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        <title>Custom Feed &#45; The BioLogos Forum</title>
    <link>http://biologos.org/resources/find/Blog/sort&#45;by&#45;Newest/sort&#45;by&#45;Newest/Human Origins,Design?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>2013-05-21T16:14:08-08:00</dc:date>    
    
    

            
            
        
      <item>
        <title>Humanity as and in Creation</title>
        <link>http://biologos.org/blog/humanity&#45;as&#45;and&#45;in&#45;creation?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/humanity&#45;as&#45;and&#45;in&#45;creation?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>Christian theology asserts that humans are spiritual creatures, a unity of body and spirit or “soul,” integrated, not reducible downwards to mere matter or upwards to mere spirit.</description>
        <content:encoded><![CDATA[<p>The second chapter of Genesis offers an enduring image for the creation of humanity: “the LORD God formed a man from the dust of the ground and breathed into his nostrils the breath of life, and the man became a living being.”</p>

<p>What does it mean for humanity to be created “from the dust of the ground?”</p>

<p>In many ancient Mesopotamian creation stories, human beings were depicted as deriving from some physical part of the gods. Often this was the result of conflict: humans arose from the blood, flesh or tears of gods slain by other gods. Humans created in this fashion were supposed to serve the gods by performing menial work that the gods had tired of doing themselves. The lot of humanity, then, was one of violence and servitude.</p>

<p>In the Israelite creation stories reflected in Genesis 1 and 2, however, humans are made from the ordinary material of creation: “dust.” Humans are made of earth-stuff, not god-stuff.</p>

<p>At first glance, it may seem that this lowers the status of the human creature. We might ask the question raised by Eliphaz in the book of Job:</p>

<blockquote><p>Can a mortal be more righteous than God?<br />
Can even a strong man be more pure than his Maker?<br />
If God places no trust in his servants,<br />
if he charges his angels with error,<br />
how much more those who live in houses of clay,<br />
whose foundations are in the dust, who are crushed more readily than a moth! (Job 4:17-19)</p>
</blockquote>

<p>Indeed, our humble origins ought to remind us of the fragility of our lives. As the Psalmist says,</p>

<blockquote><p>You turn people back to dust, saying, “Return to dust, you mortals.”<br />
A thousand years in your sight<br />
are like a day that has just gone by,<br />
or like a watch in the night.<br />
Yet you sweep people away in the sleep of death—<br />
they are like the new grass of the morning:<br />
In the morning it springs up new,<br />
but by evening it is dry and withered.</p>
</blockquote>

<p>The elements of which our bodies are made are ordinary and abundant. Science tells us that approximately ninety-three per cent of the mass in a living human body is comprised of elements first formed through nuclear fusion in the hearts of stars. Through almost unimaginably vast and ancient cycles of stellar formation and supernova explosions, this “stardust” of elements has been spread throughout the universe. It is as though God scattered the stars across space and time to seed the universe for life, including your life and mine. And we are thereby inseparably connected to each other, to the air we breathe, to the ground we tread, to all the creatures that fill the skies and crawl upon the earth and teem in the seas, to the depths of all the heavens. We are not transcendent of creation. We are creatures.</p>

<p>Yet we are creatures into which God breathed the “breath of life.” We are stardust and more than stardust. We are not reducible to our constituent chemicals. A “man” or a “woman” is not just a gooey sack of water, carbon and trace elements. Hydrogen, oxygen and carbon are not aware of their own existence. These elements cannot reason or pray or love or write poems. Conjunctions of these elements cannot carry any persistent identity across time. They do not exercise will or intentionality or agency. They are not “selves.”</p>

<p>Most of the cells in a human body are in constant flux: aging, dividing, dying, being replaced. The surface layer of human skin is renewed completely about every two weeks. An adult’s skeleton is entirely remade over approximately ten year periods. It may be that only the neurons of the cerebral cortex and a few other types of cells persist throughout the lifetime of a human body. And eventually, it all does return to “dust.”</p>

<p>Yet we think of ourselves as persisting over time, as comprising an “identity,” a “self.” Perhaps the cerebral cortex provides the stable biological platform for identity and selfhood, but something new emerges from the chemical-electrical soup, new patterns of organization, a different level of causation. We can even make choices that reshape ourselves, both physically and psychologically. The very wiring of our brains changes when we make conscious choices. Mind is both shaped by matter and supervenes on matter.</p>

<p>Materialists who wish to collapse all of human identity into brain chemistry overstep the bounds of “science.” A fundamental principle of scientific practice is testability: is it possible to demonstrate empirically whether a proposition is false ? As Saint Augustine observed many centuries ago, the fact that I acknowledge I could be “wrong” about something means that I am a “self” who is capable of making real choices about things that are in fact true or false. “<em>Si fallor, sum</em>” Augustine said – if I can doubt, if I can be wrong, then I must exist. One who is a true materialist “all the way down” cannot test his or her materialism. There is no possibility of “being” right or wrong, indeed no possibility of “being” – there is nothing but chemistry.</p>

<p>Spiritualists who wish to degrade matter in favor of the soul or spirit likewise are not expressing a Christian anthropology. Indeed, one of the first heresies that encountered the early Christian church was Gnosticism. A core belief of Gnosticism was that matter, including the human body, was essentially evil. Salvation for the Gnostics involved the soul’s escape from the prison of embodiment and materiality. The Gnostics treated the body either with disdain – engaging in extreme ascetic practices – or with antinomian abandon – engaging in extreme sexual license. Either way, their practices were rooted in the belief that matter and the body were unimportant. It’s easy to see how this view continually creeps into both our popular culture and our Church cultures.</p>

<p>Christian theology asserts that humans are spiritual creatures, a unity of body and spirit or “soul,” integrated, not reducible downwards to mere matter or upwards to mere spirit. Perhaps there is no better way to bring these themes together than with a Psalm — here is Eugene Peterson’s paraphrase of Psalm 139 in The Message:</p>

<blockquote><p>God, investigate my life; get all the facts firsthand.<br />
I’m an open book to you;<br />
even from a distance, you know what I’m thinking.<br />
You know when I leave and when I get back;<br />
I’m never out of your sight.<br />
You know everything I’m going to say<br />
before I start the first sentence.<br />
I look behind me and you’re there,<br />
then up ahead and you’re there, too—<br />
your reassuring presence, coming and going.<br />
This is too much, too wonderful—<br />
I can’t take it all in!</p>

<p>Is there any place I can go to avoid your Spirit?<br />
to be out of your sight?<br />
If I climb to the sky, you’re there!<br />
If I go underground, you’re there!<br />
If I flew on morning’s wings<br />
to the far western horizon,<br />
You’d find me in a minute—<br />
you’re already there waiting!<br />
Then I said to myself, “Oh, he even sees me in the dark!<br />
At night I’m immersed in the light!”<br />
It’s a fact: darkness isn’t dark to you;<br />
night and day, darkness and light, they’re all the same to you.</p>

<p>Oh yes, you shaped me first inside, then out;<br />
you formed me in my mother’s womb.<br />
I thank you, High God—you’re breathtaking!<br />
Body and soul, I am marvelously made!<br />
I worship in adoration—what a creation!<br />
You know me inside and out,<br />
you know every bone in my body;<br />
You know exactly how I was made, bit by bit,<br />
how I was sculpted from nothing into something.<br />
Like an open book, you watched me grow from conception to birth;<br />
all the stages of my life were spread out before you,<br />
The days of my life all prepared<br />
before I’d even lived one day.</p>
</blockquote>
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        <pubDate>Fri, 01 Mar 13 07:00:07 -0800</pubDate>
        <dc:creator>David Opderbeck</dc:creator>
        <!--<dc:date>Mar 01, 2013 07:00</dc:date>-->
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            <item>
        <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[<p class="intro">This blog was originally posted on December 10, 2010. We think it was an important one.  Note though that it was posted shortly before the discovery of <a href="http://biologos.org/blog/a-geneticists-journey.html" target="_blank">Denisovans.</a>  So now one more red bar needs be added to the figure above.</p>

<h3>Transitional Fossils</h3>

<p>Some time ago, the Discovery Institute’s Casey Luskin <a href="http://www.evolutionnews.org/2010/03/smithsonians_new_human_origins033371.html" target="_blank">commented</a> on the human origins exhibit at the Smithsonian Institution, suggesting that palaeoanthropologists use evolutionary theory to describe the progression of the human lineage even when they don’t have transitional fossils with which to work.  He writes:</p>

