Valuing Nature

Carl Zimmer has written an excellent piece in the New York Times about a very important study by Robert Costanza et al. on “Changes in the global value of ecosystem services” – in other words, how to place economic value on some of the critical functions that nature provides us for free, and how to quantify the economic fallout when these functions are degraded.

Of course, it’s difficult to put a dollar value on the esthetic aspects of natural ecosystems. And many people see it is a moral imperative to preserve these natural systems for future generations, regardless of their monetary worth.

The Costanza study, though, is based on the fact that natural ecosystems provide us with economic benefits by performing important services that, when diminished, have very real monetary costs in terms of the resulting damages and replacing the services with human-engineered solutions. Alas, many of these ecosystems and services are being rapidly and severely degraded.

Here are three of the several conclusions from Costanza et al., which I’ve taken verbatim from the highlights at the beginning of their article:

  • “Global loss of ecosystem services due to land use change is $US 4.3–20.2 trillion/yr.”
  • “Ecoservices contribute more than twice as much to human well-being as global GDP.”
  • “Ecosystem services are best considered public goods requiring new institutions.”

That last conclusion reminds me of a similar point that was made by the theologian Philip Hefner in his book The Human Factor: Evolution, Culture and Religion.  Hefner says “… in the situation to which biocultural evolution has brought us … the life not only of the human species, but of the entire planetary ecosystem is made to depend on a great wager going well. This wager is that the cultural systems of information that the co-creator [REL: that’s us humans] fashions will interface with the natural systems and with the global human culture so as to promote survival and a wholesome future.”  Hefner then says “… the wager is not going well. The cultural systems of information are not meshing adequately enough with other systems, and calamity is the prospect.” To prevent calamity, Hefner says we need “… revitalization of our mythic and ritual systems [REL: that is, our religious institutions], in tandem with scientific understandings, so as to reorganize the necessary information. This may help us to put our world together …”

I previously posted that, as a scientist, I could not accept Dr. Hefner’s fusion of science and religion. However, I agree with both Dr. Costanza and Dr. Hefner that our political, cultural, and religious institutions must support the natural ecosystems that provide vital services and valuable public goods to ourselves and to future generations.

Link to Carl Zimmer’s article in the New York Times

Link to paper by Robert Costanza et al. in the journal Global Environmental Change

Link to my response to Philip Hefner’s Theological Theory of the Created Co-Creator

[The image below is a photomosaic produced by the NASA Goddard Space Flight Center.]

NASA image of Earth

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Wonderful Life Times Two

No, I’m not talking about the movie It’s a Wonderful Life, starring James Stewart, and the eponymous book Wonderful Life by Stephen Jay Gould that presented the case for the role of contingency in the evolution of life.

Rather, I’m celebrating a wonderful end to the week and a wonderful weekend, too.

Last week, we submitted the renewal proposal to the National Science Foundation for phase two of our BEACON Center for the Study of Evolution in Action. We were led, as usual, by our amazingly wonderful director Erik Goodman, and our wonderfully superb managing director Danielle Whitaker, with major work by all of us co-PIs and input from many others. BEACON’s mission is to illuminate and harness the (wonderful) power of evolution in action to advance science and technology and benefit society. And as we move toward phase two, we’re looking forward to even more wonderful research, collaborations, diversity initiatives, training, education, and outreach.

And this weekend, one of my wonderful daughters and her wonderful husband organized a wonderful weekend in Chicago for my wonderful wife and me. We stayed with my son-in-law’s wonderful parents, and we got to spend the weekend with them and our wonderful three-year-old granddaughter. And on Saturday evening, while the in-laws babysat, we went to the wonderful Looking Glass Theater and saw a truly wonderful play, In The Garden: A Darwinian Love Story.

The play is about Charles and Emma Darwin: their childhood—they were cousins—their romance, their marriage, their trials and tribulations as Charles grappled with his science and they struggled to reconcile Emma’s religion with his science, and they both struggled to reconcile their beliefs with the death of their beloved daughter Annie, all the while remaining deeply in love with one another.

The Looking Glass Theater is a tiny, intimate setting—wonderful for an intimate play like In the Garden.

It’s a wonderful life indeed.

[Emma Darwin, in 1840, painted by George Richmond, image via Wikipedia.]

Emma Darwin

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Science and Religion: Vive la Différence

[This post is the text of a talk that I presented on October 18, 1998, in East Lansing, Michigan, as part of a forum on "Our Evolving World: Challenge to Mind and Spirit." This document is in the public domain and may be used without charge and without permission, provided the source is acknowledged.]


Preface

Let me begin by thanking Glenn Johnson and Lars Clausen for inviting me to participate in this forum, and Philip Hefner for providing a thoughtful and thought-provoking view of the relation between religion and science in his book, “The Human Factor: Evolution, Culture and Religion” (Fortress Press, Minneapolis, 1993).

