Season 2 Episode 2 - and he the end.

In this episode we discuss the extensive library on the HMS Beagle that was created by Charles Darwin and Robert Fitzroy.  Over 400 books were in the ship's library and the catalog had a heavy emphasis on travel accounts (travelogues), natural history and geology.  We discussed Humboldt and his influence on Darwin and Jeremy told the story about the dragon tree and Darwin's wish to travel the lands of Humboldt to see the same sights as Humboldt.
Dragon trees in the canary islands (picture from
Here is Humboldt's description of the dragon tree-
Although we were acquainted, from the narratives of so many travellers, with the dragon-tree of the garden of Mr. Franqui, we were not the less struck with it's enormous magnitude. We were told, that the trunk of this tree, which is mentioned in several very ancient documents as marking the boundaries of a field, was as gigantic in the fifteenth century, as it is at the present moment. It's height appeared to us to be about 50 or 60 feet; it's circumference near the roots is 45 feet. We could not measure higher, but Sir George Staunton found, that, 10 feet from the ground, the diameter of the trunk is still 12 English feet; which corresponds perfectly with the assertion of Borda, who found it's mean circumference 33 feet 8 inches, French measure. The trunk is divided into a great number of branches, which rise in the form of a candelabrum, and are terminated by tufts of leaves, like the yucca which adorns the valley of Mexico. It is this division, which gives it a very different appearance from that of the palm-tree*. [Humboldt, Alexander von. 1814-1829. Personal narrative of travels to the equinoctial regions of the New Continent, during the years 1799-1804. pgs 144-145]

Since 36% of the books in the Beagle library were travelogues, and Darwin's own Voyage of the Beagle is a travelogue, we invited Dr. Jeremy Paden, professor of Spanish Literature at Transylvania University, to discuss with us the role of travelogues in the 16th-19th century as a literature form.

During our discussion Jeremy highlighted Thomas Falkner as an influential travelogue writer who wrote  A description of Patagonia, and the adjoining parts of South America (1774).  Falkner described the region of Patagonia, a rugged area at the tip of of South America that also encompassed the Streights of Magellan.

The Streights of Magellan from Narborough, John. 1694
Unlike the map above which show the Straits of Megellan as a simple channel, the real Straits of Magellan are quite complex and convoluted as seen in the Google map below. Notice the large number of cul-de-sac inlets and waterways that can easy lead you astray.

We noted that the tip of South America looks more like a spongiform brain that has mad cow disease as shown in the image below, left image is a brain with Creutzfeldt-Jakob disease and brain on the right is normal brain.

James highlighted an unusual book in the collection - Werner's Colours, a small book that includes colour swatches that Darwin used as reference when he was taking notes of specimens.
Excerpt from Werner's Colours

You can peruse the entire Beagle library at the Darwin Online website.

At the end of the podcast we spoke with Dr. Paden about his own research and interest in poetry. James mentioned his appreciation of Jeremy's poem on the liver fluke parasite and we reprint it here-


Falling from the masticating jaws of ungulates
that clip the tips of grass blades, the black ant
escapes this evening’s immolation
and the circuitous route of cud-balls,
from stomach to teeth, stomach to teeth.

Ignorant of why it leaves the sweet feast
of slime balls secreted by common land snails,
come dusk, the ant climbs again the broad green
leaf to spend the night in sirshasana​,​
pinschers clamped ​to the end of a grass blade.

Larval lancet liver flukes, encysted
in snail-trail droppings, once eaten,​ move to​
the ganglion below the gullet,​ and force ​​
Formica fusca to climb​ the blade​ and
wait for the grazing cattle to come home.

If you are interested in reading more of Jeremy Paden's poems you can find his published book of poems concerning mining in Chile here or here.

Interlude music was Procreation by Little Glass Men

Season 2 Episode 1: Hot Coffee

 This is the first episode for Season 2 of Discovering Darwin. We have titled this season Darwin the Adventurer because we plan to explore in detail the Voyage of the Beagle, Darwin's five year around-the-world survey in which he collected the specimens and made the observations that ultimately led him to develop his theory of evolution and write On the Origin of Species.

