In The Origin of Species by Means of Natural Selection, Charles Darwin proposed to explain how one life form gave rise to another. He subtitled the book, "The Preservation of Favoured Races in the Struggle for Life." He argued that a succession of small improvements in reproductive success would gradually lead to the major changes that distinguish one species from another. This gradualist hypothesis followed the Uniformitarian principle learned from his geology professor, Charles Lyell.
Since 1859, Darwin's followers have focused on optimizing reproductive success, now called "fitness." For them, natural selection increases fitness and, thus, generates new life forms, including their sophisticated and complex adaptations.
Darwin put it this way in Chapter 6: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case."
There has always been controversy about whether random variation and natural selection for improved fitness can truly explain biological evolution over time. Today we can apply genome sequence data to test Darwin's theory. It answers clearly about gradualism.
Many genome changes at key stages of evolution have been neither small nor gradual. For example, plant breeders are familiar with rapid speciation. When we wish to create new plant species artificially, we do not use selection. We generate hybrids by mating different species. In a fine 1951 (!) Scientific American article on this subject entitled "Cataclysmic Evolution," the distinguished 20th Century evolutionist, G. Ledyard Stebbins, explained how flour wheat evolved, suddenly, by hybridization.
Hybridization frequently leads to a process of "whole genome doubling." Doubling the genome takes one generation and potentially affects all hereditary traits. Note that the production of new species with novel characters by hybridization occurs too rapidly for natural selection to act creatively.
Perhaps the most important evolutionary step of all took place at least one billion years ago, when two or more cells fused to produce the first "eukaryotic" cell having a defined nucleus. This nucleated cell was apparently the progenitor of all "higher" forms of life, including plants and animals. Such cell mergers are known as "symbiogenesis," long championed as an evolutionary force by the recently deceased biologist, Lynn Margulis .
It's remarkable that even though processes like hybridization and symbiogenesis have been well-known for decades, many neo-Darwinists firmly insist on gradualism in evolutionary change. Their position notwithstanding, living organisms have many tools at their disposal for generating sudden change.
As I described in my previous HuffPost blog, "Evolutionary Lessons from Superbugs," bacteria get new DNA information from unrelated organisms. Microbes transform into superbugs in a few minutes by "horizontal DNA transfer." Similar events confer new traits to many microbial and eukaryotic recipients, often multiple characters in a single step.
Was Darwin simply mistaken about the gradual nature of hereditary variation? Such ignorance would be unavoidable before we knew about Mendelian genetics and DNA. Or was there a deeper flaw in the theory that he (and Alfred Russell Wallace) propounded? The answer may well be that it was a basic mistake to think that optimizing fitness is the source of biological diversity.
My recent book, Evolution: A View from the 21st Century, begins: "Innovation, not selection, is the critical issue in evolutionary change." This blog expands on that assertion.
The first problem with selection as the source of diversity is that selection by humans, the subject of Darwin's opening chapter, modifies existing traits but does not produce new traits or new species. Dogs may vary widely as a result of selective breeding, but they always remain dogs.
The second problem is that Darwin understood only "numerous, successive, slight modifications" as the sources of inherited change. His neo-Darwinian followers have modified this position to assert that all mutations occur randomly. They insist there is no biological input into the change process. For them, the genome determines organism characteristics. They think of it as a read-only memory (ROM), which only changes by accident.
However, the last 60 years of molecular biology and genome sequencing have established that genome change is very much an active cellular biochemical process. I call this "natural genetic engineering." In my book, I argue that DNA biochemistry has changed our 21st-century view of the genome. We now have to consider the genome a read-write (RW) memory system.
In other words, the genome is more like an iPod than a CD.
Moreover, cells can target genome changes controlled by cell regulation and sensory inputs. Cells and organisms with RW genomes can respond creatively to life-threatening challenges.
My claim of creativity in genome change clearly requires empirical support. Decades of molecular biology research show that organism traits result from action by protein-RNA-DNA networks, which also respond to multiple sensory inputs and signals.
The genome sequence record shows that these networks and their DNA recognition sites have evolved by well-documented natural genetic engineering processes. The examples include:
• How cells generate new proteins by combining parts of existing ones
• How families of proteins expand by copying segments of DNA & RNA
• How innovations spread from part of the genome to another
• How DNA "cassettes" move through the genome (with eerie similarity to familiar human technologies).
