How has evolution successfully produced the diversity of organisms occupying virtually every ecological niche on the planet? This has been the central question in scientific evolution since thinkers in the late 18th century (including Erasmus Darwin, Charles' grandfather) introduced the idea that living organisms change over time. The big unknowns were how heredity worked, how change occurred, and how hereditary variation (called "descent with modification") transformed itself into useful biological diversity.
The Wallace-Darwin theory of "survival of the fittest" published in 1858 was the first plausible scheme for converting variation into adaptive differences. Although unable to say anything significant about the nature of hereditary transmission or variation, they proposed the following idea. Variants fittest (best able) to survive the Malthusian struggle for existence and reproduction in a world of limited resources would progressively become different and dominant. Eventually, differences would accumulate to the point that new species would form.
Darwin's 1859 Origin of Species had tremendous impact for two reasons. First, it made plausible the notion of change through differential reproduction available to the general reader. Finally, the public saw there was a scientific alternative to supernatural creation.
Second, Darwin providentially gave the name "Natural Selection" to the process ensuring "Preservation of Favoured Races in the Struggle for Life," as he subtitled his book. Proponents of evolution had a concise phrase to use when asked to explain how this new natural source of biological transformation actually worked. The satisfaction of having a short answer to a difficult question proved irresistible then, as it does today.
Did Wallace and Darwin hit the nail on the head and identify the crucial process of biological diversification? To most people, and especially to the evolutionist profession, the answer is so obviously "Yes" that even to pose the question subjects the person asking to abuse. My readers can see that from some of the comments on this blog.
Nonetheless, all questions are permissible in science. This one about evolution is particularly important. Either evolution is an exciting subject able to incorporate diverse approaches, or it is a closed subject basically solved 150 years ago, when we knew virtually nothing about heredity or hereditary variation.
Because of the public conflict between religious fundamentalism and scientific positivism (the notion that science has all the answers), public policy in science education has become linked to my question. If evolutionists are right that all basic questions have been resolved, then the atheist crusade of Dawkins and allies may have a rational basis. However, if the answer to my question is "No," then perhaps we can find a way out of this destructive dialogue of the deaf.
So, let us look more closely at the Darwinist position on evolution. Does selection for reproductive fitness lead to creative changes? Wallace once argued the reverse. He viewed selection as a stabilizing feedback mechanism, like a steam engine "governor," keeping organism features constant as long as the environment remained the same.
Darwin modeled natural selection on artificial selection by humans. He ignored the inconvenient fact that human selection for altered traits has never generated a truly new organismal feature (e.g., a limb or an organ) or formed a new species. Selection only modifies existing characters. When humans wish to create new species, they use other means.
In hailing natural selection as a blind creative force, Darwinists ignore the irony that Darwin's model of human selection is an intentional, goal-directed process with a desired outcome. It is precisely the opposite of a blind force.
Darwin was correct in believing that natural selection could only play a creative role if variation was continual and small. Based on the "Uniformitarian" idea that change had to occur in the small steps we observe under normal conditions, he originally insisted that evolutionary innovation had to be gradual. "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 out no such case" (Origin of Species, Chapter 6).
Unlike most followers, Darwin acknowledged later that significant, sudden changes could occur in a fundamentally different way. He wrote about "... variations which seem to us in our ignorance to arise spontaneously. It appears that I formerly underrated the frequency and value of these latter forms of variation, as leading to permanent modifications of structure independently of natural selection" (Origin of Species, 6th edition, Chapter XV, p. 395, emphasis added).
So a way to rephrase my question is to ask: Have we learned since 1859 about processes that can lead to organism change "independently of natural selection?" The answer is overwhelmingly positive.
Two fields principally illuminated the basic mechanisms of heredity and variation:
In combination, cytogenetics and molecular genetics have taught us about many processes that lead to biological novelties "independently of natural selection" -- hybridization, genome duplication, symbiogenesis, chromosome restructuring, horizontal DNA transfer, mobile genetic elements, epigenetic switches, and natural genetic engineering (the ability of all cells to cut, splice, copy, and modify their DNA in non-random ways). As previous blogs document and as future blogs will discuss, the genome sequence record tells us that these processes have accompanied rapid changes in all kinds of organisms. We know that many of them are activated by stress under extraordinary circumstances.
Fortunately for evolution science and science education, 20th century studies of inheritance at the cellular and molecular level have freed us from the intellectual straightjacket of gradual random change and natural selection. In the 21st century, we can think open-mindedly about the cellular and molecular processes that lead to biological diversity. Today, we can investigate how they work to achieve evolutionary success, particularly in crisis situations, when novelty is most necessary.
