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The Evolution Paradigm Shift
“Given the exemplary status of biological evolution, we can anticipate that a paradigm shift in our understanding of that subject will have repercussions far outside the life sciences. . . . How such an evolutionary paradigm shift will play out in the physical and social sciences remains to be seen. But it is possible to predict that the cognitive (psychological) and social sciences will have an increased influence on biology, especially when it comes to the acquisition and processing of information.”
–James A. Shapiro, Evolution: A View from the 21st Century
I called University of Chicago microbiologist James Shapiro, who’s now also blogging on HuffPost about science, to arrange an interview after noticing that we’d both recently been bashed by Darwinist Jerry Coyne in the same column. I reached Shapiro at home. He was engaging, although he described himself as a “reclusive person” — which he says he finds key to serious thinking. The commotion was over Shapiro’s book: Evolution: A View from the 21st Century since Coyne, also a University of Chicago professor, has an evolution text he’d like to keep relevant. I decided to have a look at Shapiro’s book and see exactly why Coyne was agitated.
Shapiro was traveling soon, so I scrambled to pick up a copy of the book. Curiously, none of the Manhattan book stores had one and neither did the libraries. Columbia University’s only two reference copies were out being read. But the New York Institute of Technology, situated in the middle of a forest on Long Island, did have one and provided the perfect canopy to immerse myself in Shapiro’s world of cognitive cells.
Shapiro says the key science journals have yet to review the book, including Nature and Science, but it’s being discussed continually on HuffPost where Shapiro has encouraged a rigorous debate on topics like “Jerry Coyne Fails to Understand Yet Again” and “What Is the Best Way to Deal with Supernaturalists in Science and Evolution?”.
Further ruffling the Darwinists, Shapiro has not been timid about engaging the Intelligent Designers on their turf at the Discovery Institute. And he graciously takes on some of the blogosphere’s notorious “Wild West” commentators as well, who frequently mistake him for an anti-evolutionist.
The University of Chicago Laboratory Schools was where James Shapiro began his scientific investigation — the same grade school that inspired symbiogeneticist Lynn Margulis. His BA is from Harvard, magna cum laude, in English Literature, which gives him a certain edge on the Internet. Shapiro’s PhD is from Corpus Christi College, Cambridge, in Genetics, where he was a Marshall Scholar. He did postdoctoral work at both the Institut Pasteur in Paris and at Harvard Medical School.
Curious about alternative forms of government, he moved to Cuba in the early 1970s where he taught Genetics at the University of Havana after leaving the research lab at Harvard Medical School concerned about the potential misuse of his work on the genetic engineering of E. coli. He returned to the US for another postdoc at Brandeis two years later. In 1973, Shapiro joined the faculty at the University of Chicago where he currently teaches in the Department of Biochemistry and Molecular Biology.
James Shapiro has served on the editorial board of a half dozen science journals, including the Journal of Bacteriology and Enzyme and Microbial Technology. He is a Fellow of the American Association for the Advancement of Science as well as the American Academy of Microbiology and a member of numerous other professional organizations, among them, the American Society for Microbiology and American Society for Biochemistry and Molecular Biology. In 2001, he was made an Honorary Officer of the Order of the British Empire for his service to the Marshall Scholarship program — having served many years as its Chicago regional chairman — which enables American students to study at some of the finest schools in the UK.
Shapiro has also been honored with a Darwin Prize Visiting Professorship at the University of Edinburgh, was a Visiting Professor at Tel Aviv University as well as a Visiting Fellow at Churchill College, Cambridge, among other distinctions.
His books include: Evolution: A View from the 21st Century (FT Press), Mobile Genetics Elements (Academic Press), and with Martin Dworkin (eds.) Bacteria as Multicellular Organisms (Oxford University Press).
James Shapiro was first to propose a detailed mechanism for replicative transposition as a means of DNA mobility in genomes. His research also encompassed pattern formation in bacterial colonies. In 1984, observing that bacterial colonies resembled flowers in organization, not unlike the patterns Nobel laureate Barbara McClintock saw in maize kernals, Shapiro later concluded that “bacterial colonies could also be viewed as multicellular organisms.”
My interview with James Shapiro follows:
Suzan Mazur: What first sparked your interest in evolutionary science — you have an undergraduate degree in English Literature from Harvard and a PhD in Genetics from Cambridge.
