Despite this usage, most of us know that randomness has something to do with probability, and that it often implies a lack of conscious intentionality. But what do mathematicians and scientists mean when they say something is random? Can a random process lead to an ordered, even predictable outcome? Is there evidence that God makes use of random processes to fulfill his creative purposes?

These are big questions, and we won’t address them all today. But I think randomness is an important topic to cover for two reasons: 1) it is integral to many processes in biology (and math, physics, chemistry, etc.), and 2) it is commonly misunderstood to be incompatible with Christianity.

As I said above, most of us know that randomness has something to do with probability. If you pick a card “at random” from a shuffled deck, you have a small probability of drawing an ace (4 out of 52, or a 7.7% chance). If you flip a coin, you have an equal probability of getting heads or tails.

Randomness also seems to imply a lack of intentionality or purposefulness. After all, you might hope for an ace when you draw a card, but you can’t choose one on purpose. You might call heads when you flip a coin, but you can’t know beforehand what the outcome will be. Thus the outcome is indeterminate, but is it purposeless? Not necessarily. Indeterminacy simply means the result cannot be predicted from the outset.

It should be noted that indeterminacy does not imply that God does not have foreknowledge of future events. Christians ought not to be uncomfortable with the idea of God interacting with his creation through chance. We often describe a seemingly-random (i.e. unplanned by us) sequence of events as being “providential,” or planned by God.

In biology, it is very hard or impossible to calculate precise probabilities for most processes, so when we say a process is random, we typically mean it is extremely unpredictable. Eventually we will discuss randomness within biological evolution, but first we must consider some simpler processes, like the self-assembly of a virus.

Viruses are remarkably efficient entities. Coiled tightly within a protein-based shell is a small amount of DNA needed for self-replication. The shell, called a capsid, is made of many repeating protein subunits and is therefore highly symmetrical (see figure). Important biomedical insights have certainly been gleaned from structural studies of viruses, but viruses also teach us about the emergence of order from non-order.

The virus life cycle has four main steps: 1) enter a host cell, 2) hijack the cell’s replication and translation machinery to make many copies of itself, 3) assemble into many virus particles, and 4) exit the cell to invade another host.

When I first learned about this process, I found it very hard to believe it just “happens.” The idea that a bunch of molecules bumping into each other inside a crowded cell could spontaneously assembly into a fully-functional virus seemed a bit far-fetched. Many viral capsids have over 100 protein subunits that must interact with each other in just the right way, or it won’t work. Surely there must be something driving this process, right?

There is! Random motion. I had to see it to believe it. I distinctly remember sitting in class during my first year of graduate school when the professor demonstrated self-assembly of a virus using a 3D model as shown in the following video. In less than 30 seconds, you can watch a jumbled heap of proteins become a beautifully ordered structure.

As the narrator explains, sub-assemblies form and break apart en route to the most stable structure, the full capsid. As the sub-assemblies begin to form, further associations with free subunits become more favorable and as a result occur rapidly, while the final steps may take considerably longer. While the subunits in the model are rigid, in reality the proteins take on multiple conformations, allowing the capsid to “breathe.”

Amazing as it is, the system we just considered—one virus capsid in a jar—is pretty simple. One wonders how self-assembly can happen in a crowded cell, where there are countless other molecules diffusing around, potentially getting in the way. We can’t directly see how it happens in a cell, but we can reconstitute the process in a test tube using different combinations of constituent molecules.

Consider two viruses, where each protein subunit in one virus is the mirror image of the corresponding subunit in the other. Putting the two viruses together by hand would be pretty tricky, because the constituent parts look so similar. But random motion can do the job in short order:

From this model, we can see clearly, in real-time, how distinct complex structures can arise from their parts randomly interacting with one another. Many large viruses also use special scaffolding proteins to assist in the assembly process, and some even use their own genomes as a scaffold. In addition, two closely-related viruses that happen to infect the same cell can exchange parts to create a new virus. This is one way viruses can evolve quickly to evade the host’s immune system.

Here we have seen how viruses demonstrate a principle inherent in God’s world—that order can emerge out of chaos from random processes. In my next post, we will look at some other biological processes that make use of—rather, depend on—randomness. This will set the stage for us to see that such processes can not only assemble a structure within seconds or minutes, but also generate complex, information-bearing molecules over billions of years. Even though the freedom inherent in nature sometimes produces unintelligently-designed structures (like viruses, which can kill us), we see that God has made, and continues to oversee by his providence, a good creation that, at least in part, is capable of creating itself.

Next weekend, we’ll continue this series about randomness and God’s divine will. Up next: how God created the body to heal itself, and how can random mutations can be both harmful and benign.

Like any theory, Darwin’s idea that evolution proceeds through natural selection was once merely a hypothesis. In this post, we’ll look at some of the early observations Darwin made on biogeography: the study of where species are distributed across the globe. These lines of evidence would later prod him to consider the possibility that species arise through a natural process of gradual change over time, rather than being independently created in each location where they are found.

The curious case of the missing mammals

As a widely-travelled naturalist on the HMS Beagle, Darwin studied a large number of different environments and documented the species he found in each. The Beagle, engaged as it was in an effort to map the coastline of South America, naturally paid call to numerous island groups along the way, including islands at a great distance from a continent (i.e.oceanic islands). One observation that Darwin made about oceanic islands is that none that he studied had terrestrial mammals on them. Later work, after his voyage, would confirm that this was a general rule. Oceanic islands lack terrestrial mammal species, except for small species that were introduced by humans. In contrast, flying mammals (i.e. bats) were found on oceanic islands, and often these species were endemic (i.e. found nowhere else in the world but the island in question).

Darwin found these observations difficult to square with his (then) working assumption that species were independently created in (and specifically created for) the locations in which they are found across the globe. He discusses these observations, and the questions they raised in his mind, in two chapters entitled “Geographical Distribution” in his Origin of Species. After discussing the similar case that amphibians (such as frogs, newts, and so on) are also not to be found on oceanic islands, he turns his attention to the missing mammals:

Mammals offer another and similar case. I have carefully searched the oldest voyages, but have not finished my search; as yet I have not found a single instance, free from doubt, of a terrestrial mammal (excluding domesticated animals kept by the natives) inhabiting an island situated above 300 miles from a continent or great continental island.... It cannot be said, on the ordinary view of creation, that there has not been time for the creation of mammals; many volcanic islands are sufficiently ancient, as shown by the stupendous degradation which they have suffered and by their tertiary strata: there has also been time for the production of endemic species belonging to other classes; and on continents it is thought that mammals appear and disappear at a quicker rate than other and lower animals. Though terrestrial mammals do not occur on oceanic islands, aërial mammals do occur on almost every island. New Zealand possesses two bats found nowhere else in the world: Norfolk Island, the Viti Archipelago, the Bonin Islands, the Caroline and Marianne Archipelagoes, and Mauritius, all possess their peculiar bats. Why, it may be asked, has the supposed creative force produced bats and no other mammals on remote islands? On my view this question can easily be answered; for no terrestrial mammal can be transported across a wide space of sea, but bats can fly across. Bats have been seen wandering by day far over the Atlantic Ocean; and two North American species either regularly or occasionally visit Bermuda, at the distance of 600 miles from the mainland. I hear from Mr. Tomes, who has specially studied this family, that many of the same species have enormous ranges, and are found on continents and on far distant islands. Hence we have only to suppose that such wandering species have been modified through natural selection in their new homes in relation to their new position, and we can understand the presence of endemic bats on islands, with the absence of all terrestrial mammals.

(As an aside, it’s important to note that Darwin, when he discusses the “supposed creative force” is not here arguing against the existence of God as creator in general, but rather against the “ordinary view of creation” common at the time: that God had episodically created species at specific geographical locations (what were called “centers of creation”) and that biogeographical patterns could be explained with limited dispersal from those centers. Darwin himself held to this common view at the start of his voyage on the Beagle, and that is the model he is attempting to refute in Origin, since it was a prevailing view among scientists at the time. Darwin and many of his scientific contemporaries also had no difficulty viewing natural processes as part of God’s regular action in the world, as is evident in Darwin’s correspondence with American botanist Asa Gray, among others.)

So, for Darwin, his biogeographical observations sat at ease with his (later) ideas of colonization and subsequent species change through natural selection, but made no sense to him if one held to an independent creation model. Many oceanic islands were very old, yet no mammals had been created there. Many oceanic islands had habitat suitable for mammals (or, indeed, for amphibians, as he notes) yet no such species had been created for that suitable habitat.

Island endemics and their continental “allied species”

Darwin noticed more than the absence of certain species groups on oceanic islands. He also noticed an interesting feature of the species that were present: an endemic species on an oceanic island would often have strong similarities with a species on the mainland closest to the island in question. Additionally, the pairing of oceanic endemic species with continental species often seemed to override expectations that species found in similar environments would be more similar to each other. These observations prompted him to reflect further on the possible means by which these “closely allied species” arose. As Darwin would write in his Origin this repeated pattern made a significant impression on him, and further caused him to doubt that endemic species had been individually created for each oceanic island. His visit to the Galapagos would prove instrumental on this point:

The most striking and important fact for us in regard to the inhabitants of islands, is their affinity to those of the nearest mainland, without being actually the same species. Numerous instances could be given of this fact. I will give only one, that of the Galapagos Archipelago, situated under the equator, between 500 and 600 miles from the shores of South America. Here almost every product of the land and water bears the unmistakeable stamp of the American continent. There are twenty-six land birds, and twenty-five of these are ranked by Mr. Gould as distinct species, supposed to have been created here; yet the close affinity of most of these birds to American species in every character, in their habits, gestures, and tones of voice, was manifest. So it is with the other animals, and with nearly all the plants, as shown by Dr. Hooker in his admirable memoir on the Flora of this archipelago. The naturalist, looking at the inhabitants of these volcanic islands in the Pacific, distant several hundred miles from the continent, yet feels that he is standing on American land. Why should this be so? why should the species which are supposed to have been created in the Galapagos Archipelago, and nowhere else, bear so plain a stamp of affinity to those created in America? There is nothing in the conditions of life, in the geological nature of the islands, in their height or climate, or in the proportions in which the several classes are associated together, which resembles closely the conditions of the South American coast: in fact there is a considerable dissimilarity in all these respects. On the other hand, there is a considerable degree of resemblance in the volcanic nature of the soil, in climate, height, and size of the islands, between the Galapagos and Cape de Verde Archipelagos: but what an entire and absolute difference in their inhabitants! The inhabitants of the Cape de Verde Islands are related to those of Africa, like those of the Galapagos to America. I believe this grand fact can receive no sort of explanation on the ordinary view of independent creation; whereas on the view here maintained, it is obvious that the Galapagos Islands would be likely to receive colonists, whether by occasional means of transport or by formerly continuous land, from America; and the Cape de Verde Islands from Africa; and that such colonists would be liable to modification;—the principle of inheritance still betraying their original birthplace.

Many analogous facts could be given: indeed it is an almost universal rule that the endemic productions of islands are related to those of the nearest continent, or of other near islands.

Rethinking independent creation

For Darwin, both of these observations (that oceanic islands lacked terrestrial mammals, and that endemic species on islands were most similar to a species on the closest mainland) had the same explanation: his hypothesis that endemic, oceanic species were the modified descendants of a colonizing species from the nearest continent. This also explained the lack of amphibians and terrestrial mammals (but allowed for bats) - simply based on the ability of these classes of life to disperse across large expanses of ocean. Those that could disperse and colonize oceanic islands would experience modification in the new environment, and species unable to colonize these islands would never appear. To Darwin’s thinking, this explanation was wholly more satisfactory than the assumption that God had independently created every endemic species in its place, and arbitrarily chosen that oceanic islands did not need terrestrial mammals and amphibians.

Despite Darwin’s musing on the biogeographical patterns he observed, and the strong suggestion these patterns made of species change over time, a mechanism for that change would take some time for him to imagine. In our next post, we’ll look at that mechanism: Darwin’s idea of natural selection, and the evidence he assembled in its support prior to publishing the Origin.