Pastor Clausen suggested that I begin by telling you briefly about my own research. I work in evolutionary biology, a field of study that seeks to understand the history and mechanisms by which life on Earth has changed during the past several billion years. Most of you probably first associate the study of evolution with dusty fossils, many of which demonstrate the existence of species that no are no longer alive today. Certain fossils provide striking evidence for evolution because the fossils have combinations of morphological traits that are no longer present in living organisms, yet were predicted from an evolutionary theory of relationships among modern-day species. For example, scientists have found fossil birds with exquisite feathers and hind-limbs like those of modern birds, but which also have teeth, clawed digits on their fore-limbs, and a long vertebral tail like their reptilian ancestors. Some of you may also know about the evidence for evolution that exists within the genes of all living organisms, including ourselves. The myriad similarities and differences among the genes of different organisms provide a material basis for evaluating the evolutionary relationships among all organisms, from bacteria to humans. These genetic similarities and differences enable scientists to determine which species are more closely related than others, using much the same logic and material that is used to establish paternity in lawsuits. The information in these genes provides independent support for the evolutionary derivation of birds from reptilian ancestors. By digging out fossil bones and sequencing genes using molecular methods, scientists can reconstruct historical events.

But I suspect that few of you think of evolution as an on-going process, one with consequences in our lifetime. And yet, evolution is happening all around us, sometimes with tangible repercussions for human welfare. Consider many disease-causing bacteria that have recently evolved resistance to the antibiotics that we use to treat infections. For example, Staphylococcus aureus, which is often acquired in hospitals following surgery, can cause potentially lethal infections; some strains of this species are now resistant to all but one of the antibiotics that were once available for its treatment. By the same token, many agricultural pests have evolved resistance to pesticides that we began using only in our lifetime. Indeed, while much of the public may regard evolutionary biology as abstract and far-removed from our present lives, in fact a substantial component of the costs of medicine and agriculture reflects an arms-race with our biological enemies. While we seek to control or eradicate diseases and pests using chemicals and other methods, these enemies are evolving genetic defenses against our best weapons. The evolution of these defenses by our natural enemies causes illness and economic devastation, and it forces us to spend more money to develop new means of combat.

And because evolution is occurring in the world around us, it is possible to perform experiments on evolution, just as one can in the fields of chemistry and physics. What is required for these experiments are organisms, such as bacteria, that have rapid generations and large populations, so that one can observe — on the time-scale of a student’s doctoral dissertation, for example — evolutionary changes that require many generations and that depend on infrequent genetic events. In my laboratory here at MSU, graduate students and I have monitored some 20,000 generations in bacterial populations that have been propagated for about ten years as part of one long-running experiment.

This experimental approach enables us to address certain evolutionary questions that would be difficult to resolve using a retrospective (historical) approach, such as studying fossils or comparing genes of living organisms. For example, on the theoretical side, how repeatable is evolution? That is, what are the relative roles of chance — from random mutation — and necessity — reflecting natural selection — during evolution? To address this question, we measure changes that take place when several initially identical populations of bacteria evolve in parallel in identical laboratory environments. On the applied side, are bacteria that have evolved resistance to antibiotics inferior to sensitive bacteria when they compete for resources, and hence for reproductive success, in the absence of antibiotic? If so, then this suggests that we may prevent, or at least slow, the spread of antibiotic-resistant bacteria by more judicious use of antibiotics.

One of the intriguing and powerful features of bacteria for this evolutionary research is the fact that they can be stored frozen, in a state of suspended animation. These frozen bacteria can be later revived to allow direct comparison, and even competition, with their own evolutionary descendants. Imagine if we could resurrect our own ancestors — from ten-thousand or a million generations ago — and then challenge them to a game of chess, or in the struggle for existence.

My students and I perform these experiments because we find them fascinating, and because evolution is a critically important process in the world in which we live. It is a process that has shaped our own being, yet it can also confound our efforts to shape the world for our well-being.

Response to Hefner’s Theological Theory of the Created Co-Creator

When Dr. Johnson told me that the focus of this forum would be the dialogue between science and religion, I listened politely but cautiously. I was pleased to hear this would not be another debate about evolution versus creation, and therefore would not pit science against religion. But as the magnitude of responding to Dr. Hefner has dawned on me, I’ve almost come to wish that this were a debate about evolution and creation! At least then it would be easy for me to disagree with another speaker’s position, and to feel that I had some expert knowledge to contribute.

Instead, my problem is this: I am a scientist, one with no special knowledge of either theology or philosophy. And yet I must respond to a distinguished theologian who has thought long and hard about the relationship between science and religion, and who has built on subtle philosophical underpinnings. So I begin by admitting that I am in over my head and hoping that I can swim, or at least dog-paddle, across this vast lake. Nonetheless, I do welcome this opportunity to respond, in order to express my admiration for Dr. Hefner’s work, but also to convey my own view of the relationship between science and religion. My view is somewhat different from the harmonious and integrated vision put forward by Dr. Hefner.

A good place to begin my reply is with a cartoon featuring Frank and Ernest, which appeared a few months ago (August 2, 1998). Ernest asks “What do you think of the idea of humans evolving, Frank?” To which Frank replies “I think it’s worth a try.” Instead of the familiar image about life emerging from the primordial ooze, or our descent from apes, this cartoon strikes us as funny because it depicts evolution in a forward-looking fashion, rather than the typical backward view. In fact, it does so at two different levels, at least for me. First, it is forward-looking in the literal sense of suggesting a future course of action. Second, Frank seems to be conveying the progressive view that not all is well with the world as it is, that humans bear some responsibility for the problems, and that therefore a new course of action is necessary.

