Is "Flat" Science "Real" Science?

In his informative - and entertaining - talk at the May meeting of the Atlanta Science Tavern, entitled Artificial evolution: a guide for hobbyists, Ichiro Matsumura, Associate Professor of Biochemistry at Emory University School of Medicine, began by reviewing the historical patterns of general scientific progress and proceeded to focus on his research efforts which attempt to explain how complex biochemical pathways of cells originate and adapt. He concluded his presentation by discussing the emerging community of unorthodox "scientists", well outside the academic and corporate mainstream, who are pursuing experiments similar to his own, but in kitchens and basements, far removed from the luster - and expense - of state-of-the-art university laboratories.

So, in some ways Ichiro's talk was a presentation of his recent discoveries about how complex cellular processes evolve, but in other ways it was a call for science to return, at least in part, to its table-top roots. Apparently, these days an amateur with a few hundred dollars and kitchen counter space to spare can purchase the materials and equipment necessary and, in short order, alter the genetic makeup of commonly available bacteria. For Ichiro this represents a "flattening" of the scientific enterprise, a welcome alternative to the "hierarchical" restrictions of conventional science that require not only professional credentials, but large sums of money, often acquired only after running the exhausting grant application gauntlet of established funding agencies.

I share Ichiro's excitement for the opportunity that these low-cost-of-entry home laboratories have created for more people to become involved in science-oriented hobbies. Like him, I think that, within the constraints demanded by public safety, this kind of experimentation should be encouraged. Also, like Ichiro, I believe that the spread of these do-it-yourself labs is inevitable. With increasing economies of scale, the costs will only drop and, with Internet resources, the essential technical information will only become more available. The genie is out of the bottle, as they say.

Where I believe I disagree with Ichiro has to do with whether this new field of DIY genetic engineering, "flat" as it is, constitutes "real" science and whether the hierarchy problem of modern science is, in some fundamental way, avoidable.

Now, although I am not prepared here to define science in any comprehensive sense, I do think that a case can be made that hobbyism, for lack of a better word, is not science. Another way of stating my position is to say, "a laboratory does not a scientist make." By making this distinction I do not intend to demean hobbyists or, conversely, to put scientists on a pedestal, but to point out what I believe is a critical feature of the scientific enterprise, and that is the obligation to communicate the details and results of one's investigations so that they can be subjected to public scrutiny and, where appropriate, correction, and so that they may also serve as a basis for further investigation.

Consider, for historical comparison, the too-much-maligned alchemists of the middle-ages. They were hobbyists extraordinaire and, in a very real sense the proto-scientists who laid the groundwork for the science of experimental chemistry that was to follow. I doubt that they lacked the brains or the temperament to be real scientists. What I do think that they lacked, in particular, were a reliable postal system and other ready means to publicize the results of their laboratory work.

The advent of the printing press and of the establishment of a network of roads and public services that made possible the routine delivery of mail over long distances addressed these deficiencies, to some extent. But these innovations were not in themselves sufficient to transform hobbyism into the science that we know today. For this to happen, "natural philosophers" who were involved in the publication of books and the exchange of letters had also to form organizations to distribute and discuss the results of their scientific investigations. In this regard, one could argue that the founding of the Royal Society in 1660 marked the beginning of what we would call modern science. It also likely marked the beginning of the kind of hierarchy problem for science that Ichiro referred to in his talk (not to be confused with the hierarchy problem that besets physics today.)

I imagine that in the 17th century the number of reports and opinions about scientific matters - even concerning a relatively specialized area of research - far exceeded what any individual could consistently review. In a world awash in scientific findings how does one begin to decide whom to trust without resorting to expert opinion? Although our democratic inclinations tend to imbue us with a reflexive disdain for "elites", we have no choice other than to rely on people whose experience and judgment are widely recognized. Once experts are designated, either, in the 17th century, as celebrated fellows of the Royal Society, or, today, as the anonymous peers who enact the review process characteristic of the contemporary funding and publication of science, a hierarchy is created.

Of course such stratification of scientific authority is not without its perils. It brings to mind the age-old conundrum, captured by the Roman poet Juvenal with the query, "who will guard the guards themselves?" A delicate - and unavoidable - balance must be maintained between what, on one extreme, would result in lifeless orthodoxy and, on the other, in intellectual chaos. This is, in some sense, the sociological challenge of modern science, to effectively filter the vast amount of new information that is generated while not censoring well-considered novel contributions that threaten the established order. It's a tough job, but someone's got to do it.

So, once again, let's hear it for those folks who are enthusiastically working away in their at-home laboratories modifying bacterial genes. Like the alchemists before them, they are involved in a personal process of discovering fascinating new things about the nature of the world. But, until their private investigations become public ones and they engage in the kind of dialog that leads to the dissemination and review of their discoveries, they will remain hobbyists, not scientists. And, like it or not, when they choose to cross the divide which demands that they publish their findings and subject them to the criticism of their peers, gatekeepers will, of necessity, arise to manage the, otherwise, overwhelming flow of information. The problem of hierarchy will be born anew. There's no way around it.

