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        <title>Custom Feed &#45; The BioLogos Forum</title>
    <link>http://biologos.org/resources/find/sort&#45;by&#45;Newest/sort&#45;by&#45;Newest/Divine Action &amp; Purpose,Evolution &#45; Evidence?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
    <description>This is a custom feed of BioLogos resources. Make a new feed at http://biologos.org/resources/find</description>
    <dc:language>en</dc:language>
    <dc:rights>Copyright 2013</dc:rights>
    <dc:date>2013-05-22T22:53:08-08:00</dc:date>    
    
    

            
            
        
      <item>
        <title>Series: Understanding Randomness</title>
        <link>http://biologos.org/blog/series/immunity&#45;and&#45;evolution&#45;the&#45;same&#45;story?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/series/immunity&#45;and&#45;evolution&#45;the&#45;same&#45;story?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>In this series, Kathryn Applegate addresses the concern that randomness implies the absence of God&apos;s activity and involvement in the natural world.  She begins by clearing up some common misconceptions about the concept of &quot;randomness&quot;, and later focuses on the mechanisms of the immune system to demonstrate that God works through random processes to preserve life.  Far from being an indication of a &quot;godless&quot; universe, one might conclude that randomness is one of God’s favorite mechanisms for creating and sustaining life!</description>
        <content:encoded><![CDATA[<p>You hear it all the time: “That’s so random!” When used by people of my generation, the word “random” can simply mean “cool” or “surprising.” Or it can mean something like “disconnected,” as in the phrase, “I had a random thought” (which returns 189,000 hits on Google, by the way—random!).</p>

<p>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?</p>

<p>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.</p>

<p>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.</p>

<p>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 <em>indeterminate</em>, but is it purposeless? Not necessarily. Indeterminacy simply means the result cannot be predicted from the outset.</p>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<p>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?</p>

<p>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 <a href="http://models.scripps.edu/" target="_blank">model</a> as shown in the following video. In less than 30 seconds, you can watch a jumbled heap of proteins become a beautifully ordered structure.</p>

<p align="center"><object height="385" width="480"><param name="movie" value="http://www.youtube.com/v/X-8MP7g8XOE&amp;hl=en_US&amp;fs=1&amp;rel=0" /><param name="allowFullScreen" value="true" /><param name="allowscriptaccess" value="always" /><embed allowfullscreen="true" allowscriptaccess="always" height="385" src="http://www.youtube.com/v/X-8MP7g8XOE&amp;hl=en_US&amp;fs=1&amp;rel=0" type="application/x-shockwave-flash" width="480"></embed></object></p>

<p>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.”</p>

<p>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 <em>see</em> how it happens in a cell, but we can reconstitute the process in a test tube using different combinations of constituent molecules.</p>

<p>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:</p>

<p align="center"><object height="385" width="480"><param name="movie" value="http://www.youtube.com/v/YbpTusoDEgA&amp;hl=en_US&amp;fs=1&amp;rel=0" /><param name="allowFullScreen" value="true" /><param name="allowscriptaccess" value="always" /><embed allowfullscreen="true" allowscriptaccess="always" height="385" src="http://www.youtube.com/v/YbpTusoDEgA&amp;hl=en_US&amp;fs=1&amp;rel=0" type="application/x-shockwave-flash" width="480"></embed></object></p>

<p>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.</p>

<p>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 <em>un</em>intelligently-designed structures (like viruses, which can kill us), we see that God has made, and continues to oversee by his providence, a <em>good</em> creation that, at least in part, is capable of creating itself.</p>

<p class="intro">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.</p>]]></content:encoded>
        <pubDate>Sat, 23 Mar 13 06:00:44 -0700</pubDate>
        <dc:creator>Kathryn Applegate</dc:creator>
        <!--<dc:date>Mar 23, 2013 06:00</dc:date>-->
      </item>
            <item>
        <title>Searching for Motivated Belief: Understanding John Polkinghorne, Part 2</title>
        <link>http://biologos.org/blog/searching&#45;for&#45;motivated&#45;belief&#45;understanding&#45;john&#45;polkinghorne&#45;part&#45;two?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/searching&#45;for&#45;motivated&#45;belief&#45;understanding&#45;john&#45;polkinghorne&#45;part&#45;two?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>To understand more clearly where Polkinghorne lies on the larger landscape of science and religion, let’s consider his approach to the Resurrection. Many contemporary thinkers, including some theologians and clergy, believe that “science” has somehow made it impossible to believe in the Resurrection, the deity of Jesus, and even belief in the transcendent God of the Bible.</description>
        <content:encoded><![CDATA[<p>In my last post, I presented John Polkinghorne’s attitude to scientific and religious knowledge and explained his approach to natural theology. Today, we briefly examine his theology of nature and his attitude toward the Resurrection.</p>

<h3>Understanding John Polkinghorne: Theology of Nature</h3>

<p>John Polkinghorne’s interest in natural theology is important, but what really sets him apart from most others is that he combines it with an equally strong interest in <strong>theology of nature</strong>, which is not the same thing. Where natural theology involves, “metaquestions about the pattern and structure of the physical world,” theology of nature involves, “metaquestions about how its historical process is to be understood.” Rather than “looking to the physical world for hints of God’s existence,” we look “to God’s existence as an aid for understanding why things have developed in the physical world in the manner that they have.” (<em>Belief in God in an Age of Science</em>, p. 13)</p>

<p>On this front, Polkinghorne advances a strongly Christocentric theology of creation, stressing Jürgen Moltmann’s notion of <a href="http://www.amazon.com/gp/product/0800628225/ref=as_li_ss_tl?ie=UTF8&amp;camp=1789&amp;creative=390957&amp;creativeASIN=0800628225&amp;linkCode=as2&amp;tag=thebiofou06-20">The Crucified God</a><img alt="" border="0" height="1" src="http://www.assoc-amazon.com/e/ir?t=thebiofou06-20&amp;l=as2&amp;o=1&amp;a=0800628225" style="border:none !important; margin:0px !important;" width="1" /> . In the context of Polkinghorne’s theology of nature, the point is that the Creator is the crucified and resurrected second person of the Trinity. Since I devoted a <a href="http://biologos.org/blog/science-and-the-bible-theistic-evolution-part-3">column to this before</a>, I won’t say more here, except to alert readers to the singular importance this particular idea has for him—especially when facing the problem of suffering. “The insight of the Crucified God lies at the very heart of my own Christian belief, indeed of the possibility of such belief in the face of the way the world is.” (<em>Belief in God in an Age of Science</em>, p. 44)</p>

<h3>Situating John Polkinghorne: The Resurrection of Jesus</h3>

<p>Many Christians today see science as posing dangerous threats to their faith, challenging their understanding of the Bible and undermining core tenets such as the bodily Resurrection of Jesus, the historical basis on which the Christian faith stands or falls. “Evolution” is <a href="http://biologos.org/blog/science-and-the-bible-theistic-evolution-part-5">often identified as the problem</a>, but the real danger is unbridled naturalism. A commitment to naturalistic methods, known as “methodological naturalism,” (MN) has been an integral part of science and medicine since the ancient Greeks. Those methods have been highly successful at producing a coherent, often very convincing picture of nature and the history of nature.</p>

<p>Advocates of Intelligent Design and some other Christians <a href="http://biologos.org/blog/science-and-the-bible-intelligent-design-part-3">reject MN</a>, but many Christians who work in the sciences and related fields (such as engineering, medicine, or the history and philosophy science) support MN as a properly grounded and properly limited way of understanding reality. In their view, a robust Christian faith is consistent with a commitment to MN, provided that the limits of scientific inquiry are not simply equated with the limits of rationally grounded belief. Polkinghorne fits squarely in this category.</p>

<p>To understand more clearly where Polkinghorne lies on the larger landscape of science and religion, let’s consider his approach to the Resurrection. Many contemporary thinkers, including some theologians and clergy, believe that “science” has somehow made it impossible to believe in the Resurrection, the deity of Jesus, and even belief in the transcendent God of the Bible.</p>

<p class="caption-left"><img alt="" src="http://biologos.org/uploads/static-content/spong_cover.jpg" /></p>

<p>A prime example is <a href="http://johnshelbyspong.com/">John Shelby Spong</a>, a retired Episcopalian bishop whose books have sold more than one million copies. Spong sees the bodily Resurrection as a figment of the disciples’ imaginations, a vestige of a theism that now we must throw away like a threadbare suit of clothes. For Spong, Christians today need to go <a href="http://www.amazon.com/gp/product/0060778423/ref=as_li_ss_tl?ie=UTF8&amp;camp=1789&amp;creative=390957&amp;creativeASIN=0060778423&amp;linkCode=as2&amp;tag=thebiofou06-20">"beyond theism"</a><img alt="" border="0" height="1" src="http://www.assoc-amazon.com/e/ir?t=thebiofou06-20&amp;l=as2&amp;o=1&amp;a=0060778423" style="border:none !important; margin:0px !important;" width="1" />&nbsp;throwing out the baby of divine transcendence—the fundamental truth of monotheism—along with the bath water of the credulity and mythology of the pre-modern authors of the Bible and the ecumenical creeds. Spong’s message is that “Christianity must change or die,” and all in the name of “science.”</p>

<p>As Spong likes to say, his work is very controversial, and not just among rank-and-file Christians. Scholars have also railed against him. “I have been attacked in books from the religious right by such people as Alistair MacGrath [whose surname is actually spelled McGrath], N.T. Wright, and Luke Timothy Johnson,” he complains (<em>Why Christianity Must Change or Die</em>, p. xvi).</p>

<p>I understand (with much sadness) that we live in a highly polarized age. Nevertheless, it’s difficult for me to grant much credibility to an author who identifies <a href="http://users.ox.ac.uk/~mcgrath">McGrath</a>, <a href="http://ntwrightpage.com/">Wright</a>, and <a href="http://www.candler.emory.edu/faculty/faculty-bios/johnson.cfm">Johnson</a>&nbsp;as representatives of the “religious right.” Indeed, if anyone here is distorting the news it is Spong, not they. As the (late) great Catholic biblical scholar <a href="http://en.wikipedia.org/wiki/Raymond_E._Brown">Raymond Brown</a>&nbsp;once observed, “I do not think that a single NT [New Testament] author would recognize Spong’s Jesus as the figure being proclaimed or written about.” (<em>Birth of the Messiah</em>, note 321 on p. 704)</p>

<p class="caption-right"><img alt="" src="http://biologos.org/uploads/static-content/resurrection_grunewald.jpg" /><br />
Matthias Grünewald, <em>The Resurrection</em> (a wing of the<br />
Isenheim Altarpiece, ca. 1515), Unterlinden Museum,<br />
Colmar, France</p>

<p>Polkinghorne certainly understands science far more than Spong does, and his conclusions about the implications of science for Christian beliefs are markedly different. With respect to the Resurrection, he is basically on the same page with his friend Wright, whose profound book, <a href="http://www.christendom-awake.org/pages/resurrection/wright_resurrection.htm"><em>The Resurrection of the Son of God</em></a>, he cites with appreciation. Belief in the Resurrection is well supported by the evidence, and the Resurrection, itself, is “the pivot on which the claim of a unique and transcendent significance for Jesus must turn.” Considering authors like Spong (although he does not explicitly name him), he adds, “it would be a serious apologetic mistake if Christian theology thought that operating in the context of science should somehow discourage it from laying proper emphasis on the essential centrality of Christ’s Resurrection, however counterintuitive that belief may seem in the light of mundane expectation.” (<em>Theology in the Context of Science</em>, pp. 135-6)</p>