<blockquote><p>What's ironic, however, is that if you ask the question How Do We Know Humans Evolved? the answer you’re given is, “Fossils like the ones shown in our Human Fossils Gallery provide evidence that modern humans evolved from earlier humans.” So whether you find fossils or you don’t, that’s evidence for evolution.</p></blockquote>

<p>Indeed, it has become an article of faith for those espousing both the young earth creation (hereafter YEC) model and many who hold to the intelligent design model that transitional fossils do not exist and therefore evolution has not taken place.  Support for this position usually entails attacking the weak areas of the fossil record, where burial processes have left us little with which to work, or the creation of straw men arguments in which transitional fossils are defined in such a way that none could ever be found.  Often this centers on the concept of “missing link,” a term that is habitually used in the popular press and young earth creation and intelligent design literature when referring to fossil remains but which has little to no meaning for biologists or palaeontologists.  As Ahlberg and Clack (Ahlberg and Clack 2006) write:</p>

<div class="see-also" id="phylo" style="display:none;">Phylogenetics is the study of evolutionary relatedness among organisms.</div>

<blockquote><p>But the concept has become freighted with unfounded notions of evolutionary ‘progress’ and with a mistaken emphasis on the single intermediate fossil as the key to understanding evolutionary transitions. Much of the importance of transitional fossils actually lies in how they resemble and differ from their nearest neighbours in the <a onmouseover="toggle_visibility('phylo');" onmouseout="toggle_visibility('phylo');">phylogenetic</a> tree, and in the picture of change that emerges from this pattern.</p></blockquote>

<p>Contrary to common misconceptions, the fossil record does not record one single lineage for any family of organisms but rather a series of branches, with many related species coexisting synchronously.  Darwin hypothesized that the evolutionary record reflected this bushiness and drew such a diagram in his journal.    At the time, though, he had little in the way of fossil evidence to back up this position.  Much has changed since his day.</p>  

<p align="center"><img src="http://biologos.org/uploads/static-content/kidder_Figure_1.jpg"></p>

<p>An analogy for understanding this “bushiness” was best described by Prothero and Buell (Prothero and Buell 2007).  They suggest that the reader consider his or her own genealogy.  You and your siblings are the direct descendents of your parents and, while you are similar to them, each of you has different characteristics not shared with them as well as characteristics that you do share.  Your parents have siblings as well (your aunts and uncles), and your grandparents are their last common ancestors. These siblings have their own children (your cousins), who have different and similar traits relative to their parents.  They are broadly recognizable as being related to you (“oh, I see you have Aunt Edna’s nose”) but three or four generations out, they will become less and less so.  These are the “nearest neighbours” that Ahlberg and Clack describe. In this analogy, each of these cousins represents a transitional form from what was (your grandparents) to what <em>will be</em> down the road.</p>

<p align="center"><img src="http://biologos.org/uploads/static-content/kidder_figure_3.jpg"></p>

<p>For example, no one would confuse a frog with a salamander but if you trace the fossil record of each back in time, eventually you encounter a fossil, <em>Gerobatrachus hottoni</em> which was recently discovered (Anderson et al. 2008) that is best described as a “frogamander,” having the basal characteristics of both frogs and salamanders. Had we seen such an animal at the time, it is likely we would not have found it remarkable because it would have resembled the species around it.  One lineage eventually diverged into frogs, salamanders and other amphibians.  Most (just like Darwin proposed in his tree diagram with the little hatch marks at the tip of many branches) went extinct.</p>

<p align="center"><img src="http://biologos.org/uploads/static-content/kidder_Figure_2.jpg"></p>

<h3>Taxonomy and the Beginnings of Human Origins</h3>

<p>All life is classified based on a system devised by Carolus Linneaus in 1735 in his remarkable work <em>Systema Naturae</em>.  This system gives all recognized species an individual place based on a system of hierarchy. The study of classification is known as taxonomy.  A taxonomic ranking for humans would be this:</p>

<p align="center"><img src="http://biologos.org/uploads/static-content/kidder_figure_5.jpg"></p>

<p>When a fossil is excavated, the first thing that the palaeontologist does is make a taxonomic assessment of where it fits in a sequence of known fossils.  Traits that are shared with other like species or genera are referred to as primitive traits.  Examples of this in humans are five fingers and the presence of three arm bones.  We share this with all mammals.  Traits that are new or are not shared with other like species are referred to as derived traits.  Examples of this in humans are the skeletal changes in the pelvis and the foot to allow for walking upright.  We do not share these with any other primates.</p>

<p>Transitional fossils in the human fossil record are distinguished at both the genus and species level.  This group includes the extinct genera <em>Ardipithecus</em> and <em>Australopithecus</em> and the current genus <em>Homo</em>.  All species except <em>Homo sapiens</em> are extinct.  Much of the recent study of early humans focuses on the transition from <em>Ardipithecus</em> (‘Ardi’) to <em>Australopithecus</em> (‘Lucy’ and similar fossils) and from <em>Australopithecus</em> to <em>Homo</em>, the genus that led eventually to us.  While each of the australopithecine species identified in the fossil record has derived characteristics that separate them from their ancestors and from each other, only one led to the genus <em>Homo</em>.</p>

<p align="center"><img src="http://biologos.org/uploads/static-content/kidder_Figure_4.jpg"></p>

<p>In future posts, I will describe the evidence for human evolution and why this evidence is compelling.  It suggests that we have had a long, varied history filled with great leaps of change, crushing defeat, and eventual expansion into all areas of the globe.</p>

<h3>Notes</h3>
<p>Ahlberg, P. & J. Clack (2006) A firm step from water to land. <em>Nature</em>, 440.</p>
<p>Anderson, J. S., R. R. Reisz, D. Scott, N. B. Frobisch & S. S. Sumida (2008) A stem batrachian from the Early Permian of Texas and the origin of frogs and salamanders. <em>Nature</em>, 453, 515-518.</p>
<p>Prothero, D. & C. Buell. 2007. <em>Evolution: What the fossils say and why it matters</em>. Columbia Univ Pr.</p>
]]></content:encoded>
        <pubDate>Mon, 21 Jan 13 06:35:46 -0800</pubDate>
        <dc:creator>James Kidder</dc:creator>
        <!--<dc:date>Jan 21, 2013 06:35</dc:date>-->
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        <title>Series: Science and the Bible: Intelligent Design</title>
        <link>http://biologos.org/blog/series/science&#45;and&#45;the&#45;bible&#45;intelligent&#45;design?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/series/science&#45;and&#45;the&#45;bible&#45;intelligent&#45;design?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>In this series, Ted Davis identifies the history, core tenets and assumptions about the Intelligent Design view.</description>
        <content:encoded><![CDATA[<h3>What’s in a name?</h3>
<p>According to <a href="http://www.merriam-webster.com/">Merriam Webster</a>, the term “intelligent design” has been used since at least 1847, in reference to “the theory that matter, the various forms of life, and the world were created by a designing intelligence.”  That’s a decent definition, also consistent with those offered by today’s proponents of intelligent design (ID). For example, the leading ID think tank, The Discovery Institute (Seattle), has <a href="http://www.intelligentdesign.org/whatisid.php">this</a>:</p>

<p style="margin: 0 0 0 10px;"><em>Intelligent design refers to a scientific research program as well as a community of scientists, philosophers and other scholars who seek evidence of design in nature. The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.</em></p>

<p>And in the opening sentence of a book he edited with philosopher Michael Ruse, ID theorist William Dembski said, “Intelligent Design is the hypothesis that in order to explain life it is necessary to suppose the action of an unevolved intelligence.” (<em>Debating Design</em>, p. 3)</p>

<p>On the other hand, while a recent contest on a prominent intelligent design (ID) <a href="http://www.uncommondescent.com/intelligent-design/contest-who-invented-the-phrase-intelligent-design-judged/">website</a> uncovered several other early uses of the term, it is important to note that it does not always mean exactly the same thing in each reference. The term itself has an interesting history, and while ID authors obviously did not invent the term “intelligent design,” they have given it specific content in recent years.  Indeed, they have even <em>removed</em> content in some cases: a point I will return to later is that, though it seems the only viable candidate for such an “unevolved intelligence” is God, ID proponents sometimes seem to do cartwheels to avoid saying as much.  When a term has such a complicated past, there simply is no substitute for looking at specific references in their own contexts as we move to seeing how ID plays out today as one of the 5 ways of relating science and the Bible. </p>

