Yves here. I’m old enough to remember when both the American government and some major private companies did a lot of basic research, such at the old Bell Labs. Per Wikipedia:
Researchers working at Bell Laboratories are credited with the development of radio astronomy, the transistor, the laser, the photovoltaic cell, the charge-coupled device (CCD), information theory, the Unix operating system, and the programming languages B, C, C++, S, SNOBOL, AWK, AMPL, and others. Nine Nobel Prizes have been awarded for work completed at Bell Laboratories.
Now it seems to be quaint to be interested in science for the thrill of discovery or even of making a fundamentally important contribution. It’s so much easier to get rich making an app or hawking a designer dietary supplement. And the rest of us wind up poorer for this misuse of potential.
KLG makes a key point below: the way that research is funded now further impedes potentially pathbreaking inquiries moving forward.
By KLG, who has held research and academic positions in three US medical schools since 1995 and is currently Professor of Biochemistry and Associate Dean. He has performed and directed research on protein structure, function, and evolution; cell adhesion and motility; the mechanism of viral fusion proteins; and assembly of the vertebrate heart. He has served on national review panels of both public and private funding agencies, and his research and that of his students has been funded by the American Heart Association, American Cancer Society, and National Institutes of Health
During the final summer of World War II Vannevar Bush, who was leader of the Office of Scientific Research and Development in the White House, wrote a report for President Truman that he called Science, the Endless Frontier. The report was recently republished with an introductory chapter by Rush Holt, Jr, a physicist and was an 8-term congressman from New Jersey from 1999 to 2015. Although Vannevar Bush was primarily an engineer, he appreciated that science, engineering, and technology are not one and the same, but that each is dependent upon the other. Science, the Endless Frontierwas a thoroughgoing brief for basic scientific research, explaining why government support of science was an essential component contributing to the wellbeing of all.
A major result of the Bush report was the establishment of the National Science Foundation (NSF) in 1950, followed by the transformation of what began as the Hygienic Laboratory in 1887 into the National Institutes of Health (NIH) we know today, with its 27 separate centers and institutes and a budget of $42B in 2020. While the Cold War tended to subvert certain priorities, a topic for another time, the Golden Age of American Science from the 1950s through the 1990s was real. Although there were ups and downs associated with budgetary constraints and politics, and there has always been some logrolling among the chosen, both agencies funded what Karl Popper would have called “good science” that was directed at answering interesting questions of what was once called “natural history.”
I am a biologist by temperament and vocation, and in this post, I will briefly tell a story of biological research that would be characterized today by reviewers and program officers at funding agencies using the killer epithet “descriptive,” but nevertheless resulted in knowledge that revolutionized cell biology in remarkable and entirely unforeseeable ways.
Bioluminescence, the emission of light by living organisms, was described by Aristotle and subsequently appeared often in the literature of natural history through the 19thcentury.[1]
Throughout the 20thcentury, this fascinating aspect of natural history yielded to biochemical approaches, as scientists in the United States, Europe, and Japan developed an understanding of the chemical nature of “cold light” and explained “how” of bioluminescence works in bacteria, protists, fungi, and animals[2]. The evolutionary “why” of bioluminescence is not as well understood across the web of life and is still mostly an outstanding question, though it is clear that deep sea anglerfish use their lures filled with bioluminescent bacteria to attract prey in the darkest ocean depths.
At the biochemical level, bioluminescence is most well understood in bacteria, fireflies, and marine invertebrates, including various Cnidaria (coelenterates, including hard and soft corals and jellyfish) and Ctenophora (comb jellies). The latter are considered to be among the earliest diverging animals, with a current nod to ctenophores, so bioluminescence is likely to be an ancient attribute of animals, though restricted in distribution among extant organisms. Here we will concentrate on the jellyfish Aequorea victoria and the sea pansy Renilla reniformis, because the mechanisms of bioluminescence in these organisms are similar and have been described in detail.