Grantees will benefit from in-person interaction through a series of summer workshops in 2013, 2014, and 2015. These meetings will not only foster a broader knowledge base, but will build a sustained network of scholars and church leaders, both young and seasoned, who are serious about addressing the concerns of the church about evolution. Also in 2015, in connection with the third summer workshop, BioLogos will host a large conference open to scientists, scholars, and church leaders from around the world.

ECF History

In January 2012, BioLogos was awarded a multi-million dollar grant from the John Templeton Foundation to fund the work of scholars and church leaders on evolution and Christian faith. In spring 2012 we worked hard to get the word out. You may have seen announcements on the BioLogos website, in our newsletters, on the Books & Culture, Leadership Journal, or First Things websites, on your professional society’s listserv, or perhaps on your friend’s blog.

The response was overwhelming: we received 225 letters of intent for a total request of $21 million—about seven times the amount we had to offer. We needed to invite the most promising applicants to submit a full proposal, but recognizing the projects with highest potential would require broad expertise. From the beginning, we envisioned that a panel of scientists, pastors, and scholars would oversee the application and review process as well as play key advisory roles throughout the project. A team of eight highly qualified individuals came on board in the early months of the project. They reviewed each proposal and together recommended that BioLogos invite 86 applicants to submit full applications.

The deadline for submissions was October 1, 2012. As in the previous round, the ECF panel evaluated each proposal. In addition, we asked 55 other experts to participate, so that each proposal received 3-4 scores. Criteria for the decision included significance of topic, project design, creativity and innovation, long-term impact potential, feasibility, and budget.

The panel then met together November 29-30, 2012, to make the final funding decisions. In the end, they recommended that BioLogos give 37 awards, ranging from $23,000 to $300,000. BioLogos staff notified applicants of their awards on December 14, 2013.

The Grantees

As part of our objective to create a network of scholars and leaders, we awarded grants to organizations across the U.S. and the world. Thirty of the 37 grantees are domestic; seven are international, hailing from Canada, France, Great Britain, Netherlands, and Spain.

Two-thirds of the accepted projects will be led by teams—some with three or more Project Leaders. We expect that the teamwork and time spent together at our summer workshops will be the start of a long-lasting network of people dedicated to helping the church think carefully about origins.

Applicants chose to apply under one of three program tracks: interdisciplinary scholarship (Track 1), intra-disciplinary scholarship (Track 2), and translational projects (Track 3). Track 1 projects focus on both the collaboration between individuals in different disciplines and the development of projects at the interface of different content areas. Track 2 projects focus on work done within a specific discipline. Track 3 focuses on projects that encourage Christians, especially those within more conservative traditions, to engage in meaningful and productive dialogue to reduce tensions between mainstream science and the Christian faith. The numbers of grantees in Tracks 1, 2, and 3 are 6, 8, and 23, respectively.

Many of the scholarly projects tackle questions about Adam and Eve, the Fall, human identity, and Original Sin—some of the most critical interpretive issues for evangelical theology.  Some examples: 

• Theologian Oliver Crisp of Fuller Seminary will take an analytic theology approach to ask to what extent a theological account of the origin of human sin depends upon the evolution of modern humans from one and only one ancestral pair—especially if that pair does not appear to correspond to what we would think of as modern human beings. 

• Pastor Michael Gulker and philosopher James Smith, leading a large team from The Colossian Forum, ask a related question: if humanity emerged from non-human primates—as genetic, biological, and archaeological evidence seems to suggest—then what are the implications for Christian theology’s traditional account of origins, including both the origin of humanity and the origin of sin? 

• Biologist Dennis Venema of Trinity Western University and New Testament scholar Scot McKnight of Northern Seminary will write a book on the evidence for evolution and population genetics, with informed theological reflection on how these issues interact with orthodox Christianity.

• Biologist David Wilcox of Eastern University will develop an updated model of human identity which reflects the complex recent scientific advances in genetics and paleoanthropology and yet is sensitive to theological concerns.  

These are just a few of the scholarly awards; check out the Grantees page for full descriptions of all Track 1 and Track 2 projects.

All projects have translational potential, but Track 3 projects are designed to meet the needs of a particular constituency within the evangelical church. These projects run the gamut from ethics to education to media production to ministry resources.  Some examples include:

• Theologian Lee Camp of Lipscomb University will produce “The Questions in Monkey Town,” an episode of Tokens, a live variety show that features musical performances, comedic sketches, brief interpretive monologues, and dialog with authors and scholars. The episode will be performed and filmed on the site of the famous Scopes Trial in Dayton, Tennessee.

• Chaplain Joshua Hayashi and Educator Diane Sweeney of the Punahou School in Hawaii will lead a team to produce multimedia curricula aimed at helping high school students connect with their biology curricula and, at the same time, deepen their Christian faith.

• Physics teacher and pastor Benoît Hébert of Science et Foi Chrétienne in France will lead an international, multi-denominational team of French speaking Evangelical scientists, pastors and church leaders to produce a large number of resources on evolutionary creation.

• Pastor Seung-Hwan Kim of Grace Truth Community Church, a Southern Baptist church in Cambridge, Massachusetts, will produce teaching and preaching materials about evolution for church leaders.

• President Gregory Wolfe and Director of Resource Development for IMAGE will gather artists and writers of faith whose work explores the dialogue between evolutionary science and faith practice, convening a conversation between them and scientists, theologians, and church leaders in private and public conferences.

Again, this is just a taste of the diversity of Track 3 projects. Read more about each project on the Grantees page. You can look forward to an incredible variety of resources coming out of the ECF program, many of which will be featured right here on the BioLogos Forum.

A common argument leveled against the theory of evolution is that scientists have not been able to produce the expected transitional fossils that show the change of one species into another. If evolution were true, wouldn’t there be instances of clear intermediary species, like, for example, a species that was half whale and half hippo to show the transition between those two? In this BioLogos podcast, Kelsey Luoma addresses this misconception about what a transitional fossil actually is. Rather than a mix between two related species, transitional fossils point back to the common ancestors that modern species share. The fact is that the number of transitional species is massive and it grows with each passing year. Given the rarity with which organisms are actually fossilized, the amazing thing is actually the completeness of the fossil record, not its incompleteness. The transitional species story strongly supports, and certainly does not disprove, evolutionary theory. ¹

1. To hear the full audio clips which have been referenced go to:

• Rational Response Debate with Kirk Cameron (from Way of the Masters)
• Behind the Scenes with Dr. Neil Shubin (from Cincinnati Museum Center)
• Mark Norell Publishes New Archaeopteryx Findings (from American Museum of Natural Sciences)
• Texas A&M Professor Discusses Findings of Autralopithecus Sediba and its Relationship to Humans (from Texas A&M University)
• Intro/outro music composed by Martin Minor (Minor2Go).

An audio only version of the podcast can be downloaded here.

With the complete genome sequence in hand, we knew the sequence and location of our genes, but what we didn’t know was how all those genes are regulated: how do the trillions of cells in our bodies know when to turn on or off all those genes? How do the hundreds of distinct cell types develop and function together, when they are all running on the same DNA “operating system?”

That’s where the ENCODE (short for Encyclopedia of DNA Elements) project comes in. Launched in September 2003, shortly after the announced completion of the Human Genome Project, the goal of the ENCODE project is “to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.” In other words, the project seeks to understand how the genome “works.”

Early this month, researchers from ENCODE released more than thirty papers presenting their findings. During a Science magazine online chat, the project’s data coordinator, Ewan Birney, explained the outcome:

The ENCODE project aimed to start our understanding of how the human genome works. We know that (nearly) all the information that determines a human is in the genome, as we all start off as single cell with this DNA. However, we had a patchy understanding of how it works, in particular away from protein coding genes.

To work out how the genome works, we used the fact there are many tiny machines (proteins and RNA - RNA is very like DNA) in each of our cells which know how to "read" parts of the genome. By monitoring where these little molecular machines are on the genome, or how parts of the DNA are copied into RNA (there are quite a few different types of RNA as well), we start to gain some insight into the genome.

We did many such experiments, across different cell types (eg, one cell type was very similar to a liver cell type; another was very similar to a white blood cell). This way not only can we see what is similar, we can also see differences between these cell types.

There is a lot more to get to know and understand here - this is definitely closer to the start than the end. But it is a substantial amount of data, and analysis, to start on this journey.

According to the abstract of one of the lead papers from Nature, this extraordinary glut of data “enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.” Only 2% of the genome codes for proteins, but 80% or more has some biochemical function. As a Science news article put it, these 30 papers “sound the death knell for the idea that our DNA is mostly littered with useless bases.”

The pro-Intelligent Design organization The Discovery Institute has heralded the discovery as the “demise of junk DNA.” Casey Luskin writes for their blog Evolution News:

Let's simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called "junk" DNA. ENCODE researchers use words like "surprising" or "unprecedented." They talk about of how "human DNA is a lot more active than we expected." But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted.

The extent to which the ENCODE project been able to identify function has been surprising—even exhilarating—though scientists have for some time been getting glimpses of the many ways in which segments of DNA can be “active.” Even in 1970 biologists knew that some non-coding DNA had function, and by 2003 there was a large body of work demonstrating that many non-coding elements acted as promoters, enhancers, insulators, and so on. Indeed, in recent years many have come to appreciate the fact that “junk” was never really an appropriate metaphor in the first place. Still, because sequencing of multiple genomes has shed such extraordinary light on key evolutionary mechanisms, many geneticists have focused on function primarily in terms of which regions do or do not contribute to the evolutionary fitness of their host, rather than whether they were merely "doing something" biochemically. What the impressive ENCODE project has done is open a treasure trove of new information that can only accelerate the pace at which researchers are able to explore the incredible subtlety and complexity of DNA, and refine the very concept of “functionality.”

So with all this in mind, is ENCODE a stunning victory for ID, as Luskin believes? Bryan College biologist Todd Wood thinks not. He writes, “I don't think that function equates to design, nor do I think that design requires or predicts function. They're not the same thing… my understanding of function does not require me to hypothesize God (or an anonymous designer, if you must) as the proximal cause.”

We agree. Indeed we would go on to say that evolution and design are not mutually exclusive. So while finding function is not sufficient to prove design, recognizing that function has arisen by way of evolution does not indicate that God was not at work. We at BioLogos believe God providentially works out his purposes—his designs—through the elegant processes of evolution, not in opposition to them.

Amazing as the new data are, it only strengthens and enhances our evidence for evolution. While much of the genome is “doing something” biochemically, it is still likely that the majority of the sequence is evolutionarily neutral (Senior Fellow Dennis Venema discusses the evidence for this “neutrality” in a post on our site, including a striking comparison between 29 different mammal genomes and the human genome). In fact, another ENCODE researcher participating in the Science magazine chat, John A. Stamatoyannopoulos of the University of Washington School of Medicine, thinks the findings align beautifully with evolutionary theory:

ENCODE's data provide a unique and powerful window through which to view evolutionary change. We can see those changes directly by lining up the genome sequences of many different organisms -- these line-ups have revealed millions of regions where all the genomes agree, indicating sequences that have been specially preserved by evolution while others have decayed away (ie freely changed their letter codes). We now see that a large proportion of these 'conserved' regions are lighted up by ENCODE annotations, indicating that they are marking spots in the genome that contain important instructions for cell function.

We’ve discussed “junk” DNA previously, including a multi-part series by Dennis Venema, and we’ve received many emails over the past few days asking for our comments on the ENCODE findings. On Monday and Tuesday, Dr. Venema will begin to offer his own thoughts on ENCODE.

A special thanks goes to Darrel Falk, Mark Sprinkle, Kathryn Applegate, Dennis Venema, and Tom Burnett for their contributions to this post.

The Denisovans, an extinct hominid group that interbred with modern humans, made the news again lately with the publication of a more detailed study of their genome. One of the many interesting findings was that the Denisovans share the same chromosome 2 fusion that modern humans have. In this post, I review what we know about the origins of human chromosome 2, and then discuss the new Denisovan findings and their implications.