James Shapiro: I became interested in biology as an undergraduate. The topic of evolution just kept coming up. As a research student at Cambridge, when I began to focus on mutagenesis, evolution was again right there because mutation was the source of the raw material of evolution. My first big lesson in evolutionary science was that the mutations I was studying in bacteria were unexpected and unpredicted. People had actually missed them because they accepted the current version of mutations just as point mutations. Here was something quite different. Pieces of DNA inserting themselves in the genome .
Later, I found unexpectedly that starvation triggers a big increase in DNA rearrangements. I also observed some genome changes occurring in patterns in bacterial colonies. All of that gave me a lively interest in evolutionary subjects.
Suzan Mazur: Do you come from a science family?
James Shapiro: No, not at all. My father was a businessman and my mother a homemaker. I was interested in lots of things growing up. I had a great science teacher in grade school — a fairly well known woman named Bertha Morris Parker at the University of Chicago Laboratory Schools I attended — who I’m sure must have had some influence on me.
Suzan Mazur: But were you always interested in nature?
James Shapiro: No I think I was interested in figuring out things, making sense of things. I didn’t collect insects and stuff like that.
Suzan Mazur: What took you to Cuba in the early 1970s where you taught for a couple of years? And what did you teach?
James Shapiro: I taught genetics. What took me there was the fact that everybody was talking about alternative forms of government, about revolution, about social change, and so forth. And here was a chance to see it up close.
Suzan Mazur: What was the conclusion that you drew from seeing it up close? Did you have a favorable experience?
James Shapiro: Well the experience had its ups and it had its downs. I don’t want to go into too many details, but I would say the take-home lesson was that human nature trumps everything. Any system has its strong points and its weak points.
Let me explain what I mean about human nature. At a benefit we were introducing the new director of an opera company where I’m on the board. He was asked to explain the season that he was planning. And he said: “Well, it’s about power and love and love of power.”
You can see those motivations in every society.
When the society works well, as ours has, you’re fortunate. We’re going through a period where we’re not so fortunate because political dialogue has broken down, much like the dialogue about evolution and science education.
Autocratic regimes sometimes can be positive. I was talking to a woman about Rwanda where Kagame is not a democrat but at least he’s trying to advance the nation. So the Rwandans are a lot luckier than the Congolese, for example.
So the human factor dominating every political system was the take-home lesson.
Suzan Mazur: You’ve now got a pretty lively blog on Huffington Post – how does this square with your description of yourself as “reclusive”?
James Shapiro: I think I am a fairly reclusive person. I think that’s necessary to do serious thinking.
Suzan Mazur: But how does that square with your lively blog on HuffPost?
James Shapiro: The blog has to do with trying to advocate a certain way of thinking about evolution and life in general. This was an opportunity presented to me by Huffington Post. They asked me if I’d like to blog. They get people to blog for free and that gives them content. And it gives those of us who have something to say the position to argue, a platform. Having published the book, I felt it was worth taking the argument forward. Also, I’m using it as a kind of test bed for learning how to write for a more general audience.
Suzan Mazur: You’re reaching out in substantive ways and getting some quality responses. Not as much of the usual rabble.
James Shapiro: Well, you do get abuse and obsession in the blog comments. On Friday, I put a note up saying that the blog was getting rather ad hominem and away from the substance. Since then the messiness hasn’t completely stopped but the comments have been somewhat more substantive. It’s the Wild West in the blogosphere.
Suzan Mazur: Statements have been attributed to you regarding a crisis in evolutionary science, and you expressed that in your 1997 Boston Review article on a “Third Way.”
Are you saying that for at least a half century or so vast billions of dollars of public money has gone to scientists whose work has been rooted in a belief system – i.e., the metaphor of natural selection, as Richard Lewontin described it in the pages of the New York Review of Books?
James Shapiro: I would say research based on theories that will be superceded is inevitable. I was quite struck when I read Thomas Kuhn who understood that. I was sitting by a swimming pool in the Dominican Republic at a meeting on plasmids and he was writing about 18th century chemistry and physics. As I was reading I was saying to myself — “Wow, that’s the way biology operates today.”