Without getting too far into the biochemical weeds, the key points, which were worked out in a series of papers from the late 1950s through the 1980s primarily from the research groups led Milton J. Cormier(Renilla) and Frank H. Johnson and Osamu Shimomura (Aequorea), are
- A chemical (substrate) called luciferin is acted upon in the presence of oxygen by
- An enzyme (protein) called luciferase
- With the production of blue light
This blue light is produced in the test tube with purified components. In each organism, however,
- The emitted light is green
And for a long time the question was, “How does that work?” To make a long story short, another protein is required for light emission in the organism: Green fluorescent protein, or GFP. The energy released during the oxidation of luciferin is passed directly to GFP, which then emits green light.
After the biochemistry and biophysics of coelenterate bioluminescence were worked out using components purified the old-fashioned way from the sea pansy and the jellyfish collected at marine laboratories, the biochemists doing the research did the next thing – they became molecular biologists and cloned the genes for Renillaluciferase, AequoreaGFP, and aequorin (here and here). Aequorin is the pre-charged luciferase-luciferin-oxygen complex triggered to emit light upon binding to Ca2+ions.
The availability of these recombinant versions of each protein led to their use as tools in molecular and cell biology. Recombinant luciferase was soon used to measure gene expression in real time in cells in which a chimeric luciferase/gene-of-interest simply by adding luciferin to the culture medium and measuring light output under experimental conditions. Aequorin purified from the jellyfish had long been used as a calcium indicator in studies of muscle contraction and the propagation of signals in nerve cells, but the availability of recombinant aequorin made it possible to extend the reach of this technique without the necessity of purifying the native protein from the jellyfish and then microinjecting it into cells manually. As with Renillaluciferase, it became possible to prepare cells expressing recombinant aequorin and measure calcium fluxes without microinjection.
These benefits from research on coelenterate bioluminescence were important advances. Light emission is easy to measure, and to a first approximation, the localization of the light-emitting molecule (aequorin or a chimeric aequorin/protein-of-interest) in a cell, tissue, or organism can be determined.
But AequoreaGFP was unexpectedly destined to be the most important result of this research. Shortly after publishing his work on the cloning and sequence of the GFP gene, Doug Prashermet Martin Chalfie and shared his GFP clone. Chalfie then expressed AequoreaGFP in the bacterium Escherichia coliand nematode Caenorhabditis elegans, and the rest is history. From the abstract of that article:
A complementary DNA for the Aequoreavictoria green fluorescent protein (GFP) produces a fluorescent product when expressed in prokaryotic (Escherichia coli) or eukaryotic (Caenorhabditis elegans) cells. Because exogenous substrates and cofactors are not required for this fluorescence, GFP expression can be used to monitor gene expression and protein localization in living organisms (emphasis added).
GFP, prosaic name that it has, is quite simply a wonder of nature. The protein folds into its native three-dimensional conformation spontaneously. Moreover, the protein is remarkably stable. Thus, a recombinant gene-of-interest containing GFP at one end or the other is easily expressed in cells of all types, from bacteria to human stem cells, and the location of this GFP-containing protein can be identified precisely using a fluorescence microscope, in real time in living cells.
Since the cloning of AequoreaGFP, it has appeared in over 45,000 publications, such that cell biology without the use of GFP is scarcely imaginable. After GFP was first used, Roger Tsien set out to produce GFP in different colors, and now we can use various shades of “GFP,” ranging from deep blue to red, often used in the same cell while studying the function of distinct proteins. Thus, Osamu Shimomura first purified and initially characterized GFP from the jellyfish; Doug Prasher later cloned the gene and then gave it to Martin Chalfie, who showed that GFP could be used as a marker of protein expression in virtually all living cells. Roger Tsien of the University of California-San Diego subsequently developed GFP in multiple colors. Drs. Shimomura, Chalfie, and Tsien were awarded the Nobel Prize in Chemistry in 2008 in recognition of their work, which has revolutionized research in cell biology.