The origins of human chromosome 2: a brief review

Though I have discussed the evidence for a fusion event leading to human chromosome 2 before, perhaps a brief review of the evidence is in order. The human genome is made up of 23 pairs of chromosomes (for a total of 46 chromosomes). This makes us something of an oddity among living great apes, all the rest of whom have 24 pairs of chromosomes (for a total of 48). Given that there are many independent lines of evidence that support the conclusion that we share a common ancestor with other great apes, this poses something of a conundrum: how is it that our species arrived at this specific chromosome number? If we were to represent this “problem” on a phylogeny, or tree of relatedness, it would look something like this (not to scale):

Our closest living relatives, chimpanzees and bonobos, both have 48 chromosomes, as do all other great apes such as gorillas and orangutans. This pattern has one of two explanations, one of which is much more likely than the other. Either the common ancestor to these species had 48 chromosomes, and there was an event that reduced that number to 46 specifically on the lineage leading to humans (option A), or the common ancestor species had 46 chromosomes, and there were independent, repeated events that increased chromosome number in all other great ape species (option B). We can compare these options by placing the required event(s) on the phylogeny (again, not to scale):

It should be obvious that the option that requires the fewest events is the more likely one – in this case option A with an event that reduces chromosome number in the lineage leading to humans. The other option, that of repeated, independent events to increase chromosome number, remains a formal, but unlikely, possibility. Events that reduce chromosome number are not frequent occurrences, so Option A is more likely than Option B.

We can also find further support for Option A, because it predicts a specific type of event, namely one that reduces chromosome number. Since loss of a large amount of chromosomal material is almost always detrimental, we need an event that reduces chromosome number without losing information. One way for this to happen is for two chromosomes to fuse together and become one. Initially, this event would produce an individual with 47 chromosomes, where two different chromosomes get stuck together. Contrary to what is often assumed, this individual would be fertile and able to interbreed with the others in his or her population (who continue to have 48 chromosomes). In a small population, over time, two relatives who both have one copy of the fusion chromosome may mate and produce some progeny with two copies of the fused chromosome, or the first individuals with 46 chromosomes. Since either a 48-pair set or a 46-pair set is preferable for ease of cell division, this population will either eventually get rid of the fusion variant (the most likely outcome), or by chance will switch over completely to the “new” form, with everyone bearing 46 chromosome pairs. While not overly likely, this type of event is not especially rare in mammals, and we have observed this sort of thing happening within recorded human history in other species. Some mammalian species even maintain distinct populations in the wild with differing chromosome numbers due to fusions, and these populations retain the ability to interbreed.

Further evidence for a fusion event in the lineage leading to modern humans comes from comparing synteny, or gene locations and orders on chromosomes within modern great apes – an issue we have discussed here before. In brief, what we see in human chromosome 2 is exactly what we would predict for a fusion event. When compared to other great apes, we see the genes on human chromosome 2 match up, in order, with two smaller ape chromosomes. We also see that sequences used at the tips of chromosomes are present at the proposed fusion site, and that human chromosome 2 has not one but two sites for the cell cytoskeleton to attach to for cell division – but that one of the sites is mutated and not functional, though it lines up precisely with the location of this site on the appropriate ape chromosome. Together, this evidence consistently supports both common ancestry for humans and great apes, and specifically that the difference we see in our chromosome numbers arose due to a single fusion event. I briefly discussed this evidence in my last post where I describe how I teach some of this material and the compelling impact it has on students exploring the evolution question for the first time.

Enter the Denisovans

With that as background, we are now prepared to appreciate a new finding that comes from genomics work done on the Denisovan hominids, an archaic species that is more closely related to Neanderthals than to us, but that nonetheless interbred with some anatomically modern humans as they migrated out of Africa and populated the globe. (For those not familiar with the Denisovans, or the evidence for our interbreeding with them, both Darrel Falk and I have written on this previously, here and here). Recently, a more detailed understanding of the Denisovan genome was published, and nested in the new information is the discovery that the Denisovans share the 46 chromosome set with the same fusion that we have. This strongly supports the hypothesis that the fusion event predates the separation of our species. If we were to represent this on a phylogeny, we can now place this event with more accuracy than before (as before, the phylogeny is not to scale):

Despite this new information, one obvious question remains. Did the Neanderthals also have the 46-pair set? From looking at the phylogeny above, we can see that the most likely answer is that they did, since the fact that the Denisovans had it strongly implies that the last common ancestor of humans and Neanderthals / Denisovans had it as well, and the Neanderthal-Denisovan split comes later. While the Denisovan DNA samples are of high enough quality to make this assessment, we do not yet have Neanderthal DNA of high enough quality to do the same analysis with current methods (though one additional feature of the new work on the Denisovan genome is developing more sensitive DNA sequencing techniques that may resolve this question in the future).

In other words, this fusion seems to be an ancient one, predating our species by several hundred thousand years. Present estimates of the last common ancestor between humans and Neanderthals / Denisovans range at about 800,000 years ago.

Implications for understanding our “becoming human”

The main implication from this work is that it places the fusion event well before the advent of our species. I’ve often chatted informally with Christians about evolution, and at times some have thought that this fusion event was what “started” our species, or made our species unable to interbreed with other groups. Some have even suggested that perhaps the fusion event was what produced the first human (i.e. Adam).

Note that thinking this way suggests a misunderstanding of how chromosome fusions occur and what effect they have on their hosts. A fusion does not precipitate a speciation event, but rather the individual with the fusion remains a part of his or her population, and able to interbreed, even if with reduced fertility. Also, there is no necessary biological effect or change that the fusion produces on the appearance of the organism. These misunderstandings aside, however,what this new evidence shows is that this fusion event took place long before modern humans arose at around 200,000 years ago. Indeed, the 800,000 years ago date for the last human - Denisovan common ancestor means that this is the most recent date possible for the fusion. While it is an interesting piece of our evolutionary history, it doesn’t seem to have much to do with how we came to acquire the traits that set us apart from, and ultimately outcompete, other similar species.

Suppose a man falls among thieves, or wild beasts; is shipwrecked at sea by a sudden gale; is killed by a falling house or tree. Suppose another man wandering through the desert finds help in his straits; having been tossed by the waves, reaches harbor; miraculously escapes death by a finger’s breadth. Carnal reason ascribes all such happenings, whether prosperous or adverse, to fortune. But anyone who has been taught by Christ’s lips that all the hairs if his head are numbered [Matt. 10:30] will look further afield for a cause, and will consider that all events are governed by God’s secret plan.

In this passage, Calvin presents belief in “fortune” as evidence of carnal reasoning, and statements like this one have contributed to a widely-held notion that modern scientific understandings of the role that randomness plays in nature is inconsistent with belief in divine providence. In other words, if “randomness” equals blind and capricious “fortune,” then how can God be said to be working all things to his ends?

But Calvin could not have known of the very different understanding of randomness held by today’s scholars. Physical scientists, mathematicians, and statisticians have not yet agreed on a single unambiguous definition of the term “randomness,” but among these scientists, the term consistently refers to a family of related concepts focusing on unpredictability of the outcomes of single events and the absence of pattern in sequences of outcomes. I like this statement by John Polkinghorne, “Chance doesn't mean meaningless randomness, but historical contingency. This happens rather than that, and that's the way that novelty, new things, come about.” In Polkinghorne’s view, chance is an agent of creativity and can be perceived as being purposeful.

In fact, there are abundant examples of phenomena in nature in which randomness plays a role one could understand as being purposeful. For example, osmosis is a marvelous mechanism that enables all 10 trillion cells in our bodies to be nourished – it depends on the random motion of molecules. The human immune system is able to defend the body against attacks from millions of different microorganisms using a relatively small number of building blocks and random combinations of these to fashion defenses specific to each adversary. We never take a breath and find it to be all nitrogen or carbon dioxide – random motion of molecules keeps oxygen close to uniformly distributed throughout the atmosphere.

In 2007, a British statistician, David Bartholomew published God, Chance, and Purpose in which he argues that God “can have it both ways”—that he can use low level randomness to accomplish divine purposes while simultaneously maintaining order at a higher level. Of course, we cannot prove that God ordained these random processes to achieve divine purposes in the world. But to a person of faith, such an interpretation in both consistent with the observations we make in science and with the Scriptural notion of God’s providential care for the world.

Considerations like these led the John Templeton Foundation to provide a generous grant of $1.69 million to support a new research initiative on the theme of Randomness and Divine providence. Beginning this past summer, the program has the purpose of providing support for solid theoretical exploration of the kinds of ideas and possibilities expressed above—involving theology, philosophy, natural science, mathematics, and statistics. The grant will support individual scholars and teams of scholars who are willing to devote a significant amount of time between March of 2013 and June of 2015 to such work, and the project’s request for proposals suggests the following as questions researchers might pursue:

• How might God work providentially through indeterminate processes? Can recent advances in understanding the nature of randomness offered by algorithmic information theory, physics, biology, and other sciences provide insight into this question?
• Can we bring clarity to the concept of "randomness"? Philosophers and scientists have tried on occasion to give precise definitions of when a process is random, but more work needs to be done on the question. How do (or should) conceptions of randomness vary across academic disciplines?
• What are some possible implications of randomness for hiding or unfolding divine creativity and purpose in the world? Could God use randomness to (1) generate creativity, (2) hide divine actions, or (3) unfold information? Why might God do so?
• How might we identify and come to understand a significant collection of nondeterministic processes in which agents could intentionally employ randomness to bring about purposeful results?
• How might we mathematically and physically model random processes in ways that help us understand how divine providence could be exercised in a "chance-governed" world?
• How do "laws and orders" in nature interplay with "chance and randomness" in bringing about results that can be interpreted as aspects of divine providence?
• Might randomness be evidence of limitations in human knowledge but nothing more? Or might it be evidence of ontological indeterminism? Might this be tested?
• What implications does randomness have for aspects of God’s relationship with the physical world such as God’s relationship to time and God’s role in causation? How might randomness be reconciled with God’s foreknowledge?
• How might an understanding of providence based on an extended Molinism and/or open theology incorporate randomness? For example, could an extended Molinism provide a plausible account of the relationship between quantum mechanics and divine providence?
• What are some theodical implications of randomness, particularly for the issue of natural evil?
• How have the theological traditions of Augustine, Maimonides, Aquinas, Luther, and Calvin addressed chance and fortune? In what ways might they incorporate ontological randomness?
• How do or could religions other than the Judeo/Christian tradition understand and incorporate randomness?
• How is the concept of randomness understood by advocates of secularism, naturalism, and new atheism? What are the strengths and weaknesses of these usages?
• How might an understanding of randomness in the world alter our conceptions of divinity, especially our understanding of divine providence?

Despite the range of issues mentioned above, research is by no means restricted only to these topics. In fact, the structure of the program is designed to foster collaboration and build community between scholars, with the end of expanding the range and integration of their work: two conferences will be held to bring scholars together with each other and then with members of the public—one at Calvin College in 2013 and the other at Fuller Theological Seminary in 2015. To get more information and to learn how to submit a proposal, see the project website; then join us in exploring the truth that all creation glorifies God—even randomness!

Darwin’s finches are some of the most visible and recognizable symbols of evolution in the world today. Biology textbooks feature them prominently, and the National Academy of Sciences has enshrined them in the entrance of their headquarters in Washington, DC. Surely the finches that Darwin collected on the Galápagos islands were a central feature of his evolutionary theory, right?

Lobby of The National Academies Building. Courtesy of CPNAS. Photo by Robert Lautman

Actually, the Galápagos finches are never even mentioned in Darwin’s famous work On the Origin of Species. Nor do they appear in Darwin’s famous notebooks on “Transmutation of Species”, in which he formulated the idea of evolution by natural selection.¹ Even Darwin’s private diary of his voyage on the HMS Beagle only mentions the Galápagos finches briefly in passing.²

It was only in 1845, in the second edition of The Voyage of the Beagle, that Darwin included a tantalizing sentence about the Galápagos finches:

Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends.³

However insightful this statement may have been, Darwin never published anything else about the Galápagos finches for the rest of his life. Nor did he publically present these birds as direct evidence for this theory of evolution.⁴

If these finches were so important to Darwin’s evolutionary theory, why did he remain silent about them? One of his comments in The Voyage of the Beagle provides us with a clue:

Unfortunately most of the specimens of the finch tribe were mingled together; but I have strong reasons to suspect that some of the species of the subgroup Geospiza are confined to separate islands.⁵

When Darwin was exploring the Galápagos himself in 1835, he had not formulated his theory of evolution yet, and thus he did know what data would be necessary to make definitive conclusions about finch evolution. In particular, he did not keep careful track of which of his specimens came from which islands. Moreover, as was customary among naturalists at that time, Darwin only collected a small number specimens—he brought home only 31 finches and 64 total birds from the Galápagos.⁶

Though Darwin sensed that these birds were truly special, he lacked sufficient evidence to reach any specific conclusions about their evolutionary origins. It would be up to the rest of the scientific community to carry out the necessary empirical research. Subsequent expeditions in 1868, 1891, 1897, and 1905 brought back thousands of Galápagos finch specimens, but instead of unlocking the mysteries of evolutionary theory, the Galápagos finches became a great enigma.⁷

A century after Darwin's voyage, scientists still struggled to explain the staggering variety of finches on this tiny, remote archipelago. By the mid-1930’s, British Museum ornithologist Percy Lowe argued that the finches presented a "biological problem of first class importance", and he told the British Association for the Advancement of Science that the finches displayed a "bewildering diversity, intergradation, and distribution".⁸ Who would be up to the challenge of making sense of such tremendous biological complexity? It was David Lack.