Kuhn captured something very quintessentially human about the scientific enterprise: that you inevitably never capture nature as it is. You only capture a portion of it that you can figure out and theorize about. And you go on exploring that portion of nature. For some period of time the explorations are extremely productive. But over time and as technology develops, partly as a consequence of what the scientific enterprise is doing, new phenomena come up and can’t be explained any longer in the same way. In the end there are always a group of people who defend the existing belief system more than is justified by the empirical observations.
Tension arises between those who say the empirical observations are telling us something different and those who defend the intellectual framework which led to those empirical observations. I am not immune to being unable to appreciate where new approaches can lead. For example, I was one of the people who initially thought genome sequencing was just an excuse for using technology without any idea of what we were going to find. I believed that people had run out of useful ideas for experimental biology and were doing DNA sequencing as a substitute. I was totally wrong about that. It turned out that sequencing has been extraordinarily revealing and far from a waste of time. No matter what kind of ideas lay behind it, it’s opened up a treasure trove of new ways of thinking about genomes and DNA in evolution.
So the answer to your question about the money is that money is always being spent based on ideas which are ultimately going to prove fallible. As I put it in a blog, if Newton couldn’t get it right, what hope is there for the rest of us? But it’s not a waste of time and money as long as the research is based on real empirical science, because the observations then lead to a more sophisticated way of thinking about things.
Suzan Mazur: With so much money being blown on war and other shenanigans and with Paul Krugman today on PBS confirming that we are now in a DEPRESSION — are you really saying that public money should continue to go to scientists, America’s most successful intellectuals in securing public funds, who agree to work to ensure the country’s health, national security and economic stability, even if they’re publicly defending a Darwinian system they won’t privately defend to other scientists? How much of the scientific establishment is doing this, by the way?
James Shapiro: I couldn’t answer that question because I only know the part of the scientific establishment — and not that much of it — that I’ve been exposed to in the course of my professional life. And the last 10 to 15 years have been fairly reclusive. I faced a major decision in 1984. I could spend all my time on the road or I could stay home and get some work done. I decided it was better to stay home than to spend my time on the road. It wasn’t necessarily the best decision professionally but it was a decision that suited me at the time.
The way I look at it, most of my colleagues exhibit a schizophrenic attitude towards new ways of thinking. Somebody will be doing research on a subject like the role of reversed transcribed DNA inserted into the genome and creation of new genetic loci. The shorthand for this is neogene formation. And that’s a totally non-Darwinian process. Certainly nothing that any of the Darwinians could ever have conceived or predicted.
The experimentalists do the research and they talk about it in appropriate new ways. In practical terms they are talking in a totally different way about how genetic change happens than fits the conventional wisdom.
However, if you say to them you’re doing non-Darwinian science, they say, “No, what are you talking about? We’re doing Darwinian science.” Because, in their minds, “Darwinian science” is synonymous with non-supernatural scientific exploration of evolution and genome change in biology.
I don’t think there’s a conscious deception going on. I describe it as a kind of schizophrenia.
Suzan Mazur: You’re saying there’s not a conscious deception going on. That’s interesting.
James Shapiro: Let me just add to that.
Naturally there are very few people who will come out as I have and say: Look the emperor has no clothes. People are not willing to do that. They probably are very wise not to. But somebody has to say it. I’m in a position to do that and so I say it.
Suzan Mazur: But if a collapse in this philosophical belief system has occurred — as you’ve said: “the DNA record definitely does not support the slow accumulation of random gradual changes transmitted by restricted patterns of vertical descent” –
James Shapiro: Yes, that’s a statement of empirical observation.
Suzan Mazur: So is science now without an acceptable explanation as to how evolution happened?
James Shapiro: No I don’t think so. We see bits and pieces of the whole process. Certainly we have paleontological evidence. We have the comparative biology. It started off as comparative anatomy but it’s gone much farther than that, of course. All of this tells us about relationships. And now we have the genome evidence, which solidifies our view in the evolutionary relationships. It complicates the picture, but it adds an element — which is the one I’ve been focusing on — the process of genome change itself that is critical. That is what I call “natural genetic engineering.”