I think this cartoon captures an important component of Dr. Hefner’s thesis. In his own words, and I quote, “… in the situation to which biocultural evolution has brought us … the life not only of the human species, but of the entire planetary ecosystem is made to depend on a great wager going well. This wager is that the cultural systems of information that the co-creator fashions will interface with the natural systems and with the global human culture so as to promote survival and a wholesome future.” Dr. Hefner then suggests that “… the wager is not going well. The cultural systems of information are not meshing adequately enough with other systems, and calamity is the prospect.” He therefore proposes “…revitalization of our mythic and ritual systems, in tandem with scientific understandings, so as to reorganize the necessary information. This may help us to put our world together …”

In a nutshell, I share Dr. Hefner’s profound concern for the future welfare of our species and planet. I agree with him that our species has evolved the unique ability to make decisions that profoundly influence the future of the world in which we live. And I share his view that this decision-making ability imposes — on all of us — a tremendous responsibility to do what it takes to ensure a wholesome future for our species and planet.

As an academic who values creative synthesis, in a world where narrow specialization has become the norm, I admire Dr. Hefner’s effort to integrate scientific and religious perspectives. But I am also troubled by the idea of integrating two such different ways of knowing. To clarify the reason for my discomfort, I must present my own views of the relationship between science and religion.

Evidence and Faith

What is the difference between science and religion? I think it is fair to say that one important difference is that science is based on evidence, whereas religion depends on faith. From some philosophical quarters, this distinction has been criticized as naïve, because science (like religion) also depends on certain fundamental beliefs that cannot be tested within the scientific enterprise. For example, science presumes that there is some correspondence between the material universe and our sensory perceptions of it. But science cannot actually prove that the world in which we live is “real” as opposed to a phantasm of our befuddled senses. I will admit, grudgingly, that I cannot prove the material reality of that wall behind me. But I invite anyone who doubts this assertion to try walking through the wall during the next break. Therefore, I will cling to the common-sense view that this distinction between science and religion — between reliance on evidence and faith — is an important one. (As a further complication to this distinction, some religious persons also claim evidence for their beliefs, as witnessed in recent days by thousands of pilgrims who visited a farm in Georgia last week to await a message they said was from the Virgin Mary. One of the pilgrims said he had on other occasions personally met both Jesus and God, and that they looked similar, except that God has more white hairs in his beard than does Jesus. But this religious evidence — unlike that required by science — cannot be reproduced or replicated on demand for a skeptic.)

While I hold to this difficult distinction between evidence and faith — indeed because I make this distinction — I would maintain that the existence of a supernatural God lies outside the realm of scientific inquiry. Science can only address natural forces in the material universe. In our work as scientists, we must assume that what we observe obeys natural laws, and that no supernatural force or being plays tricks with our experiments. Otherwise, interpretation of nature becomes arbitrary. This basic assumption applies to all scientific fields, from nuclear physics and inorganic chemistry to molecular genetics and evolutionary biology. Science therefore is unable to prove, or disprove, the existence of a supernatural God. Thus, while science is based on evidence and religion depends on faith, the two can coexist compatibly in our lives precisely because of their essential difference.

Yet despite the compatibility of science and religion at some level, science places constraints on what a religious person can believe about God, if that person also accepts a scientific world view. Let me emphasize that I don’t mean that science is infallible. Scientific claims are always liable to revision as new evidence, and even new ideas, emerge. Nonetheless, those of us who accept the validity of the scientific enterprise assume that science tends to converge toward some objective truth, even if convergence sometimes involves taking a step back before seeing the way to move two steps forward. Despite this inherent uncertainty of science, those who accept both science and religion as two sources of truth generally allow their understanding of science to constrain their personal vision of God the Creator.

For example, if a religious person accepts the scientific evidence that the Earth is several billion years old, and that all organisms including humans have evolved from a common ancestor, then that person must also accept the view that God the Creator was extremely subtle in the acts of creation, much more so than is indicated by a literal interpretation of Genesis or creation stories of most other religions. Within these scientific bounds, and recognizing the inability of science to answer questions about the supernatural, one might still imagine very different reasons for God’s subtle creativity: Perhaps God is playful and has allowed all nature the freedom to follow a path that is unknown even to God; or perhaps God is willful and directed the laws of natural creation so that they would lead to some ultimate purpose. But it would be in striking conflict with the scientific evidence to suggest that God the Creator took such direct actions as the creation stories would have us believe, if we take them as the literal truth.

Thus, one view of the relationship between science and religion is this: Science can say something about what God the Creator has done to bring about creation. This view is certainly not a new one. Over the centuries, and continuing to the present, many scientists have justified their studies on the ground that they are seeking the truth about the universe in which we live, one that God created and ultimately gave us the powers to explore. What better way to understand and even worship God than to investigate and understand God’s creation? The view that science provides insight into God’s creation, and by extension into God, seems to me entirely sensible — provided that one believes in the existence of God the Creator.

Science and Religion: Vive la Différence

I now want to suggest a slightly different view of the relationship between science and religion. It is an evolutionary view of their relationship within our culture that I personally find both plausible and liberating, in contrast to the scientific constraints that are placed on religious belief according to the previous view. As I explain this view, it should be apparent that there is an important shift in what I mean by religion from the way that I have used it previously, a shift from an emphasis on God the Creator to an emphasis on human morality. Importantly, this shift neither confirms nor denies the existence of God; instead, this view simply accepts the scientific impossibility of settling that issue.