<p>Amen.</p>

<h3>Looking Ahead</h3>

<p>This is the Easter season, and I’ll return in a couple of weeks to begin examining Polkinghorne’s approach to the Resurrection more fully, using excerpts from the chapter on “Motivated Belief” from his recent book, <em>Theology in the Context of Science</em>.</p>

<h3>References</h3>

<p>Raymond E. Brown, <a href="http://yalepress.yale.edu/yupbooks/book.asp?isbn=9780300140088"><em>Birth of the Messiah: A Commentary on the Infancy Narratives in the Gospels of Matthew and Luke</em></a>. (1992).</p>

<p>John Polkinghorne, <em><a href="http://www.amazon.com/gp/product/0300099495/ref=as_li_ss_tl?ie=UTF8&amp;camp=1789&amp;creative=390957&amp;creativeASIN=0300099495&amp;linkCode=as2&amp;tag=thebiofou06-20">Belief in God in an Age of Science</a><img alt="" border="0" height="1" src="http://www.assoc-amazon.com/e/ir?t=thebiofou06-20&amp;l=as2&amp;o=1&amp;a=0300099495" style="border:none !important; margin:0px !important;" width="1" /></em> (1998).</p>

<p>John Polkinghorne, <a href="http://yalepress.yale.edu/book.asp?isbn=9780300149333"><em>Theology in the Context of Science</em></a> (2009).&nbsp;My review for <em>First Things</em> online is <a href="http://www.firstthings.com/onthesquare/2009/07/the-motivated-belief-of-john-polkinghorne">here</a>.</p>

<p>John Shelby Spong, <em><a href="http://www.amazon.com/gp/product/0060675365/ref=as_li_ss_tl?ie=UTF8&amp;camp=1789&amp;creative=390957&amp;creativeASIN=0060675365&amp;linkCode=as2&amp;tag=thebiofou06-20">Why Christianity Must Change or Die</a><img alt="" border="0" height="1" src="http://www.assoc-amazon.com/e/ir?t=thebiofou06-20&amp;l=as2&amp;o=1&amp;a=0060675365" style="border:none !important; margin:0px !important;" width="1" /></em> (1998).</p>
]]></content:encoded>
        <pubDate>Thu, 14 Mar 13 08:00:44 -0700</pubDate>
        <dc:creator>Ted Davis</dc:creator>
        <!--<dc:date>Mar 14, 2013 08:00</dc:date>-->
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        <title>Evolution Basics: Darwin’s Early Observations on Biogeography</title>
        <link>http://biologos.org/blog/evolution&#45;basics&#45;darwins&#45;early&#45;observations&#45;on&#45;biogeography?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/evolution&#45;basics&#45;darwins&#45;early&#45;observations&#45;on&#45;biogeography?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>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.</description>
        <content:encoded><![CDATA[<p>In the previous post in this series, we discussed how scientific theories—broad, well-tested explanatory frameworks—get their start as hypotheses. As a hypothesis is used to make predictions, and those predictions are supported by experimentation, over time, scientists come to have more and more confidence in that hypothesis as a reliable guide for making predictions about the natural world. This means any current theory in science has gone through this transition, and its history can be traced.</p>

<p>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 <em>biogeography</em>: 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.</p>

<h3>The curious case of the missing mammals</h3>

<p><as a="" href="http://en.wikipedia.org/wiki/Second_voyage_of_HMS_Beagle" naturalist="" on="" the="" widely-travelled="">As a widely-travelled naturalist on the&nbsp;<a href="http://en.wikipedia.org/wiki/Second_voyage_of_HMS_Beagle">HMS <em>Beagle</em></a>,&nbsp;Darwin studied a large number of different environments and documented the species he found in each. <em>The Beagle</em>, 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.<a href="http://en.wikipedia.org/wiki/Island#Oceanic_islands"><em>oceanic</em></a>&nbsp;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).</as></p>

<p>Darwin found these observations difficult to square with his (then) working assumption that species were independently created in (and specifically created <em>for</em>) 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 <a href="http://darwin-online.org.uk/content/frameset?pageseq=364&amp;itemID=F373&amp;viewtype=text"><em>Origin of Species</em></a>. 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 <a href="http://darwin-online.org.uk/content/frameset?pageseq=411&amp;itemID=F373&amp;viewtype=side">missing mammals</a>:</p>

<blockquote><p>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.</p>
</blockquote>

<p>(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. <a href="http://en.wikipedia.org/wiki/Charles_Darwin#Religious_views">Darwin himself</a>&nbsp;held to this common view at the start of his voyage on the <em>Beagle</em>, and that is the model he is attempting to refute in <em>Origin</em>, 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 <a href="http://www.darwinproject.ac.uk/darwin-and-design-article">correspondence</a>&nbsp;with American botanist Asa Gray, among others.)</p>

<p>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)&nbsp;yet no such species had been created for that suitable habitat.</p>

<h3>Island endemics and their continental “allied species”</h3>

<p>Darwin noticed more than the <em>absence</em> 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 <em>Origin</em> 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 <a href="http://darwin-online.org.uk/content/frameset?pageseq=415&amp;itemID=F373&amp;viewtype=text">prove instrumental on this point</a>:</p>

<blockquote><p>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.</p>

<p>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.</p>
</blockquote>

<h3>Rethinking independent creation</h3>

<p>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.</p>

<p>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 <em>Origin</em>.</p>
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        <pubDate>Thu, 07 Mar 13 07:56:26 -0800</pubDate>
        <dc:creator>Dennis Venema</dc:creator>
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        <title>Series: God and Creation</title>
        <link>http://biologos.org/blog/series/god&#45;creation&#45;series?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/series/god&#45;creation&#45;series?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>In this four part series, David Opderbeck explores the interesting relationship between God and his creation. He first looks at his transcendence over the material world. In one respect, God is completely distinct from all creation, yet he is also immanent, or present within all creation. Another aspect of God reflected in creation is his Triune nature. Just as love, fellowship, and delight exist within the Trinity, so these characteristics are present in the world, and experienced by humans. He completes his thoughts with a discussion about God’s interaction with humans.</description>
        <content:encoded><![CDATA[<p class="intro">This series is drawn from David’s podcasts, which are available on his <a href="http://www.tgdarkly.com/blog/?cat=31" target="_blank">website</a>.</p>

<p>If we want to talk about God, creation, and science, where should we start? It’s easy to begin with conflict. We can claim that the rise of modern science is the root of cultural decline. We can dive right into some of the contentious questions about how the Bible and science relate to each other. We can adopt a posture of defensiveness about what Christians believe and the ways in which some people think science threatens our beliefs.</p>

<p>But this is not a good place to start. The place to start is the place where all good Christian theology must start: with God.</p>

<p>“In the beginning, God….” These are the first words of the Bible. “I believe in God….” These are the first words of the Apostle’s Creed. If we want to develop wisdom and understanding about the relation between God and creation, then we need to start with the source of everything: God.</p>

<p>But how do we know anything about God? And how can we say anything about God? As we go about our daily lives, we can’t converse with God in exactly the same way that we might talk with our families, friends or neighbors. We can’t touch or smell God like a patch of green grass or taste Him like an apple. We can’t see him like an image on our TV screens. In theological terms, there is a sense in which God is “hidden” to our human senses. Many great Christian thinkers, such as Martin Luther, spent a good part of their lives reflecting on the “hiddenness” of God.</p>

<p>It may surprise you to hear God described as “hidden.” Those of us who have been in the Church for a while often are much more familiar with talk of how God has revealed Himself to us. We seem to gravitate towards detailed and systematic explanations of what we think we can know about God. God has, of course, revealed Himself to us – or else there would be very little point in trying to speak about Him. In scripture, in the proclamation of the Church, in the created world, and most importantly, in Jesus Christ, God has made Himself known. So why start with how God is “hidden?”</p>

<p>The very fact that God cannot be directly perceived by our ordinary human senses tells us something important about God and creation. God is “hidden” because He is “other.” God is not a patch of grass, and a patch of grass is not God. God is not an apple, and an apple is not God. God is not a television image or painting or statute, and a television image, painting or statute is not God. God is not a human being, and human beings are not God. God is not matter, the stuff of the created world, and matter is not God.</p>

<p>In theological terms, God is <em>transcendent</em>. “God” and “creation” are not the same thing. This is a basic idea that distinguishes Christian understandings of God from many other philosophies and religions. In fact, this emphasis on God’s transcendence is one important difference between the Hebrew and Christian theologies of creation and the prevailing ideas in the ancient near eastern world of the Biblical writers. It also distinguishes Christian thinking about God and creation from some of the important ideas that are common today.</p>

<p>In many ancient near eastern creation myths, the material creation was derived from the body of a god.  In the Babylonian <em>Enuma Elish</em>, for example, the female god Tiamat is killed by another god, Marduk, and the two halves of Tiamat’s corpse become the earth and the skies.  In Egyptian mythology, many of the gods were related to material entities.  Ra, for example, was the god of the Sun, Nut was god of the sky, and Geb was god of the earth.  These stories reflect an ontology in which there is no sharp distinction between the gods and the material world.  The Biblical literature, in contrast, separates the nature and being of the creator-God from the nature and being of His creation.</p>

<p>In contemporary popular Western culture, two of the most common ideas about God and creation really are very old notions dressed up in new clothes.</p>

<p>One is a thought you might hearon TV talk shows, in self-help books, or in popular music or movies: that “everything is one” or that “God is in everything and everyone.”  This usually sounds like “pantheism” — the notion that God and the world around us really are essentially the same thing.  In American popular culture, this often boils down to God becoming the same thing as our own individual selves. How often have you heard a line like this in a song or TV show or movie: “<em>what you’ve been looking for has been right inside yourself all along</em>” or “<em>the most important thing is to find out who you are?</em>”</p>

<p>The truth of God’s transcendence means that the real basis for a meaningful and good life lies <em>outside</em> of our selves. We are part of creation, and therefore we are not God.    We must look outside ourselves to find the source of life. Before we become too critical here, we need to preview for a moment another important theme in Christian theology:  that God is also <em>immanent</em>. It is true that creation is an interconnected system and that God is always present throughout all of creation. It is also true that in our created humanity we are made for an intimate connection with God. It is right to look into ourselves as we seek God.  As Augustine described in his <em>Confessions</em>, an honest search of the self should reveal a nature that is not self-sufficient, that is not meant to be alone, that longs for relationship with a beauty and harmony and love that the individual self cannot sustain. Augustine called this a “God-shaped void” at the heart of every person.</p>

<p>Yet we also need to be clear that, while the search may begin within our selves, it must not stop there. God is “other,” so we must continue beyond ourselves, in fact beyond everything we think we see, in order to find Him. And the paradox here is that we can only find the true meaning and purpose of our own selves by going beyond ourselves and finding the God who is other than us and who made us.</p>

<p>The other idea often expressed in our popular culture is that “matter is all there is.” Unfortunately, for some people this idea has become the standard for supposedly “scientific” thinking about the world. But this is not a “scientific” idea at all – it is a metaphysical statement (“metaphysical” just means “beyond the physical”) with roots going back to the ancient Greek Stoics. For many educated people in Western culture, if something cannot be verified with the human senses, it is not “real,” or at least it is not worthy of consideration as a matter of “fact” or “reason.”</p>

<p>There are many reasons why this way of thinking about what counts as truth or knowledge has become so influential. Our modern intellectual, political and social systems were shaped by the period from the seventeenth to eighteenth centuries known as the “Enlightenment.”  Even modern Christianity has been tinged in significant ways by Enlightenment thought.</p>

