorance doesn’t open the door to religion, any more than it suggests that humans are gods to guinea pigs. If an expanded world exists, one that includes greater beings that remain currently unknown, it can be certain that they will be part of nature, and potentially discoverable by humans.
Several such examples exist in history, where entirely unexpected realms became manifest: discovery of a round world and new continents; electricity and magnetism; radar and radio waves; cosmic radiation and quarks. Before their discovery, these things lay hidden in and around every living human (even the new continents, where native humans lived, unaware that they remained undiscovered).
Secondly, it simply doesn’t follow that ‘intelligent design’ must be caused by a supernatural being. Other possibilities exist, and will continue to exist until scientists demonstrate conclusively how complex systems evolve. Which brings us to the next point, from page 634:
But the [intelligent design] hypothesis generates no research ideas. It stops science dead in its tracks.
This is incorrect. An hypothesis that goes something like, ‘a process of intelligent design is the source of the evolution of complex biological systems’ is a valid scientific statement, because it can be falsified by demonstrating how complex biological systems actually evolve. Research aimed at falsifying this hypothesis might be accomplished in a number of ways:
- take a simple complex system (flagella, for instance) and determine, step by genetic step, what might be needed to take place in order to evolve the system. Certain flagella are relatively simple, yet a functioning engine that appears irreducibly complex. Only a couple of dozen proteins are involved, and it might be possible to model how those proteins evolve from one stable system to another, with a credible number of mutations involved. While theories exist, they haven’t yet been validated, or accepted. Building a model that demonstrates a potential developmental path for the evolution of flagella would be a positive step forward.
- at a macro level, identify a complex system (pit vipers, for instance) and map a credible evolutionary path that requires a minimum of genetic change from one viable phenotype to another. If a model of sequential genotypes could be posited that demonstrated a viable path via incremental changes, the source of the necessary genetic changes either mutation or recombination, that would provide a decent falsification of the hypothesis.
- attempt to discover precisely how a novel feature comes into existence. Humans have been breeding dogs (and other animals) for thousands of years, resulting in a wide range of types, but without ever (to my knowledge) creating one new novel feature. Showing conclusively how a specific novel feature came into existence would be helpful.
Assume for a moment that such research is technically possible. What if after applying existing biological/genetic/evolutionary tools in a research program designed to demonstrate a viable path to biological complexity, the effort repeatedly failed to provide even one viable explanation? That in itself would represent new knowledge. (Or perhaps such things have already been accomplished, and simply didn’t make it into the text.)
Late in the book, various questions are posed and answered based on theological challenges to the theory of evolution. The tenth one (p. 643) strikes at the core of the question:
10. Complex adaptations such as wings, eyes, and biochemical pathways could not have evolved gradually because the first stages would not have been adaptive. The full complexity of such an adaptation is necessary, and it could not arise in a single step by evolution.
[the first part of the answer in the text] This was one of the first objections that greeted The Origin of Species, and it has been christened “irreducible complexity” by advocates of intelligent design.
In order to separate the substance of this question from the underlying religious undertones, it must be rephrased to something like this:
given that complex biological systems exist, and have evolved over time with increasingly complexity, how do the known mechanisms of evolutionary theory (mutation, genetic drift, recombination, various forms of selection) explain the process for a complex systems to evolve to a different—and even more complex—system, while maintaining the viability and selective advantage of the newly evolved system.
[the second part of the answer in the text] Our answer has two parts. First, many such complex features, such as hemoglobins and eyes, do show various stages of increasing complexity among different organisms. “Half an eye”—an eye capable of discriminating light from dark, but incapable of forming a focused image—is indeed better than no eye at all.
Complex systems evolve from less complex systems. The question is how. The fact that various types of biological systems of varying levels of complexity exist in nature (eyes, for instance) doesn’t settle the question of how complex systems evolve. If biologists could demonstrate, model, or explain in detail how one complex system evolved from a less complex system, that would go a long way in settling the question.
[the third part of the answer in the text] Second, many structures have been modified for a new function after being elaborated to serve a different function. The “finished version” of an adaptation that we see today may indeed required precise coordination of many components in order to perform its current function, but the earlier stages, performing different or less demanding functions, and performing them less efficiently, are likely to have been an improvement on the ancestral feature. The evolution of the mammalian skull and jaw provides a good example.
No doubt this is true (Gould calls this ‘exaptation’), and likely a major contributor to the evolution of complex systems. But it doesn’t in itself explain how complex systems in general, or in any specific case, evolve. As for the examples given, the mammalian skull and jaw do not represent a complex system. It seems easier to understand how a bone system that already exists could evolve incrementally, in terms of size, shape and function, without requiring the coordinated steps necessary for a complex system to evolve. Examples of complex systems might include eyes, the feather, the amniotic egg, flagella, and blood clotting. No doubt many more exist, along with the incredibly complex bio-chemical processes that take place within every living cell.