Suzan Mazur: In pinpointing some of the most obnoxious behavior in defense of Darwinian scenarios, I am reminded of the keynote speaker of the Rockefeller University Evolution symposium — University of Chicago biologist Jerry Coyne — who stood before an audience of distinguished scientists in the spring of 2008 to do damage control, first trashing Creationism and then declaring that he could cite 300 examples of natural selection but didn’t have enough time to do so. The speech was arranged by the National Center for Science Education — an appendage of the American Association for the Advancement of Science. I understand the AAAS has since asked for assistance steering it to scientists who are thinking about self-organization.
Are Coyne and his pal Richard Dawkins, by not publicly recognizing that a sea change has occurred, milking lucrative performances and book deals? And if so, isn’t this a disservice to science?
James Shapiro: Well that’s a loaded question.
I’ve gone on record in my blog as saying that I thought that Dawkins and his ill-conceived atheist crusade hurts science education and hurts evolutionary science. I’ve criticized Jerry Coyne for making statements that he can’t support. Both Coyne and Dawkins have been characterized as having a neo-atheist agenda in attacking religion. And it is true that many of the comments on my blog reflect a deep reservoir of anti-religious sentiment. I’ve noted in the blog that we should get out of the business of attacking supernaturalists. It’s not in science’s interest to make a war with religion or religious belief.
Suzan Mazur: And get on to the science.
James Shapiro: And get on with the science. And also to have a little bit of humility. Science never provides ultimate answers.
Both Coyne and Dawkins are doing well for themselves by being vitriolic and vehement in their campaign against religious belief and against some of the more foolish things that religious fundamentalists do. But I suspect ego gratification is the major driver more than financial gain. Obviously it’s nice if you make money at the same time.
Suzan Mazur: Bullying, which is a national issue, and misogyny, which is another national issue, continue to be rampant in evolution politics. Do you think such behavior should be reined in, that abusive scientists should answer to university misconduct panels more frequently and denied government grants rather than being allowed to hide behind tenure and the skirts of university lawyers and presses that publish their drivel without bothering any longer to check the books they sell to the public?
I am reminded of the tactics of Massimo Pigliucci, who is now entrusted with the molding of young minds at a college in the Bronx after giving up his work in the evolution lab. Pigliucci continues to pass himself off as a reformer by way of the “extended synthesis” two-day symposium he co-organized at Altenberg several years ago, while attacking as “midguided” those who really are reformers.
As recently as a few months ago, Pigliucci was still presenting natural selection front and center in his slide shows, according to Brian Enquist, who hosted Pigliucci’s talk at the University of Arizona.
Would you comment on the bullying and misogyny that go on in science?
James Shapiro: Bullying and misogyny and abuse are all deplorable, and we should do everything to eliminate them.
I’m very concerned, however, about academic freedom and worry about academics becoming untenured employees who then don’t have the same freedom to express themselves as they do now. Recognizing that all of these academic rights and prerogatives can be abused, we still have to think long and hard before we do something to put administrators and bureaucrats in judgment on academics. Inevitably, administrative controls on expression will not be used for good purposes.
Suzan Mazur: But should bullies be allowed carte blanche to mold the young minds of college students? Again, bullying is a national issue and who knows where the matter will go in terms of legislation. People are dying from bullying in this country.
Years ago we did not have proper laws on the books regarding domestic violence. In 1985, I chaired the first major benefit in New York for battered women and battered women’s shelters. I was told it hadn’t been done, that I’d need the nod from the women in Westchester. The Cuomos got behind the event along with the National and New York State Coalitions Against Domestic Violence, the Jewish philanthropies, Manhattan’s political movers and shakers — from Liz Holtzman, Bella Abzug and Gloria Steinem to Phil Donahue, Marlo Thomas and Alvin Poussaint (Harvard Medical School). In 1987, the Domestic Violence Prevention Act passed in New York, and in 1994, we saw national legislation. I have confidence that America will similarly get a handle on the bullying epidemic.
James Shapiro: I’m really interested in getting politics out of science and focusing on the scientific issues.
Suzan Mazur: At the moment, politics is a large part of evolutionary science.
James Shapiro: I would like to see, as much as possible, an emphasis on rigorous scientific debate. We should not let all these philosophical or political issues — who controls the funds, etc. — dominate. It’s counterproductive. There are real serious open evolutionary scientific issues to discuss and there are real serious alternative ways of looking at them. It’s extremely important that science move forward in new and unexpected directions.