David Lack

Ornithologist David Lack

David Lack had an exceptionally keen eye for bird-watching, and he possessed a passion to match it. By age 15, he had already observed 100 distinct species of birds, and before entering college, authored his first scientific paper. At Cambridge University in the early 1930’s, Lack was disappointed to find that his zoology professors taught “nothing about evolution, ecology, behavior or genetics, and of course nothing about birds.”⁹ In fact, at that time, there were only two professional ornithologists in all of Britain!

Thus David Lack took it upon himself to create his own learning opportunities. As an undergraduate, he became the president of the Cambridge Ornithological Club, traveled to Greenland for a bird-watching expedition, and cultivated a relationship with the prominent biologist Julian Huxley (grandson of Thomas Henry Huxley). Huxley was an inspiring mentor and encouraged Lack to expand his research further by studying tropical birds.¹⁰ Following this advice, Lack embarked on a research trip to Tanzania in the summer of 1934, but his greatest adventure was yet to come.

In 1937, Lack became fascinated by the scientific mysteries surrounding the Galápagos finches. But in order to study their behavior, Lack would need to travel to remote islands halfway around the world. How could he possibly get there? Once again, Julian Huxley was tremendously supportive and raised funds from two prominent scientific societies to pay for his expedition. After a long delay, David Lack and five companions finally set off on their journey.

Instead of residing in comfortable quarters aboard a royal naval ship, Lack’s group subsisted on a shoestring budget, traveled on commercial steamers, and stayed with local settlers. Their experience was definitely not a romantic tale of imperial expedition:

The Galápagos are interesting, but scarcely a residential paradise. The biological peculiarities are offset by an enervating climate, monotonous scenery, dense thorn scrub, cactus spines, loose sharp lava, food deficiencies, water shortage, black rats, fleas, jiggers, ants, mosquitoes, scorpions, Ecuadorian Indians of doubtful honesty, and dejected, disillusioned European settlers.¹¹

Whereas Charles Darwin spent only nineteen days on the shores of the Galápagos, Lack and his crew conducted more than five months of meticulous and exhausting study in the harsh climate. At that time, even the finches themselves provided little solace. Lack wrote,

Darwin’s finches are dull to look at, not only in their orderly ranks in museum trays, but also when they hop about the ground or perch in the trees of the Galápagos, making dull unmusical noises. Only the variety of their beaks and the number of their species excite attention.¹²

Large Cactus Finch on Española Island in the Galápagos Islands

The repetitive tedium requisite for important scientific discoveries is rarely discussed in public, and even today many bright-eyed science students become disillusioned by the painstaking work demanded by their Ph.D. programs. But one of the things that distinguishes great scientists is their unwavering commitment and tenacity in completing major projects. David Lack's efforts were not in vain:

"Despite his personal discomforts (or perhaps because of them), Lack did see something on the Galápagos that no one had ever seen before—natural selection at work among its finches through interspecies competition." ¹³

When the birds’ breeding season ended in 1939, Lack was ready to return to his home in England. But the captive finches that he had brought with him fared so badly on the voyage home that he detoured to San Francisco and put them in the care of the California Academy of Sciences. Turning this mishap into an opportunity, Lack stayed there for five additional months to study the Academy’s enormous collection of Galápagos finch specimens.¹⁴

To complete his systematic research, Lack then travelled across the United States to study the Galápagos finch collection housed at the American Museum in New York.¹⁵ Altogether, Lack examined more than 8000 specimens and specifically measured the length, width, and depth of all their beaks.¹⁶

Lack’s final obstacle was in getting his research published. Though he completed his academic manuscript “The Galápagos Finches—A Study in Variation” in 1940, paper shortages during World War II delayed its publication by the California Academy of Sciences until 1945. Were he only interested in making an original contribution to science, Lack could have stopped here and congratulated himself on a job well-done. However, his motivation sprung from a deeper source:

David Lack's drawing of 14 species of Galápagos finches, p. 19 of Darwin’s Finches

"I did not watch birds primarily for scientific reasons but for sheer enjoyment, and from the age of 15 onward returned day after day in a glow of excitement after seeing a new bird or a new habit." ¹⁷

Lack’s joyful fascination with the Galápagos finches inspired him to continue developing his conclusions long after returning from his expedition. While waiting for his academic paper to be published, he began writing a book that would enable students and the general public to share his excitement about these remarkable birds and the evolutionary processes that shaped them.

First published in 1947, Lack’s book became tremendously influential. Before this time, biology textbooks had never even mentioned the Galápagos finches. But after David Lack’s study, the finches became a primary example of evolution by natural selection, specifically adaptive radiation. Not only did textbooks fully rely on Lack’s findings, they also followed his lead in calling them “Darwin’s finches”, the title of Lack’s famous book.¹⁸

Iconic Finches

What was it about these birds that made them such a prominent symbol of evolution? As Darwin himself pointed out, the numerous Galápagos finch populations each have distinctive beaks, and he speculated that they could have evolved from an ancestral species that came to the islands. But a complete picture of finch evolution would have to wait another hundred years, when David Lack arrived.

During his five months on the Galápagos, including both the rainy and dry seasons, Lack observed that these beak differences enable the finches to subsist on different kinds of food:

The beak differences between most of the genera and subgenera of Darwin's finches are clearly correlated with differences in feeding methods. This is well borne out by the heavy, finch-like beak of the seed-eating Geospiza, the long beak of the flower-probing Cactornis, the somewhat parrot-like beak of the leaf, bud, and fruit-eating Platyspiza, the woodpecker-like beak of the woodboring Catcospiza, and the warbler-like beaks of the insect-eating certhidea and Pinaroloxias.¹⁹

Lack's image of beak adaptations from Darwin’s Finches

Specializing in such different sources of food enables these finches to live in close proximity without directly competing with each other or driving populations to extinction. The fact that so many of these closely related finches are able to co-exist is a remarkable fact in itself. As Lack himself put it, “It is not only the origin, but also the persistence, of new species which require explanation.”²⁰

But it is also fascinating to consider how these birds got to be so different in the first place. How did a finch come to have a beak like a “parrot”, “woodpecker”, or “warbler”? The answer lies in the distinct characteristics of the Galápagos. Because the islands are so remote, no actual parrots, woodpeckers, or warblers ever settled on it. In the absence of these species, the Galápagos finches were able to adopt feeding habits and forms that they would never have taken on a large continent full of other birds competing for food. The isolation of these islands offered just the right conditions for us to see living examples of adaptive radiation.²¹

Conclusion

Considering the immense popularity of the Galápagos finches, it is quite surprising to learn that Charles Darwin himself had so little to say about them. In fact, it was actually David Lack, one century later, who conducted the critical research that immortalized the finches in biology textbooks and popular lore. By naming his landmark book Darwin’s Finches,²² Lack paid homage to the man whose voyage on the HMS Beagle helped transform the study of natural history. But at the same time, Lack also obscured the fact that evolutionary biology is an enterprise conducted by a large community of brilliant scholars, not just the product of one man’s efforts.

This tendency to immortalize “great men of science” has also led many people to refer to modern evolutionary theory as Darwinism, despite the fact that it has substantially changed and developed over the past 150 years. It is important to give credit where credit is due, and if that’s the case, we should seriously reconsider how we refer to the Galapagos finches. Evolutionary biologist Dolph Schluter, who studied the finches several decades after David Lack, had this to say:

I find Lack's intuition really stunning given how little information he had. He's my hero actually… They should be called Lack's finches.²³

In the second part of this series, we’ll explore the fact that David Lack, in addition to being a world-renowned evolutionary biologist, was also a devout Christian. His study of evolutionary theory did not cause him to lose his faith; in fact, he actually converted to Christianity after completing his Galápagos finch research.

For Discussion

Further Reading

• Grant, Peter R.; Grant, B. Rosemary. How and Why Species Multiply: The Radiation of Darwin's Finches, Princeton University Press, 2008.
• Sulloway, Frank J. (Spring 1982), "Darwin and His Finches: The Evolution of a Legend" (PDF), Journal of the History of Biology 15 (1): 1–53.
• Weiner, Jonathon. The Beak of the Finch: A Story of Evolution in Our Time. Vintage Books, 1995.

Notes

1. Sulloway, F. (1983). "Darwin and his finches: The evolution of a legend." Journal of the history of biology 15(1): 32. Darwin’s notebooks on transmutation mentioned Galapagos tortoises and mockingbirds, not finches.
2. Lack, David. Darwin’s Finches. Cambridge University Press, 1947: 9. Confirmed by Sulloway (1983), p5.
3. Darwin, Charles. Journal of researches into the natural history and geology of the countries visited during the voyage of H.M.S. Beagle round the world. London: John Murray. 2d ed. 1845: 379-80. This edition of the book also contained the drawings of four different finches that have become enshrined in biology textbooks and on the walls of the National Academy of Sciences in Washington, DC.
4. Sulloway, p35. Sulloway points out that the first published evolutionary account of the Galapagos finches was not until 1876, by Osbert Salvin: "On the Avifauna of the Galapagos Archipelago." Trans. Zool. Soc. London, 9:447-51.
5. Darwin (1845), p395.
6. Sulloway, p40.
7. Sulloway, p40.
8. Larson, E. J. Evolution's Workshop: God and Science on the Galapagos Islands. New York, Basic Books, 2001: 166-67.
9. Lack, David. (1973) “My life as an amateur ornithologist.” Ibis: 424.
10. Lack (1973), 425-27.
11. Lack (1947), p1.
12. Lack (1947), p11.
13. Larson, 167-68.
14. The California Academy of Sciences sponsored an expedition to the Galapagos in 1905-06 and collected nearly 9000 Galapagos finch specimens (Sulloway, p40).
15. In New York, Lack roomed with the curator of the finch collection—German émigré zoologist Ernst Mayr. By developing this relationship, Lack had close ties with two of the biggest figures in the neo-Darwinian synthesis, Julian Huxley and Ernst Mayr (Larson, 168).
16. Larson, p168.
17. Lack (1973), p424.
18. Larson, p198.
19. Lack (1947), p60.
20. Lack (1947), p158.
21. See Lack’s concluding chapter on “Adaptive Radiation”, pp146-159 of Darwin’s Finches (1947).
22. British ornithologist Percy Lowe originally proposed the name “Darwin’s finches” in 1935, but the name did not catch on until Lack used it in his book. See P.R. Lowe, (1936) "The Finches of the Galapagos in Relation to Darwin's Conception of Species." Ibis, 13th ser., 6:310-321. (Cited in Larson, p287)
23. Schluter, in an interview with Edward Larson, 16 March 2000.

Eugene Dubois

13 years before, in 1877, Dubois had arrived in Amsterdam to study medicine, but always harboring a desire to study the ancestry of modern humans. So, after four years at the University there, he accepted an invitation to go to the University of Utrecht to study comparative anatomy and devote himself to the latest thinking about the origins of the human species. It was during his time at Utrecht (from 1881 to 1887) that Dubois became enamored of Haeckel’s views on human origins, which differed from those of Darwin. While Darwin argued that humans had evolved in Africa, the region in which our closest living relatives—the chimpanzees and gorillas—still live, Haeckel believed that the origins of humanity lay in East Asia. This was so, he believed, because of his own observations of gibbons that walk bipedally when on the ground.