While I am not a historian or a theologian, I think the case can be made that many religions have historically (and probably prehistorically) been conflicted between two distinct functions. On the one hand, religions have often sought to provide explanations about the natural world — how it came into being, and especially our own place or purpose in the world. The stories from Genesis of the creation in six days, and of the tower of Babel leading to different languages, are two familiar examples. On the other hand, religions have also sought to direct actions by explaining which behaviors were morally acceptable and which were not, and often prescribing rewards and punishments (in this life or beyond) to encourage moral behavior. The ten commandments and the parables of Jesus are examples in which religion gives moral direction. Thus, many religions, in an intellectual sense, have served two masters — understanding our place in nature and giving moral guidance.

But these two functions of religion sometimes come into conflict with one another, especially with the emergence of science as another way of explaining the natural world. This conflict has run both ways, with religious groups sometimes challenging scientific findings as heretical, and scientists (or individuals who usurped science) sometimes suggesting that their knowledge gave them special authority over issues of morality. As examples of the former, consider the trial and imprisonment of Galileo by the church for stating that the Earth revolved around the Sun; and the effort today of some fundamentalist groups to impose their creationist beliefs on the science curriculum in public schools. As examples of the latter, industrialists of the Victorian era sought to use Darwin’s principle of natural selection to justify their exploitation of the poor and weak. And Nazis borrowed pseudoscientific theories of racial differences as a supposed rationale for the irrational genocide of the Holocaust.

By viewing science and religion as two descendants of ancient religion, we can take comfort from the fact that these two interwoven realms of ancient religion — explanation of the natural world, and moral direction — continue to be present in our lives today. Moreover, by separating these two realms of understanding, each is freed from the binding constraints of the other. No longer must science be squeezed through the filter of any religious doctrine; and no longer must religion depend on justification in the natural world, which is often ruthless and unforgiving of mistakes.

Let me make it clear that I don’t believe these two realms must be kept absolutely separate. For example, we may use scientific data to inform the ethical course of action in medical practice. So, too, we need scientific information about our impact on nature, in order to weigh the moral consequences of alternative behaviors with respect to the health of our planet and all its inhabitants. And religious persons may wish to integrate a scientific understanding of the natural world into their religious framework in order to promote morality that is maximally consistent with a wholesome future, as exemplified by Dr. Hefner. By the same token, scientists ought not ignore the moral implications of their work, for example, with regard to methods of warfare or the impact of discoveries on the environment. Moreover, scientists may investigate the evolutionary origins of certain moral and religious beliefs, such as prohibitions against incest or dietary laws. And scientists may take spiritual pleasure in expanding our knowledge of the universe, whether to satisfy curiosity or to promote a wholesome future by informing effective decisions within a moral framework.

But my important point is this: Our understanding of the material world no longer depends on its agreement with any religious faith. At the same time, our moral dimension has the freedom to develop, perhaps enlightened by — but without fear of contradiction by — the natural world, which seems usually to favor selfishness over true altruism.

Conclusion

My discomfort with Dr. Hefner’s theological theory boils down to this: He weaves science and religion together so tightly as to blur the boundary between them, at least in my own reading. In a sense, he uses scientific evidence to support his religious faith; he uses what is known to support the unknowable. But this could be a hazardous enterprise. I think the same facts of evolution — with the perpetual struggle for existence and genetic rewards for selfishness — could just as easily be used to support a religion that both Dr. Hefner and I would find repugnant.

So I respect Dr. Hefner’s faith, and I admire his inclusive religious tone, even as he holds fast to the tenets of his faith. And I applaud his use of science and religion together to promote a more wholesome future for our species and our planet. But I cannot endorse his theological theory of the created co-creator, just as I could not agree with any theological theory that seeks scientific support for a matter of religious faith. Science depends on internal consistency, whereas religions span an enormous range of mutually incompatible beliefs. Some believe that God is embodied in nature, whereas others believe that God exists outside the material universe. Some believe that morality evolved from within nature, whereas others believe that morals are transcendent. Some preach tolerance, while others claim divine support for intolerance toward outsiders. Some look forward to life after death, others fear life after death, while still others view this life as the only one we have. Some even welcome the idea of an apocalypse, while others hope for generations without end.

Science can never settle these differences in faith. While individual scientists may hold diverse religious beliefs, or none at all, science is a way of knowing about the material universe only. Having evolved into two distinct cultural functions — two different ways of knowing — we can hope that science and religion together promote a wholesome future. Let the dialogue continue between science and religion. Mais vive la différence.

Postscript

I’ve spoken about the roles of science and religion in providing explanation of our place in nature and giving moral direction, but I’ve not said much about spirituality. The following poem is from a book that was written by my late mother and published a few years ago. To me, it shows the deep spirituality that can arise out of a material view of life.

 


THE FIRST GIFT

—being comprised of DNA and shared in the

first cell division, 3 to 4 billion years ago.

Take this. It’s part of me

and everything I know

about this emergent art

of getting by.

Since what I am survived

this long, this place,

my information may enable you

to live a little.

Jean Lenski (Genesis, 1993, St. Andrews College Press)


This cartoon is © by Thaves  (http://frankandernest.com/cgi/view/display.pl?98-08-02). It is shown here under the doctrine of fair use.