Suzan Mazur: Your book was published by FT Press, Pearson, parent of the FT and The Economist. I find this fascinating for a couple of reasons. First the Brits are standing behind an American scientist who is challenging Darwinian science, one of their national treasures. Also, having significantly contributed through the years to both Pearson publications, I pitched a paradigm shift story to them in 2008, which was rejected. A half dozen emails from The Economist’s science and technology editor are included in my evolution expose book, The Altenberg 16. I’m glad to see Pearson now gets it. How did you persuade them that a book on evolution paradigm shift needed to be written?
James Shapiro: I didn’t persuade them. It turns out that a man named Kirk Jensen, who edited the book that Martin Dworkin and I did on bacterial multicellularity in the late 1990s at Oxford University Press was helping FTPress launch their science book series. And Kirk knew from his work at OUP and before that at the American Society for Microbiology about mobile genetic elements and how important these things were. Mine was only one of three books. The other two by Haig Kazazian and Eugene Koonin summarized a lot of the recent molecular genetics evidence.
The production of the book was fine. The book cover is striking. I found that picture of the mimetic moth. FTPress wanted to put an iguana on the cover. I said an iguana was too traditional. Theirs was a beautiful iguana, but it was still an iguana. And I thought the moth would say a lot more than the iguana about some of the mysteries that need
to be explained in evolution.
The moth cover was ultimately chosen because the kind of exquisite mimicry it represents is an evolutionary puzzle.
How does that come about? I think gradualist explanations are difficult to sustain in the case of mimicry. Recently it’s been discovered that there are master control regions, sort of like Hox complexes but more complicated, that control wing patterns in butterflies. I suspect as people analyze those we’ll know more about how the mimetic patterns evolved.
The book hasn’t been reviewed by any of the major journals yet. Nature and Science have not reviewed it. The National Center for Science Education is reviewing it in June. I’m interested to see whether they want to show that evolution science is alive and doing novel and controversial things.
As I said in my blog, science is not doing very well in this evolution vs. religion dispute. I think part of the reason why we’re doing poorly is that the most recent and exciting science is not being presented to the public. Clearly, the issues are not being presented in a way that shows evolution science isn’t stuck in ideas from the last century and the last century before that.
Suzan Mazur: I went through the book over the weekend. It’s very thoughtful the way you’ve put it together. Would you describe your theory, which involves cells speaking to one another — cognitively, informationally. You say in reality the “gene” is “not a definite entity” — it’s “hypothetical in nature.”
James Shapiro: There are three components there.
(1) As I say in the book, cells do not act blindly. We know from physiology and biochemistry and molecular biology that cells are full of receptors. They monitor what goes on outside. They monitor what goes on inside. And they’re continually taking in that information and using it to adjust their actions, their biochemistry, their
metabolism, the cell cycle, etc. so that things come out right. That’s why I use the word cognitive to apply to cells, meaning they do things based on knowledge of what’s happening around them and inside of them. Without that knowledge and the systems to use that knowledge they couldn’t proliferate and survive as efficiently as they do.
(2) We’ve learned a great deal about hereditary variation through molecular genetics studies. I was personally involved in this back in the late 60s and 70s and since then we’ve learned about a wide variety of biochemical systems that cells use to restructure their genomes as an active process. Genome change is not the result of accidents. If you have accidents and they’re not fixed, the cells die. It’s in the course of fixing damage or responding to damage or responding to other inputs — in the case I studied, it was starvation — that cells turn on the systems they have for restructuring their genomes. So what we have is something different from accidents and mistakes as a source of genetic change. We have what I call “natural genetic engineering.” Cells are acting on their own genomes in a large variety of well-defined non-random ways to bring about change.
This is consistent with what Barbara McClintock first discovered in the 30s when she was studying chromosome repair and then later in the 40s when her experiments uncovered transposable elements. All of these natural genetic engineering systems are regulated or sensitive to biological inputs. That sensitivity is what we’ve learned about cell regulation in general. As I say, cells don’t act blindly, and they don’t act blindly when they change their genomes.
(3) So if genetic change is not a series of accidents and not a series of necessarily small changes, then how does it work out in evolution? That’s where the DNA record from genome sequencing comes in and confirms what many of us had argued for a long time: namely, all of these systems of genetic change, of natural genetic engineering, have played a major role in evolutionary change. We have a new view of how cells operate in evolution, which is much more information technology friendly.