This I Don't Believe

Let's suppose you had the opportunity to interview a judge who had recently published an opinion on an important criminal case, one in which she had found, for purposes of concreteness, in favor of the defendant. Your questions turn to the matter of the judge's objectivity, and then it is revealed that the judge has had a long-standing prior relationship with the accused.

Pressing the issue you ask whether this relationship may have influenced her decision. "No, not at all," she responds. "On the contrary, my acquaintance with the defendant didn't skew my judgment, it helped to inform my decision."

At this point in the interview you may begin to doubt - not necessarily the judge's personal integrity, since she may, after all, have had no untoward interest with regard to the outcome of the case - but her judicial faculties. Does she understand the concept of objectivity well enough to realize that it requires that she distance herself from her prejudices and, most certainly, not rely on them?

Such a failure to appreciate the meaning of objectivity is illustrated in a recent interview with Barbara Bradley Hagerty, NPR reporter and author of the forthcoming book, Fingerprints of God, by Weekend Edition Sunday host Liane Hansen. By virtue her authorship Hagerty has positioned herself as a judge of the question, "is spiritual experience real or a delusion?" Although Hansen broaches the issue that Hagerty's upbringing as a Christian Scientist might have affected her analysis, Hagerty proceeds to insist that, in fact, "Christian Science really helped me with my research."

Hagerty goes on to claim that "Christian Science was about 100 years ahead of its time," based on her dubious equation of Mary Baker Eddy's belief in prayer-healing with the emerging field of mind-body studies called psychoneuroimmunology. In this regard, she succeeds, somehow, in demeaning both religion and science. We would all agree that Christian Science is more than simply a theory about emotional health affecting physical well-being (that was hardly breaking news in the 19th century) and, likewise, we would agree that nowhere do contemporary scientific studies of the human brain presuppose supernatural influences on neurological function.

What is, perhaps, more troubling about the interview, having nothing to do with Hagerty's particular take on the religion-science debate, is that it calls into question whether NPR is adhering to its own professional standards. Specifically, the piece opens with the statement:

The golden rule of journalism decrees that reporters take nothing on faith, back up every story with hard evidence, and question everything. NPR's religion correspondent Barbara Bradley Hagerty kept that rule in mind when she decided to explore the science of spirituality.

This is hardly borne out by the exchange between Hansen and Hagerty that follows.

Is it appropriate for NPR to bestow the imprimatur of objectivity on Hagerty's tendentious opinions about religion and science without criticism? It would be one thing if she had simply endeavored to report on the contemporary scientific understanding of the origins religious experience, but Hagerty goes much further. She concludes in the interview, explicitly, that belief in God is a rational choice. This is a profound, and profoundly contentious, question that should not be presented without challenge.

Indeed, the interview and the 5-part series that it previews, Is This Your Brain on God, could be confused with a promotional campaign for Hagerty's upcoming book. Here NPR's own standing as fair "judge" could be called into question. Is Hagerty's book being featured for its merits or is it, to some extent, receiving the spotlight based on its author's long relationship as a reporter for the news organization? To the extent that Hagerty takes a disputed position on a matter of public importance, isn't it incumbent on NPR to present alternative points-of-view? I'm not sure whether NPR, like the New York Times, has a public editor to consider such concerns, but it would seem that its own journalistic standards would demand such consideration.

Cautious Darwin, a Fossil Sneeze, and the Real Octomom

Charles Darwin was a cautious scientist. More than 20 years passed between the conclusion of his voyage on the Beagle, during which he made many of the observations that would impel the development of his theory of natural selection, and the publication of his world-transforming work, "The Origin of Species". Darwin understood the potential trouble posed by the iconoclastic things he had to say, both with respect to his personal life - his wife Emma was a devout Christian - and with respect to his standing in the scientific community.

Although we imagine now that Darwin had "nailed it" when he published "Origin" in 1859, there were significant elements of his nascent theory that were subject to reasonable challenge. For one thing, Darwin had no knowledge of the mechanisms of inheritance upon which his process of natural selection relied. It would be half a dozen years before Gregor Mendel's discoveries involving plant hybridization would be published, and these would go largely unnoticed for another three decades. How, indeed, were "favored traits", so central to Darwin's hypothesis, transmitted from generation to generation? Without anything like a theory of genetics, Darwin hadn't a clue.

