In the last blog, I questioned the creative role of natural selection in evolutionary innovation. To clarify further what I had in mind, this blog will look at one of the truly creative processes of tremendous importance in evolutionary history: symbiotic mergers of two distinct organisms to generate a third new one (symbiogenesis). Without symbiogenetic mergers, we would not exist.
The classic example of symbiogenesis is the formation of lichens, the moss-like forms that live on rock surfaces. Lichens arise from a merger of a fungus and a photosynthetic microbe, either a cyanobacteria or (more commonly) an alga. The resulting lichen has both the fungus' ability to grow by spreading adherent filaments over the rocks and the photosynthetic capacity to produce food from sunlight and carbon dioxide in the atmosphere.
Lichens were considered a separate group of organisms until 1867, when Swiss botanist Simon Schwendener proposed they were a symbiotic association. It had to wait until 1939 for Eugen Thomas to artificially synthesize a lichen in the laboratory.
The great proponent of symbiogenesis as a major force in evolution was Lynn Margulis, who suddenly passed away late last year. She and her son, Dorion Sagan, summarized her ideas in the 2003 book, Acquiring Genomes: The Theory of the Origins of the Species.
Lynn was most widely known since the 1970s for championing ideas that organelles within nucleated eukaryotic cells are descended from endosymbiotic bacteria (Margulis, Origin of Eukaryotic Cells, 1970). Lynn's position was vindicated when the methods of molecular taxanomy and phylogeny, pioneered by Carl Woese at the University of Illinois (Woese 1981), made it possible to demonstrate that the oxidative energy-producing organelle of eukaryotic cells, the mitochondrion, actually descended from a specific type of bacterium.
Since all eukaryotic cells have mitochondria (or a degenerate form of this organelle), the ancestral eukaryotic cell must have had one too. Thus, the origin of the nucleated eukaryotic cell from prokaryotic (pre-nucleus) precursors involved at least one symbiogenetic event to acquire the mitochondrion.
Since all "higher" and large multicellular organisms, including ourselves, are eukaryotes, the formation of the eukaryotic cell is arguably the single most important evolutionary event since the origin of life.
It is likely, in fact, that there were additional cell mergers involved in the origins of the first eukaryote. From Woese's work, we know there are actually two kinds of prokaryotic cell: the familiar Bacteria, and other cells called Archaea because they were originally thought to be closer to the oldest (most archaic) cells. The eukaryotic cell is actually a mixture of archaea-like and bacteria-like features (Woese 1981). Thus, most theories of the origins of eukaryotes postulate a bacteria-archaea merger in addition to acquisition of the mitochondrion.
Photosynthetic organisms are the nutritional basis of most life on the planet. With the exceptions of prokaryotes that get their energy from chemical sources, sunlight provides the power for life, either directly or by providing photosynthesized food for consumption by non-photosynthetic organisms, like us.
The original photosynthetic organisms were bacteria. There are no photosynthetic archaea. There are actually three kinds of bacterial photosynthesis, and one of them produces oxygen. Oxygenic photosynthesis is also the process carried out in plants and other photosynthetic eukaryotes.
This bacterial-eukaryote similarity should hardly be surprising when we recognize that the photosynthetic organelles in eukaryotic cells, "chloroplasts" or "plastids," are all descended from an endosymbiont that belonged to the group known as cyanobacteria (blue-green photosynthetic bacteria).
In other words, all photosynthetic eukaryotes -- green plants, green algae, red algae, diatoms, and many others -- all owe their ability to use sunlight to a second, super-important symbiogenetic merger. Much of the photosynthetic capacity on earth came from cell mergers.
Symbiogenesis did not stop with two key events in the history of eukaryotes. Among photosynthetic organisms, secondary cell mergers have occurred involving both green and red algae and other lineages of eukaryotic cells. For example, diatoms (among the most abundant photosynthesizers on the planet) arose from a red algal endosymbiogenesis with a protozoan. Similarly, Euglena, a photosynthetic microorganism widely studied for its movements following light, arose from a green algal endosymbiogenesis with a protozoan relative of the sleeping sickness organism, Trypanosoma.