<p>Interestingly, many Protestant “modernist” scientists and theologians from William Jennings Bryan’s day (see my <a href="http://biologos.org/blog/science-and-the-bible-theistic-evolution-part-5">previous column</a>) unhesitatingly endorsed the idea that a designing intelligence lay behind nature. At least one such person, Nobel prize-winning physicist Arthur Holly Compton, even used the very term “intelligent design” in an address he gave at a Unitarian church in 1940: “The chance of a world such as ours occurring without intelligent design becomes more and more remote as we learn of its wonders.” (Quoting his pamphlet from 1940, <em>The Idea of God as Affected by Modern Knowledge</em>, p. 13. For more about this aspect of Compton’s views, click <a href="http://www.asa3.org/ASA/PSCF/2009/PSCF9-09Davis2.pdf">here</a>.) However, Compton regarded design as a philosophical and theological inference from science, not an explanation <em>within</em> science to be invoked when other explanations fail. He also accepted the common ancestry of humans and other organisms. This is a significant difference from the ID movement today, which offers ID as a <em>scientific alternative</em> to Darwinian evolution and (at least in many cases) seeks to undermine public confidence in common ancestry (even though ID <em>per se</em> is not actually opposed to it). </p>

<p>If any ID proponents are sympathetic to the type of religious modernism that Compton and his friends embraced, I cannot tell you who they are. In a curious, ironic twist, ID is often used by conservative Christian apologists partly to defend a cluster of traditional theological and hermeneutical positions that none of the modernists would have defended. A further irony: the intellectual descendants of the modernists—those scientists and theologians who occupy the left wing of the modern “dialogue” of science and religion—exhibit a studied avoidance of the term “design,” disconnecting them on that score from the modernists of the 1920s. </p>

<p>Many other contemporary writers, including some evangelical TEs, are also reluctant to use the word “design,” precisely because in their view it has been co-opted by ID proponents and they do not want readers to misunderstand their position(s). They may agree with ID proponents that certain features of the universe reflect divine design, but because they do not see design as a <em>scientific</em> explanation they employ other language. (Likewise, the YECs have co-opted the word “creationism” to mean just one specific understanding of God’s creative activity, leading most advocates of other views either to provide their own definitions of the word or else to avoid using it altogether. Politics dogs this conversation at every turn.)</p>

<h3>Core Tenets or Assumptions of Intelligent Design</h3>
<p>With that bit of historical context for the term “Intelligent Design,” let’s now look at the first of the Core Tenets of this perspective in its current state, and as it is most often used by those associated with the Intelligent Design movement.</p>

<p><strong>(1) The Bible is <em>NOT</em> to be mentioned (at least for now); ditto for “God” and “theology” as far as possible.</strong></p>

<p>This is a deliberate strategy, adopted for political reasons to keep arguments at the level of philosophy and science. Here, “political” refers to the American political system, with its constitutional disestablishment of religion, not to partisan politics. Since the 1980s, federal courts have consistently ruled that “creationism” (which was specifically of the YEC variety in the relevant cases) is sectarian religion, not science, and therefore it cannot be taught in public school science classes. Anxious to avoid a similar fate, proponents of ID always want to ensure that they are not perceived as advocates of “creationism.” The less they mention God and the Bible, the reasoning goes, the less likely they are to fall afoul of those decisions.</p>

<p class="caption-center"><img src="http://biologos.org/uploads/static-content/first_amendment.jpg" alt="" height="331" width="424"  /><br />The First Amendment to the U.S. Constitution, pertaining to the freedom of religion and the freedom of the press. <br />Source: http://www.rochester.edu/college/psc/images/Courses/Spring2008/FirstAmendment.png</p>

<p><a href="http://en.wikipedia.org/wiki/Phillip_E._Johnson">Phillip Johnson</a>, the former law professor who effectively began the ID movement some twenty years ago, has put it bluntly: “To put things on a more rational basis, the first thing that has to be done is to get the Bible out of the discussion.” He quickly adds, “This is not to say that the biblical issues are unimportant; the point is rather that the time to address them will be after we have separated materialist prejudice from scientific fact.” (<a href="http://www.touchstonemag.com/archives/article.php?id=12-04-018-f">“The Wedge: Breaking the Modernist Monopoly on Science,”</a> <em>Touchstone: A Journal of Mere Christianity</em>, July/August 1999, p. 22.) </p>

<p>If God and the Bible are really to be left out for the time being, then why am I discussing ID in a series on “Science and the Bible”? It’s a fair question. I simply don’t see any way meaningfully to avoid talking about ID apart from the culture wars in which it is embedded (I’ll say more about this in a subsequent column), and the Bible is never far from the surface when the battle being fought involves origins. Conservative Christians sense that ID really <em>is</em> about God—Dembski’s “unevolved intelligence”. As Dembski himself <a href="http://www.leaderu.com/offices/dembski/docs/bd-the_ac.html">has said</a>, “no intelligent agent who is strictly physical could have presided over the origin of the universe or the origin of life”, and there aren’t a lot of candidates for that job. Many Christians also identify strongly with the ways in which ID seeks to confront the secular establishment, in an explicitly-stated effort to combat what Johnson calls “the modernist scientific and intellectual world, with its materialist assumptions.” (“The Wedge,” p. 23.) They see it as a way of getting traditional theistic perspectives and Christian values back into the academy, once “design” has become an acceptable academic talking point—and it isn’t very far from there to conversations about “science and the Bible.” If this were not so, then why would so much ID literature be published by Christian presses? Indeed, when I tell church audiences with a straight face that ID purports not to be about the Bible at all, I’m usually met with considerable skepticism.</p>

<p>When I’m back in about two weeks, we’ll look at further Core Tenets of ID—the ones that have even less to do with the Bible, explicitly, and more to do with the way we approach the  study of the natural world.</p>
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        <pubDate>Tue, 18 Dec 12 07:00:11 -0800</pubDate>
        <dc:creator>Ted Davis</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>
        <guid>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</guid>
        <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>Series: Asa Gray and Charles Darwin Discuss Evolution and Design</title>
        <link>http://biologos.org/blog/series/asa&#45;gray&#45;and&#45;charles&#45;darwin&#45;discuss&#45;evolution&#45;and&#45;design?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/series/asa&#45;gray&#45;and&#45;charles&#45;darwin&#45;discuss&#45;evolution&#45;and&#45;design?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>Many Christians believe that they face a painful choice&#45;&#45; either life was designed by God or it is an evolutionary product of natural selection.  Charles Darwin himself believed in this dichotomy, and people ever since have felt the need to &quot;choose sides&quot;.  However, looking back at history, we find that one of Darwin&apos;s chief scientific colleagues, Asa Gray, did not share this perspective. In this three&#45;part essay, part 1 charts the relationship of Asa Gray and Charles Darwin.  Part 2 describes Darwin&apos;s struggle with the problem of natural evil and design in nature, and part 3 explores how Asa Gray was able to embrace evolution without rejecting the idea of design.</description>
        <content:encoded><![CDATA[<h3>Asa Gray</h3>

<p class="caption-left"><img src="http://biologos.org/uploads/static-content/asa_gray_image_3.jpg" alt="" height="374" width="250"  /><br />Asa Gray</p>

<p>If Thomas Huxley earned the title of "Darwin's bulldog," then Asa Gray should be remembered as "Darwin's dove." Whereas Huxley enjoyed a good fight in his defense of Darwin's theory, Gray sought to mediate and bring sides together around a common understanding of "good science." As Darwin's strongest and most vocal scientific ally in the United States, Gray recognized the scientific importance of Darwin's efforts for the growing professionalism of biological researchers.</p>

<p>But as an orthodox Christian, a Presbyterian firmly devoted to the faith expressed in the Nicene Creed, Gray saw in Darwin's theory both evidence for his philosophical commitment to natural theology and support for his opposition to the idealism advocated by Louis Agassiz and the <em>Naturphilosophen</em> in both Europe and America. Indeed, Agassiz's advocacy of Platonic forms as a basis of biological understanding (e.g., "A species is a thought of the creator")<sup>1</sup> would be a major source of American opposition to Darwin's theory.</p>

<p>Professor of botany at Harvard during most of the middle half of the nineteenth century, Gray was one of the few members of the scientific community to whom Darwin revealed his theory before the publication of <em>On the Origin of Species,</em> and, from what I can tell, the only American. Gray and Darwin met briefly in January 1839 during one of Gray's visits to England. Later, during the 1850s, Darwin wrote Gray on several occasions requesting information--a practice that Darwin frequently employed.  In 1854, Darwin's friend and confidant, Joseph Hooker, showed Darwin Gray's review of Hooker's <em>Flora of New Zealand</em>, in which Gray had argued strongly against Louis Agassiz's idealism and had raised questions from his own work on the stability of species. Gray was not yet ready to deny their permanence, but hybrids and other observations were beginning to trouble him.</p>