To make matters worse, Darwin was painfully aware of the problems presented by what he called "the imperfection of the geological record", enough so that the topic merited a chapter of its own in his book. The absence of fossil evidence for transitional species - so-called missing links - was a vulnerability that Darwin addressed as best he could. Today we can make allowances for the fact that the collection and identification of paleontological specimens was then still in its infancy as a systematic enterprise - a defense that was hardly available to Darwin at the time. Much to the chagrin of creationists, who - contrary to the wealth of discoveries made in the last 150 years - insist that these deficits in the fossil record remain, few missing-links have gone missing. In fact, the contemporary fossil record is rich in finely graduated intermediate forms.

It does turn out that Darwin was wrong about one claim he made in "Origin" with regard to fossilization, one that underscores his cautious expectations. In enumerating the many limitations of geological evidence, he despaired that "no organism wholly soft can be preserved." Shells and bones are all that we could count on, according to Darwin, and even they "can disappear when left on the bottom of the sea".

Meet Keuppia levante, a 95-million-year-old octopus, whose fossilized remains were recently discovered by Dirk Fuchs and fellow researchers from the Freie Universität Berlin and announced March of this year. Since octopuses consist pretty much of muscle and skin, what isn't eaten almost immediately by scavengers upon their demise, decays rapidly into a blob of slime. The odds of finding a fossil octopus have been compared to those of finding a "fossil sneeze". Looking at this Cretaceous-era octopus, so exquisitely preserved in Lebanese limestone, it would appear it is about time - finally - for someone offer an appropriate "fossil gesundheit".

What is, perhaps, more remarkable, according to Fuchs and his colleagues, is how closely this ancient specimen resembles its present-day descendants. Such invariance in form would have come as a surprise to Darwin, since his conception of evolution by natural selection imagined the accumulation of favored differences - gradually, but inexorably - over time. To him, the probability of a particular species remaining largely unmodified over the eons of geological time would have seemed to have been astronomically small.

(As an aside I'll note that this "error" on Darwin's part serves to remind us that, although his were the first words in the theory of evolution, they are certainly not the last. Unfortunately, there is a tendency in some quarters to equate Darwin's hypotheses in "Origin" with our current understanding of the process of natural selection. Enough confusion exists that some suggest, "let's get rid of Darwinism," declaring to the world, in all deference to the master, that we have, in the last 150 years, moved significantly beyond many of his original proposals. I think they have a point.)

But, although Darwin could possibly be faulted for not anticipating that, by dint of the hard work of 21st century paleontologists such as Dirk Fuchs, fossil sneezes, such as Keuppia levante, would ultimately be unearthed, there is a method available today to evolutionary science to probe the biological past that he could never have anticipated in his wildest dreams - namely, the analysis of the DNA of living creatures.

With this in mind, allow me to introduce Megaleledone setebos or, as I call her, the real octomom.

Thirty million years ago octomom or, more accurately, members of a species quite similar to hers, roamed the waters surrounding Antarctica. Sea ice was, for the first time, massing on the surface, removing fresh water from the Southern Ocean and leaving below it a highly saline environment enriched in oxygen - a fitting octopus habitat. As the climate continued to cool and the Antarctic ice shelf grew, streams of these salty, oxygenated waters flowed northward along the ocean floor carrying with them octomom's sisters and cousins, who would, themselves, become the founding mothers of new, distinct deep-water octopus species in other parts of the globe.

How do we know the details of this octopus "out of Antarctica" saga? Since they are so exceedingly rare, scientists couldn't use fossilized octopus remains to reconstruct this prehistoric exodus, so, absent a fossil record, they turned to the genetic one, the record written in the DNA of the cells of octopuses living today.

Thanks to the work of the Census of Marine Life, a decade-long project begun in 2000 "to assess and explain the diversity, distribution, and abundance of marine life", specimens representing a number of the living species of deep-sea octopuses were collected and delivered to researchers at Queens College in Belfast. There, by analyzing extracted DNA, biologist Jan Strugnell was able to formulate a family tree for these creatures which not only demonstrated the extent they were related to one another, but also resulted in a calculated genetic profile for their common ancestor, who, although 30 million years older, turns out to be a dead ringer, so to speak, for Megaleledone setebos, our very own octomom.

Darwin's misstep in doubting the possibility of the fossilization of organisms consisting almost entirely of soft tissue is quite understandable. How could he have anticipated the discovery of a fossil sneeze? His concerns about the deficiencies in the geological record have been - and continue to be - addressed and rectified by the diligent work of paleontologists, who, from all appearances, leave no stone unturned. To augment these traditional methods of evolutionary investigation researchers use the tools of molecular biology and genetic science now at their disposal. These allow them to peer into the deep time of the history of life on earth using DNA from the cells of living organisms - a window into the past that Darwin could not have imagined.

All said, Darwin would, no doubt, be astounded by and proud of what his scientific heirs have made of the simple - and cautious - beginnings of his theory of evolution by natural selection.


Cautious Darwin, a Fossil Sneeze, and the Real Octomom by Marc Merlin is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 United States License.
Based on a work at thoughtsarise.blogspot.com.