Since cell mergers involve independent cells with their own genomes, the symbiogenetic cells that result each has two or more genome compartments. In fact, we know the mitochondrion and plastids are descended from bacteria because we can isolate and sequence their DNA. When secondary symbiogeneses occur, the merged cells often have at least four genome compartments: the nucleus, the mitochondrion, the plastid, and a "nucleomorph" descended from the nucleus of the endosymbiotic alga.
In all these cases, there is active DNA transfer between genome compartments. Typically, DNA sequences travel from the organelle genomes to the nuclear genome. Thus, the nucleus actually encodes most of the proteins in each of its organelles, even though they have their own genomes and protein synthesis machinery.
Restructuring of both nuclear and organelle genomes is an important aspect of evolution. Some groups of organisms are actually identified by the organization of their mitochondrial DNA.
We see from the few examples discussed here that symbiogenesis by cell mergers has been an essential component in the evolution of life on earth. Once formed, symbiogenetic organisms have to succeed in the struggle for existence. But nothing about their origins involves Natural Selection.
Symbiogenesis is responsible for some of the most important innovations in evolution. It illustrates clearly why we have to think about the precise cellular and genomic events that create new organisms.
Making one organism out of two is far from a simple process. There are countless questions still to be answered about what makes these mergers succeed. The existence of so many unanswered questions illustrates that science is, as Vannevar Bush called it, the "endless frontier."
There can be few ideas less scientific than the argument that we have things all worked out, even in principle.
REFERENCES
"tiede.fi keskustelut (conversations) Evoluutio ja fossiilit" with pseudonym P.S.V. I am intuitively sure that his way is very relevant.
Thanks for your help in getting the word out. One of the best things to do is post the link to the web page for my book, which links to videos and lots of specialized and relevant bibliographies: http://shapiro.bsd.uchicago.edu/evolution21.shtml.
I still remember eating the split salmon on wooden planks cooked in the glow of burning coals in one of the main squares in Helsinki. Very delicious.
http://www.evolutionnews.org/2012/08/coyne_disses_sh063541.html
It contains a link to the lecture. Of special interest during the Q & A session is a comment by Dan Hartl (at 1:05) "I don't think anyone seriously disputes what you said".
Thanks for your comment. Judging by some of the other, more hostile commentaries posted here, one might think my arguments were so outrageous that no one should take them seriously. But the vitriol in those statements only reflects on the jaundiced views of the commentators themselves, who have no real knowledge of serious scientific discourse.
Whoever said anything else? You simply have natural selection conflated with all of evolution.
Looking back over the exchanges with you on natural genetic, engineering, symbiogenesis and selection, it has become clear to me that it is essential to distinguish several aspects of evolution:
1. The change processes involved. These include symbiogenesis and NGE. Neither is a biological product of evolution (i.e. cell or organism).
2. The nature of changes that occur to cells during evolution. These can be cell mergers, as in symbiogenesis, or genome changes, as in NGE. NGE generates all manner of genome changes, ranging from single base substitutions to major DNA rearrangements.
3. The altered cells and organisms that result from the change processes. These can be symbiogenetic fusions, mutants with minor alterations, or cells and organisms that have new genome structures. The structural changes to the genome or cell will result in novel biological properties or phenotypes. This is why I say that these change processes are the creative aspects of evolution.
4. The ecological fate of the novel cells and organisms. This is where natural selection operates. It tests the adaptive utility of new characters and works to eliminate those that are detrimental and facilitate the spread of those that provide an advantage in the prevailing ecology.
My impression is that these distinctions have not been clear to everyone.
3. When people talk about a character--let's say a modern bird wing--coming into being, the process which molded it from the previous forelimb was a combination of variation-producing processes coupled with natural selection. And the same will be true for just about any character you pick--maybe there were a couple big jumps like a domain shuffling event or chromosome duplication--but that event alone isn't very often enough to produce the cumulative overall phenotypic changes that we talk about.