<p>The next year Gray wrote a lucid and penetrating positive evaluation of Alphonse De Candolle's two-volume <em>Géographie botanique raisonnée</em>, a pioneering work dealing with plant geography and distribution from a statistical perspective. Hooker had sneeringly dismissed the work. In A. Hunter Dupree's authoritative biography of Gray, he describes Gray's puzzlement at Hooker's response in these terms:</p>

<blockquote>Although in the long view Gray's evaluation of the epoch-making nature of De Candolle's book was more justified than Hooker's sneers, [Gray was confused by his response, for] Hooker seemed to be talking with a more comprehensive theory definitely in mind, some reason for taking his position, which he did not divulge and which his friend [Gray] did not possess.<sup>2</sup></blockquote>

<p>Darwin, however, saw in both Gray's review of Hooker's book and in his comments on De Candolle's tome that Gray was troubled by some of the same empirical data that had been bothering him. In April 1855, Darwin wrote Gray to urge that Gray update his <em>Manual of the Botany of the Northern United States</em> first published in 1848, and especially to address the issue of the range of Alpine plants in the United States. Specifically, he said: "Now I would say it is your duty to generalise as far as you safely can from your as yet completed work."<sup>3</sup></p>

<p>Behind this request was Darwin's desire to test his impression that Gray could make a good ally. Gray passed the test, and finally, in July 1857, Darwin let Gray in on his theory of the transmutation of species. Gray was never an uncritical supporter, and there are many evidences in the correspondence between these two scientists that Gray was willing to challenge Darwin and disagree with some of his conclusions. Nevertheless, Gray saw the importance of Darwin's work and the ways in which it provided answers to the troublesome issues that he had confronted in his own botanical efforts.</p>

<p class="caption-center"><img src="http://biologos.org/uploads/static-content/asa_gray_image_2.jpg" alt="" height="294" width="570"  /></p>

<h3>Gray responds to Darwin's theory</h3>

<p>After considerable interchange--one might even say debate--among Gray, Darwin, and Hooker, Gray wrote to Hooker in October 1859 (one month before the publication of <em>On the Origin of Species</em>) saying that he had absolutely no problem with cognate species arising by variation. He did, however, raise a concern that would be the source of much future discussion. He wondered about Darwin's "carry[ing] out this view to its ultimate and legitimate results,--how [do] you connect the philosophy of religion with the philosophy of your science." He added: "I should feel uneasy if I could not connect them into a consistent whole--i.e., fundamental principles of science should not be in conflict."<sup>4</sup></p>

<p>When <em>Origins</em> was published, Gray wrote a clear, positive, yet critical review in <em>The American Journal of Science</em>. Aware of mounting religious opposition, he ended his review by arguing that whereas one could use Darwin's theory in support of an atheistic view of Nature, one could use any scientific theory in that way. He wrote:  "The theory of gravitation and ... the nebular hypothesis assume a <em>universal and ultimate</em> physical cause, from which the effects in nature must necessarily have resulted."<sup>5</sup> He did not see the physicists and astronomers who adopted Newton's theories as atheists or pantheists, though Leibniz earlier had raised such reservations.  And a similar situation existed with the origin of species by natural selection.  Darwin, Gray continued: "merely takes up a particular, proximate cause, or set of such causes, from which, it is argued, the present diversity of species has or may have contingently resulted. The author does not say necessarily resulted."<sup>6</sup></p>

<p>This far Gray could go with Darwin. But there was a point at which he parted company, and that was the fortuitous <em>randomness</em> of the process that Darwin's theory seemed to imply.</p>

<p class="intro"> In part 2, Dr. Miles describes Darwin's struggle with the problem of natural evil and design in nature.</p>

<h3>Notes</h3>

<p class="date">1. Cited in A. Hunter Dupree, <em>Asa Gray: American Botanist, Friend of Darwin</em> (Baltimore: The Johns Hopkins Press, 1959), 151.
2. Ibid., 236.<br> 
3. Charles Darwin, <em>More Letters of Charles Darwin</em>, ed. Francis Darwin, (New York: D. Appleton and Company, 1903), 252.<br>  
4. Dupree, <em>Asa Gray</em>, 266. <br> 
5. Asa Gray, "The Origin of Species" in <em>Darwiniana</em> (Cambridge, MA: The Belknap Press of Harvard University, 1963), 44. <br> 
6. Ibid.</p>
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        <pubDate>Sat, 04 Aug 12 07:21:11 -0700</pubDate>
        <dc:creator>Sara Joan Miles</dc:creator>
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        <title>Being Human (Infographic)</title>
        <link>http://biologos.org/blog/being&#45;human&#45;infographic?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/being&#45;human&#45;infographic?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>The BioLogos Forum is pleased to present this infographic about the current anthropological understanding of human evolution, which takes into account research into both physiological and cultural developments among our ancient ancestors.</description>
        <content:encoded><![CDATA[<a href="http://biologos.org/uploads/static-content/Human-Evolution-Infograpic_full.png"><img src="http://biologos.org/uploads/static-content/Human-Evolution-Infograpic_570.png" alt="" height="1008" width="570"  /></a>
<p><strong>(Click Image for Full Resolution)</strong></p>]]></content:encoded>
        <pubDate>Mon, 30 Jul 12 10:06:50 -0700</pubDate>
        <dc:creator></dc:creator>
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        <title>Hominids Lived Millions of Years Ago, but How Can We Tell? (Videocast)</title>
        <link>http://biologos.org/blog/hominids&#45;videocast?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/hominids&#45;videocast?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>This BioLogos videocast addresses the age of recently discovered hominid fossils and how scientists are able to obtain those dates.</description>
        <content:encoded><![CDATA[<p>Today we present the fifth entry in our on-going BioLogos videocast series. The latest episode addresses the age of recently discovered hominid fossils and how scientists are able to obtain those dates. The script was written by biology student Joy Walters, with help from BioLogos president Darrel Falk.</p>

<p>For more, be sure to read our FAQs <a href="http://biologos.org/questions/ages-of-the-earth-and-universe">How are the ages of the Earth and universe calculated?</a> and <a href="http://biologos.org/questions/what-scientific-evidence-do-we-have-about-the-first-humans">What scientific evidence do we have about the first humans?</a>, as well as our recent infographic <a href="http://biologos.org/blog/how-do-we-know-the-earth-is-old-infographic">How Do We Know the Earth is Old?</a>.</p>

<h3>Author's Note from Joy Walters</h3>
<p>As I mentioned in my first post, I grew up skeptical of the whole idea of evolution. One contributor to my disbelief was the lengthy timescale for the “tree of life” that was presented with the theory. I would hear, for example, that dinosaurs lived hundreds of millions of years ago, but there was no explanation of why this was true; it was just given as a fact. No one explained the methods of dating, and so I thought biologists simply estimated the ages of species to fit their preconceived notions of how long it would take for one species to emerge from another. It also seemed like the ages were periodically revised and extended farther back in time, and I figured scientists needed to manipulate numbers to make evolution plausible. This, in my mind, made the theory both unbelievable and dismissible.</p>

<p>Once I learned about the techniques used to date fossils, I realized that my first impressions were wrong; the ancient ages of species are scientific determinations rather than scholarly conjectures. However, I have found in recent conversations that Christians remain skeptical of old ages and the evolutionary time scale. For this reason, I wanted the videocast to address the process of fossil dating (what the methods are and why they are accurate) while focusing on cases where hominid fossils were discovered and dated using these very methods. My hope is that Believers would be informed about the evidence for human evolution and its scientific grounding.</p>]]></content:encoded>
        <pubDate>Thu, 26 Jul 12 05:00:03 -0700</pubDate>
        <dc:creator>Joy Walters</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>
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        <title>Fine&#45;tuning and the “Fruitful Universe”</title>
        <link>http://biologos.org/blog/fine&#45;tuning&#45;and&#45;the&#45;fruitful&#45;universe?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/fine&#45;tuning&#45;and&#45;the&#45;fruitful&#45;universe?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>I ask the question, “Why is the universe so special?” Now scientists don’t like things to be special; we like things to be general, and our natural anticipation would have been that the universe is just a common specimen of what a universe might be like.</description>
        <content:encoded><![CDATA[<p align="center"><iframe src="http://player.vimeo.com/video/17950307" width="400" height="300" frameborder="0"></iframe></p>