I think the first blog I put out was quoting a December 2011 paper where they went through the human genome using the 29 mammalian genomes that had recently been aligned. The authors concluded that, at a minimum, there were 280,000 different components, defined functional elements in the genome, that came from mobile genetic elements.
The point is that natural genetic engineering systems have played major roles in evolutionary change. We also see in the DNA record that evolutionary change has not just been a slow accumulation of random changes.
A good way of summarizing this is to compare the genome to storage systems in computers. The conventional view is that the genome is a read-only memory (ROM) system that changes only by copying errors. Incorporating what we have learned at the biochemical level about the cellular and molecular processes of DNA change, we can formulate a fundamentally different view. The contemporary idea is that the genome is a read-write (RW) storage system that changes by direct cell activity. How cell control circuits guide that change activity is the scientific issue of the moment.
Suzan Mazur: So what the gene is, how it first appeared and when are an old way of thinking about things.
James Shapiro: The gene first appeared at the beginning of the 20th century with the rediscovery of Mendelism. Gregor Mendel called them factors, which is fine because it’s nondescript. Then Wilhelm Johannsen came up with the term “gene.” And over time the gene became endowed with a whole bunch of properties. There’s a 1948 Scientific American article by George Beadle in which he called the gene the basic unit of life.
Suzan Mazur: I mean in evolutionary time. This thinking that the gene arrived at some point in the emergence of life. It seems to be an old way of thinking now because the definition of the gene has become much more ambiguous.
James Shapiro: When three scientists rediscovered Mendelism at the turn of the century, in 1900, breeders started seeing discrete hereditary differences that could be passed on from generation to generation. And so the idea that you could have a particulate or atomistic view of the genotype built up, and then the individual components were called genes.
We now have a more sophisticated understanding of hereditary. You’ve got an integrated, super-sophisticated storage system called the genome. You can’t just try and reduce it to any one of its components.
I don’t use the word “gene” because it’s misleading. There was a time when we were studying the rules of Mendelian heredity when it could be useful, but that time was almost a hundred years ago now.
The way I like to think of cells and genomes is that there are no “units.” There are just systems all the way down. This idea came to me unexpectedly in conversation during a visit to give a lecture at Michigan State. A colleague said that his goal was to discover the basic units in the genome. Without thinking about it consciously, I responded, “What if there are no units?” At that moment, I realized that this answer was something I had been thinking about for a long time.
There have been lots of surprises and lots of discoveries along the way to a systems view of the genome: coding sequences being broken up into exons and introns, non-coding sequences which serve as signals for expression of coding sequences, different ways of reading the coding sequences, and so forth. When you have all of that complexity in genome expression, you no longer can give any kind of simple unitary definition of what you mean by a particular piece of the genome.
With George Beadle and Edward Tatum in the 1940s, you had the one gene-one enzyme hypothesis. It was thought that we could say definitively that the business of “genes” is to determine the structure of proteins. But now we have all of this so-called ”noncoding” information in the genome. In our own human genomes, “non-coding” sequences greatly exceeds the the protein coding capacity. A lot of that “non-coding” DNA is clearly functional and very important for genome action. So we’re beginning to develop a far more sophisticated idea of what a genome is and how it operates. That’s all a part of bringing evolutionary science into the 21st century.
Suzan Mazur: But how far back in time would you say were cells talking to one another without genetic systems, i.e., programs?
James Shapiro: I think I make it explicit in the book that we don’t have enough knowledge yet of how cells came into being in the first place.
Suzan Mazur: When do you anticipate that might become more clear?
James Shapiro: We need to understand how the cells that exist today operate. That’s going to require another shift in our thinking because we have a very mechanical, again a very atomistic view of that.
We don’t yet understand how cells and organisms are integrated functionally and informationally. When we understand that integration, then we’ll have a better idea than we do right now of what the basic requirements are for life and for reproduction.
I expect there will also be technological changes in paleochemistry aiding the search for traces of early life. We don’t have this right now. It’s possible we may never have it. On the other hand, science always amazes us with what it’s able to find. I don’t want to be in a position to say we can’t work something out scientifically because very often we do succeed in unexpected ways.
Suzan Mazur: When did multicelluarity first happen?