<p>The Enlightenment, of course, was not all bad. It gave us some great gifts, including the contemporary scientific method and the political frameworks, such as the U.S. Constitution, that support the freedoms we now take for granted.</p>

<p>But like many exciting moments in history, the Enlightenment produced some unbalanced perspectives. The ways in which human beings can know things in addition to observation of the tangible world around us were lost. The sorts of intuitions and experiences that human beings throughout history had understood to reach beyond reason were discredited. The thought that a transcendent God might have broken into history to reveal anything about Himself was mostly set aside.</p>

<p>Christian theology has always asserted that because God is transcendent, human observation and human reason are neither the starting point nor the ending point for true knowledge, wisdom and understanding. If matter is not all there is, then our search for truth cannot be limited to the material world alone. In fact, the beginning of knowledge and wisdom is the realization that God is beyond and other than the created world.
Again, a word of balance is in order. Human observation and reason do matter, precisely because God created us as part of a world that is in important ways orderly and knowable. The great Christian thinker Anselm said that knowledge is the act of “faith seeking understanding.” “Understanding” – the sometimes difficult process of bringing all our resources, including reason, to bear on the search for truth – depends on and follows “faith.”</p>

<p>God’s transcendence means that the physical world does not represent the limits of what is true and real. Indeed, the physical world is not the beginning or end of what is true and real. The “beginning and end,” the “alpha and omega,” is the God who is beyond all our thoughts and imaginings.</p>]]></content:encoded>
        <pubDate>Fri, 01 Mar 13 07:00:07 -0800</pubDate>
        <dc:creator>David Opderbeck</dc:creator>
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        <title>Evolution and Christian Faith Grantees Announced</title>
        <link>http://biologos.org/blog/evolution&#45;and&#45;christian&#45;faith&#45;grantees&#45;announced?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/evolution&#45;and&#45;christian&#45;faith&#45;grantees&#45;announced?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>Congratulations to the 37 winners of the Evolution &amp; Christian Faith (ECF) grants competition! ECF is a new BioLogos program designed to support projects and network&#45;building among scholars, church leaders, and parachurch organizations.</description>
        <content:encoded><![CDATA[<p>Congratulations to the 37 winners of the Evolution &amp; Christian Faith (ECF) grants competition!&nbsp; ECF is a new BioLogos program designed to support projects and network-building among scholars, church leaders, and parachurch organizations. Each project takes a different approach to address theological and philosophical questions commonly voiced by Christians about evolutionary creation. ECF places a premium on scholarship with high “translational” potential—that which leaves the academy and makes an impact on the church. The program runs through August 2015.</p>

<p>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.</p>

<h3>ECF History</h3>

<p>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 &amp; Culture, Leadership Journal, or First Things websites, on your professional society’s listserv, or perhaps on your friend’s blog.</p>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<h3>The Grantees</h3>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<p>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.&nbsp; Some examples:&nbsp;</p>

<ul>
<li><p>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.&nbsp;</p>
</li>
<li><p>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?&nbsp;</p>
</li>
<li><p>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.</p>
</li>
<li><p>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.&nbsp;&nbsp;</p>
</li>
</ul>

<p>These are just a few of the scholarly awards; check out the <a href="/ecf/grantees">Grantees page</a> for full descriptions of all Track 1 and Track 2 projects.</p>

<p>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. &nbsp;Some examples include:</p>

<ul>
<li><p>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.</p>
</li>
<li><p>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.</p>
</li>
<li><p>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.</p>
</li>
<li><p>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.</p>
</li>
<li><p>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.</p>
</li>
</ul>

<p>Again, this is just a taste of the diversity of Track 3 projects. Read more about each project on the <a href="/ecf/grantees">Grantees page</a>. 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.</p>
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        <pubDate>Wed, 13 Feb 13 05:25:03 -0800</pubDate>
        <dc:creator>Kathryn Applegate</dc:creator>
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        <title>Where are the Transitional Fossils?</title>
        <link>http://biologos.org/blog/where&#45;are&#45;the&#45;transitional&#45;fossils?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/where&#45;are&#45;the&#45;transitional&#45;fossils?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>A common argument leveled against the theory of evolution is that scientists have not been able to produce transitional fossils that show the change of one species into another.  In this podcast, we address a common misconception about what transitional fossils actually are.</description>
        <content:encoded><![CDATA[<p align="center"><iframe src="http://player.vimeo.com/video/31875051?title=0&amp;byline=0&amp;portrait=0" width="570" height="428" frameborder="0" webkitAllowFullScreen allowFullScreen></iframe></p>

<p>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. <sup>1</sup></p>

<p class="date">1. To hear the full audio clips which have been referenced go to:</p>
<ul><li><a href="http://www.youtube.com/watch?v=X6EmOQLf25s&feature=BFa&list=PLACF41F3DDBCA4565&lf=results_video&noredirect=1" target="_blank">Rational Response Debate with Kirk Cameron (from Way of the Masters)</a></li>
<li><a href="http://www.youtube.com/watch?v=FN9wyn9xVko&feature=related" target="_blank">Behind the Scenes with Dr. Neil Shubin (from Cincinnati Museum Center)</a></li>
<li><a href="http://www.youtube.com/watch?v=fVNXXLLUYFM' target="_blank">Mark Norell Publishes New Archaeopteryx Findings (from American Museum of Natural Sciences)</a></li>
<li><a href="http://www.youtube.com/watch?v=VmtDGjfMajM" target="_blank">Texas A&M Professor Discusses Findings of Autralopithecus Sediba and its Relationship to Humans (from Texas A&M University)</a></li>
<li>Intro/outro music composed by Martin Minor (<a href="http://www.looperman.com/users/profile/159051" target="_blank">Minor2Go</a>).</li> </ul> </p>

<p><strong>An audio only version of the podcast can be downloaded <a href="http://biologos.org/uploads/resources/fossil_podcast_final.mp3" target="_blank">here</a>.</strong></p>
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        <pubDate>Fri, 01 Feb 13 08:57:28 -0800</pubDate>
        <dc:creator>Kelsey Luoma</dc:creator>
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        <title>Series: Decoding ENCODE</title>
        <link>http://biologos.org/blog/series/decoding&#45;encode&#45;series?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/series/decoding&#45;encode&#45;series?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>The BioLogos Foundation explains to the findings of the Encyclopedia of DNA Elements (ENCODE) project and responds to the claims that its discoveries challenge the theory of evolution, especially regarding so&#45;called &quot;junk DNA&quot;.</description>
        <content:encoded><![CDATA[<p>In 2003, under the leadership of BioLogos founder Francis Collins, the Human Genome Project sequenced the full human genome, showing us for the first time the order of the 3.2 billion chemical “bases” that make up the rungs of DNA’s double helix structure. The project identified and mapped 23,000 genes that code for proteins, but those genes make up less than 2% of the total sequence—far fewer than originally predicted, given the complexity of humans. While many non-coding sequences were identified as having function as well, there were still vast swaths of the genome that had no obvious function. In fact, what was known about certain classes of sequences suggested that they had no functional role for humans—such as the sequences identified as either transposons or transposon fragments that make up nearly half of our genome. These sorts of sequences seemed to fit into what was popularly known as the “junk DNA” category. </p>

<p>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?”  </p>
<p>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.”</p>

<p>Early this month, researchers from ENCODE released more than thirty papers presenting their findings. During a <em>Science</em> magazine <a href="http://news.sciencemag.org/sciencenow/2012/09/live-chat-figuring-out-what-dna.html">online chat</a>, the project’s data coordinator, Ewan Birney, explained the outcome:</p>

<blockquote>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.<br /><br />

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.<br /><br />

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.<br /><br />

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.</blockquote>

<p>According to the abstract of one of the <a href="http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html">lead papers</a> from <em>Nature</em>, 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 <em>some</em> biochemical function.  As a <em>Science</em> <a href="http://www.sciencemag.org/content/337/6099/1159">news article</a> put it, these 30 papers “sound the death knell for the idea that our DNA is mostly littered with useless bases.”</p>

<p>The pro-Intelligent Design organization The Discovery Institute has heralded the discovery as the “demise of junk DNA.”  Casey Luskin writes for their <a href="http://www.evolutionnews.org/2012/09/junk_no_more_en_1064001.html">blog</a> <em>Evolution News</em>:</p>

<blockquote>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.</blockquote>

<p>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.” </p>

<p>So with all this in mind, is ENCODE a stunning victory for ID, as Luskin believes? Bryan College biologist Todd Wood thinks not.  He <a href="http://toddcwood.blogspot.co.uk/2012/09/everyones-excited-about-encode.html">writes</a>, “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.”  </p>

<p>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—<em>through</em> the elegant processes of evolution, not in opposition to them.</p>

<p>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 <a href="http://biologos.org/blog/understanding-evolution-is-there-junk-in-your-genome-part-1">post</a> on our site, including a striking comparison between 29 different mammal genomes and the human genome).  In fact, another  ENCODE researcher participating in the <em>Science</em> magazine chat, John A. Stamatoyannopoulos of the University of Washington School of Medicine, thinks the findings align beautifully with evolutionary theory:
</p>

<blockquote>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.</blockquote>

<p>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.</p>

<p class="intro">A special thanks goes to Darrel Falk, Mark Sprinkle, Kathryn Applegate, Dennis Venema, and Tom Burnett for their contributions to this post.</p>]]></content:encoded>
        <pubDate>Wed, 26 Sep 12 05:00:35 -0700</pubDate>
        <dc:creator>Stephen Mapes, Dennis Venema</dc:creator>
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        <title>Denisovans, Humans and the Chromosome 2 Fusion</title>
        <link>http://biologos.org/blog/denisovans&#45;humans&#45;and&#45;the&#45;chromosome&#45;2&#45;fusion?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
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        <description>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.</description>
        <content:encoded><![CDATA[<br> </br><p>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. </p>

<h3>The origins of human chromosome 2: a brief review</h3>
<p>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):</p>

<p class="caption-center"><img src="http://biologos.org/uploads/static-content/denisovans_fig_1.jpg" alt="" height="357" width="434"  /></p>
 
<p>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): </p>

<p class="caption-center"><img src="http://biologos.org/uploads/static-content/denisovans_fig_2.jpg" alt="" height="300" width="570"  /></p>
 
<p>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.</p>

<p>We can also find further support for Option A, because it predicts a specific type of event, namely one that reduces chromosome number. Since <em>loss</em> 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. </p>

<p>Further evidence for a fusion event in the lineage leading to modern humans comes from comparing <em>synteny</em>, or gene locations and orders on chromosomes within modern great apes – an issue we have discussed <a href="http://biologos.org/blog/signature-in-the-synteny">here</a> 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 <a href="http://biologos.org/blog/the-sorrows-and-joys-of-teaching-evolution">last post</a> 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. </p>

<h3>Enter the Denisovans</h3>
<p>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, <a href="http://biologos.org/blog/a-geneticists-journey">here</a> and <a href="http://biologos.org/blog/understanding-evolution-neanderthals-denisovans-and-human-speciation">here</a>). Recently, a more detailed understanding of the Denisovan genome <a href="http://www.nature.com/news/new-dna-analysis-shows-ancient-humans-interbred-with-denisovans-1.11331">was published</a>, and nested in the new information is the discovery that the Denisovans share the 46 chromosome set with the same fusion that <a href="http://johnhawks.net/weblog/reviews/denisova/denisova-chromosome-2-2012.html">we have</a>. 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): </p>

<p class="caption-center"><img src="http://biologos.org/uploads/static-content/denisovans_fig_3.jpg" alt="" height="452" width="513"  /></p>
 
<p>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).</p>

<p>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.</p>

<h3>Implications for understanding our “becoming human”</h3>
<p>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). </p>