<p>I ask the question, “Why is the universe so special?” Now scientists don’t like things to be special; we like things to be general, and our natural anticipation would have been that the universe is just a common or garden specimen of what a universe might be like.</p>
 
<p>But we’ve come to understand a lot about the history of the universe. We know that our universe started 13.7 billion years ago, and it started extremely simple, just an almost uniformly expanding ball of energy, about the simplest physical system you could possibly think about. But a world that started so simple has of course become rich and complex. With you and me, in fact, the most remarkable and complex consequences are its history, at least of which we are aware. The human brain is far and away the most complicated physical system we have ever encountered anywhere in our exploration of the universe.</p>

<p>That fact itself might suggest that something has been going on in cosmic history rather than just one thing after another. But we’ve also come to understand many of the processes by which this rich fruitfulness has come to birth. As we’ve come to understand these, we’ve come to see that though these processes are of course evolving processes, they took long periods of time – the universe was 10 billion years old before any form of life appeared in it, at least as far as we know anyway – and life of our complexity only appeared yesterday.</p>
 
<p>Nevertheless, the universe is pregnant with life, pregnant with the possibility of life, essentially from the beginning onwards. By which I mean the given laws of nature had to take a very specific, very finely tuned form, if the universe was to have so fruitful a history.</p>

<p>That’s a very remarkable discovery, and let me give you some examples of why we believe that. If you’re going to have a fruitful universe, one of the first things you have to get right is that you have to have the right stars in the universe. The stars are going to have a very important role to play. First of all, you must have some stars that are going to be very long lived, live for billions of years, steadily burning, steadily producing energy which will enable the development of life on one of the encircling planets. We understand what makes stars burn in that sort of way very well, and it depends on a delicate balance between the strength of gravity and the strength of electromagnetism. Electromagnetism is the force that holds matter together. The seats on which you are sitting are held together by electromagnetism and in fact you are held together by electromagnetism.</p>

<p>If you alter that balance a little bit in one direction the stars will begin to burn intensely, furiously, just pouring out energy and they will only live a few million years rather than a few billion years. If you move it a little bit in the other direction they will burn so slowly they will be brown stars and they will not produce enough energy to fuel the development of life. So you have to have a very delicate finely tuned balance between the strength of gravity and the strength of electromagnetic forces in a fruitful universe.</p>

<p>Remember, science takes the laws of nature, takes the given strengths of gravity, the given strength of electromagnetism, uses that to explain processes in the world, how things happen, but it doesn’t explain where those laws of nature come from. They are just brute facts as far as science is concerned.</p>

<p>And the stars have another absolutely indispensible role to play. The stars are the place where the heavier elements essential for life are made in the interior nuclear furnaces. There are many elements that are necessary for life, of which carbon is perhaps the most essential. Carbon is the basis of the long chain molecules, which are the biochemical basis of life. The early universe only makes the simplest elements; it makes hydrogen and helium and it makes no carbon at all. Carbon only begins to be made when the universe, which started uniform, begins to condense and become lumpy and grainy with stars and galaxies. As the stars condense they heat up, nuclear processes begin again in their interiors. And it’s those nuclear processes in the stars that make carbon and the heavier elements. Every atom of carbon in your body was once inside a star. We are people of stardust made in the ashes of dead stars.</p>

<p>And that’s a very beautiful process that takes place in that sort of way. And one of the great triumphs of astrophysics and the second half of the 20th century was to unravel that process. One of the people who did some of the most important work on that was a senior colleague of mine in Cambridge called Fred Hoyle. And they were trying to figure out how to make carbon. They got helium, and if you can make three helium nuclei stick together that will produce carbon, but when you have something as small as a nucleus it is impossible to get three to stick together at one time, they’re just too small.</p>

<p>Ok, so let’s do it step by step. Stick two together gives you berylium. Helium 4 gives you beryllium-8, hope it stays around for a bit, another helium comes along, attaches itself, and bingo, you’ve got carbon-12. That’s the obvious thing to think about but it doesn’t work in the obvious way, and the reason it doesn’t work in the obvious way is that beryllium-8 is terribly unstable. It doesn’t oblige you by staying around long enough to catch that third helium, at least in an ordinary, straightforward way.</p>

<p>But Fred realized that it would be just possible for this to happen if there was a very large enhancement effect, in the trade we call it resonance, occurring in carbon at just the right energy, it has to be the right energy, which would enable that attachment process to catch that third helium much much more quickly that you might have thought, in fact so quickly that some of them would get caught before the beryllium-8 disappeared. It was a very good idea, and he must have felt pretty pleased with himself and he went off to just check in the nuclear data tables of this particular resonance’s energy levels, and it wasn’t in the tables, but he knew it must be there, he’s carbon based life like you and me.</p>

<p>So he rang up some friends in the States, a father and son team who were good experimentalists and he said, “Look, you missed something. There’s a resonance and energy level in carbon that you haven’t spotted, and I’ll tell you exactly where to look for it. I know exactly where this energy has got to be. You go look for it.” And they said, “No, no, we don’t want to do that, we have more interesting things to do.” But Fred was very determined and he bullied them into looking for it and they found it.</p>

<p>Now that’s a wonderful achievement, to predict an energy level in carbon on the basis of how it might have been made in the stars is a fantastic scientific achievement. But it’s more than that. Fred had a lifetime conviction of atheism, realized of course that if the laws of physics had been just a little bit different that resonance wouldn’t have been there, and the possibility of carbon-based life is too significant for it just to be a happy accident in his view, so he says in a Yorkshire accent that is beyond my power to imitate, he said that the universe is a put-up job. Fred didn’t like the word God, and so he said some Intelligent, capital “I” Intelligence, must have monkied with the laws of nature to make carbon production possible. What that could possibly be I don’t know, but the more sensible thing to say is that creation is ordained, that the laws of nature would be such, as to enable the fruitfulness of carbon-based life.</p>

<p>We’ll come back to evaluating that possibility in a minute, but before we do, let me give you two other examples of how specific, how special, our universe has to be for us to be able to be here today to think about. We live in a universe that is immensely big, beyond our powers to imagine really. There are a hundred thousand million stars in our galaxy in the Milky Way, of which our sun is just a common or garden specimen, and there are about a hundred thousand million galaxies in the observable universe, of which our Milky Way is a pretty common or garden specimen. So we live in a world that is unimaginably vast, and sometimes we might feel upset by that and think, “What could be the significance of us who are simply inhabitants of a speck of cosmic dust, as you might say, in this vast, vast universe?”</p>

<p>Nevertheless, if all those stars were not there, we would not be here to be upset at the thought of them. Because there is a direct connection between how big a universe is and how long it lasts, and a universe that is significantly smaller than our universe would not have been able to last the 14 billion years, which is the necessary time to produce beings of our complexity. So that’s another condition of the world that has to be right for human beings, or something like human beings, to be a possibility.</p>

<p>One final example, which is the finest tuning of all: quantum theory suggests that there should be an energy attached to space itself. In quantum theory the vacuum, so called empty space, is not just a void. There are things called vacuum fluctuations which occur in a continual sort of seething mass of things coming into being and going out of being all the time. So while there is nothing there that doesn’t mean there is nothing happening. That may sound strange and paradoxical but believe me that’s what quantum theory implies. And of course these happenings, these fluctuations, generate a certain amount of energy, we call it “zero point energy”, and that energy is spread out over the whole of space. So we expect there to be energy associated with space.</p>

<p>And just recently the astronomers have discovered something called dark energy which is driving the expansion of the universe, which is just such an energy associated with space. Well that’s very good, you might say. However, when we estimate, just from thinking about quantum theory, how much energy there should be in space it turns out to be a fantastically large amount, and when we see the amount of energy there actually is per volume in space, it turns out to be very, very small in relation to that expected size. In fact, it turns out to be smaller by a factor of 10<sup>-120</sup>. That means by a factor of 1 over 1 followed by 120 zeros. You don’t have to be a great mathematician to see that’s a fantastically small number. So some fantastic cancellation has taken place to turn that big number into the tiny number that we actually observe, and if it hadn’t taken place we wouldn’t be here to observe it because significantly higher energy would simply have blown the whole show apart too fast for anything interesting to happen. That’s the finest tuning that we know in the universe: one part in 10<sup>120</sup>.</p>

<p>So we live in a world that is very remarkably finely tuned, and we have to consider that. And all scientists would agree about what I have been telling you; this is non-contentious. Where the contention comes in is what we might make of that, what is the further significance of it.</p>