Haeckel also believed that there had once been a large landmass called Lemuria between the continents of Africa and Asia. In his view, Lemuria had since become submerged, leaving the modern islands of Madagascar and the East Indies as its only remains. The idea of submerged continents was not unusual for the late 19th-century, as people struggled to understand the character of biological diversity present in the world and why there were such striking similarities between animals that were geographically dispersed. The geographical distribution of marsupial fossils in South America and Australia is an example of this sort of problem, and one that was not solved until the second half of the 20th century when continental drift reconstructions suggested that ancient marsupials had used Antarctica as a conduit between the other two continents. Not only did such theories make sense of modern distributions, they were confirmed with later discoveries of marsupial fossils in Antarctica.

In any case, in 1888 Dubois joined the army and set out for the Dutch East Indies to pursue his ideas. For the next two years, he would comb Sumatra attempting to locate the hominin remains that Haeckel promised would be there. In hindsight, what Dubois was attempting was something that had never been done before: discovery of hominin material through the tools of archaeological excavation. Up to this point, all of the human fossils had been found on the surface, eroding out of the side of a bank, or as a result of farming. It had not occurred to anyone to go looking for human ancestors.

Now, with his supply of prison workers dwindling due to desertion and fever, he had almost run out of options and was on the verge of failure. Using almost all of his remaining resources, he decided to abandon his excavations on Sumatra and turn to the nearby island of Java. Emboldened by the fact that early modern human fossils had been discovered there (at Wadjak), he arrived and settled in at Trinil, on the banks of the Solo River, in 1890.

Figure 1: Dubois' Pithecanthropus erectus

The very next year, Dubois’ long-standing efforts were finally rewarded, first with the discovery of a skullcap (calvaria) of a hominin cranium, and then with an intact femur (Figure 1). Judging by what he knew of cranial anatomy, Dubois estimated that the skull would have been approximately 900 cubic centimeters (cc) in volume, placing it below even the lowest threshold of modern humans. Further, he noticed that it was not like modern humans in shape, being too long and low. He concluded that it showed “evidence of a form intermediate between man and the anthropoid apes” (Dubois, 1896). Dubois envisioned a sequence of forms in which the gibbon gave rise to a form of chimpanzee called Anthropopithecus sivalensis, which then gave rise to the form represented by the Trinil remains, after which Homo sapiens arose (Turner, 1895).

Dubois spent the next twenty years on the road with his find, trying to drum up support for its place in human prehistory. As with Raymond Dart’s discovery of the first australopithecine thirty-three years later, Dubois did not receive a warm reception. Most critics simply said that he had gotten it wrong and that the femur did not belong to the same individual as the obviously-primitive skull cap. Some of the criticism Dubois suffered could have been mitigated had he been more open to sharing the Trinil materials; but, instead, he allowed very little access to the bones, so that very few people knew exactly what they looked like. Adding to Dubois’s credibility problems was the 1911 “discovery” of Piltdown. This intentional hoax turned the paleoanthropology world on its head for forty years, sending researchers down innumerable rabbit holes. As I noted in a previous post, the Piltdown remains made all of the other hominin finds appear too “ape-like” to be on the road to humanity and informed many opinions about finds such as those from Trinil.

On the other hand, some critics of Dubois’ new hominin claim were vicious, and questioned both his academic abilities and his judgment (Shipman & Storm, 2002)—in addition to the interpretation of the find itself. It was in reference to Dubois’ work that the term “Missing Link” was first used with reference to a particular human fossil, originating with Charles Lyell (1863) and describing palaeontological gaps. And ironically, it was in one of the most stinging criticisms of Dubois’ work that the name that would eventually stick was first used: “Homo erectus.” Eventually, many other finds in the same general area and across Southeast Asia demonstrated that what Dubois had found was a real, previously-unknown hominin form, and the first to colonize the Asian continent and the islands leading off towards Oceania.

Homo erectus across South East Asia:

Figure 2: Sangiran 17

Sangiran

The earliest point at which Homo erectus appears to have begun to colonize the greater East Asian region is around 1.8 million years ago, represented first by the partial child’s skull found at the site of Modjokerto, and then, at around 1.66 million years ago, at the site of Sangiran, in Trinil, where Dubois had made his landmark discovery. This site was rich, yielding the remains of many crania, perhaps best represented by Sangiran 17 (Figure 2), an almost complete skull.

The material from the Sangiran site is very diverse morphologically, with some crania having capacities of as little as 700 to 800 cc, and other, larger heads with volumes in the range of 1000 cc. As with the late Homo ergaster finds from Africa, the remains from Sangiran yielded crania that were still widest at their bases, possessing large brow ridges. Some have thick cranial bones and are very robust (Sangiran 4), while others are very gracile (Sangiran 31). What this variation means is not clear, but most workers believe it represents a very diverse diachronic population (that is, one group living and moving around over a long period) rather than separate species inhabiting the area. The Sangiran site yielded fossil material in an almost continuous succession from approximately 1.66 million years ago to less than 800,000 years ago.

Because the area of the excavations—the Sangiran Dome—is a volcanic deposit, the layers have been securely dated by the ⁴⁰Ar/³⁹Ar method, although questions remain about the historical sequence and distribution of other animals that lived there through the ages (its faunal succession). The problem is that many of the fossils were not found in context, and relating them directly to the stratigraphy is tenuous. Despite this, most workers are comfortable with the earliest hominins in the region being at least 1.5 million years old.

One of the things hampering workers in this region is the comparative paucity of recovered stone tools. Those that have been found suggest a technological stage similar to the late Oldowan design, equivalent to that being created by the Homo ergaster populations inhabiting the area of Dmanisi and East Africa. Unfortunately, none of the tools have been associated with the hominins directly so it is not exactly clear who made them.

Figure 3: Sambungmacan 3

Sambungmacan

Another major find from the area where Dubois brought Homo erectus to light is the cranium from the site of Sambungmachan. This skull was reportedly found in 1977 but was then illegally sold to the antiquities market, where is spent considerable time in different collections before being “rediscovered” in 1998—in a New York nature curio shop called Maxilla and Mandible, Inc. (Delson et al., 2001). This was an almost-complete calvaria (Figure 3), with only part of the base missing. It is equivalent in size to the fossils from Sangiran, with a cranial capacity of around 1000 cc. It has a large brow ridge extending all of the way across the top of the eyes, a long, low cranium with a sloping forehead and a maximum width near the cranial base—all features that are also characteristic of the late African H. ergaster and Sangiran crania. Although we will never know exactly how old this cranium is, its morphology is consistent with that of the material from Sangiran.

Figure 4: Ngandong 6

Ngandong

Later in time, but also located on the Solo River, is the site of Ngandong, excavated by Oppenoorth in the early 1930s. At this site, fourteen calvaria have been discovered, all of which show advanced Homo erectus characteristics: long and low in shape, with thick-bones and a distinctive brow-ridge. (Figure 4). As with the other Indonesian finds, dating the Ngandong material has been problematic. The deposits at the site were originally thought to be around 100,000 years old, but this interpretation was turned on its head in 1996, when Swisher and colleagues claimed that the deposits were no older than between 27,000 and 53,000 years old (Swisher et al., 1996). These age estimations were made on the associated fauna, however, and as Rainer Grün and the late Alan Thorne pointed out, the faunal material does not match the skulls either in color or in texture and is likely not from the same time. Recently, Swisher and colleagues revisited the dating of the site and derived internally-consistent dates of at least 143,000 years before the present (Indriati et al., 2011). As with the Trinil remains, however, there are no associated stone tools.

Homo erectus in China

The Chinese Homo erectus material is very widely scattered and working in the region has presented many difficulties for researchers in terms of transport, language barriers and funding. Consequently, we know less about this region and its previous inhabitants than we do about most other areas of the Old World. Although there are between ten and fifteen sites that have yielded Homo erectus material, I will only touch on the most important ones.

Lantian:

Figure 5: Lantian

In the early 1960s, a cranium and mandible were found in the cave of Lantian, Shaanxi province, whose characteristics matched other remains from China designated as Homo erectus. Paleomagnetic dating has yielded a date no earlier than 1.15 million years ago for the skull, with the consensus being that it is around 800,000 years old. A date of approximately 650,000 years before the present was derived for the mandible. The cranium is heavily encrusted and suffered from postmortem deformation (Figure 5). When reconstituted, it was found to have a capacity of around 780 cc (low for Homo erectus) and the bones on the sides of the head are the thickest yet recorded. At this site some flake tools, mammal remains, and an ash deposit were all recovered, suggesting hunting and control of fire.

Figure 5: Hexian

Hexian

Another almost-complete calvaria was found at Longtandong cave in the province of Hé Xiàn, dated to between 400,000 and 500,000 years ago. This find exemplifies typical Homo erectus in many ways in that it is long and low, with heavy muscle markings toward the base and the rear of the skull (Figure 6). The cranial capacity is around 1000 cc, a third-again greater than that of the Lantian calvaria. Its cranial shape is very similar to those found in Southeast Asia, suggesting that it straddles the Southeast Asian and Chinese boundary.

While both Lantian and Hexian were significant finds, another site in China boasted the single largest collection of Homo erectus fossils ever found at one site, as well as presenting one of the greatest mysteries in paleoanthropology. Tomorrow, in the conclusion of our look at Homo erectus in Asia, we’ll peer into the Zhoukoudian caves and consider how this species fits into the lineage of man.

There are two opposite errors which need to be countered about the fossil record: 1) that it is so incomplete as to be of no value in interpreting patterns and trends in the history of life, and 2) that it is so good that we should expect a relatively complete record of the details of evolutionary transitions within all or most lineages.

What then is the quality of the fossil record? It can be confidently stated that only a very small fraction of the species that once lived on Earth have been preserved in the rock record and subsequently discovered and described by science.

There is an entire field of scientific research referred to as "taphonomy" -- literally, "the study of death." Taphonomic research includes investigating those processes active from the time of death of an organism until its final burial by sediment. These processes include decomposition, scavenging, mechanical destruction, transportation, and chemical dissolution and alteration. The ways in which the remains of organisms are subsequently mechanically and chemically altered after burial are also examined -- including the various processes of fossilization. Burial and "fossilization" of an organism's remains in no way guarantees its ultimate preservation as a fossil. Processes such as dissolution and recrystallization can remove all record of fossils from the rock. What we collect as fossils are thus the "lucky" organisms that have avoided the wide spectrum of destructive pre- and post-depositional processes arrayed against them.

Soft-bodied organisms, and organisms with non-mineralized skeletons have very little chance of preservation under most environmental conditions. Until the Cambrian nearly all organisms were soft-bodied, and even today the majority of species in marine communities are soft-bodied. The discovery of new soft-bodied fossil localities is always met with great enthusiasm. These localities typically turn up new species with unusual morphologies, and new higher taxa can be erected on the basis of a few specimens! Such localities are also erratically and widely spaced geographically and in geologic time.

Even those organisms with preservable hard parts are unlikely to be preserved under "normal" conditions. Studies of the fate of clam shells in shallow coastal waters reveal that shells are rapidly destroyed by scavenging, boring, chemical dissolution and breakage. Occasional burial during major storm events is one process that favors the incorporation of shells into the sedimentary record, and their ultimate preservation as fossils. Getting terrestrial vertebrate material into the fossil record is even more difficult. The terrestrial environment is a very destructive one: with decomposition and scavenging together with physical and chemical destruction by weathering.

The potential for fossil preservation varies dramatically from environment to environment. Preservation is enhanced under conditions that limit destructive physical and biological processes. Thus marine and fresh water environments with low oxygen levels, high salinities, or relatively high rates of sediment deposition favor preservation. Similarly, in some environments biochemical conditions can favor the early mineralization of skeletons and even soft tissues by a variety of compounds (eg. carbonate, silica, pyrite, and phosphate). The likelihood of preservation is thus highly variable. As a result, the fossil record is biased toward sampling the biota of certain types of environments, and against sampling the biota of others.