<p>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.</p> 
<br> </br>]]></content:encoded>
        <pubDate>Thu, 06 Sep 12 13:07:21 -0700</pubDate>
        <dc:creator>Dennis Venema</dc:creator>
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        <title>Did David Hume &quot;Banish&quot; Miracles?</title>
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        <guid>http://biologos.org/blog/did&#45;david&#45;hume&#45;banish&#45;miracles?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>“I flatter myself,” Hume triumphantly proclaimed, “that I have discovered an argument . . . which, if just, will, with the wise and learned, be an everlasting check to all kinds of superstitious delusion, and consequently, will be useful as long as the world endures.”</description>
        <content:encoded><![CDATA[<p class="intro">Alvin Plantinga’s series on <a href="http://biologos.org/blog/divine-action-in-the-world-part-1">Divine Action in the World</a> gives considerable attention to the question of miracles and whether they are “contrary to science”.  To follow up on this contentious issue, we’d like to feature this excerpt from Rick Kennedy's book <a href="https://wipfandstock.com/store/Jesus_History_and_Mt_Darwin_An_Academic_Excursion" target="_blank">Jesus, History, and Mount Darwin: An Academic Excursion</a>.  During Rick’s climb into the Evolution Range of the High Sierras of California, he reflected on why historians are so loath to accept accounts of supernatural events.  Many academics point to the Enlightenment scholar David Hume as offering the most compelling argument against the possibility of miracles.<br><br>

For more of Rick Kennedy’s reflections, see his full BioLogos <a href="http://biologos.org/blog/series/mount-darwin-series">series</a>.</p>

<h3>Keeping History Safe</h3>

<p>In the cold morning air with the sun not yet over the ridge, the place to begin preparation for summiting Mount Darwin is to ponder the reasonableness of miracles.  Many <em>Totalizers</em> would like to ban miracles from university consideration and inquiry.  Trouble is: human history is awash with credible people reporting miracles. </p>

<p>Modern academic tradition tends to try and maintain order. For historians it behooves us professionally to avoid accounts of alleged spiritual events.  We find comfort in a little logical gymnastics that keeps history safe for us to wander in, a deceptively formulaic avoidance method that helps us avoid what people are telling us about extraordinary events in the past.</p>

<p>David Hume popularly articulated this logical gymnastics in an essay titled “Of Miracles” that was eventually printed in <em>Enquires Concerning Human Understanding</em> (1748). “I flatter myself,” Hume triumphantly proclaimed, “that I have discovered an argument . . . which, if just, will, with the wise and learned, be an everlasting check to all kinds of superstitious delusion, and consequently, will be useful as long as the world endures.” </p>

<p>His everlasting check on superstition begins with a circular argument that because miracles can’t happen, a reasonable person should not even listen to reports of them. Hume taught that though the normal job of a historian was to listen to the testimony that comes down to us from the past, there is a point at which you can close your ears. Hume knew that historical testimony can get wild, so he came up with a way to domesticate the wildness, a way to make history a zoo rather than allow it to be a jungle. His “Of Miracles” has been tremendously influential in the discipline of human history over the last two hundred and fifty years, not because his ideas are strong, but because his ideas are useful. Get rid of “superstitious delusions,” and the discipline of history can be turned from a safari into a form of home economics.
Hume’s domestication of history is seductively simple. Instead of following the Aristotelian tradition of linking the credibility of hard-to-believe testimony to the credibility of the testifier, Hume recommended disregarding the testifier and focusing only on the testimony. This effectively removed the persuasive power from hard-to-believe testimony. Miracles need the credibility of an eyewitness in order to have persuasive power. Hume cut the power source from the unwanted testimony.  </p>

<p>Essentially, Hume adopted the modeling technique that Darwin later used and is best seen in Global Positioning System (GPS) units. Hume recommended gathering testimony from the past and every region to create a general model of what humans generally experience. Using this mass of information, one should generalize standards of common experience. Now if anyone reports a miracle, the alleged event can’t be true because it does not conform to the generalized standards of common experience. (Of course, Hume had already refused to allow that any reports of miracles could be used even to generalize common experience.) It’s tricky. Its logic is circular. But it works to weed out awkward, quirky information. It is as if a domineering GPS unit created a sphere to serve as an abstraction for the earth, then insisted that the earth can’t have wobbling poles and flattening in the upper latitudes because the sphere in the GPS shows it can’t be true. Given a useful and trustworthy GPS, don’t listen to a scientist who might tell you something different than what the GPS tells you.</p>

<p>The circularity of this argument has been noted ever since Hume first proposed it, but Hume was a good writer and said what a lot of people wanted to hear.  Miracles are impossible so miracle reports can’t be true. Don’t even listen to reports of them.</p>

<h3>Balancing Likelihoods</h3>

<p>Also embedded in Hume’s essay is the awkward “rule of logic,” most often called “Balancing Likelihoods.” By combining math and logic in an odd way, Hume’s “Of Miracles “ offered another way for historians to avoid thinking about miracles.  Balancing Likelihoods has many names but is probably best stated by David Hackett Fischer, in his <em>Historians’ Fallacies: Toward a Logic of Historical Thought</em>, as “the rule of probability:”</p>

<blockquote><p>“[A]ll inferences from empirical evidence are probabilistic. It is not, therefore, sufficient to demonstrate merely that A was possibly the case. A historian must determine, as best he can, the probability of A in relation to the probability of alternatives. In the same fashion he cannot disprove A by demonstrating that not-A was possible, but only by demonstrating that not-A was more probable than A. This is the rule of probability.”</p></blockquote>

<p>This seems to be practical but is impossible.  Balancing Likelihoods, in the way described by Fischer, cannot be used by historians in any normal practice. It is a talisman to keep history mentally safe from the wildness that is reported to exist.  Logicians, especially mathematicians, have long criticized intellectual constructions like this.  The “probability” that Fischer writes about is seemingly mathematical, but the math is simply implied to give a sense of strength to human feelings.</p>

<p>Before Hume wrote “Of Miracles” probabilistic logic had been advancing rapidly and there was a great hope that mathematical analogies would strengthen human thinking—even Christian apologetics.  “Pascal’s Wager,” the most famous mathematical apologetic from the seventeenth century, equated eternal salvation with mathematical infinity and then applied it to a gambling formula.  Antoine Arnauld, in <em>The Port-Royal Logic</em> (1662), and John Locke, in his <em>Essay Concerning Human Understanding</em> (1690) and <em>Discourse on Miracles</em> (1706), carried probabilistic math and logic into the handling of reported miracles.  A half-century later, however, Hume reacted against Arnauld and Locke’s teachings that mathematical analogies could help in the discussion of the credibility of miracles.  Hume insisted that to handle a reported miracle, a historian had to create two separate ratios, pro and con, for believability. The ratios were then to be weighed against each other. This is Fischer’s “rule of probability” quoted above. In the language of Hume’s era, this was proclaimed as the “calculus of good sense.”</p>

<p>Lorraine Daston, in <em>Classical Probability in the Enlightenment</em> (1988), offers an excellent study of Hume and the many eighteenth-century mathematicians who wanted to help bring rigorous quantitative thinking to what today would be called the humanities. Daston writes that by the 1840s, mathematicians realized that “the ‘calculus of good sense’ had become antithetical to good sense,” and that today most of what these early probabilists were trying to do is considered “patently absurd.”</p>

<p>In 1901, one of America’s preeminent philosopher-mathematician-logicians, Charles Sanders Peirce, wrote three essays attacking the way historians had adopted Hume’s bad logic: “A Preliminary Chapter, Toward an Examination of Hume’s Argument Against Miracles, in its Logic and in its History,” “Hume’s Arguments Against Miracles, and the Idea of Natural Law,” and “On the Logic of Drawing History from Ancient Documents especially from Testimonies.” Peirce showed that historians are in error when they talk of judging testimony by balancing probabilities because “in a scientific sense, there are no ‘probabilities’ to be judged.”</p>

<p>Probability, Peirce wrote, “is the ratio of the frequency of occurrence of a specific event to a generic event.” A testimony “is neither a specific event, nor a generic event, but an individual event.” Peirce further pointed out that what people were justifying by claiming Balancing Likelihoods was really simply relating “what they prefer to do” to what they don’t prefer. “Likelihood is merely a reflection of our preconceived ideas.”</p>

<p>Historians like me who teach in universities about the reasonable credibility of Jesus’ resurrection need to be students of Peirce not Hume on the subject of assessing the credibility of reports that come down to us from ancient history. Dealing wisely with reports of events verging on the incredible is just part of the normal job of being grounded in the social study of our complex human past.</p>

<p>“Come to history as a doubter,” Richard Marius advises in a historical methods manual. “Skepticism is one of the historian’s finest qualities. Historians don’t trust their sources. . . . Nothing is quite so destructive to a historian’s reputation as to present conclusions that prove gullibility.”</p>

<p>But Marius is wrong. In practice, historians have to trust more than doubt. In practice, historians, especially ancient historians, can’t rely on doubting. Historians have to be close listeners, discerning listeners, wise listeners, who sometimes have to make harmonies and stretch for belief.</p>]]></content:encoded>
        <pubDate>Wed, 05 Sep 12 05:00:44 -0700</pubDate>
        <dc:creator>Rick Kennedy</dc:creator>
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        <title>Series: Divine Action in the World</title>
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        <description>In this talk, Professor Plantinga addresses the fact that many contemporary thinkers—including many theologians—believe that God cannot perform miracles, providentially guide history, or interact in the lives of people, as these activities would be contrary to science.   Plantinga, on the other hand, makes the case that this popular view is mistaken; excluding divine action in the world is not a central feature of natural science itself, but a philosophical or theological preference that has been added on to science (and can just as readily be removed).   Plantinga concludes that it is completely logical to accept the miracles of the Bible and support contemporary science.</description>
        <content:encoded><![CDATA[<p>My talk is entitled “Divine Action in the World.”  I want to talk about a certain kind of objection to Christian belief that some people raise. They claim that central thoughts, central doctrines of Christianity, are contrary to science, and therefore, are suspicious or incredible or such that one can’t sensibly hold them—can’t be rational in accepting them.</p>

<p>There are several different kinds of arguments that people bring along these lines; I want to talk about just one. So first… the Heidelberg catechism, one of the forms of unity of the church I go to (the Christian Reformed Church), says </p>

<blockquote>Providence is the almighty and ever-present power of God, by which he upholds as with his hand heaven and Earth and all creatures and so rules them, that leaf and blade, rain and drought, fruitful and lean years, food and drink, health and sickness, prosperity and poverty. All things, in fact, come to us not by chance, but from his fatherly hand.</blockquote>

<p>And part of the way it comes to us—not by chance, but from his fatherly hand—part of the way God has designed our world, is that there is a great deal of regularity and dependability in our world. Of course, if it were not for this regularity and dependability, we couldn’t do the things that we actually do. I mean, for example, if I just wanted to walk off the stage—if, for example, all the sudden those stairs over there suddenly turned into a ladder going up—well, that would make it really difficult.</p>

<p>If you are trying to build a house, for example, you have this hammer, but all the sudden the hammer turns in to a goose or a pigeon. Again, that would make things really difficult…or if the nail turned into a worm…or if you get in the car and turn the key and the car turns into a camel, things would be really hard, much harder than they are. This regularity and dependability in our world is an essential condition of our being able to live in the world in which we actually do.</p>