Frank and Ernest 02-Aug-1998

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On Time and Space

The long-term evolution experiment (LTEE) began in 1988, and the E. coli populations are approaching 60,000 generations.  That’s a long time for an experiment, and I hope it continues for much, much longer.

But when I give talks about the LTEE, I also try to remind people that 26 years is only a drop in the proverbial bucket of evolutionary time.  If you were to add these experimental populations to the tree of life—or even to a tree showing only other E. coli strains—they would not be visible to the eye because the branches they represent—tiny twigs, really—would be so short (in time) and so close (in genetic distance) to their ancestors.

On Time and the LTEE

Life has existed on Earth for roughly 3.5 to 4 billion years.  That’s about 140 million times longer than the LTEE has existed.  Expressed the other way around, this experiment has been running for about 0.0000007% of the time that life has been evolving on our planet.

As a said, a mere drop in the bucket of time …

That’s a somewhat mixed metaphor, though, with “a drop in the bucket” being a statement about space and relative volumes, not about time.  And that got me wondering about the spatial scale of the LTEE relative to the spatial scale of the biosphere.

If the LTEE is just 0.0000007% as old as life on Earth, what fraction of the space—of the total biovolume—of life on our planet exists in the confines of the LTEE?

On Space and the LTEE

That’s a harder a question to answer.  We know the volume of the LTEE:  there are 12 flasks, one for each of the evolving populations, and each flask contains 10 milliliters (mL) of liquid medium.  (In medicine, by the way, a drop has been defined as 1/20th of a mL, so each flask in the LTEE contains 200 drops.)  If we sum across the populations, then the LTEE occupies 120 mL.

Before you read further:  What’s your quick intuition?  Is the LTEE larger on this spatial scale than on the temporal scale?  Or is the LTEE smaller?

 

Volumes and Numbers

How should we estimate the volume of Earth’s biosphere?  Here are three back-of-the-envelope approaches to get a rough sense of the scale.

1)  Most of the Earth is covered by its oceans, which are full of life.  While life is not equally abundant throughout the oceans, none of that space is entirely devoid of life.  The total volume of Earth’s oceans is about 1.3 billion cubic km.  That’s a lot of mL!  A mL is a cubic centimeter, or cc, and that’s 1/(100^3) = 1 millionth of a cubic meter.  A cubic meter is 1/(1000^3) = 1 billionth of a cubic kilometer, and the oceans contain over a billion of those cubic kilometers.

So the 120 mL in the LTEE correspond to 120 / (1.3 x 10^9 x 10^9 x 10^6), or about 9 x 10^-22 of what  the oceans contain.  That’s just 0.000000000000000000009% of the volume of the oceans.

By this calculation, then, the temporal scale of the LTEE is ~75 trillion times greater than its spatial scale, when both are expressed relative to nature.  If the LTEE is “a drop in the bucket” with respect to time, then that drop has to be diluted by a factor of 75 trillion with respect to the oceans.

2)  Let’s try another quick-and-dirty calculation.  Most life, in the oceans and on land, is near the Earth’s surface.  The surface area of our planet is about 510 million square kilometers.  If we take just the top meter, that’s equivalent to 510/1000  = 0.51 million cubic kilometers.  That’s about 1/2600 of the volume of the ocean.  But even this conservative estimate of the volume of the biosphere makes the relative scaling of the LTEE with respect to time and space differ by a factor of 30 billion.

3)  Here’s one more approach—it’s based not on the volume of the physical environment but, instead, on the number of organisms in the LTEE and in the biosphere.  When grown to stationary-phase density in the LTEE environment (i.e., when the limiting resource, glucose, is depleted), the ancestral bacteria could achieve a maximum density of ~5 x 10^7 cells per mL.  Most populations have evolved so that they now produce slightly fewer, but larger, cells; and one population has evolved the ability to use the citrate that is also in the medium, and it now reaches a density that is several times greater than the other populations.  In any case, given 10 mL of medium for each population, and 12 populations, the total population size across the LTEE is on the order of 10^10 cells.

And how many cells exist in the Earth’s biosphere?  Whitman et al. (1998, PNAS) estimated that there are more than 10^30 prokaryotes—bacteria and archaea combined—in the biosphere, and they make up the great majority of all living things.

So by this approach, using the number of cells as a proxy for the spatial scale, the size of the biosphere is over 10^20 (a hundred-million-trillion) times larger than the LTEE.  We’re back into the trillions in terms of the relative scaling of the temporal and spatial scales of the LTEE.

On Time, Space, and the LTEE

By all three approaches, then, the LTEE is vastly older with respect to the history of life on Earth than it is large with respect to the size of Earth’s biosphere.

The LTEE really is a long-running experiment, as experiments go.

But the LTEE is a “drop in the bucket” with respect to how long life has been evolving on Earth.  And it is a vastly more miniscule “drop in the bucket” when compared to the spatial extent and number of living organisms on our planet.

Maybe I should give the LTEE a new name—the “incredibly tiny but relatively long-term evolution experiment.”

[Photo of a water drop on a leaf taken by tanakawho and shared on Wikipedia (en.wikipedia.org/wiki/File:Water_drop_on_a_leaf.jpg).]

Water drop from Wikipedia

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An Absence of Posts, an Abundance of Talks, and More

Dear Reader:  No, I have not given up on this blog.  But I’ve been busy, busy, busy!