In this episode we introduce the three major characters involved in the famous voyage- Captain Robert Fitzroy, Charles Darwin and the ship the HMS Beagle.
HMS Beagle in the Galapagos (painted by John Chancellor)

Josh introduced us to Pringle Stokes, the original captain of the Beagle during its maiden voyage (1826-1830) to South America on a survey voyage to map the Straits of Magellan at the tip of South America. However the HSM Beagle, a Cherokee class brig-sloop which were often derogatorily referred to as "coffin brigs", was a difficult ship to control in the severe winds, strong currents, high seas, and rogue icebergs that were typically encountered around Cape Horn. Josh explained how Pringle Stokes commits suicide on the ship in 1828 and Robert Fitzroy is assigned to captain the ship after Stokes demise.
Robert Fitzroy - photo by Hemus, Charles 1849?-1925
[Public domain], via Wikimedia Commons

We talked about the contingencies of history and how some tierra del fuegian children became the nexus for Fitzroy, Darwin and the HMS Beagle.  We will dedicate a later episode to the depressing tale of Jemmy Buttons, York Minister and Fuegia Basket, kidnapped tierra del fuegians who rejected their roles as Christian missionaries for England and forever haunted Robert Fitzroy and many others back in England.
Drawings by Robert Fitzroy

Because of Robert Fitzroy's short temper and willingness to lash out to those crew members he felt were wanting he was given the nickname "Hot Coffee" by the crew.  A meticulous man and data collector, Fitzroy would often retrace his sailing path to confirm his charts and maps, a level of meticulousness that would exasperate his crew and Darwin.
Fitzroy's iterative approach to sailing. Map from
Add caption

The opening and closing theme to Discovering Darwin is "May" by Jared C. Balogh. 

Chapter XV - Recapitulation and Conclusion

In this episode we discussed Chapter XV - Recapitulation & Conclusion from Darwin's Origin of Species. It is our final podcast of this season and we chose not to recapitulate as much as discuss how Darwin's book was received at the time and how Darwin handled the release of his book.

Although only 1250 copies of Origin of Species was published in the first edition, Darwin purchased 80 or so copies himself and Mudie's Circulating Library purchased 500 copies for use in their subscription service library, a service widely used by many middle class British folk.

It was through the subscription library that allowed Darwin's ideas to be widely distributed to the general public while fevered debates occurred in churches and academic halls.

The original 1859 publisher of Origin of Species was the Murray Publishing House book and the publisher was very generous in allowing Darwin to make corrections after the first printing run which is why the 2nd edition of OoS has a 1860 publication date.

We discussed how Darwin was often portrayed as an ape in cartoons published at the time. When we discussed the infamous images of monkey-like Darwin James erroneously associated those images with the famous Punch magazine but it turns out the ones he was thinking of came from other magazines of the time.
Charles Darwin considering the fashion of the time - the bustle (Fun magazine 1872)

 from The Hornet magazine, 1871

We really appreciate you listening to our podcast and we hope you return later this fall when we return with Season Two - Darwin the Adventurer.

The opening and closing theme to Discovering Darwin is "May" by Jared C. Balogh. 

Interlude music is bensound retro soul

Chapter XIV Embryology

This episode discusses Chapter XIV where Darwin applies his ideas of evolution and descent with modification to explain the developing "natural system" of classification, the unity of embryos and why organisms have rudimentary or vestigial organs.  

From the most remote period in the history of the world organic beings have been found to resemble each other in descending degrees, so that they can be classed in groups under groups. This classification is not arbitrary like the grouping of the stars in constellations. The existence of groups would have been of simple significance, if one group had been exclusively fitted to inhabit the land, and another the water; one to feed on flesh, another on vegetable matter, and so on; but the case is widely different, for it is notorious how commonly members of even the same sub-group have different habits.

Cuvier in 1817 proposed a system of classification that recognized animals as belonging to one of four forms  - Vertebrata, Mollusca, Articulata (arthropods) and radially shaped animals (Radiata).
image from
Darwin argues that the hierarchical system of classification mirrors his idea that new species formation mirrors the pattern of inheritance and genealogy we see in family tree. 
 A nice example is the phylogeny of placental mammals, those are mammals different from marsupial mammals (kangaroos, opossums, etc.) and monotremes (egg laying mammals like platypus)  in that they retain the embryo internally in a placental sac where they feed and protect the developing embryo. Placental mammals represent the majority of extant species of mammals today and seem to have evolved from three major geographical locations - Africa, Laurasia and South America. This is a a beautiful artistic representation of the placental mammal phylogenetic tree.

A comparison of early development of placental mammals from the Afrotheria clade (left most branch) shows similarities and divergences in the different types of mammals.

 [A.. Tenrec [tenrecoidea], B. Golden mole [Chrysochloridae] C. Elephant shrew [Macroscelididae] D. aardvark [Tubulidentata] E. Bush elephant [Proboscidae] F. dugong [Sirenia] G. hyrax [Hyracoidea] Image from Hautier, Lionel, et al. "Patterns of ossification in southern versus northern placental mammals." Evolution 67.7 (2013): 1994-2010.