<p>If the world were irregular enough, we would not even be able to live in it, but there are also, according to classical Christianity here (the Heidelberg catechism, for example) there are also special divine actions; sometimes God does things specially. There are miracles in Scripture: the parting of the Red Sea, for example, Jesus walking on water, Jesus changing water into wine. There are miraculous healings: Jesus rising from the dead, Jesus raising Lazarus from the dead, and so on. And according to classical Christians, many of them, perhaps most of them, are special divine actions. God, for example, responds to prayers. He works in the hearts and minds of his children to effect sanctification. There is, what Calvin called, the internal testimony or witness of the Holy Spirit, and there is what Thomas Aquinas called the internal instigation of the Holy Spirit. So, these things are all special actions on the part of God. God constantly causes events in the world. Ok, so far fair enough—what is the problem?</p>

<p>Many theologians seem to think there is a science-religion problem here. I don’t think any of the theologians of Biola think this, (I don’t know, but I doubt it) but many theologians do. For example, Rudolf Bultmann says, “The historical method,” which of course he thinks that is the method we should use, “includes the presupposition that history is a unity in the sense of a closed continuum of effects in which individual events are connected by the succession of cause and effect. This continuum, furthermore, cannot be rent by the interference of supernatural, transcendent powers.”</p>

<p>That’s what he says. Alright, there is this continuum that cannot be rent by the interference of supernatural (that would be God) or transcendent powers. So, it is a little bit like the laws of the Medes and Persians. You probably remember Daniel. Daniel was a favorite of King Darius, and well, the other courtiers became jealous of Daniel (they didn’t like it that the king liked him so well). So, they came to the king and said, “Oh king, live forever, we think it would be a great idea if you passed an edict to the effect that you alone can be worshipped. Everybody has to worship you and nothing else.”  Well the king thought that over for a minute, and that sounded pretty good to him so he said, “I guess that it is a pretty good idea.” So he made this edict; he made this declaration: “Only King Darius is to be worshipped—no one else, nothing else.”</p>

<p>These courtiers knew that Daniel worshipped God, and they thought probably Daniel would keep right on worshipping God despite this edict. So they were watching Daniel, and he was, in fact, worshipping God. So they came to the king.  Now the penalty for worshipping something else was to be thrown into the lion’s den and they said, “Well, king live forever, looks like Daniel has been violating this edict. You have got to throw him in the lion’s den.”</p>

<p>Well, the king didn’t want to do this because he really liked Daniel. He thought this was a miserable way to proceed, and he didn’t want to do it, but then they said to him, “O king live forever, and remember a law of the Medes and Persians cannot be abrogated, even by the king himself.” So once it’s put in place, not even the king himself can change it or abrogate it or go against it.</p>

<p>That is sort of the suggestion that you get here from Bultmann. Bultmann thinks, “Maybe God created the world and set it up in a certain way, but once he did that, not even he can interfere in it”—he uses that word interference—“not even he can do anything in it. He just has to keep hands off.” It is like the law of the Medes and the Persians.</p>

<p>Another theologian who agrees is John Macquarrie, who says,</p>

<blockquote>The way of understanding miracle (and that would be one kind of special divine action) that appeals to breaks in the natural order and to supernatural intervention belongs to the mythological outlook, and cannot commend itself in a post-mythological climate of thought. The traditional conception of miracle is irreconcilable with our modern understanding of both science and history. Science proceeds on the assumption that whatever events occur in the world, can be accounted for in terms of other events that also belong within the world, and if on some occasion, we are unable to give a complete account of some happening, the scientific conviction is that further research will bring to light further factors in the situation that will turn out to be just as imminent and this worldly as the factors already known.</blockquote>

<p>Ok again, no room there for special action. And the third thinker here, Langdon Gilkey (still another theologian), says something similar, but I will pass. I will not read that one in the interest of saving a little bit of time, but these three theologians, plus many others want to assert that there is something wrong with the idea of God acting in the world, acting in the world in a way that goes beyond creation and sustaining, or creation and holding things in existence. So they think, “Ok, God created the world; God sustains it in existence”…that is ok with them, but anything beyond that, God performing any miracles, raising Jesus from the dead, or for that matter working in somebody’s heart and mind in a special way, that, they say, is a real problem.  The question is, what is the problem?</p>

<p>Well, the next little bit here…according to the Christian and theistic idea, God is a person; he has knowledge, loves, and hates. He has aims and ends. He acts on the basis of his knowledge to achieve his ends. He is all-powerful, all-knowing, and wholly good. Thirdly (noted above by the Heidelberg catechism), God has created the world. Fourth is God conserves and sustains and maintains in being this world he created, but fifth, at least sometimes, God acts in a way going beyond creation and conservation in miracles, but also in his providential guiding of history, his working in the hearts of people, his internal instigation of the Holy Spirit, and so on, and it is with that fifth category that these people have a problem. It is God’s special action in the world—action beyond conservation and creation—and miracles would be an example.</p>

<p>So we might think of these theologians as endorsing what we could call hands off theology. God has got to keep his hands off. God could create the world. God conserves the world, sustains it in being, but he can’t do anything else—that is as far as he could go. It is hands off theology, and Bultmann, even in this context, even talks about interfering. I mean if God did something in the world that would be interfering, which, when you think about it, is a sort of strange thing to say—I mean if God created the world, he is the omnipotent, omniscient, holy, good creator of the world—when you accuse someone of interfering, you are saying they are doing something they should not be doing, right?</p>

<p>So Bultmann thinks if God did something in the world that would be interfering, and he should be ashamed of himself. Ok, now why is this a problem? Their suggestion is that somehow it is contrary to science. It is contrary to science the suggestion that God acts specially in the world. I didn’t read that bit, but Gilkey says, "The causal nexus in space and time which the enlightenment science and philosophy introduced into the western mind is also assumed by modern theologians and scholars. Since they participate in the modern world of science, both intellectually and existentially, they can scarcely do anything else.”</p>

<p class="intro">From a presentation sponsored by Biola University’s <a href="http://cct.biola.edu/" target="_blank">Center for Christian Thought</a>, and delivered February 12, 2012 at EV Free Church, Fullerton, CA.  Used by permission.</p>]]></content:encoded>
        <pubDate>Tue, 04 Sep 12 04:00:33 -0700</pubDate>
        <dc:creator>Alvin Plantinga</dc:creator>
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        <title>The Randomness Project</title>
        <link>http://biologos.org/blog/the&#45;randomness&#45;project?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/the&#45;randomness&#45;project?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>It is not uncommon to hear voices proclaiming that biology and physics have shown us that—at fundamental levels—nature is random, hence meaningless, purposeless, and without a creator.  But how might God work providentially through indeterminate processes?  The John Templeton Foundation has provided a generous grant of $1.69 million to support a new research initiative on the theme of Randomness and Divine providence.</description>
        <content:encoded><![CDATA[<p>It is not uncommon to hear voices proclaiming that biology and physics have shown us that—at fundamental levels—nature is random, hence meaningless, purposeless, and without a creator.  In fact, chance (or randomness) has often been seen as inconsistent with Christian faith by Christians, too, not just by those opposed to faith.  For instance, none other than John Calvin wrote:</p>

<blockquote><p>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. </p></blockquote>

<p>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? </p>

<p>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 <em>unpredictability of the outcomes of single events and the absence of pattern in sequences of outcomes</em>.  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. </p>

<p>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.  </p>

<p>In 2007, a British statistician, David Bartholomew published <em>God, Chance, and Purpose</em> 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.</p>

<p>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:</p>

<ul><li>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?</li>
<li>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?</li>
<li>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?</li>
<li>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?</li>
<li>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?</li>
<li>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?</li>
<li>Might randomness be evidence of limitations in human knowledge but nothing more?  Or might it be evidence of ontological indeterminism?  Might this be tested?</li>
<li>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?</li>
<li>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?</li>
<li>What are some theodical implications of randomness, particularly for the issue of natural evil?</li>
<li>How have the theological traditions of Augustine, Maimonides, Aquinas, Luther, and Calvin addressed chance and fortune?  In what ways might they incorporate ontological randomness?</li>
<li>How do or could religions other than the Judeo/Christian tradition understand and incorporate randomness?</li>
<li>How is the concept of randomness understood by advocates of secularism, naturalism, and new atheism?  What are the strengths and weaknesses of these usages?</li>
<li>How might an understanding of randomness in the world alter our conceptions of divinity, especially our understanding of divine providence?</li></ul>

<p>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 <a href="http://www.calvin.edu/mathematics/randomnessproject/">project website</a>; then join us in exploring the truth that all creation glorifies God—even randomness!</p>
]]></content:encoded>
        <pubDate>Fri, 31 Aug 12 05:00:42 -0700</pubDate>
        <dc:creator>James Bradley</dc:creator>
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        <title>David Lack and Darwin’s Finches</title>
        <link>http://biologos.org/blog/david&#45;lack&#45;and&#45;darwins&#45;finches?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/david&#45;lack&#45;and&#45;darwins&#45;finches?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>Considering the immense popularity of &quot;Darwin&apos;s finches&quot;, it is quite surprising to learn that Charles Darwin himself had very 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.</description>
        <content:encoded><![CDATA[<h3>Darwin’s Finches? </h3>

<p>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?</p>

<p class="caption-left"><img src="http://biologos.org/uploads/static-content/Lacks_Finches_NASlobby.jpg" alt="Lobby of the National Academy of Sciences" height="350" width="570"  /></br>Lobby of The National Academies Building.  Courtesy of CPNAS. Photo by Robert Lautman</p>

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

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

<blockquote>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.<sup>3</sup>
</blockquote>

<p>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.<sup>4</sup> 
</p>

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

<blockquote>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.<sup>5</sup> </blockquote>

<p>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.<sup>6</sup>   </p>

<p>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.<sup>7</sup>  </p>

<p>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".<sup>8</sup>   Who would be up to the challenge of making sense of such tremendous biological complexity? It was David Lack.</p>
 
<h3>David Lack</h3>

<p class="caption-right"><img src="http://biologos.org/uploads/static-content/David_Lack.png" alt="Ornithologist David Lack" height="291" width="250"  /></br>Ornithologist David Lack</p>

<p>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.”<sup>9</sup>  In fact, at that time, there were only two professional ornithologists in all of Britain!</p>

<p>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.<sup>10</sup>  Following this advice, Lack embarked on a research trip to Tanzania in the summer of 1934, but his greatest adventure was yet to come. </p>

<p>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.</p>

<p>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:</p>

<blockquote>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.<sup>11</sup></blockquote>

<p>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,</p>
	
<blockquote>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.<sup>12</sup> <strong></strong></blockquote>

<p class="caption-left"><img src="http://biologos.org/uploads/static-content/Lacks_Finches_Cactus_Finch.jpg" alt="Large Cactus Finch–the Galapagos." height="215" width="320"  /></br>Large Cactus Finch on Española Island in the Galápagos Islands</p>

<p>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: </p>

<p><em>"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."</em> <sup>13</sup></p>

<p>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.<sup>14</sup> </p>

<p>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.<sup>15</sup>   Altogether, Lack examined more than 8000 specimens and specifically measured the length, width, and depth of all their beaks.<sup>16</sup> </p>

<p>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:</p>

<p class="caption-right"><img src="http://biologos.org/uploads/static-content/Lacks14finches_sm.jpg" alt="David Lack's illustration of 14 Finches" height="455" width="300" /> </br>David Lack's drawing of 14 species of Galápagos finches, p. 19 of <em>Darwin’s Finches</em></p>

<p><em>"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."</em> <sup>17</sup></p>

<p>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.</p>

<p>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 <a href="http://en.wikipedia.org/wiki/Adaptive_radiation">adaptive radiation</a>.  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.<sup>18</sup> </p>