<p class="intro">In the <a href="http://biologos.org/blog/john-polkinghorne-on-natural-theology-part-iv">conclusion</a> to Dr. Polkinghorne’s lecture, he looks at two explanations for the "fine-tuning" principle -- the multiverse theory and the existence of a divine intelligence -- and explains why natural theology alone is not sufficient to make the case for a God who interacts and cares for his creation. To make the case for theism, he argues, we need revelation, God's self-disclosure. This is manifest in various ways, including that which we experience personally, including ethics and aesthetics.</p>]]></content:encoded>
        <pubDate>Fri, 01 Jun 12 05:00:10 -0700</pubDate>
        <dc:creator>John Polkinghorne</dc:creator>
        <!--<dc:date>Jun 01, 2012 05:00</dc:date>-->
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            <item>
        <title>Adam&apos;s Dream</title>
        <link>http://biologos.org/blog/adams&#45;dream2?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/adams&#45;dream2?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>While the specific “how” of our being made into the image of God will probably always remain a mystery, the Bible and creeds are clear on the “why” of our creation: we were made to worship the Lord, and be in relation with Him and each other.</description>
        <content:encoded><![CDATA[<p>Discussion about Adam as the first divine "Image-bearer" often turns on the perceived conflict between scientific evidence contradicting belief in a single biological ancestor of all living human beings and Scriptural testimony that humans were made different from the rest of the creation: we have capacity to reflect the image of God.</p>

<p>Many posts on this Forum have suggested that the cosmological narrative in Genesis 1 is best read as being primarily about God’s identity and agency, rather than about the physical make-up or material history of the natural world.  Similarly, we demonstrate our highest regard for Genesis 2’s account of the creation of Eve—the second fully human being—by looking to its meaning in terms of spiritual and interpersonal relationships, rather than genetic ones.  While the specific “how” of our being made into the image of God will probably always remain a mystery, the Bible and creeds are clear on the “why” of our creation: we were made to worship the Lord, and be in relation with Him and each other.  That intimate, conscious and deeply symbolic knowledge of our maker and fellow human beings is a profound difference that sets us apart from the other creatures.</p>

<p>I have frequently argued that poets are often the most clear on some of the important issues of our faith, including this one.  Today we feature a work by Robert Siegel, who identifies the imagination as the faculty by which we recognize and name those spiritual relationships.  As he says, “It's the imagination, hence language and art, that establishes the connections”; it is the imagination that allows us to conceive of and name the links between ourselves and creation, ourselves and each other, ourselves and the Creator God.</p>

<p>Though we often focus on Adam’s naming of the animals, and then even of Eve, Siegel helps us remember that it was in <em>hearing</em> his own name that Adam’s whole humanity came into being: he experienced the richness of being called by God to bear His likeness, but also of being called to by one that was profoundly “like him.”  Put another way, we are speakers, but also equally hearers. May we, too, be awakened to ourselves and our image-bearing identity by a still, soft voice saying our name. May we, too, in gratitude and delight, call upon the name of the one, Jesus, who is both our God and our fellow man.</p>


<h3>“Adam’s Dream”</h3>
<p>by Robert Siegel</p>

<p><em>The Imagination may be compared to Adam's dream:<br />
he awoke and found it truth</em>. --Keats</p>

<p>He saw the garden spreading past the trees<br />
he'd been warned to avoid (yet keep a special eye on).<br />
He'd learned by scents, transported by the breeze,<br />
myriads of roses and how, by hand, the scion<br /><br />
of one to graft on another--and what was edible:<br />
whole families of legumes, grasses, roots,<br />
melons, peaches, apples, pears. Incredible,<br />
the variety of tastes just from the fruits!<br /><br />
But it wasn't enough. Even the breathing animals<br />
with friendly grunt or sigh, silken warm side,<br />
and large affectionate eye were not able<br />
to speak. When he named them, none replied:<br /><br />
His words fell dead on the air--though he said<br />
them everywhere, walking or running to each place:<br />
to the mountain, which echoed back the sounds he made,<br />
or the still pool, returning his own gaze.<br /><br />
But no one answered him until one night in a dream<br />
he woke and heard a soft voice speak his name.</p>

<p>“Adam’s Dream” first appeared in issue 3 of <a href="http://stonework03.blogspot.com/2005/11/stonework-issue-3.html" target="_blank">Stonework</a>, the literary journal of Houghton College. &copy; 2001 Robert Siegel</p><br> </br>

<p class="intro">Robert Siegel is the author of nine books of poetry and fiction, most recently <a href="http://www.amazon.com/gp/product/1557254303/ref=as_li_ss_tl?ie=UTF8&tag=thebiofou06-20&linkCode=as2&camp=217145&creative=399369&creativeASIN=1557254303">A Pentecost of Finches: New and Selected Poems</a><img src="http://www.assoc-amazon.com/e/ir?t=&l=as2&o=1&a=1557254303&camp=217145&creative=399369" width="1" height="1" border="0" alt="" style="border:none !important; margin:0px !important;" />. He has received prizes and awards from Poetry, Prairie Schooner, The Transatlantic Review, the Ingram Merrill Foundation, and the National Endowment for the Arts, and his poems have appeared in numerous journals and anthologies.  His fiction includes Alpha Centauri and the Whalesong trilogy, which received the Golden Archer and Matson awards.  With degrees from Wheaton, Johns Hopkins, and Harvard, Siegel has taught at Dartmouth, Princeton, and Goethe University in Frankfurt, and for twenty-three years at the University of Wisconsin-Milwaukee, where he directed the graduate creative writing program and is currently professor emeritus of English. He is married to Ann Hill Siegel, a photographer, and lives on the coast of Maine.</p><b></br>]]></content:encoded>
        <pubDate>Sun, 20 May 12 05:39:50 -0700</pubDate>
        <dc:creator>Mark Sprinkle</dc:creator>
        <!--<dc:date>May 20, 2012 05:39</dc:date>-->
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            <item>
        <title>Caution! Design Arguments Ahead</title>
        <link>http://biologos.org/blog/the&#45;wonder&#45;of&#45;the&#45;universe&#45;caution&#45;design&#45;arguments&#45;ahead?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/the&#45;wonder&#45;of&#45;the&#45;universe&#45;caution&#45;design&#45;arguments&#45;ahead?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>Design arguments have been around forever and expressed in various ways. Most of them fall into what we call natural theology, which is the process of inferring something about the existence and nature of God by the inspection of nature.</description>
        <content:encoded><![CDATA[<h3>A Short History of Design Arguments </h3>

<p>Design arguments have been around forever and expressed in various ways. Most of them fall into what we call <em>natural theology</em>, which is the process of inferring something about the existence and nature of God by the inspection of nature. The story of creation in Genesis launches the discussion in the Judeo-Christian tradition when it speaks of God ordering nature and driving back chaos. On the fourth day “God created the sun, moon, and the stars to give light to the earth and to govern and separate the day and the night. These would also serve as signs to mark seasons, days, and years.” All this suggests design and purpose. Job speaks of God making “water drops evaporate” so the clouds can “shower abundantly on mankind.” (Job 36:27-28 HCSB). The psalmist expresses awe at the grandeur of the night sky but remarkably does not comment on the grandeur of his own existence:</p>

<p><blockquote>When I observe Your heavens,
the work of Your fingers, . . . 
what is man that You remember him? (Psalm 8:3-4 HCSB) </blockquote></p>

<p>In the New Testament, Paul speaks of the created order testifying clearly to the reality of God, arguing that, “the invisible things of [God] from the creation of the world are clearly seen, being understood by the things that are made” (Romans 1:20 KJV). Biblical scholars have interpreted this to mean that an open-minded seeker can infer the existence of God by studying the creation. 
As theologians reflected on the nature of the creation these arguments were repeated and refined. Augustine in the fourth century, Thomas Aquinas in the thirteenth century, Luther and Calvin at the time of the Reformation in the sixteenth century—all were understandably convinced that the world had a grand design that was readily discernable. After all, nobody had any other explanation for why birds were adapted to fly, fish to swim and constellations to mark the seasons. </p>

<p>By the time we get to Isaac Newton in the latter part of the seventeenth century, we have the first carefully constructed scientific arguments. Newton, as we learned in high school, explained how gravity from the sun keeps the planets in their orbits. This explanation replaced previous medieval explanations that included the possibility that the planets moved because angels pushed on them. (It also replaced Galileo’s explanation that they moved because of a “circular inertia,” which turned out to be as much a fantasy as the pushing angels.) But Newton’s theory didn’t explain why the planets all go around the sun in the same direction and in almost the same plane. In fact Newton could not imagine any natural process that could produce such elegant design, so he argued that God must be the explanation. </p>