Modern phylogeny and classification is based on Darwin's ideas of descent with modification and we now use DNA, RNA, and protein sequences to expand and improve our understanding of the relatedness of organisms


We have seen that the members of the same class, independently of their habits of life, resemble each other in the general plan of their organisation. This resemblance is often expressed by the term "unity of type;" or by saying that the several parts and organs in the different species of the class are homologous. The whole subject is included under the general term of Morphology. This is one of the most interesting departments of natural history, and may almost be said to be its very soul. What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include similar bones, in the same relative positions?

Homologous bone structure of tetrapod limbs

James attempted to differentiate homologous structures from analogous structures but showed how complicated it can be when discussing flying adaptations in mammals. As you can see in the figure above, the limbs of birds, bats, humans, seals and turtles contain the same bones in the same configuration making them homologous in morphology. What changes in the relative size to each other not their relative position. In vertebrates, the evolution of powered flight occurred independently three times - in Pterosaurs (reptiles), bats (mammals), and birds (again reptiles) so their wings are functionally analogoussince they are wings constructed of different specific materials. James erroneously said that the pterodactyl wing was from a super elongated index finger but in fact it is the 4th digit what we associate with the pinky finger.  We colored the figure below of a pterodactyl wing to conform to the color legend in the figure above.


Earnst Haeckel was a famous scientist in Darwin's time who applied Darwin's idea of the evolution of organisms in his studies of the embryonic stages of chordates

As Sarah mentioned this set of illustrations were updated but the overall conclusion does not differ. Follow this link to read a wonderful summary of the Haeckel embryo controversy with modern drawings and interpretation. Overall embryo development does show that chordates exhibit very similar and distinct stages of development whereas the adult forms can be quite different in form.

Rudimentary Organs
 Humans exhibit a number of traits, that we see in other mammals, but are degraded or rudimentary in their form. Some classic examples we discussed were the coccyx (tail bone), wisdom teeth and appendix but failed to mention the degrading nictating membrane in the corner of our eyes. In other chordates it is semitransparent film that can over the eye to clean and protect it. Ours is reduced to a little nubbin in the corner of our eye.

The opening and closing theme to Discovering Darwin is "May" by Jared C. Balogh.

interlude music is Otrov by Black Bear Combo

Geographical Distribution: Chapter XII-XIII

In this episode we gather our liquid strength and courage to work our way through two chapters of Origin of Species, Chapter XII - Geographical Distribution and Chapter XIII - Geographical Distribution continued.  Although Sarah predicted the podcast would last 3 hours we luckily were able to restrain ourselves to 1 hour and 28 minutes.

We do have two corrections to make-
#1  Although Josh declared that Noah's Ark came to rest on the top of Mt. Sinai the general view is that it actually settled on Mt. Ararat.

#2 James mentioned the relationship between flightless birds (ratites) and the breakup of paleocontinent of Pangea when he should have said Gondwanaland instead.

Chapter XII-XII
These two chapters have been present in OoS since the first edition and it is in these chapters that Darwin defends his model against the prevailing view of the time - special creation. To make his argument Darwin uses modern distribution patterns of plants and animals on continents and islands, the success of introduced species to new habitats, experiments he conducted at Down House and data he collected from citizen scientists.

Geographical Distribution 

There is hardly a climate or condition in the Old World which cannot be paralleled in the New—at least as closely as the same species generally require....Notwithstanding this general parallelism in the conditions of the Old and New Worlds, how widely different are their living productions!

Sarah discussed the idea of the monkeys from Africa (Old World Monkeys) are quite different from the monkeys found in South America (New World). In Madagascar are found the prosimians "almost monkeys" like lemurs, aye-aye, and sifakas.

By Joseph Meyer - MKL online at Retro Bibliothek, work 149, 2009, Public Domain,

On the continent of Africa are a large diversity of primates that range from leaf-eating species like the colobus monkeys to the generalist species like the vervet monkeys and baboons.  In addition gorillas and chimps which are tail-less apes are also in Africa (we realize that these are not monkeys but they needed to be mentioned none-the-less).
The New World monkeys are quite different in form, long limbed with many species having a prehensile tail which they can use as a 5th limb.

Josh talked about the rich diversity of marsupial mammals found in Australia, the most striking is(was) the Tasmanian Wolf, a marsupial carnivore that looks like a dog but it is more closely related to a kangeroo! Here is a haunting silent 1936 film of the last known living Tasmanian wolf filmed in captivity.