In addition to these preservational biases, the erosion, deformation and metamorphism of originally fossiliferous sedimentary rock have eliminated significant portions of the fossil record over geologic time. Furthermore, much of the fossil-bearing sedimentary record is hidden in the subsurface, or located in poorly accessible or little studied geographic areas. For these reasons, of those once-living species actually preserved in the fossil record, only a small portion have been discovered and described by science. However, there is also the promise of continued new and important discovery.

The forces arrayed against fossil preservation also guarantee that the earliest fossils known for a given animal group will always date to some time after that group first evolved. The fossil record always provides only minimum ages for the first appearance of organisms.

Because of the biases of the fossil record, the most abundant and geographically widespread species of hardpart-bearing organisms would tend to be best represented. Also, short-lived species that belonged to rapidly evolving lines of descent are less likely to be preserved than long-lived stable species. Because evolutionary change is probably most rapid within small isolated populations, a detailed species-by-species record of such evolutionary transitions is unlikely to be preserved. Furthermore, capturing such evolutionary events in the fossil record requires the fortuitous sampling of the particular geographic locality where the changes occurred.

Using the model of a branching tree of life, the expectation is for the preservation of isolated branches on an originally very bushy evolutionary tree. A few of these branches (lines of descent) would be fairly complete, while most are reconstructed with only very fragmentary evidence. As a result, the large-scale patterns of evolutionary history can generally be better discerned than the population-by-population or species-by-species transitions. Evolutionary trends over longer periods of time and across greater anatomical transitions can be followed by reconstructing the sequences in which anatomical features were acquired within an evolving branch of the tree of life.

For more, be sure to read Randall Pruim's recent series Randomness and God’s Governance, Kathryn Applegate's post That's Random: A Look at Viral Self-Assembly, and our FAQ How Do Randomness and Chance Align with Belief in God's Sovereignty and Purpose?.

Author's Note

I am so thankful that I grew up in a Christian environment, which both kindled and nurtured my relationship with Jesus Christ. The Biblical instruction I received from my parents, pastors, and teachers has been invaluable as I walk out my love for the Lord from day to day. However, there was one specific topic growing up which was not fully addressed, namely evolutionary theory.

Coming from a conservative Christian background, evolution was given little or no thought because of its seeming contradiction to the creation story in Genesis. To me, evolution meant a monkey became a human, and as far as I knew, I had never seen that happen! So, of course, it appeared too improbable to hold any truth. When it was discussed, an inadequate picture of its ideas was often painted, which caused immediate suspicion and rejection of the theory. I don’t think this was intentional, but most Christians have never learned an unbiased, in-depth theory of evolution that is completely detached from societal agendas and philosophical conclusions. Therefore, their explanations of the theory are often misinformed.

My senior year of high school, I took AP Biology, and finally learned the scientific reasoning supporting this theory. I was surprised by how logical and obvious the mechanisms of change (such as mutations, natural selection, genetic drift, and so on) were that gave rise to new species. My subsequent response was, “No wonder people believe evolution occurred.” At that point, I was convinced that microevolution (evolution within a species) existed, but I was still questioning macroevolution.

Now, being at Point Loma Nazarene University as an undergrad in the Biology-Chemistry major and a year-round, student intern at BioLogos, my understanding of evolution has expanded enormously. I have enjoyed critically thinking through the evidence for evolution and reading articles that tackle difficult issues at the interface of science and Christian faith. Ultimately, I know that God has created all things, but the processes he used surpass my small understanding.

My personal wrestling with evolution and quest for truth has led to times of prayer and studying God’s Word, which has deepened my love for him in ways I cannot express. The first chapters of Genesis, in particular, have come alive. My whole life, the creation story was a straightforward list of facts about the creation of the world; I never searched further. I didn’t even perceive the truths Genesis declared over my very identity and God’s character. The more I study his Word and handiwork, I glimpse the awesomeness and majesty of the Creator, who loves me much more than I know. There is still so much to learn, but I am confident that he will lead me into all truth as I seek him out.

I desire to give others the opportunity to see evolution accurately and to distinguish it from the traditional, philosophical, and personal conclusions that too often cloud the scientific theory. I believe these conclusions alienate Christians from evolution more than the scientific theory itself. Ultimately, I do not mean to convince someone about evolution, but simply to give them the freedom to understand it.

Therefore, my goal for this podcast is two-fold:

• First, to offer a new perspective on randomness within natural processes that removes its negative connotations (especially as it relates to evolution).
• Second, to expose why evolution is powerless to support conclusions beyond the physical realm.

This will hopefully encourage others to study evolutionary theory and draw their own conclusions about its meaning in the framework of their faith.

Many of the games I enjoyed playing involve a combination of strategy and randomness: card games of various sorts, backgammon, and board games like Monopoly and Parcheesi. Some games that rely exclusively on chance (like War and Candy Land) or too heavily on chance (like Sorry) quickly became uninteresting to me. In fact, for Sorry, War, and several other games, I introduced additional rules to change the balance of strategy and luck—for example, by allowing each player to hold a hand of cards rather than merely flip a card and follow its bidding.

When my children were young, I played many games with them, especially those involving some amount of chance. I always play to win, so games of pure strategy like chess gave me too great an advantage—at least when they were still young. I still remember the first time I played the German game Mitternachtspartie with my children and some of their cousins. The game uses a die on which the number 5 has been replaced with the image of Hugo the ghost. Each player rolls the die and moves one of his figures the specified number of squares, unless Hugo is rolled, in which case Hugo moves instead.

I quickly worked out the expected distance Hugo would move for each of my turns and the expected number of squares I would get to move my own figures each turn. Using that information, I could strategically place my figures in the opening portion of the game. I fully expected to win this first game, since my young children were going to have to learn from experience what I already knew by the mathematics of probability. I lost—badly. As it turned out, the die had two Hugos on it. So compared to my expectations, Hugo moved twice as often, and my figures moved slightly less far. That combination turned the carefully calculated positioning of my figures into a disaster.

From Fun and Games to Science

I still enjoy playing games, including games that involve chance. But these days I encounter randomness even more often in my profession. I was trained as a mathematician and now work at the intersection of mathematics, statistics, and computer science. Like many scientists, I use randomness on a daily basis as part of our toolkit for modeling and investigating all sorts of phenomena. Models known as stochastic models, which explicitly incorporate random components, often via simulation in computer software, are used to model everything from diffusion to genetics to quantum mechanics. Insurance companies and financial institutions use stochastic models to manage risk. If we include all the applications of statistics, then almost no area of science is untouched by the use of randomness.

Most of the time, scientists and game players alike don’t devote much thought to just what makes randomness tick. But they both know that the better they understand the probabilities, the more successful they are. Nevertheless, if you ask many of them what it means for something to be random, they may struggle to put it into words. I won’t try to give a precise definition either, but it is important that we have some idea what we are talking about, so let’s consider one of the prototypical examples of randomness: the tossing of a fair coin.

If I flip a coin, the result could be heads or tails. Until I flip the coin, I don’t know which it will be. In this sense, the coin toss is unpredictable. If the coin is fair, each result is equally likely, so while I cannot say in advance whether a particular result will be heads or tails, I can say something about a large number of flips: approximately half should be heads and the other half tails.

A little mathematics even allows me to determine a range around 50% in which the percentage will almost surely lie. For example, if I flip a fair coin 1,000 times, the percentage of heads will most likely be between 45% and 55% (where “most likely” means a 99% chance). If the percentage of heads lies outside this range—especially if it is quite far outside this range—I am going to be suspicious that the coin flipping process is not fair. That’s one of the key ideas in statistics: not only can we calculate the frequency with which an event occurs, but we can compare data to a stochastic model to see if they are compatible or incompatible.

There are several interesting things we can learn by considering a coin toss. First, probability calculations rely on assumptions. If the assumptions are incorrect, then the probability calculations will also be incorrect. For example, if the coin is biased (such as one that is heads 60% of the time), but we assume it is fair, then the probability calculations given above will be wrong. Of course, if the assumptions are not too far from correct, the results may still be sufficiently accurate for scientific conclusions. If we have an appropriate way to collect data, then we can test our assumptions by comparing data to projections made based on the assumptions.

Second, “random” does not imply “equally likely.” A fair coin should have equal probabilities of heads or tails, but a biased coin is no less random. It’s just different. It is not as simple to handle arithmetically as a situation in which all outcomes are equally likely, but it is not otherwise special. It is a common mistake to assume random events are equally likely when they are not (or when that assumption is not justified).

Third, randomness is about the process. It is a fun experiment to flip a penny 100 times, then spin a penny 100 times and record the side that is showing when it finally tips over, then to stand the penny on end (this takes a steady hand and a little practice) and record which side is showing after pounding the table. These are three different processes, and they do not yield the same results.

Fourth, random processes produce patterns. I sometimes ask my students to mentally flip a coin and record the results as a sequence of letters (e.g., “HTTHHTHT”). Then I have them actually flip a coin and record the results. If the sequences are long enough, I can almost always tell them which is which. The sequences imagined by the students tend to have too few runs of consecutive heads or tails. The sequences based on real coin flips usually include several heads in a row. People not familiar with randomness are often surprised at the patterns that result and assume that the process must not have been random when they perceive a pattern. Our eyes and minds are drawn to similarities and patterns—even those that are produced purely randomly. This can lead us to draw false conclusions from coincidences of all sorts.

Consider the image in Figure 1. It was constructed using a computer to randomly throw 300 darts at a square board. Every position on the board was equally likely to be hit by a dart. This does not, however, mean that the dots are evenly spaced. There are 100 smaller squares. The average is three dots per square. But your eye is likely drawn to some clusters and voids. My eye also catches a graceful downward swoop in the lower part of the upper left quarter. All of this is exactly what we should expect from this random process. If we repeated this experiment, we should expect similar results. Several of the smaller squares would be empty and some others would have two or three times the average number of dots, but these clusters and voids would appear in different places.

Finally, randomness can be used to produce patterns intentionally. Consider the two pictures in Figure 2. You may think the two pictures are identical, but they are not. However, they were each constructed using the same random process:

1. Start at the lower left corner of the big triangle.
2. Randomly choose one of the three corners of the big triangle.
3. Move half way to that corner, placing a dot at the new location.
4. Repeat steps 2 and 3, 50,000 times.

The first few steps of this process for each image are illustrated in Figure 3. Although the final images look very similar, the route taken to get there is very different. In fact, the only point the two images have in common is the starting point. As the creator of the program that generated these images, I knew full well that the result would resemble a fractal image known to mathematicians as Sierpinski’s Triangle, even though I did not know or exercise any control over how the individual points would be selected.

Despite our familiarity with children’s games and the importance of stochastic models throughout the sciences, many Christians have a reaction to randomness that falls somewhere between uneasy and antagonistic. And yet, those same Christians may well watch the evening news to learn about public opinion polls forecasting upcoming elections, take prescription drugs approved by the FDA based on statistics found in clinical trials, obtain electrical power from a nuclear power plant that uses random fission reactions, and insure their cars with companies that rely on stochastic models to set the rates. The foundation of each of these activities is a thorough understanding of randomness that begins with the simple description above.

So where does the uneasiness come from? Likely it comes from the feeling that taking randomness seriously means not taking God seriously. Or put more strongly, it comes from a fear that believing in randomness means not believing in God. Next week we’ll address that problem by asking the question, “Could God use randomness to achieve his purposes?”

In the 1950s, Cage began using various methods of “casting lots” to determine how elements of his music would be chosen and arranged—principally the Chinese system of I Ching. His controversial program was to distance himself from his own creative process, and he explored many additional strategies to transform the role of “creator” into one of “observer.” Most famous of these was his musical composition, “4.33,” which consisted of a pianist sitting at the instrument doing nothing at all for four minutes and thirty-three seconds, while musician and audience listened to the ambient sounds of the concert hall. Yet contrary to that main thrust of Cage’s work, a description of the activities during the week-long residency at the Mountain Lake Workshop where the New River Watercolor Series were made suggests that choice, constraint, and intention were integral and inescapable tools in putting randomness to work for creative ends.