In the last four weeks alone, I have traveled to the University of Arizona, Harvard University, Duquesne University, and Princeton University.  Besides giving talks at each place (two public lectures and two academic seminars, with cumulative audiences of well over a thousand people), I have met with dozens and dozens of amazing scientists, from graduate students and postdocs to faculty both young and old.  It’s been a blast:  an exhausting blast, but a blast all the same!

And next week?  I’m hosting four terrific colleagues from two continents who will work with me to begin making sense of hundreds of newly sequenced genomes from the LTEE.

Oh, and we have some more job searches starting next week.

And did I mention?  We just had a fascinating (if I may so myself) and complex paper come out today in Science (on-line express for now) on the most deeply divergent (i.e., oldest sustained polymorphism) of the 12 LTEE populations.  And no, it’s not about the citrate eaters from population Ara–3.

Plucain, J., T. Hindré, M. Le Gac, O. Tenaillon, S. Cruveiller, C. Médigue, N. Leiby, W. R. Harcombe, C. J. Marx, R. E. Lenski, D. Schneider.  2014.  Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.  Science.

It’s population Ara–2 instead, where two lineages—dubbed the Larges (L) and Smalls (S)—have coexisted for several tens of thousands of generations.  In superb research led by Dr. Jessica Plucain that she did in the lab of my long-time collaborator (and dear friend!) Prof. Dom Schneider (Grenoble, France), Jessica led the work to identify—out of hundreds of mutations—three that are sufficient to allow a “constructed” S ecotype (i.e., the ancestor plus three derived alleles) to invade and stably coexist with the evolved L ecotype.  Ecological context and specific genetic interactions are key to establishing this “half” of the polymorphism … and the other “half” of the story— what makes the L ecotype special—might well turn out to be just as complex, or perhaps even more so.

The S and L types are especially challenging (even painful!) to work with because this population became a mutator very early on—before the two lineages diverged—and so there are many, many mutations to contend with; moreover, they make colonies on agar plates that are quite challenging to score and count.  So congratulations to Jessica, Dom, and other members of Dom’s lab for their perseverance in studying this extremely interesting population.

Also on the list of authors are Prof. Chris Marx and two members of his lab.  They performed metabolic analyses showing how the carbon fluxes through the central metabolism of the S ecotype have diverged from both the ancestor and the L ecotype.  Chris was a postdoc in my lab almost a decade ago, but most of his work (then and since) has been on experimental evolution using Methylobacterium, and so this is the first paper we’ve co-authored.

There was a production error, though, in the on-line version of our paper; the final sentence of the abstract was dropped (except for one word).  The abstract, in total, should read as follows:

“Ecological opportunities promote population divergence into coexisting lineages. However, the genetic mechanisms that enable new lineages to exploit these opportunities are poorly understood except in cases of single mutations. We examined how two Escherichia coli lineages diverged from their common ancestor at the outset of a long-term coexistence. By sequencing genomes and reconstructing the genetic history of one lineage, we showed that three mutations together were sufficient to produce the frequency-dependent fitness effects that allowed this lineage to invade and stably coexist with the other. These mutations all affected regulatory genes and collectively caused substantial metabolic changes. Moreover, the particular derived alleles were critical for the initial divergence and invasion, indicating that the establishment of this polymorphism depended on specific epistatic interactions.”