Given these well-documented examples of molecular innovation by natural genetic engineering, the new century may be an appropriate time to revisit our basic assumptions about the sources of biological diversity. Perhaps natural genetic engineering plays a more important role than natural selection.
As Barbara McClintock predicted three decades ago, the 21st Century brings us new insights about how cells adapt to challenges. Let us hope that we acquire nature's wisdom. Just as life has survived by repeated innovation, we humans can solve our own daunting problems by learning the lessons cells have to teach.
There was not space to do epigenetics justice. Epigenetic control is a key aspect of the life history - genome restructuring connection and should be the subject of its own posting. It was implicit in the mention of genome restructuring as a response to life-threatening challenges. Contrary to what conventional theorists may pretend, evolution has many dimensions. The known and potential roles of epigenetic processes certainly add to the multidimensionality. Sorry not to be able to deal with everything at once, but life and evolution are complex affairs.
I thought the article was great. I am enamored with the evidence concerning epigenetics currently and felt that epigenetics would have fit well in your article. I would very much enjoy another article by you on epigenetics. I'm sure it would be fascinating! Thanks for your time in replying.
Berthajane Vandegrift
A Few Autistic Questions about Freud, Marx and Darwin.
You may be interested in the following publications:
Bray, D. Wetware A Computer in Every Living Cell 279 (Yale University Press, New Haven, CT, 2009).
Danchin, A. Bacteria as computers making computers. FEMS Microbiol Rev 33, 3-26 (2009). http://www.ncbi.nlm.nih.gov/pubmed/19016882.
And we use intelligence to do it, too, don't we? Personally, I think there's an intelligent designer behind everything. This universe, including life itself, is no happy accident, IMO.
Beyond a thinking, planning designer? For lack of a better descriptor, you can call it "Spinoza's God," like Einstein did, if you like. Or just plain "God," if you'd like to cut to the chase.
>>>do the laws of physics apply to this 'creature', etc>>>
Physics, as we know them, may not even apply in another universe out there. For all we terribly intelligent humans think we know, we really don't know all that much. We don't even know what caused the Big Bangeroo.
>>>I'm not that sure that surviving in nature is/ has been that pleasant of an experience>>>
Maybe it's not intended to be a pleasant experience for one and all.
Also, Darwin's suggestion of development of structures based upon incremental steps still holds, a bigger than normal step that succeeds just speeds up the process. Fitness improves by a bound rather than a step, yet nevertheless, for a brilliant innovative adaptation to spread through a non-bacterial population selection is still required: it may be fast, but it's there.
Furthermore, plant breeders operate far from natural conditions. They tend and weed and scrutinize. Trays and trays of seedlings are cast aside when compared with the better results of their own genetic algorithms.
There seems a presumption that gradualism provides something of a barrier, or at least a speed brake, to runaway genetic change.
Put another way: given the breadth and scale of genetic 'tinkering' going on, should your perspective give us pause and a re-evaluation?
The fact that genetic engineering is natural serves as a double-edged sword with respect to
genetically-modified organisms (GMOs). On the one hand, human genetic manipulations are not in any way "unnatural." So the fear of creating a monster we cannot control is not the same as it was to many people in the 1970s. On the other hand, all that we have learned about DNA mobility should make us aware that our laboratory constructs will inevitably escape in the wild. There is already evidence for this. So prudence is the watchword, not complacency.
The author lists some interesting phenomena that biologists in Darwin's era had no idea about. But one thing remains true: for any evolutionary change in phenotype to persist, it must confer some benefit to its own means of replication. Unless the author has discovered the immortal Eldar, I'm afraid that all of the neat genetic tricks (most of which are extremely rare in animals) still must survive the generations. And if you want to survive the generations, you better make your hosts more "fit" (that is, reproductively successful).
Do you mean to say there can be no scientific alternatives to Darwin's theory of evolution? If you read some of the other comments or look at the history of evolutionary thinking, you will see there have always been alternatives. Molecular biology and genome sequences allow us to specify alternatives with greater precision, which is what I have tried to do. Is there anything wrong in that?
Genome analysis is increasingly revealing important cases of whole genome doubling (WGD) events. Often these indicate that an interspecific hybridization has taken place. For example, the emergence of vertebrates as whole is marked by one WGD, and the separation of jawed vertebrates is marked by another. The emergence of bony fish includes another WGD, and the separation of the Salmonids involves another. Moreover, although they are rare (as far as we know) in animals, there are numerous examples of WGDs in protists, fungi and plants. So this one cause of major and rapid genome change has played a significant role in genome evolution.