James discussed Darwin's interest in the flightless birds like the ostrich, cassowary, rhea, emu, tinamou and kiwi and Josh reminded us of the extinct Moa. This picture shows the relative sizes of the kiwi, ostrich and moa with the eggs. Notice how large the egg of the Kiwi is relative to its body size. It is the largest egg per body size while the ostrich egg is one of the smallest relative to the body size!
Until recently the prevailing view of flightless bird evolution was that the early flightless bird evolved before the continent of Gondwana broke up into the separate continents and then each lineage of flightless bird evolved on their prospective continents - Rheas in South America, ostrich in Africa, Emu in Australia and Kiwi and Cassowary in New Zealand. Recent molecular evidence has challenged that view and actually argues that "flightlessness" evolved independently three times.

We discussed the various experiments Darwin conducted with seed dispersal in salt water or in the guts of birds and fish as well as insects and seeds being dispersed on the feet of duck, swans and other semi-aquatic birds. James was reminded of a childhood story in a Dr. Dolittle book, Doctor Dolittle's Garden in which a beetle recounts being brought to England on the foot of a duck.

Sarah brought up the idea of endemics, and how unique species with limited geographic distributions are often found on islands or high elevation habitats which supports Darwin's model of isolation and speciation. Sarah used the Silversword as an example, a beautiful plant that is found only on the high elevations of Halaekala on the island of Maui in Hawaii. James exposed the beauty and elegance of the plant so here is a picture he took last May 2015.
Flowering silversword - photo by James Wagner

The opening and closing theme to Discovering Darwin is "May" by Jared C. Balogh.

interlude music Octopussy by Juanitos.

Chapter XI -On the Geological Succession of Organic Beings

Let us now see whether the several facts and laws relating to the geological succession of organic beings accord best with the common view of the immutability of species, or with that of their slow and gradual modification, through variation and natural selection.

In this episode we explore Chapter XI that deals with the fossil record and how patterns in the fossil record fit with Darwin's model of descent with modification. We begin the discussion with Darwin's views on extinction and how this phenomenon is part of his model of evolution. Sarah introduced the idea that extinction occurs at two different rates - normal background rate of extinction where species themselves have a measured lifespan based on how long they exist in the fossil record. Current analysis of the fossil record indicates that many species persist for a period of time and then go extinct. From this  data scientists calculate an average lifespan for a species - That is, how long in the geological record does a species typically persist? Many authors have written about this idea and many of their findings have been summarized in Extinction Rates, a book edited by J. Lawton, and R. May (1995).

Generally species lifespans are varied and biased by the size of the organisms. Small unicellular marine dinoflagellates have species "lifespans" in the 10's million years whereas large multicellular Cenozoic animals had a species 'lifespan" of 1-2 million years. These normal background rates of extinctions in the fossil record are punctuated by five massive extinction events where 75%-96% of all species went extinct. Sarah mentioned the dramatic "soot' line that demarcated the mass extinction event called the K-Pg (formally called the K-T) extinction event that occurred 66 million years ago. This extinction event was correlated with a thin layer of metal iridium that is visually and chemically distinct from rock material layers above and below the line. This layer was now thought to be have been created when a small asteroid impacted the earth near the Yucatan peninsula contributing to massive habitat destruction and climate change. These massive changes in climate are thought to have contributed to the extinction of all non-avian dinosaurs.

image from

Sarah recommended a book on extinctions by Peter Ward called Under a Green Sky: Global Warming, the Mass Extinctions of the Past, and What They Can Tell Us About Our Future (Harper 2008).

Affinities of past to current organisms

Let us now look to the mutual affinities of extinct and living species. All fall into a few grand classes; and this fact is at once explained on the principle of descent.

We discussed how many of the organisms in the fossil record can be directly related to species we see today - the wide array of extinct elephants themselves are a dramatic example of extinct forms being related to extant forms today.
image from

James spent some time explaining the background story of the archeopteryx fossil that was found in 1861 in Germany just after Darwin published Origin of Species.
Photograph: Jason Edwards/Getty Images
On the photo above notice the fingers on the wing and the long bony tail that extends off of the pelvis region. Museums are now creating displays that highlight the feathered dinosaurs that have been found in the past 10 years.  In 2016 the American Museum of Natural History opened a display that highlighted many new feathered dinosaurs.
 The relationship between organisms we see today to extinct versions in the fossil record is one of the stronger pieces of evidence that supports Darwin's model of descent with modification. In the next episode we will discuss how this relationship between extinct and extant organisms is actually restricted geographically, that is the mammals in the fossil record of South America are similar to the mammals you find in South America today, whereas they are different from those mammals you find, either in the fossil record or living, in Europe, Africa, Australia or Asia.