[Edited on 07-Mar-2014:  The on-line PDF at Science Express now has the complete abstract.]

~~~

The picture below shows Dom Schneider and Richard Lenski in Paris in 2013.  They are holding a petri dish that Jessica Plucain made to celebrate the 25th birthday of the LTEE.

Dom and Rich, Paris, 2013

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Resources for People Interested in Learning about Evolution

Over on Twitter, a poster was interested in learning more about evolution and how it works.

I suggested the poster begin with Evolution 101, a website produced by the University of California Museum of Paleontology.

I then recommended four superb books (including one suggested by another poster).  These are all written with wonderful style and terrific content by world-class authors.

I’d begin with Carl Zimmer’s Evolution: The Triumph of an Idea.  This beautifully illustrated book was written as a companion to the PBS series on Evolution that aired in 2001.

The next three books are a bit more advanced, but still very accessible, and they could be read in any order.

The Greatest Show on Earth: The Evidence for Evolution by Richard Dawkins

Why Evolution is True by Jerry Coyne

Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body by Neil Shubin

I could make many, many more suggestions.  But that’s a start, and now I’ll let others weigh in with suggestions in the Comments below. 

Please label your selections as for the Beginner, Intermediate, or Advanced student (and by student, I mean anyone, regardless of age or prior studies, who wants to learn about the science of evolution).

Please include only one link per post; otherwise, the spam filter may delete your post.  Also, I will delete any inappropriate suggestions.

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Zachary Blount on “Ham on Nye” Debate, Follow-up #3

I’m very pleased to present this guest post written by Dr. Zachary Blount, aka Dr. Citrate, as an in-depth follow-up to the “Ham on Nye” science versus creation debate.  Zack did his undergraduate studies at Georgia Tech, and then obtained a masters degree from the University of Cincinnati.  After that, he came to MSU, where he completed his Ph.D. in 2011.  With his doctoral work generating so many interesting results and new questions, Zack stayed on here as a postdoctoral researcher.  His current research is funded by a grant from the John Templeton Foundation Program on Foundational Questions in Evolutionary Biology.

Zack has devoted years to studying the evolution of the ability to grow on citrate that occurred in one of the 12 populations from the long-term evolution experiment (LTEE) with E. coli.  We still don’t fully understand all of the steps involved.  But a simple “on/off” switch it is not!

However, even if it had been a single, simple mutation that allowed the cells to grow on citrate, that still would have been evolution … it still would have been a beneficial mutation in the context of the experiment … and it would still have demonstrated the acquisition of new information encoded in the genomes of the bacteria that fits them to their environment.  Of course, if it were so easy as a single, simple mutation, then we would have seen that capability evolve in many or all of the populations. But after almost 60,000 generations to date, only one population has evolved that ability.

You can read about the technical details of our findings in two papers here and here, as well as in a recent paper from a team at the University of Texas, Austin.

In what follows, the nomenclature Cit+ refers to the bacteria that evolved the ability to grow on citrate in the presence of oxygen, while Cit refers to the bacteria – their ancestors and other E. coli – that lack that ability.

 – Richard Lenski

* * * * *

My work on the evolution of aerobic growth on citrate in one of the LTEE populations has received a fair amount of attention over the years.  (Sometimes there is a bit of a dream-like quality to it all.  I still have a hard time conceiving that people unknown to me know about what this here kid from north Georgia has done.)  The attention is rather gratifying because I’ve spent many years and a great deal of effort in school and in the lab to become an evolutionary biologist. But why did I do all that in the first place? Because I find evolution to be endlessly fascinating, beautiful, and even inspiring.

It means a lot to know that the work I spent several thousands of hours toiling away on has made a contribution to science.  Even more satisfying is that my work has come to be viewed as a go-to example of evolution in action that may, perhaps, inspire in others some of the same feelings that have motived me.

Of course, this attention has also been a bit troubling because it has led to repeated disparagement, dismissal, distortion, and misrepresentation of my work by both professional and amateur creationists.  These creationists often get entirely wrong the work my colleagues and I toiled long and hard to do, likely because they haven’t bothered to read our papers, learn the details and methods, or think much about the results.  (I suspect some duplicity is in there, too.)  Reflexive, unthinking dismissal bothers me – maybe because my parents and devoutly Southern Baptist Granny told me when I was a child that this is something that civilized folk simply should not do.

This brings me to the recent debate between the legendary science educator Bill Nye and the legendary obfuscator and anti-science showman Ken Ham.  It was the standard sort of set-up, with Nye defending evolution and science against creationism, and Ken Ham, well, doing what Ken Ham does.

Twice during the debate, Ham discussed my work with the LTEE population that evolved the capacity to grow aerobically on citrate.  The first time was at about 44 minutes, and included a video clip of Dr. Andrew Fabich, a “Biblical creationist” microbiologist at Liberty University.  [You can read the transcript here.]

The evolution of the new Cit+ function is, and has been discussed as, an instance of evolutionary innovation that arose in a controlled experiment in which we can drill down and figure out how it evolved. Ham and Fabich, however, dismissed Cit+ as an innovation or even an instance of evolution using two arguments suggesting that neither knows the work well at all and likely have not read our papers.  (In Ham’s case, this wouldn’t be surprising, as he has been called “willfully ignorant” even by other creationists, which is a bit like being called unkempt by Pig-Pen or in need of a haircut by Cousin Itt.  In Fabich’s case, however, it would betray a lack of professional courtesy, at best.)

First, Ham repeatedly said that some of the bacteria in the LTEE “seemed” to have developed the ability to grow on citrate.  This wording suggests either stupidity or duplicity on our part, as though we either didn’t check or just lied, but the fact of the matter is that there is no “seem” about it.  The Cit+ bacteria do grow on citrate, and they do so under conditions that E. coli normally does not.  This ability is something that is easy to demonstrate, and which I and my colleagues – not only in the Lenski lab but also other labs that are now working with these bacteria – have documented.  And it’s not as though we don’t have the evidence – as Rich has pointed out to another anti-evolution critic, we have many, many, many vials full of them in our freezers.

The second argument was more direct.  Both Ham and Fabich asserted that the Cit+ function did not evolve because using citrate did not involve “any kind of new information … it’s just a switch that gets turned on and off.”  (Fabich went on to state that this “switch” is what we reported.  That is emphatically not true.  It beggars belief that anyone, much less a trained microbiologist, could actually read our 2012 paper, where we reported the genetic basis of Cit+, and come away thinking this.) Variations on that wording are often used by creationists who discuss the citrate work because it implies that Cit+ arose because of a pre-existing regulatory switch and involved no evolution at all.  But that simply is not the case – that wording, dare I say it, is a lie.