Steven Paul Leiva: Science Is Not a Frog: Don't Dissect It Before You Appreciate It
"How has evolution successfully produced the diversity of organisms occupying virtually every ecological niche on the planet? This has been the central question in scientific evolution since thinkers in the late 18th century (including Erasmus Darwin, Charles' grandfather) introduced the idea that living organisms change over time."
No, the question doesn't need and shouldn't include the word "successfully". By inserting that word you're asserting or at least implying that there's a lofty goal for evolution beyond survival and reproduction. Apparently you've forgotten about extinction and that most of the species that have ever lived are extinct.
Give me the full quotes, and I'll reply. Typos happen. Do you never make them?
You're right that Darwin accepted the inheritance of acquired characteristics.
Eva Jablonka is the big Lamarck proponent. If you're interested, her 2007 book with Marion Lamb, Evolution in Four Dimensions, would be of interest. You can also look up her papers.
Now that we know environmental stimuli can induce transgenerational epigenetic effects, there is a potential molecular connection between experience, the genome and selection. I expect a great deal will be made of that.
It becomes lying for g_d in defence of own faulty thinking. Critical thinking starts with own cultural "truths". The farther from reality a god belief are, the harder they have to defend it. Truth becomes relative and "lies" becomes truths. Poor souls.
Dawkins and Coyne believe that mutation is random.
Shapiro believes that mutation can be directed.
I would love to see a debate between them that concentrates specifically on this question.
You get the point. You might look at some of my earlier blogs on just this subject (http://www.huffingtonpost.com/james-a-shapiro/genetic-engineering-immune-system-evolution_b_1255771.html, http://www.huffingtonpost.com/james-a-shapiro/barbara-mcclintock_b_1223618.html?ref=science, http://www.huffingtonpost.com/james-a-shapiro/immune-cells-dna-engineering_b_1395040.html, http://www.huffingtonpost.com/james-a-shapiro/variation-and-selection-w_b_1522314.html, http://www.huffingtonpost.com/james-a-shapiro/natural-genetic-engineering-evolutionary-outcomes_b_1572730.html, http://www.huffingtonpost.com/james-a-shapiro/network-evolution-genetics_b_1594000.html). That should keep you busy for a little while.
http://richarddawkins.net/news_articles/2012/8/22/james-shapiro-goes-after-natural-selection-again-twice-on-huffpo#.UDZywtBYv5g
As soon as I started commenting at Shapiro's blog postings, I realized he was doing a grave disservice to his scientific colleagues and causing great harm towards public understanding of science. It's great to get additional confirmation of this from the likes of Coyne and Dawkins IMHO.
You're in hallowed company.
I have difficulty understanding where you are coming from. As parody of some of the more extreme comments, this is brilliant. But I wonder whether you are serious or not. Please clarify.
Sometimes I have difficulty understanding the subtle points some commentators are making. Such is the case here. The following is my understanding of what you are saying:
It is not legitimate to ask how evolution produced life as it now exists. The reason for this is that we have no record of the failed evolutionary novelties.
This has some interesting implications. Any scientist who tries to explain how a particular evolutionary novelty came to be cannot in principle come up with a valid answer, because the very question he is pursuing is invalid. In fact the entirety of VALID evolutionary science is contained in the statement "evolution produced life as we see it, but we have no idea how this happened".
http://richarddawkins.net/news_articles/2012/8/22/james-shapiro-goes-after-natural-selection-again-twice-on-huffpo#.UDZywtBYv5g
Dawkins Comment:
"Jerry has done a good job of demolishing this silly article. I would emphasise even more strongly the point about explaining the illusion of design. All the processes that Shapiro lists may or may not have an effect on evolution:-
"independently of natural selection" -- hybridization, genome duplication, symbiogenesis, chromosome restructuring, horizontal DNA transfer, mobile genetic elements, epigenetic switches, and natural genetic engineering (the ability of all cells to cut, splice, copy, and modify their DNA in non-random ways"
I don't think you've paid attention to my argument. It's not the testing role of selection that is at issue. It's the creative aspect of the evolutionary process that is in question.
You wrote: "And whats gradual or rapid got to do with anything?" The point is that natural selection can only play a guiding role for gradual changes. Even Richard Dawkins recognized that.
I suggest you read through the comments and responses to get a clearer idea of where the critical questions are. It's just not possible to have a two word answer to all the issues in evolution.
BTW evolution involves lots of organisms that are not animals. In fact, the not-animals are the vast majority.
I'm not familiar with everything that Dawkins has ever said or what he may recognize but the word "gradual" does not have to be construed as meaning slow. Changes, such as mutations, can be slow or fast (two more words with variable meanings) but they will be filtered by NS regardless of the speed in which they come about. Some changes will get through the NS filter and some will not.
I'm curious, what do you think of this statement?:
Evolutionary processes/events, including natural selection, have created the diversity of life.
Or this one:
Natural evolutionary processes/events, including natural selection, have created the diversity of life.