<h3>Iconic Finches</h3>

<p>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.</p>

<p>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:</p>

<blockquote>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 <em>Geospiza</em>, the long beak of the flower-probing <em>Cactornis</em>, the somewhat parrot-like beak of the leaf, bud, and fruit-eating <em>Platyspiza</em>, the woodpecker-like beak of the woodboring <em>Catcospiza</em>, and the warbler-like beaks of the insect-eating <em>certhidea</em> and <em>Pinaroloxias</em>.<sup>19</sup>  </blockquote>

<p class="caption-left"><img src="http://biologos.org/uploads/static-content/finchbeaks_sm.jpg" alt="" height="270" width="350"  /> </br>Lack's image of beak adaptations from <em>Darwin’s Finches</em></p>



<p>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.”<sup>20</sup> </p>

<p>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.<sup>21</sup> </p>

<h3>Conclusion</h3>

<p>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 <em>Darwin’s Finches</em>,<sup>22</sup>  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.</p>

<p>This tendency to immortalize “great men of science” has also led many people to refer to modern evolutionary theory as <em>Darwinism</em>, 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:</p>

<blockquote>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.<sup>23</sup></blockquote>

<p class="intro">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 <em>converted</em> to Christianity after completing his Galápagos finch research.</p>

<h3>For Discussion</h3>
<strong>We’ve seen in this essay that the term “Darwin’s finches” is misleading, especially since Charles Darwin himself didn’t make the Galapagos finches famous.  Is it also problematic that people refer to modern evolutionary theory as “Darwinism”?  What misunderstandings can arise by associating an entire field of science with just a single person? Share your thoughts in the comments section below.</strong></p>

<h3>Further Reading</h3>
<ul><li>Grant, Peter R.; Grant, B. Rosemary. <em>How and Why Species Multiply: The Radiation of Darwin's Finches</em>, Princeton University Press, 2008.</li>

<li>Sulloway, Frank J. (Spring 1982), "Darwin and His Finches: The Evolution of a Legend" (<a href="http://www.sulloway.org/Finches.pdf">PDF</a>), <em>Journal of the History of Biology</em> 15 (1): 1–53.</li>

<li>Weiner, Jonathon. <em>The Beak of the Finch: A Story of Evolution in Our Time</em>.  Vintage Books, 1995.</li></ul>

<h3>Notes</h3>
<p class="date">1.  Sulloway, F. (1983). "Darwin and his finches: The evolution of a legend." <em>Journal of the history of biology</em> 15(1): 32. Darwin’s notebooks on transmutation mentioned Galapagos tortoises and mockingbirds, not finches.<br>
2.  Lack, David. <em>Darwin’s Finches</em>.  Cambridge University Press, 1947: 9.  Confirmed by Sulloway (1983), p5. <br>
3.  Darwin, Charles. <em>Journal of researches into the natural history and geology of the countries visited during the voyage of H.M.S. Beagle round the world</em>. 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.  <br>
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." <em>Trans. Zool. Soc. London</em>, 9:447-51.<br>
5.  Darwin (1845), p395.<br>
6.  Sulloway, p40.<br>
7.  Sulloway, p40.<br>
8.  Larson, E. J. <em>Evolution's Workshop: God and Science on the Galapagos Islands</em>. New York, Basic Books, 2001: 166-67.<br>
9.  Lack, David. (1973) “My life as an amateur ornithologist.” <em>Ibis</em>: 424. <br>
10.  Lack (1973), 425-27.<br>
11.  Lack (1947), p1.<br>
12.  Lack (1947), p11.<br>
13.  Larson, 167-68. <br>
14.  The California Academy of Sciences sponsored an expedition to the Galapagos in 1905-06 and collected nearly 9000 Galapagos finch specimens (Sulloway, p40).<br>
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).<br>
16.  Larson, p168.<br>
17.  Lack (1973), p424.<br>
18.  Larson, p198.<br>
19.  Lack (1947), p60.<br>
20.  Lack (1947), p158.<br>
21.  See Lack’s concluding chapter on “Adaptive Radiation”, pp146-159 of <em>Darwin’s Finches</em> (1947).<br>
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." <em>Ibis</em>, 13th ser., 6:310-321.  (Cited in Larson, p287)<br>
23.  Schluter, in an interview with Edward Larson, 16 March 2000.</p>
]]></content:encoded>
        <pubDate>Wed, 01 Aug 12 04:43:25 -0700</pubDate>
        <dc:creator>Thomas Burnett</dc:creator>
        <!--<dc:date>Aug 01, 2012 04:43</dc:date>-->
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        <title>Series: The Human Fossil Record</title>
        <link>http://biologos.org/blog/series/human&#45;fossil&#45;record?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/series/human&#45;fossil&#45;record?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>In this series, James Kidder provides an intriguing study on transitional fossils and the evolutionary history of modern humans.  He begins by discussing the fossil record, explaining how new forms are classified. He then explains the physically distinguishing trait of humankind—bipedalism.  From the discovery of Ardipithecus, the earliest known hominin, to the australopithecines, the most prolific hominin, Kidder focuses on the discovery, the anatomy, and the interpretation of these ancestral remains.</description>
        <content:encoded><![CDATA[<h3>Discovery</h3>

<p class="caption-left"><img src="http://biologos.org/uploads/static-content/Eugene_Dubois.jpg" alt="" height="320" width="240"  /></br>Eugene Dubois</p>
It was 1890 and <a href="http://en.wikipedia.org/wiki/Eugene_Dubois">Eugene Dubois</a> was tired.  He had searched everywhere in Sumatra for the human ancestors that were supposed to be there—at least according to the theories of his mentor, famed German naturalist Ernst Haeckel.  Instead, he had found only heat and malaria.</p>

<p>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. </p>

<p>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.</p>

<p>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.  </p>

<p>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. </p>

<p class="caption-right"><img src="http://biologos.org/uploads/static-content/kidder_10_1_1.jpg" alt="" height="377" width="318"  /><br />Figure 1: Dubois' <em>Pithecanthropus erectus</em></p>

<p>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 <em>Anthropopithecus sivalensis</em>, which then gave rise to the form represented by the Trinil remains, after which <em>Homo sapiens</em> arose (Turner, 1895).  </p>

<p>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 <a href="http://biologos.org/blog/the-dispersal-of-the-australopithecines">previous post</a>, 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.  </p>

<p>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: “<em>Homo erectus</em>.” Eventually, many other finds in the same general area and across Southeast Asia demonstrated that what Dubois had found <em>was</em> a real, previously-unknown hominin form, and the first to colonize the Asian continent and the islands leading off towards Oceania. </p>

<h3><em>Homo erectus</em> across South East Asia: </h3>

<p class="caption-left"><img src="http://biologos.org/uploads/static-content/kidder_10_1_2.jpg" alt="" height="180" width="215"  /><br />Figure 2: Sangiran 17</p>

<h4><em>Sangiran</em></h4>

<p>The earliest point at which <em>Homo erectus</em> 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.  </p>

<p>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 <em>Homo ergaster</em> 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.  </p>

<p>Because the area of the excavations—the Sangiran Dome—is a volcanic deposit, the layers have been securely dated by the <a href="http://en.wikipedia.org/wiki/40Ar/39Ar"><sup>40</sup>Ar/<sup>39</sup>Ar method</a>, although questions remain about the historical sequence and distribution of other animals that lived there through the ages (its <a href="http://en.wikipedia.org/wiki/Faunal_succession">faunal succession</a>).  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.  </p>

<p>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 <em>Homo ergaster</em> 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.  </p>

<p class="caption-left"><img src="http://biologos.org/uploads/static-content/kidder_10_1_3.jpg" alt="" height="343" width="228"  /><br />Figure 3: Sambungmacan 3</p>

<h4><em>Sambungmacan</em></h4>

<p>Another major find from the area where Dubois brought <em>Homo erectus</em> 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 <em>H. ergaster</em> 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.  </p>

<p class="caption-right"><img src="http://biologos.org/uploads/static-content/kidder_10_1_4.jpg" alt="" height="185" width="233"  /><br />Figure 4: Ngandong 6</p>

<h4><em>Ngandong</em></h4>

<p>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 <em>Homo erectus</em> 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.  </p>

<h3><em>Homo erectus</em> in China</h3>

<p>The Chinese <em>Homo erectus</em> 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 <em>Homo erectus</em> material, I will only touch on the most important ones.  </p>

<h4><em>Lantian</em>:</h4>

<p class="caption-right"><img src="http://biologos.org/uploads/static-content/kidder_10_1_5.jpg" alt="" height="164" width="192"  /><br />Figure 5: Lantian</p>

<p>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 <em>Homo erectus</em>.  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 <em>Homo erectus</em>) 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.  </p>

<p class="caption-left"><img src="http://biologos.org/uploads/static-content/kidder_10_1_6.jpg" alt="" height="144" width="204"  /><br />Figure 5: Hexian</p>

<h4><em>Hexian</em></h4>
	
<p>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 <em>Homo erectus</em> 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.</p>

<p>While both Lantian and Hexian were significant finds, another site in China boasted the single largest collection of <em>Homo erectus</em> 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 <em>Homo erectus</em> in Asia, we’ll peer into the Zhoukoudian caves and consider how this species fits into the lineage of man.
</p>]]></content:encoded>
        <pubDate>Sun, 29 Jul 12 04:59:44 -0700</pubDate>
        <dc:creator>James Kidder</dc:creator>
        <!--<dc:date>Jul 29, 2012 04:59</dc:date>-->
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        <title>What evidence do we have for evolution besides fossils and genes?</title>
        <link>http://biologos.org/questions/what&#45;evidence&#45;do&#45;we&#45;have&#45;for&#45;evolution&#45;besides&#45;fossils&#45;and&#45;genes?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/questions/what&#45;evidence&#45;do&#45;we&#45;have&#45;for&#45;evolution&#45;besides&#45;fossils&#45;and&#45;genes?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>Scientists have found multiple lines of evidence for evolution, not just one or two.  These types of evidence are independent of each other, coming from sources as different as ancient fossils and modern genetics labs. Evidence also comes from comparing the anatomy of creatures living today.  All creatures with four limbs (whether mammals, birds, or reptiles) have the same bone structure in each limb, pointing to their descent from a common ancestor. More evidence comes from biogeography.  Isolated islands are missing common species found on the mainland, but are filled with many unique species that can be related by a common ancestor. Finally, evidence comes from embryonic development.  As an embryo of a mammal grows, its heart develops through stages similar to fish, amphibians, and reptiles.  God’s creation declares the history of life in many different ways. All these ways are pointing to a consistent picture of God creating through evolution.</description>
        <content:encoded><![CDATA[<em>Coming soon.</em>]]></content:encoded>
        <pubDate>Fri, 13 Jul 12 13:25:46 -0700</pubDate>
        <dc:creator></dc:creator>
        <!--<dc:date>Jul 13, 2012 13:25</dc:date>-->
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        <title>The Fossil Record</title>
        <link>http://biologos.org/blog/the&#45;fossil&#45;record?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/the&#45;fossil&#45;record?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>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.</description>
        <content:encoded><![CDATA[<h3>The Fossil Record:  Is there enough evidence ?</h3>

<p>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.</p>

<p>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 <a onmouseover="toggle_visibility('pop1');" onmouseout="toggle_visibility('pop1');">science</a>.</p>

<div class="see-also" id="pop1" style="display:none;">A more expanded discussion of this topic can be found in Miller, K.B., 2003, “Common descent, transitional forms, and the fossil record,” IN, K.B. Miller (ed.), <em>Perspectives on an Evolving Crreation</em>, Wm. B. Eerdmans, Grand Rapids.</div>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<p>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.</p>    