You are quite correct to say that mutations are of vital importance to the evolution of new life forms.
Mutations (and natural selection) were both required for the phenomenon of symbiogenesis to occur.
Mutations are grist to the mill of natural selection. Symbiogensis is one of the most amazing results of the power of these two natural processes. Natural engineering indeed!
Of course, natural engineering, like natural selection isn't teleological in nature. Teleological explanations have no place in modern science. Do they? Underlying chemistry is the physics of quantum mechanics. We would not want to introduce quantum woo into biochemistry. Teleology is woo too.
You are asking for a complex response.
Natural genetic engineering does not exactly mean mutation (broadly interpreted as any kind of genome sequence or structure change). By natural genetic engineering, I mean the cell processes that restructure the genome. It's like the distinction between construction as a process and as a building. The one (genome change) is the result of the other (natural genetic engineering).
I use the engineering metaphor because cells actually cut and splice their genomes in a variety of ways. For anyone who has worked on mobile genetic elements, as I have, the parallel is inescapable. I am not the first person to use that terminology. I recall seeing a retrovirologist use it to refer to oncogenesis by tumor viruses.
Thinking of genome change as natural genetic engineering helps us understand processes that are inherently more efficient than random change and selection, such as exon shuffling in protein evolution (http://www.huffingtonpost.com/james-a-shapiro/genetic-engineering_b_1541180.html). Even without any regulation, such processes generate useful novelty more rapidly and with higher probability than accumulating random changes.
However, we know that cells can regulate and target natural genetic engineering (http://shapiro.bsd.uchicago.edu/TableII.7.shtml and http://shapiro.bsd.uchicago.edu/TableII.11.shtml). Do they use these capabilities to bias natural genetic engineering in some demonstrable way towards functional novelty? That needs to be answered experimentally.
"Thinking of genome change as natural genetic engineering helps us understand processes that are inherently more efficient than random change and selection, such as exon shuffling in protein evolution."
Given that genome change is mutation and NGE is the process (or processes) responsible for mutation, allow me to tidy things up: NGE helps us understand processes that are inherently more efficient than random change and selection.
Which processes do you mean? Exon shuffling is a NGE process. It makes no sense to say that NGE processes help us to understand NGE processes.
When you claim to be quoting someone you have a responsibility to do so accurately. You state Shapiro claims that "natural genetic engineering" does predict the occurrence of "Irreducibly complex" biological structures and functions.
This is not true; he stated NGE could explain them. If you are unfamiliar with the distinction between 'predict' and 'explain' please consult a dictionary.
At best that is clumsy. Less kindly, it's plain wrong.
Symbiogenesis represents one of the most important developments in the evolution of life.
I'm not sure what point you are making. Let's take the "less kindly" road; "Symbiogenesis is responsible for some of the most important innovations in evolution" is a false statement. That being the case its negation is true. The negation is:
'Symbiogenesis is not responsible for any of the most important innovations in evolution.'
Is this your position?
An objection to your conception of evolution that seems to come up repeatedly in the comments thread is that it doesn't really matter how variation is produced, it is all subject to natural selection. I get the impression that you have responded to this point repeatedly. Darwin thought that the origin of complex biological systems or features needed to be understood in terms of the accumulation of simple or trivial biological changes or features. The origin of the eukaryotic cell seems a plausible counter-example to this way of thinking, for reasons you have discussed here. One may want to respond with the claim that the organisms that combined to form the eukaryotic cell were themselves the products of mutation and natural selection (and nothing else besides), but this is more an a priori assumption than a substantive empirical consideration. Darwin's gradualistic or incremental conception of evolutionary change seems to have been overlooked in many (but not all) of the negative comments posted here and it is difficult to conceptualise symbiogenesis in this kind of way.
Just what mutational changes, incremental or otherwise, brought about the evolution of the eukaryotic cell is an interesting question to pursue. Time will tell, perhaps.