Or this one:
Evolutionary processes/events, including natural selection, have resulted in the diversity of life.
"I wouldn’t go after Shapiro except that... naive readers might get the impression that biologists are beginning to doubt that natural selection isn’t important. Well, as far as evolutionary biologists regard adaptations, it is: natural selection is the only game in town."
So Jerry agrees with what I said about professional evolutionists and their belief in the all-purpose explanatory powers of natural selection. I'll have more detail tomorrow.
Here are excerpts from the response I asked Jerry to post on his web site.
Jerry,
“Well, as far as evolutionary biologists regard adaptations, it is: natural selection is the only game in town.”
Thanks for making this so clear and easy for me. That is just what I claimed professional students of evolution believe, and you have confirmed it. With that kind of an attitude, it is hard to avoid turning natural selection into a Deus ex Machina that can explain everything (and, consequently, nothing). I personally would prefer to limit natural selection to testing the adaptive value of new characters. That is an important but not all-powerful role.
Unlike you, I do not claim to have an all-encompassing explanation or, as you put it in an earlier posting, “all the facts are on my side.” It’s not clear to me how you know what “all the facts” are since so much research remains to be done. Molecular genetics and genome sequencing have opened up a whole new world in evolution science that takes us way beyond the conventional wisdom you repeat. It shows us what a fascinating, complex and multidimensional process evolution is. Natural selection plays an important role, but we have to learn to put each component of biological change over evolutionary time into proper perspective. Making natural selection the be-all and end-all is not the way to do that.
I think you are fundamentally missing his point. He's not saying that he won't consider any evidence that contradicts saying "natural selection is the only game in town" he is saying that there is over whelming evidence FOR natural selection and none for the alternatives you mention.
http://richarddawkins.net/articles/646837-james-shapiro-goes-after-natural-selection-again-twice-on-huffpo
The link has gone dead for some reason. But not to worry, Jerry's fulminations can be found at http://whyevolutionistrue.wordpress.com/ below his comments on Fred Astaire. I'll have more to say tomorrow.
As a geneticist, I did not think of it as a disparagement. There is a considerable discussion of just this point farther down in the comments. Now that I am aware that professional students of evolution do not like to be called by the name of their subject, I will try to find other options that do not strike the same sensitive chord. Curious psychology, if you ask me.
when I first responded to your article, I challenged your use of loaded terms in part because your article was peppered with them: so many loaded words! It was only after reading your papers on your university website that I realized you appear to be an orthodox researcher who could take me to school on graduate-level biochemistry (makes me wish I lived in Chicago) and not an undercover ideologue (there are many here).
While you may agree with me (as a biochemist) that keeping terms precise is important, you may not have noticed that precision is not just based on dictionary definitions, but also on cultural understandings of words: your exposure to criticism on this post is probably heavily based on this. This is where these comments can be helpful: to expose you to definitions not found in a dictionary.
I ran into a similar problem as a child when I tried to use an innocuous word in English with native Spanish speakers--cynical. While the word has the same definition in both languages, Spanish speakers generally use "cynical" to describe folks who behave in disreputable ways as a result of adherence to this ideology while English speakers usually imply "distrust of selflessness" and not necessarily acting in disreputable ways. So calling someone cynical in English can be a compliment (you're a critical thinker) while in Spanish it can be an offense (you're a corrupt person), even if both dictionaries define it exactly the same.
I replied hours ago, but HuffPost seems to be jammed.
Since I have no problem being called a "geneticist" or a "microbiologist," I did not think "evolutionist" would be considered pejorative for students of evolution. As you can see from the comment trails below, I have learned to appreciate the special sensitivities these colleagues have. So I will try to use only other, more neutral terms.
Come now. You are disingenuous when you claim not use the word "evolutionist" pejoratively. Prefacing with a reference to the "public conflict between religious fundamentalism and scientific positivism", you state:
"If evolutionists are right that all basic questions have been resolved, then the atheist crusade of Dawkins and allies may have a rational basis."
Does being called a "geneticist" or a "microbiologist" mean that you believe that "all basic questions have been resolved"?
I don't know whether or not to thank you. On the one hand, you validate what I am saying about evolutionary processes. But on the other hand, you don't understand and disparage my argument.
What I am trying to say here is the we need to disentangle the various steps in the evolutionary process and ask where functional novelties originate. As long as one could assume that variation was a succession of small changes, there was an argument for natural selection playing that role. I don't agree with it, but I can see the logic behind it.
However, now that we know natural selection often confronts large genome changes and tests their adaptive merit, we have to ask where to locate the source of novelty in a successful innovation. I argue that it must be in the cell processes that produce the genome changes because their phenotypic consequences are presented to natural selection all at once.
Please let me know if this clarifies the argument, independently of whether you accept it or not.