<p>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.</p>]]></content:encoded>
        <pubDate>Fri, 13 Jul 12 05:00:15 -0700</pubDate>
        <dc:creator>Keith Miller</dc:creator>
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        <title>What scientific evidence do we have about the first humans?</title>
        <link>http://biologos.org/questions/what&#45;scientific&#45;evidence&#45;do&#45;we&#45;have&#45;about&#45;the&#45;first&#45;humans?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/questions/what&#45;scientific&#45;evidence&#45;do&#45;we&#45;have&#45;about&#45;the&#45;first&#45;humans?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>In recent decades, scientists have discovered more about the beginnings of humanity.  The fossil record shows a gradual transition over 5 million years ago from chimpanzee&#45;size creatures to hominids with larger brains who walked on two legs.   Later hominids used fire and stone tools and had brains as large as modern humans.  Fossils of homo sapiens in east Africa date back nearly 200,000 years.  Humans developed hearths for fire, stone points for spears and arrows, and cave paintings by 30,000 years ago.   By 10,000 years ago, humans had spread throughout the globe.   Genetic studies support the same picture.  Humans share more DNA with chimpanzees than with any other animal, suggesting that humans and chimps share a relatively recent common ancestor.  Also, the same defective genes appear in both humans and chimps, at the same locations in the genome—an observation difficult to explain except by common ancestry. Genetics also tells us that the human population today descended from more than two people. Evolution happens not to individuals but to populations, and the amount of genetic diversity in the gene pool today suggests that the human population was never smaller than several thousand individuals.  Yet all humans, of all races, are descended from this group.  Humanity is one family.</description>
        <content:encoded><![CDATA[<em>Coming Soon</em>]]></content:encoded>
        <pubDate>Thu, 12 Jul 12 14:34:24 -0700</pubDate>
        <dc:creator></dc:creator>
        <!--<dc:date>Jul 12, 2012 14:34</dc:date>-->
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        <title>Randomness and Evolution: Is There Room for God? (Videocast)</title>
        <link>http://biologos.org/blog/randomness&#45;and&#45;evolution&#45;is&#45;there&#45;room&#45;for&#45;god&#45;videocast?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/randomness&#45;and&#45;evolution&#45;is&#45;there&#45;room&#45;for&#45;god&#45;videocast?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>This BioLogos videocast addresses the idea of randomness as a part of natural selection, and whether it challenges the possibility of God using the evolutionary process as a means of creation.</description>
        <content:encoded><![CDATA[<p>Today we present the fourth entry in our on-going BioLogos videocast series. So far we have looked at the fossil record and genetic evidence for evolution, as well as speciation and macroevolution. The latest entry addresses the idea of randomness as a part of natural selection, and whether it raises questions about the possibility of God using the evolutionary process as a means of creation. The script was written by biology student Joy Walters, with help from BioLogos president Darrel Falk.</p>

<p>For more, be sure to read Randall Pruim's recent series <a href="http://biologos.org/blog/series/randomness-and-gods-governance">Randomness and God’s Governance</a>, Kathryn Applegate's post <a href="http://biologos.org/blog/thats-random-a-look-at-viral-self-assembly2">That's Random: A Look at Viral Self-Assembly</a>, and our FAQ <a href="http://biologos.org/questions/chance-and-god">How Do Randomness and Chance Align with Belief in God's Sovereignty and Purpose?</a>.</p>

<h3>Author's Note</h3>

<p>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. </p>

<p>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. </p>

<p>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.  </p>

<p>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. </p>

<p>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.</p>

<p>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. </p>

<p>Therefore, my goal for this podcast is two-fold:</p>

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

<p>This will hopefully encourage others to study evolutionary theory and draw their own conclusions about its meaning in the framework of their faith.</p>]]></content:encoded>
        <pubDate>Fri, 15 Jun 12 05:00:15 -0700</pubDate>
        <dc:creator>Joy Walters</dc:creator>
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        <title>Series: The God Who Acts: Robert John Russell on Divine Intervention and Divine Action</title>
        <link>http://biologos.org/blog/series/the&#45;god&#45;who&#45;acts&#45;robert&#45;russell&#45;on&#45;divine&#45;intervention&#45;and&#45;divine&#45;action?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/series/the&#45;god&#45;who&#45;acts&#45;robert&#45;russell&#45;on&#45;divine&#45;intervention&#45;and&#45;divine&#45;action?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>Does God need to supernaturally &quot;intervene&quot; in order to bring about the diversity of life that we observe today? Is that kind of action different from God’s ordinary action?  We begin our three&#45;part series with Robert John Russell’s description of how views of divine action have changed throughout history, excerpted from his book Cosmology: From Alpha to Omega.  Part 2 addresses why “intervention” in the natural world is a problem philosophically, theologically, and scientifically; and Part 3 explains Russell’s own theory of divine action in the natural world.</description>
        <content:encoded><![CDATA[<h3>Introduction</h3>

<p><em>(Written by the BioLogos editorial team)</em></p>

<p>In a recent lecture in Washington, D.C., Intelligent Design advocate Stephen Meyer noted that scientists and theologians are generally uncomfortable with the idea of "supernatural intervention" in natural processes such as evolution.  He then posed the question, “What's so bad about supernatural intervention?”  Meyer’s comment touches on a point of particular tension among Christians engaged in understanding how our science and our theology interact: the nature of <em>divine action</em>.</p>

<p>Much of the confusion in this area, however, stems from the inexact meaning of <em>intervention</em>, which—like evolution or Darwinism—implies different things to different people.  All Christians affirm that God works powerfully in the world, doing extraordinary acts of creation and salvation.  In common conversation, then, <em>intervention</em> tends to mean simply “acts that are recognizably or obviously God’s,” whether as dramatic as the parting of the Red Sea or as subtle as an individual believer hearing a clear call to repentance or to mission from the Lord.  Even in this most casual sense, <em>intervention</em> tends to mean special occasions of God’s providential care, rather than his ordinary sustaining work.</p>

<p>But to Christian scientists and philosophers trying to understand God’s action in creation—especially how he might go about his sustaining role—<em>intervention</em> has another connotation: namely, that recognizing something as “divine action” requires it to be in violation of the natural laws which God himself established.  Put another way, many Christian thinkers associate the word <em>intervention</em> with the idea that to act <em>in</em> the world God “must” act from <em>outside</em> the world. That view is a central tenet of deism, not Christianity.  One response to Meyer’s comment, then, is to ask whether <em>intervention</em> is the only (or even a helpful) way of thinking about God’s work in biological creation.  Is there another way of talking about “divine action” that does not restrict God's work to only extraordinary events?  Can we conceive of divine action in a way God is never absent, distant, or in any way removed from the creation he sustains at every moment?</p>

<p>Finding such an alternative vocabulary to talk about the different ways God acts in his creation is the purpose of this short series introducing the work of theologian and physicist Robert John Russell.  Russell’s book <em><a href="http://store.augsburgfortress.org/store/product/3874/Cosmology-From-Alpha-to-Omega" target="_blank">Cosmology: From Alpha to Omega</a></em> explores the history of Christian thinking about divine action and proposes one model for how we might understand it in light of Scripture, the traditions of the church, and contemporary scientific explorations of the material world.</p>

<p>To be clear, Russell argues that God does unmistakably act in the world.  He singles out the bodily resurrection of Jesus not only as a prime example, but as a truly unique event distinct even from Christ’s other miraculous acts during his ministry on earth.  That is, the resurrection was an in-breaking of God’s new reality into the present one, something “beyond miraculous.”  This series, though, offers his perspective on the more basic issue of how God might be at work in what we have called the “ordinary processes” of his world. </p>

<p class="intro">We begin our three-part series below with Professor Russell’s description of how views of divine action have changed throughout history (excerpted from Chapter 4 of <em>Cosmology: From Alpha to Omega</em>).</p>

<h3>Historical background to the problem of divine action</h3>

<p>The notion of God’s acting in the world is central to the biblical witness. From the call of Abraham and the Exodus from Egypt to the birth, ministry, death and raising of Jesus and the founding of the church at Pentecost, God is represented as making new things happen. Through these “mighty acts,” God creates and saves. Rather than seeing divine acts as occasional events in what are otherwise entirely natural and historical processes, both the Hebrews and the early Christians conceived of God as the creator of the world and of divine action as the continuing basis of all that happens in nature and in history.</p>

<p><img src="http://biologos.org/uploads/static-content/john_calvin.jpg" alt="" height="299" width="220" style="float:right; margin:0px 0px 10px 10px;" />The view that God works in and through all the processes of the world continued throughout Patristic and Medieval times. For example, God was understood as the first or <em>primary cause</em> of all events—where all natural causes are instrumental or <em>secondary causes</em> through which God works. The conviction that God acts universally in all events, and that we act together with God in specific events, was maintained by the Reformers and the ensuing Protestant orthodoxy. John Calvin (1509-1564) argued that God is in absolute control over the world and at the same time maintained that people are responsible for evil deeds. Questions about human freedom and the reality of evil were seen more as problems requiring serious theological attention than as reasons for abandoning belief in God’s universal agency.</p>

<p>Moreover, faith in God the creator was articulated through two distinct but interwoven doctrines: <strong>creation</strong> and <strong>providence</strong>. The doctrine of <strong>creation</strong> asserts that the ultimate source and absolute ground of the universe is God. Without God, the universe would not exist, nor would it exist as “universe.” Creation theology, in turn, has often included three related but distinct claims: 1) the universe had a beginning; 2) the universe depends absolutely and at every moment on God for its sheer existence; and 3) the universe is the locus of God’s continuing activity as Creator. The first two have traditionally been grouped in terms of <em>creatio ex nihilo</em>(creation from nothing), and the third in terms of <em>creatio continua</em> (continuing creation).</p>

<p>The doctrine of <strong>providence</strong> presupposes a doctrine of creation, but adds significantly to it. While creation stresses that God is the cause of all existence, providence stresses that God is the cause of the <em>meaning and purpose</em> of all that is. God not only creates but guides and directs the universe towards the fulfilling of God’s purposes. These purposes are mostly hidden to us, though they may be partially seen after the fact in the course of natural and historical events. The way God achieves them is hidden, too. Only in the eschatological future will God’s action throughout the history of the universe be fully revealed and our faith in it confirmed. General providence refers to God’s universal action in guiding all events; special providence refers to God’s particular acts in specific moments, whether found in personal life or in history.</p>

<h3>Divine intervention arises in the Enlightenment</h3>

<p><img src="http://biologos.org/uploads/static-content/Pierre-Simon_Laplace.jpg" alt="" height="267" width="200" style="float:left; margin:0px 10px 10px 0px;" />The rise of modern science in the seventeenth century and Enlightenment philosophy in the eighteenth, however, led many to reject the traditional views of divine action. Although Isaac Newton (1643-1727) argued for the essential role of God in relation to the metaphysical underpinnings of his mechanical system, and in this way defended the sovereignty of God in relation to nature, Newtonian mechanics depicted a causally closed universe with little, if any, room for God’s <em>special</em> action in specific events—and then only by intervention: that is, by acting as from outside that closed system. A century later, Pierre Simon Laplace (1749-1827, pictured left) combined the <em>determinism</em> of Newton’s equations with <em>epistemological reductionism</em> (the properties and behavior of the whole are reducible to those of the parts) and <em>metaphysical reductionism</em> (the whole is simply composed of its parts), to portray all of nature as a causally closed, impersonal mechanism. This in turn led to the concept of interventionism: if God were really to act in specific events in nature, God would apparently have to break the remorseless lock-step of natural cause and effect by intervening in the sequence and violating the laws of nature in the process. </p>