<p>About two centuries later the most famous design argument was developed by William Paley whose <em>Natural Theology</em> Darwin read voraciously as a young scientist. “Suppose I had found a watch upon the ground,” asked Paley, “and it should be inquired how the watch happened to be in that place. . . . [W]hen we come to inspect the watch, we perceive . . . that its several parts are framed and put together for a purpose. . . . [T]he inference, we think, is inevitable, that the watch must have had a maker.” Paley goes on to compare the watch to an eye, arguing that if a watch implies a watchmaker, then an eye implies an eye-maker. The eye-maker, of course, can only be God. </p>

<p>Newton’s argument about the planets and Paley’s about the watch have the same logical form: We find something in nature that appears too ingeniously arranged to have been produced by known natural processes, so we infer that a Designer from outside the natural order—God— must be the source of the design. Their arguments differ, however, on the question of purpose. It was not clear to Newton or anyone of his day exactly why the planets needed to be going about in the orderly way they were observed. If the order was indeed provided by God, no explanation for it could be discerned other than the creation of order for the sake of order. In contrast, the designs that Paley highlighted were clearly purposeful. Our eye is remarkably designed for a purpose other than to elicit awe at its complexity. We see with our eyes. We don’t do anything with Neptune’s nice orbit, other than admire it. </p>

<h3>Red Flags</h3>

<p>Arguments that the universe is designed are complicated. We certainly live in a remarkable universe with many features that inspire awe. Many of those features connect in astonishing ways to the habitability of the universe. The psalmist’s wonder at the heavens has only grown stronger as we have learned more about those heavens. The universe certainly does not become ever more boring and bland as we come to understand it better.</p>

<p>But we also live in a world with earthquakes, plagues and tsunamis. Our sun will burn out at some point, incinerating the earth in the process. The prospects of securing our future by colonizing other planets seem remote. The long-term prognosis of the universe, by the cold logical lights of science, is not good. Its temperature will continuously drop as it expands for billions of years. Eventually there won’t be enough heat left for any form of life, and finally there won’t even be enough heat for atoms and molecules to interact. This sterile icy blackness is frightening to contemplate. No matter what we do as a species, we and our cultural achievements are destined to perish. </p>

<p>No simple overriding explanation that makes sense of everything comes into view as we learn more about the universe. And experience with past arguments raises red caution flags. For example, Newton’s design argument about the planets was an argument from ignorance that now bears the label “god of the gaps.” There was a gap in Newton’s explanation for the planets. He could explain why their orbits were elliptical and what kept them in their orbits. But he could not explain the uniformity of their orbits, so he invoked God as the explanation to plug this gap—hence the label for such arguments—god of the gaps. </p>

<p>A century after Newton, French physicist Pierre Simon de Laplace dispelled the mystery of the structure of the solar system. He showed that a better understanding of gravity and how solar systems originated could explain the things that Newton attributed to the direct action of God. Laplace’s work did not refute the existence of God, of course. But it did dismantle Newton’s argument that the planetary orbits must have been set up by God, thus eliminating an argument that some had been using to argue for God’s existence. </p>

<p>In a similar way, Darwin’s theory of evolution offers an explanation for the design that Paley marveled at in the eye. Scholars of Paley’s generation knew nothing of natural selection, mutations or genetics, so they could not imagine how nature might craft something so remarkable as an eye. Paley’s argument, like Newton’s, turns out to be another god of the gaps explanation that disappears with further scientific insights into the way the world works. </p>

<p>So this is the first red flag to note—design arguments are all-too-often based on gaps in our knowledge and will disappear when those gaps are filled. </p>

<p>The second red flag concerns the apparent purpose of any design. “Design” can point in many directions or no direction at all. The science museum in Boston has a grand contraption that does nothing except move balls around to no end. The only possible purpose is to impress a visitor with the juxtaposition of complex design and lack of purpose. There is likewise no significance to the patterns of the stars that we call constellations. The “design” of the Big Dipper is simply interesting. The fine-tuning of the universe for life, on the other hand, encourages us to wonder if life may be important in some way. But it does not specify which life forms are relevant and why. And we must note that some features of our world exhibiting a high level of design—like the AIDS virus or the poison of the rattlesnake—seem to have the purpose to destroy human life. If rattlesnakes could reflect on their existence, they could marvel at the carbon resonance that makes that existence possible. </p>

<p>A third red flag we must note is bad design. If marvelous design in the universe motivates reflection on the possibility that God created the world what do we do about the counterarguments? Consider asteroids. A gigantic asteroid struck the Yucatan Peninsula 65 million years ago and so disrupted the ecosystems and the atmosphere of the earth that the dinosaurs went extinct. Absolutely nothing prevents the same thing from happening again. We are protected today largely by the vastness of space and the structure of our solar system with large outer planets that “vacuum up” a lot of stuff that could hit the earth. These various protections make collisions of the sort that wiped out the dinosaurs unlikely. But they offer no guarantees. If the Goldilocks features of our universe are intended to make it habitable, then why does the universe also have anti-Goldilocks features? </p>

<p>Many such issues complicate the process of figuring out why the universe is the way it is. And as we have learned somewhat reluctantly in the last few centuries, the great explanatory power of science disappears entirely when questions of purpose enter the conversation. Science is quite extraordinary at telling us how the world is but quite unable to tell us why the world is like that. Science illuminates the remarkable features of our universe that make life possible, but it goes silent when we ask whether any particular life form is the reason why the universe is the way it is. That deeply religious question has to be explored somewhere else. </p>

<p>These challenges caution us against naively selecting—cherry-picking we call it—a few Goldilocks features of the universe, assuming the friendly design work is for our benefit, and jumping to the conclusion that everything points simply and unambiguously in the direction of God as Creator. </p>
]]></content:encoded>
        <pubDate>Tue, 15 May 12 05:00:56 -0700</pubDate>
        <dc:creator>Karl Giberson</dc:creator>
        <!--<dc:date>May 15, 2012 05:00</dc:date>-->
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        <title>Understanding Evolution: The Evolutionary Origins of Irreducible Complexity, Part 1</title>
        <link>http://biologos.org/blog/understanding&#45;evolution&#45;the&#45;origins&#45;of&#45;irreducible&#45;complexity&#45;part&#45;1?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/understanding&#45;evolution&#45;the&#45;origins&#45;of&#45;irreducible&#45;complexity&#45;part&#45;1?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>I will take some time to clarify exactly how Michael Behe, the biochemist and Intelligent Design (ID) proponent who has most extensively developed the &quot;irreducible complexity&quot; argument, uses the term.</description>
        <content:encoded><![CDATA[<h3>The Intelligent Design argument from Irreducible Complexity (IC)</h3>

<p>Since this post, and those that will follow it, depend on an accurate representation of the argument for irreducible complexity (IC), I will take some time to clarify exactly how Michael Behe, the biochemist and Intelligent Design (ID) proponent who has most extensively developed the IC argument, uses the term. For Behe, the argument for IC is a critique of gradual evolutionary processes, of the kind that Darwin saw as necessary for his theory to hold. When Behe introduces and defines IC in his book <em>Darwin’s Black Box</em>, he has a key quote from Darwin on gradualism explicitly in view: </p>

<blockquote>Darwin knew that his theory of gradual evolution by natural selection carried a heavy burden: "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."<br /><br />

It is safe to say the most of the scientific skepticism about Darwinism in the past century has centered on this requirement… critics of Darwin have suspected that his criterion of failure had been met. But how can we be confident? What type of biological system could not be formed by “numerous, successive, slight modifications”?<br /><br />

Well, for starters, a system that is irreducibly complex. By <em>irreducibly complex</em> I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. (<em>Darwin’s Black Box</em>, p. 39)</blockquote>

<p>The definition of an IC system is thus straightforward: it is a matched group of components, where all the components are necessary for the function of the system. The necessity of each component can be demonstrated by attempting to remove it – if the system no longer works if even one component is removed, it is by definition IC. Since an IC system requires all the components to be present for its function, it is not possible for the system, in its current state, to have been produced directly from a non-functional precursor. If one grants this premise, it leaves two options: that the IC system was derived indirectly, from a system that is not IC, or that the system was assembled by fiat and thus represents the actions of a designer. Behe’s criterion for distinguishing between these choices is based on evaluating the probabilities of these competing options:</p>