Why is this interesting, to me and other biologists and to those interested in scientific research as one of our methods useful for understanding the world around us? Because the research upon which this revolution was based developed straight out of Vannevar Bush’s vision of basic research, which should be funded and supported in the absence of a particular goal. This research had no instrumental justification, other than to understand an interesting puzzle of natural history. There is no way that anyone could have pictured where the early funding from NSF to Osamu Shimomura, Frank Johnson, Milton Cormier and several others would take us.
That was indeed a different world. Current guidelines from the NSF Cellular Dynamics and Function Cluster, which would be a likely source of funding for the research on bioluminescence are here:
The cluster seeks theory-driven investigations of diverse cellular and subcellular systems. Research proposals are encouraged that use multidisciplinary physical, chemical, mathematical and computational approaches to providenovel techniques and integrative insight into fundamental cellular functions. Innovative proposal using plants, microbes, and nontraditional model species are encouraged. Proposals that rely heavily on descriptive approaches are given lower priority.
The cluster encourages proposals in the following areas:
- Predictive understanding of the behavior of living cells through integration of modeling and experimentation.
- Evolutionary approaches to understanding the rules governing cellular functions.
- Integration of function with emerging cellular properties across broad spatiotemporal scales, including ideas that consider cellular organization from the standpoint of soft condensed matter are encouraged.
The cluster recognizes that technological advancement can have profound and catalytic influences on the field of cell biology. These advances are often the result of technology in one scientific field being borrowed and applied to another in new and creative ways. The cluster encourages proposals to develop or adapt innovative tools with potential to enable new avenues of cellular investigation.
This is word salad of the worst kind, rivalling that of the typical American politician (which come to think of it, NSF has a .gov suffix). The description at Systems and Synthetic Biology may be worse. But let us unpack some of this.
Theory-driven investigations. Theory is in the eye of the beholder, and theories in biology have an undistinguished past. This in particular reminds me of the “axiomatic biology” developed by J.H. Woodger during the 1930s,[3]during one of Biology’s periodic extended bouts of physics and engineering envy. Aside from the Gene Theory, the Central Dogma of Molecular Biology, and the Modern Synthesis of Evolutionary Biology, biology is too granular, i.e., biological molecules and cells have a meaningful evolutionary history of almost 3 billion years, for grand overarching theories of any kind.
Multidisciplinary. Interdisciplinary, perhaps, but then such collaborations and conflations, seldom work, especially when forced, although they are popular with politicians. Novel techniques and integrative insights…innovative tools with potential to enable new avenues of cellular investigation. Anyone who proposes something truly novel or innovative in a grant proposal to NSF will be disappointed with an inevitable version of “she has not proved she can do this or that it will work” from at least one reviewer. One is enough. And it is usually Reviewer Number 3.
And now to my favorite: Proposals that rely heavily on descriptive approaches are given lower priority. I think they forgot “incremental,” which is the twin of “descriptive” in the Program Officer/Proposal Reviewer universe of disdain. I will simply point out that none of the solid research that led to the revolution in cell biology described here would have met the standards of the current NSF. The objective of those scientists 50-60 years ago was to understand nature, at whatever appropriate level they pursued.
Because Biology is not amenable to “theory” except in the most trivial of contexts, virtually all biological research is primarily descriptive. It is also incremental. Leaps are few and far between, including the structure of DNA although James Watson in The Double Helix tried his damnedest to make it so for DNA and nearly succeeded.
Other major advances in biology in the past 50 years that were “descriptive and incremental” include our understanding of the cell cycle, which was worked out using yeasts and marine invertebrates as experimental organisms after the use of “higher” cells and models proved fruitless. The first cell lineage map of a multicellular organism was accomplished using the nematode C. elegans, and this led to the discovery of programmed cell death (apoptosis), which is the objective of much cancer therapy.
Every high school biology student knows the importance of the fruit fly in the development of genetics, but the genes responsible for pattern formation in virtually every animal came out of research by a largely solitary, independent scientist who described fruit flies that looked strange. As Joram Pitiagorsky pointed out several years ago, those responsible for choosing the winners and losers in what has become the Great Grant Lottery, from policymakers to reviewers to Program Officers, should remember always that the answers to biological questions cannot be known in advance – there is no biological equivalent of the Higgs boson– and that the answers to these questions often lead to advances in scientific knowledge, and scientific practice, that are as unimaginable and unpredictable as they are revolutionary.