Here’s art historian and theorist Howard Risatti’s description of Cage’s plan of action for the New River Watercolors, from the website of artist Ray Kass, who runs the Mountain Lake program and was Cage’s collaborator for his work there:

Following upon [a previous (1983) Mountain Lake workshop] “painting experiment,” stones collected from the New River were sorted into three groups according to size, which were separately numbered; numerous and varied brushes were divided into two separately numbered groups; likewise, feathers to paint with, colors and washes, and papers were also divided and numbered. In this way, chance procedures using pages of random numbers that were now generated by a computer program could be used to determine the specific materials utilized for each painting (e.g., which painting instruments, what type of paper and which colors, how many washes, which stones to paint around, where to locate the stones on the paper).

While this list enumerates all the specific variables that Cage and his team submitted to chance, there was an incredible level of personal engagement with the materials: Cage didn’t just show us drawings of where the I Ching said the rocks ought to be, he (or his assistants) placed them on the paper and used them as guides to paint around. Large custom brushes were constructed to lay on washes of color, and even the paints were hand mixed, combined, and diluted according to his desires.

Cage’s use of chance, then, was not a “hands off” process, but neither was it a matter of total control: Cage selected processes to create a space of play between himself and the materials he used: the feather between himself and the paper, for instance, introduced variability of resistance and spring, its ability to hold paint, the width of the line. All of these things were elements of material ‘freedom,’ areas in which Cage asked the stuff he used to make the paintings to take part in the process—to contribute its own identity to the intentional, purposeful, and determined work of creating “based on chance.” This should not be surprising, as all art, all creation that we can observe, happens as a dialectic between materials and the creator, and such engagement and interaction in no way lessons the purpose of making, the end in sight.

Kass’ book The Sight of Silence: John Cage’s Complete Watercolors, gives a much more complete account of the tools, processes, and interpersonal reactions between Cage, Kass, and the team of student assistants who helped at almost every stage of the creation of the works. The book goes to great length to honor Cage’s ideal of being present in but not controlling the outcomes (not least by nearly always putting words like “choice” in quotation marks), but the description of his process makes the centrality of Cage’s personal aesthetic and artistic motives inescapable, even more than his physical engagement. What comes through perhaps even more than the way Cage intended to allow chance to ‘guide the creative process’ is that way Cage, himself, not only set the parameters of the chance he allowed into the system, not only engaged directly with the materials during the process, but also exercised judgment over the results, both in process and at the end:

“Cage decided he didn’t want the images of the stones to overlap or go off the sides of the paper. To guarantee this restriction, he created conditions and rules to limit their possible placements.” (p. 51)

“For this single painting [Series IV, #1, pictured above] Cage chose to confine the images of the rocks to a lower area of the paper that represented the proportion of the “golden rectangle. . .” (p. 57)

“While “choice” established much of the work’s nature, “chance” highlighted the intrinsic nature of the materials to reveal a refreshing presence.” (p. 59)

“[H]e initially decided to remove [the first painting of Series III] from the group, and then, liking it more, changed his mind and returned it to the group that would be signed.” (p. 56)

This last note is particularly interesting in that it highlights the fact that Cage was claiming these paintings, naming himself as their author, and was attentive to which ones he approved of enough to call his own. There is no way around the fact that Cage was subjectively as well as objectively the maker of these works: the author of the procedures by which they came to be, but well as the judge (and sometimes redeemer) of the results. For Cage, randomness was a tool, no different than the brushes or rocks or paints is that its specific parameters were chosen at the outset, and always used within the context of his over-arching vision. Perhaps we may likewise think of God’s use of chance—constrained by and tuned to the material conditions he established at the birth of the cosmos—as a way to both engage with and allow freedom for the creation itself.

With any work of art it is reasonable to ask, “Is it beautiful?” or more tellingly, “Would I hang this on my wall?” Seeing Cage’s watercolors for first time without any knowledge of the process or the relative fame of Cage himself, some might be intrigued by the structure of the work (the proportions of the golden rectangle, the overlapping stone shapes, the colors of the paint) while others would be completely uninterested, perhaps even after hearing about how they were made and seeing them in the context of the rest of the New River Watercolor series. But if you had been there in the shop as an assistant, or even observer, if you had been party to the relationships that developed even over the few days Cage spent at the Mountain Lake Workshop, your sense of the beauty of these paintings (and perhaps even scraps of paper Cage used to try out brushes or washes), would take on a different meaning, in much the way we treasure the crayon drawings of our children not because they are spectacular art, but because they are tokens of our relationship.

I make that observation to emphasize one other aspect of Cage’s creative process: that Cage was the instigator first and foremost of relationships of creation. His process created not only paintings but the fellowship that developed as the work was being done. That social, interpersonal dimension is what gives the objects a depth of meaning beyond their material composition, and suggests the particular roles humanity has been given by God. One role is to join into the creative process as lesser, but not unimportant co-creators with him; the other is to observe, recognize and celebrate his activity in the world. Where some will see randomness as evidence of an absent God, our knowledge of this most personal and participatory aspect of creation points us to the God who is with us.

With God’s creation as with human art, we may (or may not) marvel at any one particular “work,” or even think the specifics of how it was made are interesting or attractive; but knowledge of and fellowship with the artist transforms our appreciation of the process as well as its results. When we know the maker, we come to recognize and treasure even the most “random” bits of his handiwork, and name them as his, nonetheless.

For Further Reading:

Ray Kass. The Sight of Silence: John Cage’s Complete Watercolors, 2011.

Website for John Cage Centennial Festival, Washington, DC. September 2012.



]]> Sun, 13 May 12 12:53:04 -0700 Mark Sprinkle http://biologos.org/blog/understanding-evolution-theory-prediction-and-evidence-2?utm_source=RSS_Feed&utm_medium=RSS&utm_campaign=RSS_Syndication http://biologos.org/blog/understanding-evolution-theory-prediction-and-evidence-2?utm_source=RSS_Feed&utm_medium=RSS&utm_campaign=RSS_Syndication We have already discussed hind limb and hair loss in whales, and now we turn to one of the remaining questions: tooth loss in the lineage leading to modern toothless whales. One of the challenges for discussing evolution within evangelical Christian circles is that there is widespread confusion about how evolution actually works. In this (intermittent) series, I discuss aspects of evolution that are commonly misunderstood in the Christian community. In this post, we continue to explore how whale evolution is supported by converging lines of evidence from developmental biology and genetics.

In the previous post in this series, we explored how evolution can force science into making predictions that seem counter-intuitive. For cetacean (whale) evolution, we saw that the preliminary lines of evidence (the fact that whales are vertebrates, and mammals, for instance) pointed to the prediction that modern whales are descended from four-limbed, land-dwelling ancestors. As we then noted:

Instantly this prediction raises a host of uncomfortable questions: where did their hind limbs go? How did they acquire a blowhole on the top of their heads when other mammals have two nostrils on the front of their faces? How did they transition to giving birth in the water? What happened to the teeth of the baleen whales? What happened to the hair characteristic of mammals? and so on. In some ways, evolutionary thinking about whales creates more difficulties than it appears to solve.

And yet, these difficulties are the stuff of science. If indeed our “educated guess” of terrestrial, tetrapod ancestry for whales is correct, the evidence will show that these transitions, challenging though they may seem, did indeed occur on the road to becoming “truly cetacean”.

We have already discussed hind limb and hair loss in whales, citing evidence from embryonic development in modern whales that shows how hair and hind limbs develop early in their embryogenesis, but then are lost at later stages. We now turn to one of the remaining questions: tooth loss in the lineage leading to modern toothless whales (order Mysticeti). To obtain their food these whales pass seawater through a baleen, a large sieve-like structure that filters out plankton, small fish and other food items. Some recent genetics sleuthing has investigated a portion of this riddle, and adds further details to the story of how the baleen whales came to be.

Evolution: A Theory with Bite

If indeed modern whales are descended from ancestral, four-limbed, terrestrial ancestors, then those ancestors, like mammals in general, had teeth. Modern toothed whales (order Odontoceti) have retained those teeth to the present day, but baleen whales have adopted a new way of life as filter-feeders. Researchers were curious to see if traces of a “toothed past” could be found in the genomes of modern baleen whales, so they went hunting for remnants of genes devoted to making teeth. Such defective gene remnants would be examples of pseudogenes, and we have discussed pseudogenes previously in this series. While pseudogenes in and of themselves are powerful evidence for evolution, pseudogenes that are “out of place” are especially so. One such example we have seen before is the human vitellogenin pseudogene, the remains of a gene used for yolk production in egg-laying organisms found in the exact location in the genome that evolution would predict for it. As mammals that receive embryonic nourishment through a placenta, we have no need of egg-yolk genes. Similarly, baleen whales have no need for genes responsible for making teeth, and finding the remnants of such genes would make a strong case for an evolutionary origin of baleen whales as the modified descendents of toothed whale ancestors.

Independent Lines of Evidence, but Contradictory Stories?

Some of the genes known to be used in all mammals for tooth formation were the obvious candidate genes to start with: the products of the ameloblastin, amelogenin, and enamelin genes are all used in the formation of tooth enamel, the hardest structure in the vertebrate skeleton. Researchers went looking for these genes in several Mysticete (i.e. toothless whale) species. The results showed that all the species studied did indeed have these three genes present as pseudogenes (and more specifically, as unitary pseudogenes, a special class of pseudogene we have discussed in detail previously). Finding these genes as pseudogenes in toothless whales was exactly what evolution predicted, but there was a catch: none of the mutations that removed the functions of these three genes were shared between different species, suggesting that these genes lost their function independently in the species studied. This finding was at odds with data from the fossil record, which suggested that teeth were lost only once, and early in the lineage leading to all modern toothless whales. So, the researchers seemed to have two lines of evidence that at face value contradicted each other. The fossil record suggested that tooth loss occurred once in the common ancestor of all toothless whales, but these three genes seemed to have been inactivated independently, several times over, suggesting that loss of teeth should be happening later in Mysticete evolution, and more than once.

One proposed explanation for the apparent discrepancy (among several put forward) was to predict that a fourth gene required for enamel formation was lost early in Mysticete evolution. The loss of any one gene necessary for forming enamel would be enough to prevent the process altogether. In this case, the loss of this fourth gene would prevent tooth enamel from forming, even though the genetic sequences of the other three enamel genes would still be intact. Once enamel function was lost, random mutations in the remaining enamel genes could then accumulate later in Mysticete evolution after speciation in this group was already underway. To test this hypothesis, the research group went hunting for other enamel genes in toothless whales.

Signature in the SINE

The smoking gun for tooth loss in Mysticetes turned out to be exactly what was predicted: a fourth gene, necessary for enamel production, and mutated with the same inactivating mutation in all modern toothless whales. The gene in question, named enamelysin, was destroyed when a mobile genetic element called a SINE transposon inserted into it, breaking it into two halves and removing its function:

The fact that the same SINE insertion mutation at an identical location is found in all modern Mysticete species indicates that this mutation happened once in a common ancestor and then was inherited by the entire group. Since this must have occurred early in the evolution of toothless whales in order to happen in the common ancestor of the entire group, the picture from the genetics and the fossil record match. Once again, findings in one discipline (in this case, paleontology) can be used to make very detailed predictions about what another, unrelated discipline (comparative genomics) should reveal. These results are also entirely consistent with the observation, made in the 1920s, that toothless whales form tooth buds during embryogenesis that are later reabsorbed prior to the point when the deposition of enamel would begin. As with the hind limb story in whale evolution, lines of evidence from genetics, paleontology and embryology converge to support the hypothesis that modern toothless whales descend, through modification, from toothed ancestors.

In the next post in this series, we’ll examine a few more lines of evidence for whale evolution, and extend our discussion to converging lines of evidence for the evolution of our own species.

For further reading:

Meredith, R.W., Gatesy, J., Cjeng, J., and Springer, M.S. (2011). Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales. Proceedings of the Royal Society B: 278 (1708); 993 – 1002. Available online: http://rspb.royalsocietypublishing.org/content/early/2010/09/16/rspb.2010.1280.full.pdf

Ridewood, W.G. (1923). Observations on the skull in foetal specimens of whales of the genera Megaptera and Balaenoptera. Philosophical Transactions of the Royal Society of London B: 211; 209 - 272. Available online: http://rstb.royalsocietypublishing.org/content/211/382-390/209.full.pdf

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Perusing the writings of atheistic scientists and philosophers like Daniel Dennett, one could easily get the impression that arriving at a simpler explanation for something equates to a revelation that things are “lower, cruder, and more trivial.” But at the heart of Barr’s critique is the observation that in fundamental physics and advanced mathematics, “simpler” does not mean more chaotic and inchoate, but rather more elegant and beautiful. Those who hold to a philosophical reductionism “overlook the hidden forces and principles” that govern the processes of cosmic evolution.