Thanks for making that point. The whole argument that selection is a purifying rather than a creative force in evolution depends on the size of the changes presented to it. Even Dawkins accepts that. The DNA evidence shows many large-scale changes of various types. We'll discuss more in blogs to come. Stay tuned.
Unfairly I think, within the context of my other comments. So to speak more clearly: cell fusion is a consequence of evolution. The process of mutation and natural selection led directly to the novel event of cell fusion and the more evolved form of cell fusion which we observe today.
Natural selection subsequently favoured the mutation responsible for the first ever occurrence of symbiogenesis. It may have been the case that several fortuitous mutations were involved, divided between the two cells. However it happened, it happened because of mutation in the genome of at least one of the two cells which fused together.
How else can it be explained?
The title of this topic is pure nonsense. The evolution of symbiogenesis. There is a subject worthy of study.
I agree that the evolution of symbiogenesis is worthy of study. The rest of your points have been more than adequately covered in numerous replies. No need to point out some of the conflations in your statements. Interested readers should now be in a position to figure them out on their own.
One of them mentions the difficulty of explaining irreducible complexity on the basis of Darwin's own belief of incremental change. This is not a problem for present day understanding of evolutionary mechanisms. The same paper suggests that natural genetic engineering could explain the phenomenon. That is true.
Natural genetic engineering is nothing other than cell processes which derive from evolution.
Natural genetic engineering is nothing other than more of the same.
Natural genetic engineering is nothing other than evolution by mutation and natural selection.
Still in the attempt to do just that, I shall have one last try.
You do accept that all the processes that fall under what you term as "natural genetic engineering" had to evolve by means of mutation - however those mutations may have arisen - and natural selection, don't you?
And all of these processes may give rise to mutations, themselves? Am I correct? If they go wrong for some reason and cause heritable alteration to the genome, for example. In which case natural selection will take its course.
Then what other way can "natural genetic engineering" processes possibly affect the course of evolution? Surely there is no other way?
That being so, we don't appear to have gone beyond mutation and natural selection. It would be an immense surprise if we had. But we haven't. "Natural genetic engineering" doesn't explain anything about evolution than we already understand.
You still have to explain clearly what point you are trying to make.
At a time when some people are asking me to stop blogging, your appreciation is most welcome. I hope others share your opinion.
My question is, why do these critics object to making the public at large aware of what has been happening in molecular evolution science? What are these critics afraid the public will learn? That science has more questions than answers? That science is continually learning it was ignorant or mistaken in the past? I think the public knows this already.
What has damaged evolution science in the eyes of the public is not the fact that many questions remain open. It is the arrogance to pretend that the opposite is true and that simple phrases provide answers to difficult questions. The public knows that's phony, and we do not help science education by denying that science is continually in the business of asking rather than answering questions.
How many of these types of relationships have evolved and failed?
We don't know, just as we don't know how many types of cells existed besides the three we know about today (bacteria, archaea and eukarya). Cells that existed in forms that did not leave fossil remains but went extinct are presently unknowable to us. The discovery of the archaea 40 years ago reminds us that we cannot assume there never were other kinds of cells.
The fact that there have been secondary and tertiary endosymbioses involving photosynthesis, which is easy to spot, suggests that there may have been other kinds of symbiogenetic events. Lynn Margulis and others have proposed several, but the molecular evidence is lacking.
Dawkins said it with exquisite clarity a few years ago: “Darwin made it possible to be an intellectually fulfilled atheist”. Nothing, absolutely nothing will convince evolutionists of this persuasion that NS has not totally explained all life as we now see it and will see it in the future. Imagine trying to convince Duane Gish that God didn’t create individual species de novo.
There is a significant issue with the majority demographic that visits this blog. If you copy and paste screen names of the most consistent and viscous detractors into Google the results are not surprising. You will notice an overlay of users. Many of the same names appear on pro neo-Darwinism blogs. These people make up a large percentage of those who comment. For some reason they feel the need to defend their stance across many different sites. It ultimately creates a discussion that isn't very healthy.