<p><img src="http://biologos.org/uploads/static-content/immanuel_kant.jpg" alt="" height="277" width="220" style="float:right; margin: 0px 0px 10px 10px;" />The eighteenth century also saw the rise and fall of deism, in which the scope of divine agency was limited to an initial act of creation. According to deism, the universe was like a clock which, once built and set in place, proceeded to run on its own.  David Hume (1711-1776) challenged the deistic (and theistic) arguments for God as first cause and as designer. In response, Immanuel Kant (1724-1804, pictured right) constructed a new metaphysical system which emphasized the mind’s role in organizing sense-data through universal categories of intuition and forms of sensibility. According to Kant, the sphere of religion lies not in our knowing (the activity of pure reason) but in our sense of moral obligation (the activity of practical reason). It is our ethical system, not our knowledge of nature, that requires us to postulate God, freedom and the immortality of the soul. The consequence of Kant’s thought for the West was the philosophical separation of the domains of science and religion into “two worlds”—a move which was to have an immeasurable effect on Christian theology up to the present. </p>

<h3>Theology splits into conservative and liberal interpretations of divine action</h3>

<p><img src="http://biologos.org/uploads/static-content/schleiermacher.jpg" alt="" height="350" width="220" style="float:left; margin: 0px 10px 10px 0px;" />As a consequence of the philosophical division of science and religion, theology in the nineteenth century was faced with a fundamental challenge not only to its contents and structure, but even to its method. The variety of responses to this challenge tend to fall into two groups: “liberals” largely accepted and worked within the terms of the discussion that modernity dictated while “conservatives” upheld traditional formulations and tended to reject “modernity.” The earliest and most influential figure among liberals was Friedrich Schleiermacher (1768-1834), who responded to Kant by locating religion as neither a knowing nor a doing. Instead religion is grounded in personal piety—the feeling of absolute dependence. </p>

<p>Schleiermacher held that theological assertions emerge from the immediacy of the religious self-consciousness. He understood God’s relation to the world in terms of “universal divine immanence” [the idea that God is present to the entire cosmos at all times], and he blurred the distinction between creation and providence by collapsing the later into the former. In a famous move he defined miracle as “. . . simply the religious name for event. Every event, even the most natural and usual, becomes a miracle, as soon as the religious view of it can be the dominant.” Schleiermacher’s arguments became characteristic of liberal Protestant theology throughout the nineteenth century and continued into much of twentieth century theological work.</p>

<p>The second half of the nineteenth century saw the rise of Darwinian evolution, which combined random variation and natural selection to explain biological complexity. To some in the nineteenth and twentieth centuries, the fundamental role of chance in nature seemed to undercut any notion of divine action in the world; to others, such as the Anglo-Catholic liberal movement in Britain and America, Darwinian evolution could be accommodated and even integrated into theology without interventionism, since God works immanently in and through the very processes of nature. In contrast, religious conservatives tended either to reject evolution as a whole or give it a limited acceptance with the proviso that the objective acts of special providence constitute divine interventions in nature.</p>

<h3>The rise of neo-orthodoxy in the twentieth century</h3>

<p><img src="http://biologos.org/uploads/static-content/kant.jpg" alt="" height="171" width="250" style="float:right; margin: 0px 0px 10px 10px;" />Protestant theology in the first half of the twentieth century was largely shaped by Karl Barth. In his rejection of nineteenth-century liberal theology, Barth returned theology to its biblical roots and focused it on the God who is “wholly other.” Recognizing that a religion founded exclusively on subjective experience is vulnerable to the critiques of Feuerbach and Freud, Barth and his followers held fast to the objective action of God in creating and redeeming the world. “The Gospel is . . . not an event, nor an experience, nor an emotion—however delicate! ... It is a communication which presumes faith in the living God, and which creates that which it presumes.” The ‘God who acts’ became a hallmark of the ensuing “biblical theology” movement which arose in the 1940s and 1950s. To many this movement seemed to offer a <em>tertium quid</em> between liberal and conservative theologies. </p>

<p>But do Barthian neo-orthodoxy and the biblical theology movement actually produce a credible account of divine action? On the one hand neo-orthodoxy attempts to distance itself from liberal theology by retaining biblical language about God acting through wondrous events and by viewing revelation as including an objective act. Yet on the other hand, it, like liberalism, accepts the modern premise that nature is a closed causal system, as depicted by classical physics. The result is that neo-orthodoxy seems to assert a contradiction: God does act objectively in nature (as conservatives believe) and God does so without intervening, violating, suspending or obstructing the ordinary processes of nature understood as a closed causal system (as liberals believe).</p>

<h3>A third way between liberal and conservative theologies</h3>

<p>Any purported “third option” will require an intelligible concept of objectively special providence which does <em>not</em> entail divine intervention. Such a concept could serve as a <em>genuine tertium</em> quid to conservative and liberal notions of special providence, combining strengths borrowed from each. Specifically, we will seek to speak about special divine acts in which God acts objectively in an unusual and particularly meaningful way in, with, and through events which serve to mediate God’s action. We will seek to do so without entertaining—in fact by refusing—the additional claim that God must intervene in, or at least suspend, the laws of nature.  Those laws are themselves the result of and description of God’s continuous creation, after all. I call this type of divine action <em>Non-Interventionist Objective Divine Action</em> (NIODA).</p>

<p class="intro">In part 2 of this series, Tom Burnett will explore in more depth what Russell takes to be wrong with the Enlightenment concept of “supernatural intervention.”  Part 3 will explain and clarify Russell’s theory of NIODA.</p>

<p><em>From Chapter 4, “Does ‘The God Who Acts’ Really Act? New Approaches to Divine Action In Light Of Contemporary Science,” in <a href="http://store.augsburgfortress.org/store/product/3874/Cosmology-From-Alpha-to-Omega" target="_blank"><em>Cosmology: From Alpha to Omega</em></a>  by Robert John Russell, copyright © 2008 Fortress Press. Reproduced by permission of Augsburg Fortress Publishers. All rights reserved. No further reproduction allowed without the written permission of the publisher.</em></p>
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        <pubDate>Fri, 25 May 12 04:59:18 -0700</pubDate>
        <dc:creator>Robert John Russell, Thomas Burnett</dc:creator>
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        <title>Series: Randomness and God’s Governance</title>
        <link>http://biologos.org/blog/series/randomness&#45;and&#45;gods&#45;governance?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/series/randomness&#45;and&#45;gods&#45;governance?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>In this three&#45;part series from Pruim’s chapter in the book Delight in Creation: Scientists Share Their Work with the Church, mathematician Randall Pruim explains what scientists and mathematicians mean when they speak of something being “random”. He also addresses God&apos;s use of apparent randomness in creation as a part of his sovereign rule.</description>
        <content:encoded><![CDATA[<p>I’ve enjoyed playing games as long as I can remember. Among my earliest memories are playing <em>Candy Land</em>, <em>Chutes and Ladders,</em> <em>Don’t Break the Ice</em>, and <em>Don’t Spill the Beans</em>. When I was a child, whenever someone did not know what to get me for a birthday or Christmas present, a game was always a good choice. Today, in the back room of our house, we have a closet filled with games that my children and I have accumulated over the years. The rest of our games are either in a closet upstairs or in one of several large boxes in the attic. Periodically we rotate the location of the games for variety.</p>

<p>Many of the games I enjoyed playing involve a combination of strategy and randomness: card games of various sorts, backgammon, and board games like <em>Monopoly</em> and <em>Parcheesi</em>. Some games that rely exclusively on chance (like <em>War</em> and <em>Candy Land</em>) or too heavily on chance (like <em>Sorry</em>) quickly became uninteresting to me. In fact, for <em>Sorry</em>, <em>War</em>, 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.</p>

<p>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 <em>Mitternachtspartie</em> 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. </p>

<p>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.</p>

<h3>From Fun and Games to Science</h3>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<p>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.</p>

<p>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).</p>

<p>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.</p>

<p>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. </p>

<img src="http://biologos.org/uploads/static-content/Pruim_Randomness_1_1.png" alt="" height="528" width="500"  />

<p>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.</p>

<img src="http://biologos.org/uploads/static-content/Pruim_Randomness_1_2.png" alt="" height="757" width="476"  />

<p>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: 

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

<p>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.</p>

<img src="http://biologos.org/uploads/static-content/Pruim_Randomness_1_3.png" alt="" height="816" width="487"  />

<p>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.</p>

<p>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?”</p><br></br>
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        <pubDate>Mon, 21 May 12 05:00:55 -0700</pubDate>
        <dc:creator>Randall Pruim</dc:creator>
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        <title>Chance Creation</title>
        <link>http://biologos.org/blog/chance&#45;creation?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/chance&#45;creation?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>It should not be surprising that John Cage asked the stuff he used to make paintings to take part in the process—to contribute its own identity to the intentional, purposeful, and determined work of creating “based on chance.”</description>
        <content:encoded><![CDATA[<p>Mathematician Randall Pruim ended the <a href="http://biologos.org/blog/randomness-and-gods-governance-part-1">first installment </a>of his series on randomness and God’s governance by noting that “many Christians have a reaction to randomness that falls somewhere between uneasy and antagonistic” because they think that “taking randomness seriously means not taking God seriously.” While Pruim will continue to explore randomness as a mathematical concept, I’d like to approach the counterintuitive idea that God would “intentionally” use chance processes in his creative work by looking at the practice of John Cage, an artist whose music and visual art was built around the use of chance. One set of Cage’s visual works in particular—the New River Watercolor series from 1988—can help us think about how “allowing” for chance is actually an opportunity for positive and intimate engagement with the created world. I’d like to offer this instance of human making using randomness as an analogy for thinking about how God uses randomness in his own making, and suggest that “chance” is always both limited and guided by the intentions of the creator.  To do that, though, we need to spend a little time understanding how Cage used chance in his work.  </p>

<p>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 <em>I Ching</em>.  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.</p>

<p>Here’s art historian and theorist Howard Risatti’s description of Cage’s plan of action for the New River Watercolors, from the <a href="http://www.raykass.com/html/Cage/cage01.html">website</a> 
 of artist Ray Kass, who runs the Mountain Lake program and was Cage’s collaborator for his work there:</p>

<blockquote><p>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).</p>
</blockquote>

<p>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<em> I Ching</em> 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.</p>

<img src="http://biologos.org/uploads/static-content/Cage_2txt.jpg" alt="" height="604" width="250" style="float:right;margin:0px 0px 0px 10px;"  />

<p>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.</p>

<p>Kass’ book <em>The Sight of Silence: John Cage’s Complete Watercolors</em>, 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:</p>


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

<p>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.</p>

<p>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.  </p>

<p>I make that observation to emphasize one other aspect of Cage’s creative process: that Cage was the instigator first and foremost of <em>relationships</em> 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.</p>

<p>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.</p>

<h3>For Further Reading:</h3>

<p>Ray Kass. <a href="http://books.upress.virginia.edu/detail%2Fbooks%2Fgroup-3985.xml?q=kass">The Sight of Silence: John Cage’s Complete Watercolors</a>, 2011.


<p><a href="http://www.johncage2012.com/watercolors.html">Website</a> for John Cage Centennial Festival, Washington, DC. September 2012.<br> </br>

<img src="http://biologos.org/uploads/static-content/Cage_3txt.jpg" alt="" height="207" width="500"  />

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        <pubDate>Sun, 13 May 12 12:53:04 -0700</pubDate>
        <dc:creator>Mark Sprinkle</dc:creator>
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