If you take E. coli from a medium in which it is growing on glucose, and move it into a medium where the only thing to eat is something else, like lactose, it turns off the expression of some genes specific to growth on glucose, and it turns on other genes necessary to grow on lactose.  That is what is called gene regulation, and that is what biologists mean when they talk about switching functions on and off – existing genetic circuitry that allows an organism to respond to changes in the external and internal environment.  If you transfer normal, Cit E. coli from a glucose medium to a medium with only citrate to eat, they don’t grow.  They just sit there and starve.  Regular E. coli cells have no existing genetic regulatory circuitry that “flips a switch” to allow them to start growing on citrate in the presence of oxygen.  On the other hand, if you do the same thing with the Cit+ cells that evolved in the long-term experiment, the Cit+ cells will start growing happily on citrate.  This difference is not a matter of gene regulation, but an evolved difference between the ancestral strain and the Cit+ lineage that allows Cit+ cells to grow on citrate.

No, the ability to grow on citrate is not a matter of simply flipping a pre-existing regulatory switch.  Continuing the electrical metaphor, the evolved Cit+ function is instead about rewiring.  My dear little Cit+ cells gained their ability to partake of the previously forbidden citrate by a genetic duplication involving a gene, called citT, which encodes a transporter protein that is used during anaerobic growth on citrate.

This duplication did something very special.  You see, one of the major aspects of gene regulation is that genes have associated regulatory DNA sequences, including what are called promoters that control when genes are expressed.  The citT gene is normally controlled by a promoter that tells the cell to turn it on only when there is no oxygen present.  As shown in the Figure below, the gene duplication put one copy of citT next to, and under the control of, a promoter that normally controls another gene called rnk.  The rnk gene is normally turned on when oxygen is present.  The new association between citT and the rnk promoter – what we call the rnk-citT regulatory module – turns citT on when oxygen is present, and allows Cit+ cells to use citrate under the conditions of the LTEE.  (To really feast on the citrate involved additional evolutionary changes, both before and after this rewiring, but I’ll leave that point aside for this post.)

There is a very interesting consequence of how the rnk-citT module originated. While Ham did not make this argument, other creationists have asserted that Cit+ arose simply by a loss of gene regulation, because they have the notion that evolution can only break things.  However, the duplication that gave rise to the rnk-citT module caused no such thing.  There is still a copy of citT that is linked to the same adjacent DNA sequence as before, and there is still a copy of rnk that is under the control of its own promoter.  In other words, the cell got something new without losing anything old.

When they actually bother to explain all of that, creationists still dismiss Cit+ as being an instance of evolutionary innovation because it involved the rearrangement of existing components.  True, the duplication responsible for Cit+ did rearrange components that were already there, but that rearrangement generated a new association between components that did not previously exist, and it produced a new function that also did not previously exist.  To argue that rearrangements cannot produce innovation is akin to arguing that a novelist has done nothing creative in writing her novels because she only used words that already existed.

Ham also made a demand that is common among creationists that betrays a fundamental misunderstanding of evolutionary theory. In the later debate segment [starting at ~2:30], Ham says, “What Bill Nye needs to do for me is to show me example of something…uh, some new function that arose that was not previously possible from the genetic information that was there. And I would claim and challenge you that there is no such example that you can give… you’d have to show an example of brand new function that never previously was possible.  There is no such example, uh, that you can give anywhere in the world.”

According to Ham, evolution cannot be true if this burden can’t be met.  Consider that wording for a moment, though: “… show an example that never previously was possible.”  Not possible?  That’s kind of a high bar given that impossible things don’t happen by definition.  Moreover, it is clear from Ham’s words that he won’t regard any capacity that arises from modification of an existing genome to be an innovation, which means that he must think that evolutionary theory holds that new genes just pop into existence fully formed, without precursor states, like Athena from the head of Zeus.

This goes to the larger problem with how Ham, Ray Comfort, Michael Behe, Georgia Purdom, and others of their ilk approach evolution – they just don’t know much about it, and so what they end up arguing against isn’t the science, but a caricature of the science that exists only in their minds.  Evolutionary novelty does not arise from genes just popping into existence.  That is a silly idea, and one that no evolutionary biologist holds!

Instead, evolution innovates and creates through descent with modification of what already exists, a process that Nobel laureate François Jacob called “evolutionary tinkering”.  This modification arises by random mutations: base changes, deletions, duplications, insertions, and so on – and, depending on the organisms, horizontal genetic exchange and sexual recombination.  Natural selection then preserves and accumulates the useful changes – those that enhance survival and reproduction of the organism in its environment – across the generations.  Often, such innovations are based on just what we see with the Cit+ bacteria – novel rearrangements of old components.  Indeed, Jacob wrote that, “(Evolutionary) novelties come from previously unseen association of old material.  To create is to recombine.”

So Ham and other creationists dismiss how evolutionary theory says evolution works as not being evolution, and then they demand the impossible.  That strikes me as neither fair nor honest.  But in the end, their lies, distortions, misrepresentations, and ignorance don’t matter, just as debates, entertaining though they may be, don’t matter, because nature doesn’t care.  To paraphrase a bumper sticker I once saw, they may not believe in evolution, but nature does!

While they go on cycling through their old and ossified rhetoric according to their fixed and incorrect notions, evolution proceeds, MacGyvering the new from the old. Natural selection can’t do the impossible, but it is pretty darn spiffy at doing the improbable with the rare.

If you are interested in learning more, please visit my website, where you will find my papers available for download.  You can also watch my Ph.D. defense presentation, in which I go into much more detail about the evolution of the Cit+ E. coli.

– Zachary Blount

* * * * *

The figure below shows schematically the tandem duplication in the population that evolved the new ability to grow on citrate.  This duplication produced the new rnk-citT regulatory module by placing the second copy of the citT gene adjacent to the rnk promoter region.  The figure comes from Blount et al., 2012, Nature; it is shown here under the doctrine of fair use.

tandem duplication

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