James Shapiro: At the first cell division. Life for as long as we know it has been multicellular. The single celled organism is — not exclusively, but by and large — a synthetic construct devised partly to analyze how cells operate and partly as a consequence of Koch’s postulates and the germ theory of disease. In studying bacterial pathogenesis, the emphasis was on isolating a pure culture from a single cell. But in nature very few cells exist isolated from other cells.
Suzan Mazur: When do you think evolution began? How do you think about it?
James Shapiro: This is part of what I think is a new understanding of what it takes to be alive. I would include the ability to change as a fundamental feature of living organisms, as a basic vital function.
Suzan Mazur: Are we including pre-biotic evolution?
James Shapiro: There are people who want to speculate about pre-biotic evolution. I don’t think we can talk about it in a serious scientific way.
Suzan Mazur: Interesting.
James Shapiro: I think we need to come to terms with the biology that exists in front of us before we’re able to speculate about what might have preceded it. And I think we’re very far from being finished with that enterprise.
Suzan Mazur: So you must have some interesting things to say about astrobiology.
James Shapiro: I don’t have anything interesting to say about astrobiology.
Suzan Mazur: Freeman Dyson wrote a piece for the NYRB recently in which he said that credentialled string cosmologists and amateurs are essentially on equal footing because they’re both dealing with the abstract. Is that also the state of affairs in evolutionary science today — particularly theories regarding origin of life? By the way, the man who many consider the father of string theory told me a year or so ago that everything he knows about evolutionary science he learned in Dawkin’s book The Selfish Gene.
James Shapiro: Heaven help him.
Suzan Mazur: Should amateurs who are seriously challenging Darwinian scenarios be welcome to the evolutionary science discourse rather than bludgeoned?
James Shapiro: Well I don’t see how you can exclude anybody. The point is not who’s saying something or what their credentials are but the value and substance of what they’re saying. Having started off my career as an amateur with a degree in English rather than in biology, I think sometimes that’s an advantage because you are without prejudices. You’re freer to understand and interpret data.
I wasn’t the first person to see mutations caused by transposable elements in bacteria but for some reason I was the first one to be able to free myself of thinking that there had to be point mutations, base substitutions or frame shifts, which was the reigning theory of mutation at the time.
There’s even a paper by Crick and Brenner and colleagues called “The Theory of Mutagenesis” that was published shortly before my own work which said that base changes and frameshifts were the substance of genetic change.
I was able to say, maybe my mutations are additions of DNA, and it turned out to be correct. That’s how we started to study transposable elements in bacteria. People working on antibiotic resistance soon found that antibiotic resistances hopped around. So yes, people can come in from all kinds of backgrounds. It’s the substance of what they’re observing and saying that matters.
Suzan Mazur: Would you wrap up your view of 21st Century evolution and where we’re headed?
James Shapiro: We have the three components, which are:
(1) Cells act in what I call a cognitive way or an information processing way. Some people like to say “computational.” The only reason that I don’t use the word computational is that it doesn’t include the sensory aspect of how cells operate. And the sensing and it’s molecular bases are all very firmly established scientifically. There’s no question about it.
What we don’t understand is how everything is integrated, how the information is processed and how the cells end up doing the appropriate thing. We know a lot about the components involved in signal transfer and decision-making, but we don’t know how the whole system works. That I think is the key frontier in the 21st century. The research will not only impact biology, but it will possibly revolutionize computation as well.
(2) Cells engineer their own genomes and they do it in a wide variety of ways that are subject to sensory inputs and which can be targeted within the genome. I document that pretty extensively in the book.
(3) We know from the DNA record that natural genetic engineering systems have been important in the evolution of new life forms.
The key questions that I see in evolution science besides learning more about those three components are:
(i) What is the link between ecological change and genome change in organisms?
(ii) What is it about the natural genetic engineering processes and how they are regulated and controlled that biases them towards creating new functionalities?
We know we can stimulate rapid genome change in the laboratory by starving cells, or putting them under pressure or in high salt and other stress conditions. Similarly, by manipulating their genomes the way McClintock did so they don’t operate normally. Or by hybridizing, as in horticulture, having different species mate or different populations mate. All of those things will trigger very significant episodes of genome restructuring. And we know genome restructuring has played a role in evolution and evolution is marked by the appearance of biological functional innovations.