To Dr. Shapiro: For the sake of quality discussion moving forward you should read this:
http://en.wikipedia.org/wiki/Online_disinhibition_effect
Also have you ever considered creating a Twitter/Facebook (will help bring new people on board) and/or a separate blog (so you can post a variety of things as often as you want)? If combined with this blog I think your audience would increase quickly and more efficiently.
Thanks for the encouragement and link on disinhibition. I have had a relatively rapid education in the psychology of blog readers.
Huff Post invited me to blog. It already takes more time than I can really spare from keeping up with the new literature and preparing my next book. Managing Twitter and Facebook as well would be too much, I'm afraid.
You're beginning to get the point. Localized mutations result from the action of lesion bypass mutator polymerases. Duplications require coordinated biochemical activities of various sorts. These activities are all independent of natural selection. It is their phenotypic consequences that are subject to scrutiny by selection after the fact.
You point is silly, trivial. You have take the narrowist posible view of selection and twisted it to present the generation of variants as an alternative to natural selection. Variation is a central feature of the theory of evolution by natural selection. Darwin dedicated multiple chapters to it.
Without variants the is no such thing as evolution by natural selection. It is a theory ABOUT variation and it's consequences.
Unclear what the referant for "when" is. Please clarify.
What I am looking for from you is to stop claiming that natural selection plays some minimal role in evolution when it clearly does.
Do you claim that you can you get from two completely independent and non-interacting organisms to a single integrated organism without natural selection? Do you claim that you can get from dinosaurs to birds without natural selection?
I presume your answer has to be no, and that you are focusing on the specific singular events that happen and generate variation that natural selection can act on. Which is fine and good. But you aren't completely overturning and displacing natural selection in doing so. You're increasing the size of jumps that can happen in a single generation, but it is more a difference of magnitude over, not a difference of kind. No matter how you get variation, evolution cannot occur without natural selection.
For what it is worth there are other reputable scientists who are convinced that NS is not the dominant driver of evolution:
"The exclusive focus of Modern Synthesis on natural selection acting on random genetic variation has been replaced with a plurality of complementary, fundamental evolutionary processes and patterns (see Figure 13-1). In the new evolutionary biology, natural selection is but one of the processes that shape evolving genomes—and, apparently, not the quantitatively dominant one. To a large extent, neutral processes such as genetic drift and draft define evolution."
Koonin, Eugene V. (2011-06-23). The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press Science) (Kindle Locations 6475-6478). FT Press. Kindle Edition.
I think we agree.
I am arguing against using natural selection as a catch-all explanation for the complicated business of evolution. I have no interest in saying that selection does not occur.
We might differ as to the relative importance of selection, especially as a creative, formative influence in evolution, but there is no question that organisms compete for survival and reproduction and that success in that competition is critical to evolutionary outcomes.
I object to evolutionary biologists like Coyne and Dawkins invoking natural selection as a full and complete explanation of how evolution occurs. Coyne just repeated this in critiquing my last two blogs. It is important and worthwhile to examine just what the contribution of selection is. That makes it possible to think more clearly about other contributors to evolution, such as cell fusions and the way cells manipulate DNA.
Statements like "But nothing about their origins involves Natural Selection." are exactly the problem. Where you object to others casting natural selection as a full and complete explanation of evolution (though I don't believe they are even doing that), you instead take the exact opposite tack and reduce it to almost nothing.
Cell Mergers and the Evolution of New Life Forms: Symbiogenesis BY Natural Selection
The process of endosymbiosis is Natural Selection in action. From the first mutations that allowed the joining to occur where none had before to the numerous subsequent modifications and their decent.
I enjoy dialoguing with you. But I have to say, you are fixated on attributing functions to natural selection it does not have. That is common among people who study evolution because "natural selection" has provided them with a simple explanatory phrase when they confront a truly challenging evolutionary problem. You can rewrite this as much as you like. The real phenomenology will not change.