Barr’s article lays out the way that the work of scientists and mathematicians exploring the fundamental principles of physics (from Kepler to Einstein to those currently running the Large Hadron Collider in Switzerland) actually suggests “that order does not really emerge from chaos, as we might naively assume; it always emerges from greater and more impressive order already present at a deeper level.” This excerpt gives his first example, the starting point from which he guides us into strangely beautiful world of particle physics, and towards the discovery that “matter, although mindless itself, is the product of a Mind of infinite profundity and infinite simplicity.”

Fearful Symmetries

“Let’s start with a simple but instructive example of how order can appear to emerge spontaneously from mere chaos through the operation of natural forces. Imagine a large number of identical marbles rolling around randomly in a shoe box. If the box is tilted, all the marbles will roll down into a corner and arrange themselves into what is called the “hexagonal closest packing” pattern. (This is the same pattern one sees in oranges stacked on a fruit stand or in cells in a beehive.) This orderly structure emerges as the result of blind physical forces and mathematical laws. There is no hand arranging it. Physics requires the marbles to lower their gravitational potential energy as much as possible by squeezing down into the corner, which leads to the geometry of hexagonal packing.

At this point it seems as though order has indeed sprung from mere chaos. To see why this is wrong, however, consider a genuinely chaotic situation: a typical teenager’s bedroom. Imagine a huge jack tilting the bedroom so that everything in it slides into a corner. The result would not be an orderly pattern but instead a jumbled heap of lamps, furniture, books, clothing, and what have you.

Why the difference? Part of the answer is that, unlike the objects in the bedroom, the marbles in the box all have the same size and shape. But there’s more to it. Put a number of spoons of the same size and shape into a box and tilt it, and the result will be a jumbled heap. Marbles differ from spoons because their shape is spherical. When spoons tumble into a corner, they end up pointing every which way, but marbles don’t point every which way, because no matter which way a sphere is turned it looks exactly the same.

These two crucial features of the marbles—having the same shape and having a spherical shape—should be understood as principles of order that are already present in the supposedly chaotic situation before the box was tilted. In fact, the more we reduce to deeper explanations, the higher we go. This is because, in a sense that can be made mathematically precise, the preexisting order inherent in the marbles is greater than the order that emerges after the marbles arrange themselves. This requires some explanation.

Both the preexisting order and the order that emerges involve symmetry, a concept of central importance in modern physics, as we’ll see. Mathematicians and physicists have a peculiar way of thinking about symmetry: A symmetry is something that is done. For example, if one rotates a square by 90 degrees, it looks the same, so rotating by 90 degrees is said to be a symmetry of the square. So is rotating by 180 degrees, 270 degrees, or a full 360 degrees. A square thus has exactly four symmetries.

Not surprisingly, the hexagonal pattern the marbles form has six symmetries (rotating by any multiple of 60 degrees: 60, 120, 180, 240, 300, and 360 degrees). A sphere, on the other hand, has an infinite number of symmetries—doubly infinite, in fact, since rotating a sphere by any angle about any axis leaves it looking the same. And, what’s more, the symmetries of a sphere include all the symmetries of a hexagon.

If we think this way about symmetry, careful analysis shows that, when marbles arrange themselves into the hexagonal pattern, just six of the infinite number of symmetries in the shape of the marbles are ex-pressed or manifested in their final arrangement. The rest of the symmetries are said, in the jargon of physics, to be spontaneously broken. So, in the simple example of marbles in a tilted box, we can see that symmetry isn’t popping out of nowhere. It is being distilled out of a greater symmetry already present within the spherical shape of the marbles.”

In the full essay, Barr gives a richer description of how this most basic kind of symmetry is just one sort of order, and how even this form points to other much more complex kinds of symmetry whose properties may be described only through the tools of complex mathematics. As he says, “the symmetries that characterize the deepest laws of physics are mathematically richer and stranger than the ones we encounter in everyday life.” But even more important than the fact that such mathematical concepts exist and are beautiful, more important even than the way such esoteric mathematical symmetries have suggested imminently practical experimental projects, is the way they point to a universe that is anything but brutish and trivial, though its elegance may be hard to see:

“It is true that the cosmos was at one point a swirling mass of gas and dust out of which has come the extraordinary complexity of life as we experience it. Yet, at every moment in this process of development, a greater and more impressive order operates within—an order that did not develop but was there from the beginning. In the upper world, mind, thought, and ideas make their appearance as fruit on the topmost branches of an evolutionary tree. Below the surface, we see the taproots of reality, the fundamental laws of physics that shimmer with ideas of profound simplicity.”

This essay appears with the permission of First Things. To read Barr’s complete essay, please click here.

In our previous post, we examined processed pseudogenes – transcribed gene copies that randomly insert into genomes. Unitary pseudogenes, however, are different: unlike processed pseudogenes, they are unique sequences in genomes, and not copies. They have the features one expects of “real” genes: regulatory sequences, introns, and protein coding sections – but with mutations that prevent them from being transcribed or translated. Like buildings in various states of repair, there is a similar range for unitary pseudogenes. If they have only been recently inactivated, they will be largely intact – like a recently abandoned building with a few broken windows. Others are further along in their degradation, like a stone building without a roof and grass growing up through the floor. Some are so far gone that one needs to peel back the turf to search for what remains of the foundation. Despite their various states of disrepair, they remain recognizable – in some cases, they can persist for millions of years before they slowly mutate beyond recognition.

The reason for these defective genes is straightforward: the organism that had the original mutation that removed the function of the gene was not significantly impacted by the loss. One example I have previously discussed is the human GLO pseudogene. The functional GLO gene is part of the biochemical pathway for making vitamin C, something that humans and other primates are not able to do: if we don’t get enough in our diet, we get scurvy. In an environment with adequate dietary vitamin C, however, the loss of the GLO gene is no big deal – and mutations that remove its function would not have been a disadvantage. The mutations that remove GLO function in humans are the same mutations we see in other species – they are an example of mutations in a nested hierarchy, the type of pattern that relatedness produces. This indicates that the mutations happened once, in a common ancestral species, and have been inherited by several species that descend from that ancestor, ours included.

So, what’s a defective gene like you doing in a species like this?

While it makes sense that mammals ought to be able to make vitamin C (even if humans and other primates cannot), in some cases pseudogenes seem much more “out of place.” One example from the human genome that we have discussed in the past, is the vitellogenin gene, a gene required for egg yolk formation in egg-laying organisms. This gene is present in the human genome as a pseudogene, even though humans are placental mammals – human embryos are nourished through a placenta, not egg yolk. This pseudogene was located in the human genome by predicting that its genomic location relative to its neighboring genes would be retained for a long time, even after its inactivation. Accordingly, researchers found a functional vitellogenin gene in the chicken genome, and noted the genes on either side of it (let’s just call them “Gene A and Gene B” for convenience). Gene A and Gene B are also side by side in the human genome, so the researchers looked between them for the signs of vitellogenin gene remains – and found them in that precise spot, still visible despite approximately 300 million years since we last shared a common ancestor with chickens:

Other examples like this abound: whales, for example, have unitary pseudogene remnants of genes devoted to an air-based sense of smell, even in cases where the whale species in question does not have an olfactory organ. A second example from whales are pseudogene remnants of visual pigments adapted for wavelengths of light found in terrestrial settings, not aquatic environments. These examples make perfect sense in light of the terrestrial ancestry of whales, but are challenging to account for from an antievolutionary perspective.

Pseudogenes: evolution’s silver bullet?

Unitary pseudogenes with shared mutations in nested hierarchies among related species are far from the only evidence for evolution, and are not even necessarily the line of evidence most convincing to specialists. Specialists can see the broad pattern of multiple lines of converging evidence that support common ancestry to an extent non-specialists cannot easily appreciate. Unitary pseudogenes, however, are valuable tools for demonstrating a sampling of those lines of evidence, and providing a window into the world of comparative genomics that, to paraphrase Dobzhansky’s famous quote, would make absolutely no sense except in the light of evolution.

Yes, the implications of unitary pseudogenes such as these are easy for even non-specialists to grasp: whales have the defective remnants of genes adapted to terrestrial vision and air-based smelling because they descend from terrestrial ancestors. Placental mammals, including humans, have a defective remnant of a gene used to make egg yolk because they descend from egg-laying ancestors. Unitary pseudogenes share identical mutations across related species because they were inactivated in a common ancestor, and were inherited by every species that descended from that ancestral species.

No special training in genetics is required to appreciate the strength of the evidence that these examples provide. Nor does it require special insight to see that attempts made by antievolutionary groups to refute this evidence face an uphill battle. Its daunting nature notwithstanding, some have undertaken just that task, since the evidence is too compelling to ignore, and too risky to leave unanswered.

Bringing it together: antievolutionary approaches to pseudogenes, unitary and otherwise, miss the mark

Now that we have covered significant ground with respect to what various classes of pseudogenes are and how they arise, we are now able to properly evaluate antievolutionary arguments put forward in an attempt to discredit these lines of evidence for evolution. Attempts to discredit unitary pseudogene evidence generally have one or both of the following two approaches, which we will evaluate in turn:

Approach 1: Discuss rare examples of processed pseudogenes that have acquired function, and imply that all pseudogenes, including unitary pseudogenes, will similarly be shown to have function.

This approach is a fairly common one in the antievolutionary literature, and examples abound. We have examined previously how processed pseudogenes may, in rare cases, acquire a function and come under selection. Note well: the vast, vast majority of processed pseudogenes are not functional and are slowly mutating beyond recognition as DNA not under selection. While rare examples that have acquired function are very interesting from a scientific perspective, they do not “confer functionality” on the remainder of processed pseudogenes, let alone on unitary pseudogenes.

The other issue with this argument is that in many cases we know what the function of the unitary pseudogene once was. We know what the function of vitellogenin is, for example – and we can find this gene in modern-day egg-laying animals. When we see the remnants of this sequence in the human genome it is a stretch to argue that it has another, as of yet unknown function. When we see the human pseudogene sitting between two other genes in the human genome the same order as we observe in the chicken genome, it stretches credibility well past the breaking point.

Approach 2: Claim that unitary pseudogenes with mutations shared across species are the result of non-random mutations that occurred independently in the two species, and are not inherited from a common ancestor.

This argument, though having an appearance of validity, is similarly doomed to frustration. While mutations are not entirely random (certain regions of the genome mutate more readily than others) there is no known mechanism that could create the precise, repeated pattern of shared mutations we observe between related species. The most significant attempt to mount this type of argument against unitary pseudogenes in general was directed at the GLO pseudogene, and I have already discussed the specific details of why that attempt was inadequate. No refinement of that argument, to my knowledge, has been put forward since.

In summary, pseudogenes in general, and unitary pseudogenes in particular, remain a significant thorn in the side of antievolutionary groups. In the next post in this series, we’ll cast our net wider and explore an example of how multiple, convergent lines of evidence support evolution, often in unexpected ways.

For further reading:

http://biologos.org/blog/signature-in-the-pseudogenes-part-1
http://biologos.org/blog/signature-in-the-pseudogenes-part-2
http://biologos.org/blog/a-tale-of-three-creationists-part-3

In our previous BioLogos podcast, we looked at the question of transitional fossils, and how the transitional species story strongly supports evolutionary theory. In this podcast, we look at genetic evidence for evolution. The discovery of DNA has revolutionized our understanding of common descent, particularly in the past few decades. Mutated genes spread through populations over generations, leading to the change we know as evolution. Amazingly, deeper study of DNA lines up with Darwin's initial observations of the larger natural world. While it would take weeks to highlight all the genetic evidence for evolution, today we focus on a few specific examples: the similarity of genomes for related species, psuedogenes, and genetic markers left by retroviruses.

For more, be sure to read Dennis Venema's series "Signature in the Psuedogenes" and "Understanding Evolution".