You seem to be arguing that natural selection is not the source of diversity, but I took this already as a given. I thought natural selection was acting on the source of diversity and selecting for traits that survive - though really thats just a nice way of saying if an animal/plant has a mutation that stops it surviving then it tends not to.
'Mutation' is the engine going on here, but as you say we have discovered much diversity in this engine. Horizontal gene transfer, chromosome restructuring etc etc. This is all what natural selection acts on, but it isn't causing it. the causes are down to the chemistry and physics of the molecules themselves and what events occur during replication. Or at least that's what I remember from paleontology.
There is a response put here hours ago. I don't know what is holding HuffPost up. Please be patient, and you will get a full reply to your comment.
The changes which aid the organism in dealing with the environmental challenge spread through out the population of course with the aid of NS.
Note carefully the clear difference in the role of NS in these two cases: in the first NS is a key component. Without it the small individual beneficial mutations would never accumulate into a package and be spread through the population. In the second NS has no role except to purge the population of failed engineering experiments. The genomic changes generated by the experiments are themselves in no way influenced by NS.
I think your description is basically correct. I hope it helps people understand what I have been trying to explain.
The only thing I would add, is to point out that there are two competing explanations of how adaptive systems build up in genomes.
(1) In the conventional view, they arise gradually in a step-by-step process. As you point out, natural selection is an essential part of that gradualist process because each small step has to spread through the population before the next step has a reasonable probability of occurring.
(2) The alternative argument, based on DNA sequence evidence for rapid genome changes in evolution, is that adaptive DNA constructs are formed by the cell using and regulating its natural genetic engineering tools. That argument can be investigated experimentally because we do not have to wait eons for changes to accumulate. They can be detected and studied in real time.
Page 132: That is why the term engineering seems to be more appropriate for the built-in processes of self-modification that have operated over the course of evolution.
I do not believe we are in a position to say what does or does not happen. The relevant experiments have not been performed.
Cells can respond to all kinds of inputs and challenges in adaptive ways. Just read any modern cell biology textbook. So it does not seem implausible to me that life history inputs can also influence the kinds of genome changes that occur when stimulated by circumstance.
We know quite well that a wide of stimuli activate natural genetic engineering (http://shapiro.bsd.uchicago.edu/TableII.7.shtml). Do they also influence the nature of the changes that occur or bias them in a potentially productive direction? I have suggested how to look at this experimentally (http://www.huffingtonpost.com/james-a-shapiro/experimental-evolution-ho_b_1619171.html and http://www.huffingtonpost.com/james-a-shapiro/natural-genetic-engineering_b_1638823.html).
When we have done those experiments, and others that I have not thought of, then we will know what cells can and cannot do.
I notice that there is a lot of confusion with regard to how Prof. Shapiro understands the role of Natural selection in the evolutionary process. Here is my take based on reading his book and carefully following his blogs. I am sure he will correct me if I am misrepresenting his position.
If evolution is primarily driven by the accumulation of small beneficial mutations then NS is essential to make possible this accumulation and guarantee that the accumulated mutations spread through out the population. In this scenario NS acts as an ‘accumulator’ of small beneficial mutations, thus creating a package of mutations which is beneficial. In a very real sense NS creates this beneficial package from the raw materials of random beneficial mutations.
Based on large amounts of data gathered in recent decades it is Shapiro's assertion that evolution is driven by a very different mechanism: A process which he designates by 'natural genetic engineering' (NGE) results in a large genomic change in a single individual. NS has no role in the generation of this change. There is no accumulation of small mutations; the genomic change results entirely from the cell exercising its NGE tools. NS does come into play however. Some of these engineered changes may be failures – they do not aid the organism in overcoming the environmental challenges which triggered them in the first place. Such failures are ‘purged’ by NS.
I think we need to proceed step-by-step in learning what NGE can do. I posted two blogs on this (http://www.huffingtonpost.com/james-a-shapiro/experimental-evolution-ho_b_1619171.html and http://www.huffingtonpost.com/james-a-shapiro/natural-genetic-engineering_b_1638823.html). You can look at them to see how we might start this research. We have to learn to walk before we can learn to run.
On the other hand if the mutation activates external change then there doesn't need to be a pathway for external factors to affect our genes. In such a case our genes would therefore be possessed of a limited number of permutations built in to their mathematical foundations. They would only be possessed of a survivability cut off by the limited number of external factors that they are initially designed to activate. In this case, however, the question must be asked- what triggers this mutation? Certainly not external factors. Are our genes therefore full of ticking time bombs waiting to be set off in order to facilitate external changes? Who knows.
Not sure I follow your argument. However, we know that a wide variety of external stimuli activate DNA change operations. You can find a list and the pertinent references at http://shapiro.bsd.uchicago.edu/TableII.7.shtml.