Is there a way forward for biology? Yes, but things must be changed. In my first two contributions to this series (here and here) I undoubtedly came across as one who is disenchanted with science. Nothing could be further from the truth.
But I have seen good science, bad science, and indifferent science in a career that began as a dishwasher in a teaching laboratory. I hope I have contributed to the first of these, and I have no doubt that I have been party to some of the latter. Nevertheless, I am about to break Horowitz’s Law, named for my Introductory Sociology professor when I was a freshman many years ago: “Never generalize about your own limited experience!”
Horowitz was right, and his teaching has served me well for 40 years. But my experience has now been extensive at every level of research in the biomedical sciences. When the early work on bioluminescence described here commenced, grant review panels met to decide which applications not to fund. This does not mean that obtaining grant support was ever easy. But there was a time when positive expectations were reasonable, when the word “grantsmanship” did not exist.
I have written and reviewed grant applications for more than 30 years, and more recently I served for 10 years as co-chair and chair for a national review panel of a prominent funding agency. During this time, it became clear to me that a review panel can (just possibly) decide which applications are in the top third of the pool and should be funded and which are in the middle third and should be funded upon revision. A 67% success rate is about right. Most scientists are serious minded and willing to work hard. Preparing a research grant application is certainly hard work that can take a year or more. Those in the bottom third will remain hopeless for the duration.
Believable success rates for major public funding agencies are hard to come by because definitions of research awards are sometimes incommensurate with one another. But at NIH the recent pay line for extramural research project grants is ~20%. Or as we should view it: 80% of all research proposals remain in purgatory. In some institutes the success rate is in the single digits. I have a close colleague doing some very promising research on cancer. With the pay line of 8-9% at the National Cancer Institute, she, as someone who is not already a member of the club, she has virtually no chance.
The opportunity costs of such low success rates are not calculable, but they are large. What are we missing by picking the winners ahead of time, ranking one grant in the top-5% while there is no difference between that application and one that ranks in the top-30%? Had the current neoliberal project reigned in the 1950s would bioluminescence of obscure “primitive” animals have been funded? Probably not. Would someone have eventually figured out that GFP from a jellyfish could be used as the indispensable tool in cell biology? Probably not.
So the solution to this problem is similar to the solution to so-called evidence-based medicine: Scientific research funded with an open mind and disinterested expectations. Will some of the research yield indifferent results, or even no results. Of course, it will. But some if it will be revolutionary. We cannot know which ahead of time.
And in the long run, it will be less expensive to have an enlarged NSF and NIH (yes, we can afford both) fund the ideas that do not work while making sure that those that will work get the chance they deserve.
As a final note, while I was reviewing the literature referred to here, I noticed that the research groups who did the work were often small and the number of publications by the principal investigators not ridiculously large. There is something to this, alluded to by Karl Popper: “My own misgivings concerning scientific advance and stagnation arise mainly from the changed spirit of science, and from the unchecked growth of Big Science (certainly including Big Pharma), which endangers great science.” This great science is often done by very small groups of committed individuals.
If we as a nation are serious about building back better, this is one of many good places to begin.
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[1]E. Newton Harvey, A History of Luminescence from the Earliest Times until 1990. Philadelphia: The American Philosophical Society, 1957. Bioluminescence, New York: Academic Press, 1952.
[2]F.H. Johnson and Y. Haneda, eds. Bioluminescence in Progress, Princeton: Princeton University Press, 1966; P.J. Herring, ed.Bioluminescence in Action, New York: Academic Press, 1978.
[3]The Axiomatic Method in Biology(1937). Yes, I read this to the extent that was possible. It has been a long time, but the notation reminded me of Principia Mathematicaby Bertrand Russell and Alfred North Whitehead. A library with open stacks in a major research university is a wonder of the modern world.
