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.

An Ode to Darwin's Pigeons and to Wikimedia Commons

"... from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved. " With these words Charles Darwin closes his own most beautiful and most wonderful book, "The Origin of Species". But Darwin's case for his theory of natural selection therein has its own simple beginning, and not one having to do with an ancient or exotic organism, but with the species Columba livia, the humble rock-pigeon, that unremarkable denizen of our urban landscape.

I came to appreciate the importance of Columba livia to Darwin's argument only recently, as a result of undertaking a re-reading of "Origin" at the suggestion of Josh Gough, the organizer of the Atlanta Science Tavern Meetup. Although I was eager to re-familiarize myself with the famous text, to put it honestly, I wasn't looking forward to slogging my way through chapter 1, "Variation under Domestication", again. My interest in biology has always been with its most abstract concerns, so taxonomy, the naming, description and classification of animals and plants had never held much allure for me. But I had learned in the years since my first reading of "Origin" that Darwin's section on selection of domestic species, specifically pigeons, was crucial to the presentation of his greater theory. I was determined to understand why this was so, and I wanted to write about it.

This is where Wikimedia Commons came to my rescue.

In their own words, "Wikimedia Commons is a media file repository making available public domain and freely-licensed educational media content (images, sound and video clips) to all." To my good fortune, this repository contained a photo or illustration that was representative of each of the 10 or so domesticated pigeon breeds that Darwin mentions in his book. Their ready availability made this essay possible and the images themselves allowed me to see for the first time why the variation exhibited by these pigeon breeds was so central to Darwin's argument.

Take a moment to take a look at the following slide show, created with photos from Wikimedia Commons, which I've annotated with descriptions from "Origin", and, unless you are already a student of pigeons, you will be struck, as I was, with the astonishing differences among these breeds. (If you have trouble with the slide show or want to view larger images, please follow this link.)




To understand why the variation resulting from the domestication of pigeons was essential to Darwin's presentation of his theory of natural selection, one must fully appreciate the difficulty that Darwin faced in persuading his readers of the possibility that any ancestral population could generate, over time, individuals quite unlike themselves. How could it be that organisms as different as crocodiles and crocuses are related by common descent? Without recourse to knowledge of the mechanisms responsible for the modification and transmission of biological traits - much less a theory of genetics - why should anyone believe that living things possess the kind of intrinsic malleability that such enormous variation in form would demand?

Cue the pigeons.

These breeds, so different from one another, provided Darwin with compelling evidence that the potential for evolutionary change was, in fact, present in a single species, Columba livia. The implication was that, if such variation could be achieved with pigeons by means of breeding choices over the course of human history, then, perhaps, it was not unreasonable to imagine that the enormous variety of the biological world could have been achieved by means of natural processes over the the vast expanse of geological time.

For Darwin to make his case, though, it was not enough for him to demonstrate the striking variation in breeds of pigeon, he had to convince his readers that these breeds were, in fact, breeds of rock-pigeon, and not themselves each a descendant of a different "aboriginal" pigeon species. Darwin does this through several lines of argument. He speculates that is was improbable that "uncivilized man" had undertaken the domestication of so many different pigeon species; he notes the absence of existing wild populations of the hypothetical aboriginal types; he describes how crosses within each of the breeds exhibit markings of the proposed rock-pigeon ancestor; and, anticipating the modern definition of biospecies, he observes that the various pigeon breeds are capable of producing fertile "mongrel offspring". Finally Darwin concludes, "I can feel no doubt that all our domestic breeds have descended from Columba livia."

Using these pigeons Darwin developed a plan in "Origin" to fend off the challenges faced by any scientific theory based, not upon reproducible experiment, but upon historical evidence. Variation under domestication was the closest thing Darwin had to a laboratory to "test" his ideas. He understood that this "experiment" with pigeons was the unassuming foothold he needed in his book before he could begin his ascent to his bold and comprehensive view of the origin of the range of living organisms. The highly-varied domestication of Columba livia was Darwin's simple beginning, and his theory evolution by natural selection was its beautiful and wonderful descendant.


An Ode to Darwin's Pigeons and to Wikimedia Commons 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.

The Physics of Silly Names

Physicists are a silly lot, especially when it comes to naming things. Given some of the humdingers that they have come up with, you might think that they might have their very own Ministry of Silly Names (MoSN), something like the Ministry of Silly Walks, featured in a 1970 sketch from the "Monty Python's Flying Circus" television show.

Take, for example, the names given to the various types of quarks, those reclusive, fractionally-charged, point-like particles that are the building blocks of protons and neutrons. First, it would have to be conceded that the name quark, itself, is pretty silly - not surprising, given that it was selected because it sounds like the call of a duck. This silliness is only compounded when one notes that quarks don't come in types, they come in flavors - as though specifying a fundamental characteristic of some of the tiniest bits of matter was akin to ordering an ice cream cone at the neighborhood Baskin Robbins.