Suzan Mazur: But do you think scientists are now moving onto the same page around the world regarding evolution or do you think European science is heading in a different direction than American science, for example?
James Shapiro: European science — and this was one of the virtues of doing a PhD in England and a postdoc in France — European scientists have always taken a more intellectual view of what they do. American science is very operational and highly technological and much less conceptual than science in Europe. I think sometimes there is more openness and sometimes more hostility towards new ideas in the States.
Suzan Mazur: But ultimately do you think there will be a coming together and that the public will be served by these different approaches.
James Shapiro: I think we have to realize that there are a whole range of new players coming into the science game.
Suzan Mazur: Right.
James Shapiro: The Japanese have always been very important. It was the Japanese who first figured out transmissible antibiotic resistance, which solved one of the big evolutionary events that we’ve observed happening in real time, which is the emergence of multiple anitbiotic resistance in bacteria.
Suzan Mazur: And then the Chinese coming in. Important research centers in the Middle East.
James Shapiro: The Singaporese, Russians and Indians. All of that’s going to be good — scientists coming from different cultural and philosophical traditions who are not bound by the history of European or American science.
Suzan Mazur: So an Anglo-American approach to evolutionary science is no longer enough, it’s got to be more inclusive.
James Shapiro: That’s always been the history of science.
Suzan Mazur: Hasn’t it been pretty much Anglophile?
James Shapiro: There’s a large period when the French dominated science. And the Germans and German-speaking dominated. Johannes Kepler was a German. Carl Linnaeus was a Swede. Nicolaus Copernicus a Pole. Pre-Rennaissance science was largely carried out by Chinese and Arab researchers.
Suzan Mazur: But it’s Darwinian evolutionary science that’s taken root. And that’s Anglophile.
James Shapiro: Yes, there is an aspect of nationalism there that’s gotten bound up in the Darwin – Lamarck rivalry. Whether that’s positive or negative I don’t really know.
I think we’re headed to a more diverse scientific culture because people from these countries have their own traditions. The Chinese think differently about things than we do. They like to make lists, for example.
Suzan Mazur: So it’s going to be a while before there’s a real coherence to evolutionary science.
James Shapiro: Well I suppose. People are always going to try to unify, and other people are going to be diversifying. The unifications are always going to involve trying to impose artificial constraints on natural phenomena, and I think they’re doomed to failure.
We have this terrible dilemma in science. We need to be reductionists to get meaningful results and make observations. But when we take the observations and try to understand what they mean, then we have to stop being reductionists and become integrationists to understand how the things we’ve identified and singled out fit into the whole picture.
We’ve lost sight of that need for integration with the successes of molecular biology. But I think we’re getting back to an integrationist view now because people are studying complex problems like cell biology and multicellular development using molecular tools. It’s becoming clear that there’s an interaction between the parts and the whole which is far more complex and multidirectional than people used to think.
I think that that shift from reductionism to integrationism actually needs to happen in the physical sciences as well. They still hang on very much to the idea that you can have “a theory of everything.” I’m rather dubious about that.
Again, my experience in science has taught me that you should never say that something can’t happen because we’re continually discovering things we’ve been told can’t happen. It’s just been a few years since we’ve realized cells can pick up fragments of sequence from invading DNA. Whether they do it at the DNA level or the RNA level is not entirely clear yet. But they can pick up fragments of a sequence from invaders, incorporate them into their genomes and then defend themselves. We were told that was impossible based on the Luria-Delbrueck experiment.
Being more inclusive and more open to new ideas and imaginative approaches will serve us best. It should be difficult for new ideas to become accepted because that’s how you really test their worth, their value. But it does not make any sense from a truly scientific point of view to exclude things a priori.
Suzan Mazur: People should be encouraged to put their theories out there.
James Shapiro: Yes. It’s an Anglo-Saxon idea, the marketplace of ideas. People who try to erect artificial barriers are making a big mistake.
Suzan Mazur is the author of The Altenberg 16: An Expose’ of the Evolution Industry. Her reports have appeared in the Financial Times, The Economist, Forbes, Newsday, Philadelphia Inquirer, Archaeology, Connoisseur, Omni and others, as well as on PBS, CBC and MBC. She has been a guest on McLaughlin, Charlie Rose and various Fox Television News programs. She can be reached at: firstname.lastname@example.org