Several possibilities certainly exist:
- It could be that scientists genuinely understand how complex systems evolve, and have yet to provide a convincing statement to the public.
- Or such convincing statements have been published, and I am simply unaware of them.
- It’s also possible that the evolution of complex systems is simply one of many biological mysteries that remain unsolved (like how life originated on Earth, say, or how enzymes evolve, an example given earlier), and biologists are busy researching what they consider more important topics, ones related to health care, for instance.
If, however, the evolution of complex biological systems remains a genuine scientific mystery, and if the scientific community continues to minimize or deny the magnitude of that mystery (as reflected in this text, for instance), then the possibility of that mystery ever being properly researched, let alone resolved, remains problematic.
Texts like this are being taught to future scientists, and those future scientists are getting the impression that the question of how complex biological systems have evolved has already been answered, or soon will be.
And it remains possible that even if scientists are not yet in possession of all the detailed answers, they remain confident that the simple extension of what they already know, in terms of evolutionary processes (mutation, recombination, genetic drift, various forms of selection) along with biochemical processes and further genetic research, will result in bridging those final gaps in our understanding. And then all will be explained, with nothing genuinely new to be discovered.
But consider for a moment if that isn’t the case. What if the current gaps in scientific knowledge are genuine gaps, ones that cannot be bridged by known processes. What if there are additional elements of the natural world, ones that pertain solely to biological systems, ones that emerge from the physical and chemical substrate, that remain as yet undiscovered?
In the history of science, such gaps have been surprisingly bridged many times by completely unexpected phenomenon. Continental drift is a good example, something that nobody could believe absent the proof that scientists ultimately provided. But perhaps a better example lies in 19th century physics, when the scientific world was content with Newton’s view of the physical world, with but a few troubling anomalies. And yet those anomalies that confounded the scientific paradigm were wrenched wide to reveal a new world of quantum, relativity, uncertainty, and E=mc2.
There are so many things in the biological world that we don’t understand:
- the fundamental difference between life and non-life
- how every process within each living cell functions
- how to create the simplest form of biological life from non-biological elements
- in general, how to trace an unbroken causal chain between the genetic code resident in DNA to the specific development of an organism
- more specifically, how the genetic code in a particular case manifest into specific organs, with specific structure and functions
- how the genetic code provides the mechanisms to control and coordinate all of the intertwined and incredibly complex biological systems that lead directly to development, survival and reproduction
- how instinctual behavior is encoded in genes, and becomes manifest
Unlike the example of 19th century physics, these gaps in our knowledge are not insignificant: they are broad and deep, and worthy of the utmost attention. The book makes the following point (p. 634):
Despite loose talk about “proving” hypotheses, most scientists agree that the hypothesis that currently best explains the data is provisionally accepted, with the understanding that it may be altered, expanded, or rejected if subsequent evidence warrants doing so, or if a better hypothesis, not yet imagined, is devised. Sometimes, indeed a radically new “paradigm” replaces an old one; for example, plate tectonics revolutionized geology in the 1950s, replacing the conviction that continents are fixed in position.
Does such a possibility exist in the biological sciences? It is possible that currently unknown aspects of nature underlie many of the biological processes that we don’t understand? For instance (and I am not suggesting this as an answer, only pointing to another frontier of scientific knowledge), what if the physical model that posits the existence of additional dimensions turns out to be an accurate depiction of our actual universe? These additional dimensions would be sub-microscopic and in principle undetectable by humans, yet might possibly manifest actual consequences.
I don’t mean to seriously speculate, only to emphasize the breadth of our ignorance. Richard Dawkins reflects this ignorance in The Blind Watchmaker:
The theory of evolution by cumulative natural selection is the only theory we know of that is, in principle, capable of explaining the existence of organized complexity. Even if the evidence did not favor it, it would still be the best theory available.
This is very weak tea, and hardly inspires confidence in the current scientific orthodoxy. Arguing that it is the best theory because it is the only theory simply demonstrates inadequacy. Such an argument would never be used to support plate tectonics, or countless other scientific explanations.
This state of affairs can be blamed on undue influence of the religiously faithful. Allowing the culture wars and the fear of Intelligent Design ideologues to push scientists into untenable theoretical corners and slamming the door on further inquiry seems dangerous and unscientific. Perhaps the most brilliant biologist should heed the following (p. 634):
Indeed, much of science consists of seeking chinks in the armor of established ideas, and few successes will burnish a scientist’s reputation more than showing that an important orthodox hypothesis is inadequate or flawed.
The opportunity exists, I believe, to do just that: show that the current theory of evolution falls short of explaining the full range of biological processes extant in nature. Doing so has the potential to blaze trails into uncharted, and currently unknown, new worlds.