Ontongeny Recapitulates Phylogeny

Josh introduced the idea that embryos of organisms can reveal their evolutionary past since they often exhibit structures during development that are more fitting to earlier evolutionary forms. It was formally developed by the famous biologist Ernst Haeckel (1834-1919) in which he argued that organisms have developmental stages that represent earlier stages of their evolutionary heritage.
By Romanes, G. J. - Romanes, G. J. (1892). Darwin and After Darwin. Open Court, Chicago., Public Domain,
Although the drawing above has been discredited because Haeckel was said to have taken liberties in scale and overly emphasizing some structures, it is clear that early embryonic stages of many chordates exhibit clear gill arches and a well developed tail that becomes greatly reduced or lost during development. Josh queried us about what type of tail we would most prefer - foxy tail was by the far the best choice.

interlude music is

Chapter X - On the Imperfection of the Geological Record must the number of intermediate varieties, which have formerly existed, be truly enormous. Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely-graduated organic chain; and this, perhaps, is the most obvious and serious objection which can be urged against the theory. The explanation lies, as I believe, in the extreme imperfection of the geological record.  [406]

This episode focused on Darwin discussing the state of the fossil record, why he felt transitions may be rare and why he does not think the imperfection in the geological record was fatal to his theory. We discussed three of his major issues with the fossil record and then discussed the age of the earth and the sudden appearance of diversity in the fossil record. A phenomenon often referred to as the Cambrian Explosion.

How to make a fossil? 

One of the challenges of creating a fossil is avoiding the rapid decay and destruction of the organic material by bacteria, fungi and other decomposers.  The majority of the decomposers require oxygen to live so a successful fossilization event requires the remains to settle in an area that is anaerobic (anoxic for aquatic systems) (without oxygen). Anaerobic conditions occur in deeper waters where oxygen is slow to replenish from the surface, or it can occur in wet terrestrial systems like bogs or river banks where wet saturated soils can become anaerobic. We didn't mention in the podcast the amazingly preserved 1,000-2,000 year old humans discovered in peat bogs in Europe. These acidic and anoxic environments deter the growth of most bacteria and fungi.
image from:

This is a picture of a sheep that fell into a ditch that was then frozen over, although it is not technically a bog, it does show the difference between access and lack of access of decomposers to a body.
image from:
Ultimately the conditions that favor fossilization result in a bias in who gets fossilized which greatly biases and restricts the fossil record. In general you can say that to become a fossil you should be:
  • Small and abundant. The more abundant you are in the environment the more likely you could experience the rare opportunity to become fossilized. 
  • Live in or near an aquatic environment.
  • Have hard body parts than can resist decay. Scales, shells, bones, exoskeletons and woody material often resist decay whereas flesh, hair and soft tissue not so much.
  • If you are small, blind, sessile and attached to the sea floor you are more likely to become a fossil or fossil imprint than if you are large, active and run across the Serengeti or swim in the shallow, wave disturbed seas.
Although the fossil record is biased towards small, aquatic organisms there are museums full of large and dramatic fossils that contradict the rules above. So when you consider the improbability of a creature becoming a fossil the fossil record is actually quite impressive!

photo of Sue by James Wagner

Is evolution predictable?

James mentioned that evolution tinkered with different materials or metabolic pathways but ultimately settled on a few systems that are widely utilized across the diversity of life. In particular we discussed how evolution utilized many different chemical mixtures to create a hard support system (endoskeletal, shell, or exoskeleton) with an interesting alternative seen today in the "glass" sponges. Glass sponges utilize silica to create their hard spicules, the support material utilized by sponges to give strength and support to the jumbled array of barely specialized cells that constitute a sponge. Unlike most sponges which create individual spicules which they assemble with the organization that resembles a game of pick up sticks,

spicules by

the glass sponge silica spicules fuse into a large basket-like structure that remains intact after the sponge dies.
We discussed the crazy idea that early evolution experienced a fork in the road when it came to building a mineral based hard skeleton - it could have used silica as the material or calcium carbonate/phosphate. Josh mentioned the downside if we had evolved a glass skeleton.

We also discussed the other major evolutionary fork in the road - green versus purple photosynthetic systems. Here is a beautiful picture showing a mat of purple photosynthetic sulfur bacteria floating among a pad of green algae.

If we rewound the tape and replayed evolution could we have ended up in a purple world with fragile glass skeletons?

The opening and closing theme to Discovering Darwin is "May" by Jared C. Balogh. 
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Interlude music is Little Lilly Swing by Tri-Tachyon which is licensed under a Attribution License.