A little dignity is restored by the fact that the two "original" quark flavors have the unremarkable names up and down. To a good approximation, protons are constructed from 2 up quarks, designated, conventionally, by the letter 'u', and one down quark, designated by 'd'; neutrons, likewise, from 2 down quarks and one up quark.

The second generation of quarks flavors - more massive than up and down, so it took collisions created by high-energy particle accelerators to produce them in abundance - were given the apparently silly names, strange ('s') and charm ('c').

Strange, it turned out, was not all that silly a choice. When particles called K-mesons, or kaons, were first created, they were observed to decay into a triplet of garden-variety pions, but they took their good time doing so. Something "strange" was keeping them from decaying as quickly as had been expected. A special property was proposed, strangeness, to account for the kaon's longevity. Such a property, called a conserved quantity, is difficult, if not impossible, to shed - sort of like a bad cosmological penny. Thus, the kaon is stymied in its routine attempts to self-destruct, and must resort to slow-as-molasses assistance from the feeble weak interaction to get the job done. You see, the weak interaction doesn't hold strangeness in any special regard and would just as soon eradicate it as keep it around, of course taking in its own sweet time.

I wish I could say that there was a similarly dignified story to account for the origin of the designation charm as a quark flavor, but, to be frank, once strange found its way into the particle physics lexicon, a kind of silliness mania took hold. Indeed, the flavors of the third generation of quarks, then yet to be discovered, were christened beauty and truth by some silly researchers. There were fears - smirking hopes in some quarters, actually - that it would just be a matter of time before newspaper headlines would appear proclaiming such things as: "Beauty Revealed by Fermilab Scientists" or "Particle Physicists Seek Truth with New Accelerator". Something had to be done.

As a result, the Ministry of Silly Names put its foot down and a silly-name reformation was launched. When the quark dust settled, charm, old enough to sound quaint, was, graciously, grandfathered in, but beauty and truth were sent packing, replaced with the names bottom ('b')and top ('t'). How the silly how fallen!

Not going down without a fight, the forces of silliness mounted a rear guard action, so to speak. When the b quark was first created in particle collisions, it was always produced in conjunction with its antimatter counterpart, the b antiquark. So, given the way matter and antimatter cancel each other out, the particle that they formed possessed no net "bottomness". This was just the kind of opening that the silliness resistance needed. The search was on for creating a so-called B meson, a particle containing a single, unbalanced b antiquark, one that would brazenly show its "bare bottom". It was a last hurrah for quark name silliness.

Well, silly or not, the sextet of quarks - up, down, strange, charm, bottom, and top - have now all been detected, advancing the cause of the Standard Model of elementary particles, if not the cause of respectable physics names, considerably. This is as close as physicists have come so far to a long-sought theory of everything (ToE), and by that I mean a comprehensive theory of matter and energy and (most of) the forces of nature that has undergone rigorous experimental tests.

There is, though, one important piece still missing from from the Standard Model puzzle and it is called the Higgs particle, an eponym, named for the theoretician Peter Higgs, so hardly a silly name. Unfortunately, because of the pivotal role the Higgs plays in bestowing mass on other particles in the Standard Model, Leon Lederman, who, it turns out, was a co-discoverer of the b quark, nick-named it the God Particle. No doubt this nickname will be the inspiration for silly headlines when the Higgs is detected, as is likely to be the case, in the next couple of years. There's not much that can be done to avoid this embarrassment. Particle nicknames - much like Bush-era financial markets - are pretty much unregulated.

To put things in perspective, and to give the silly physicists their due, let's turn to the book of Genesis for some guidance about the challenge posed by naming things.

In the creation myth of the first chapter, after creating man in His image, God grants him dominion over every living thing. And in the creation tale of chapter 2, immediately after fashioning Adam out of dust,

the Lord God formed every beast of the field, and every fowl of the air; and brought them unto Adam to see what he would call them: and whatsoever Adam called every living creature, that was the name thereof.

How formidable a task for Adam - himself just now created - to be called upon to name things, things not only unfamiliar to him, but things entirely new to the world!

I imagine that Adam, struggled and stumbled, yet persevered, and came up with names for the animals, as commanded. No doubt, some of these names were fitting and clever, while others were out-and-out silly. But, what choice did Adam have? To have dominion over a thing means you have to call it by name.

To the list of attributes that have been used to characterize to our species - "thinker", "tool maker", "culture bearer" - perhaps, "namer" should be added. Physicists, as scientists, have taken on the task of discovering things entirely new to the world and, with that assignment, they have taken on the responsibility of giving names to the things they discover. We can hardly fault them for struggling and stumbling. We can hardly fault them, now and then, for coming up with silly names.