<blockquote><p>Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin's criterion of failure has been met skyrockets toward the maximum that science allows. (<em>Darwin’s Black Box</em>, p. 40)</p></blockquote>

<p>As we will examine in an upcoming post, Behe attempts to determine the precise limit of what evolutionary processes can (and cannot) achieve in a second book, <em>The Edge of Evolution</em>. For our present purposes, however, it is enough to note that the strength of the argument from IC depends on the perceived implausibility of the opposing explanation – that of an indirect evolutionary route that produces an IC system from a non-IC precursor system. </p>

<h3>Building IC, one step at a time?</h3>
<p>The presence of IC systems in biology as Behe has defined them is not contentious: there are many biological systems that cease to function when parts are removed. Indeed, the success of classical genetics in “dissecting” which genes are needed for certain functions largely rests on the ability to see some effect on function when a gene is removed from a system by mutation. What scientists dispute, however, is Behe’s claim that identifying IC systems is a hallmark of design. The evolutionary model for building IC is quite simple, and Behe has set it out as an option: an indirect route where non-essential parts are added to a system, and then over time the system comes to depend on those parts. We can diagram this model as follows: </p>
 
<p align="center"><img src="http://biologos.org/uploads/static-content/ic_post_1.png" alt="" height="526" width="570"  /></p>

<p>The key to the model is that new parts can be added to a system, and that these parts are <em>not essential</em> when they are added. The resulting system is thus not IC, since it has parts that are not essential to its function, even if the new parts are advantageous in some way. If the new component is taken away at this stage, the system merely reverts to the precursor system. The second part of the model is that these intermediate, non-IC systems then may become IC if small changes make the new parts essential. </p>

<p>The addition of new, non-essential parts can be accomplished in several ways, such as a change in an existing protein that allows it to bind to a “precursor system”. More extreme would be the generation of a new protein that then adds to a precursor system as a non-essential component. Brand new genes, by definition, cannot be essential when they arise, since they arise in an organism that, up to that point, had no need of them. Looking to see if new genes then later <em>become essential</em> would be very good experimental support for the evolutionary model for how IC systems arise. </p>

<p> In practice, it takes a lot of scientific effort to tease out changes to an existing protein that allow it to become part of an intermediate system and then progress to an IC system, though we have examined one such example <a href="http://biologos.org/blog/evolution-and-the-origin-of-biological-information-part-3-csi-on-steroids">in a previous post</a>. Looking for brand new genes, however, is much easier – and some recent work in  several fruit fly species (<em>Drosophila</em>) has done just that. </p>

<h3>The Young and the Restless</h3>
<p>So, how to go about finding genes that are new? We have already discussed, in the context of duplicating an entire genome, how <a href="http://biologos.org/blog/evolution-and-the-origin-of-biological-information-part-5">duplication of genes</a> may lead to the two copies picking up new functions over time. While duplication may happen rarely at a whole-genome scale, small-scale duplication of small numbers of genes happens quite frequently as an error during cell division. At the time of the duplication, the two copies are the same, and therefore functionally equivalent. Over time, however, the two copies may become different and acquire distinct functions. </p>

<p>One way to look for genes that have arisen due to a recent duplication event is to compare the genomes of closely related species and look for genes that are present in one species but not another, or in a subset of related species. Duplicated genes will show up in a nested hierarchy, much like how pseudogenes appear in the same nested pattern, as we have discussed previously <a href="http://biologos.org/blog/signature-in-the-pseudogenes-part-1">here</a>. </p>
 
<p align="center"><img src="http://biologos.org/uploads/static-content/ic_post_fig_2.jpg" alt="" height="505" width="570"  /></p>

<p>The complete genome sequences for a number of fruit fly species are available, so researchers used this method of comparison to look for new genes that mostly arose “recently” (over the last 35 million years) within flies. Since the speciation times for the various fly species are known to a good approximation, the time of the various duplication events can be estimated as well.  </p>

<h3>Putting the argument for IC to the test</h3>
<p>Using this method, researchers identified 195 recent, “young” genes that arose through duplication events. (Note: this finding, in and of itself, is problematic for the ID argument that significant amounts of new information cannot arise through evolutionary mechanisms). More problematic for the argument from IC, however, is that just less than <em>one third of these new genes are now essential for development</em> in the species that carry them. This fraction is approximately the same for “old” genes – about one third are essential for development. </p>

<p>The implications are easily grasped: many new genes have arisen through duplication, and a sizeable fraction are now part of IC systems. When they arose, they could not have been essential, but now they are emphatically so. As such, they must have been added to previous 
systems, and become IC over time. Moreover, this effect is not a rare, one-off event, but rather has been repeated time and again in recent evolutionary history. </p>

<p>In the next post in this series, we’ll delve into some of the details about how these new genes arose, and what sort of functions they have.  </p>

<h3>For further reading:</h3>
<p>Behe, M.J. <em>Darwin’s Black Box: the Biochemical Challenge to Evolution</em>. Free Press, New York, 1996. </p>
<p>Behe, M.J. <em>The Edge of Evolution: the Search for the Limits of Darwinism</em>. Free Press, New York, 2007. </p>
<p>Chen, S., Zhang, Y, and Long, M (2010). New genes in Drosophila quickly become essential. <em>Science</em> 330; 1682-1685. </p>
]]></content:encoded>
        <pubDate>Thu, 19 Apr 12 05:51:09 -0700</pubDate>
        <dc:creator>Dennis Venema</dc:creator>
        <!--<dc:date>Apr 19, 2012 05:51</dc:date>-->
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            <item>
        <title>Beginning with the End in Mind</title>
        <link>http://biologos.org/blog/evolutionary&#45;convergence?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/evolutionary&#45;convergence?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>In today&apos;s video, Oxford physicist Ard Louis discusses the famous debate between renowned evolutionary biologists Stephen Jay Gould and Simon Conway Morris over the idea of evolutionary convergence.</description>
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<p class="intro">Today's video is courtesy of filmmaker Ryan Pettey, director/editor of Satellite Pictures and features physicist Ard Louis.</p>

<p>In today's video, Oxford physicist Ard Louis discusses the famous debate between renowned evolutionary biologists Stephen Jay Gould and Simon Conway Morris. Gould believed (and wrote in his book <em>Wonderful Life</em>) that if the "tape" of evolution were rerun, the chance that anything like human intelligence would emerge is essentially zero. In other words, humanity is here through random accident. Gould pointed to the work of Morris and fellow scientists in their research of the Burgess Shale as evidence for this view.</p>

<p>However, Morris himself disagrees, pointing to what is called evolutionary convergence. As Morris notes, there are numerous examples of identical features evolving multiple times throughout the history of life independently. Morris believes that if the tape of life were replayed, we would see something like humans emerge. A Christian might say, it looks like we were planned.</p>


<p>Some Christians might find Simon Conway Morris' viewpoint, with its implicit teleology, more attractive. Others, perhaps motivated by a high view of providence, may find Gould's emphasis on contingency equally congenial to their faith.  What do you think?</p>]]></content:encoded>
        <pubDate>Thu, 15 Dec 11 05:51:27 -0800</pubDate>
        <dc:creator>Ard Louis</dc:creator>
        <!--<dc:date>Dec 15, 2011 05:51</dc:date>-->
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        <title>Dead Bones with a Living Message</title>
        <link>http://biologos.org/blog/our&#45;family&#45;tree?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/our&#45;family&#45;tree?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>In this video, Pääbo covers a lot of ground, noting several lines of genetic evidence for the evolution of modern humans from earlier hominids in Africa, as well as for the interbreeding between early humans and Neanderthals.</description>
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<p>As we noted in <a href="http://biologos.org/blog/biologos-and-the-june-2011-christianity-today-cover-story">our response</a> to the June article in <em>Christianity Today</em> “The Search for the Historical Adam,” the evidence for gradual creation is overwhelming, with more studies supporting the evolutionary process being published each year. We’ve looked at many of these evidences: from fossils, from comparative anatomy, from genetics. Today, we’d like to highlight for our readers a compelling video from the annual TED Conference featuring geneticist Svante Pääbo. You may remember Pääbo from his efforts to extract and sequence DNA from 30,000(+) year old Neanderthal bones (we mentioned his work <a href="http://biologos.org/blog/a-geneticists-journey">here</a>).</p>

<p>In this eighteen minute video, Pääbo covers a lot of ground, noting several lines of genetic evidence for the evolution of modern humans from earlier hominids in Africa, as well as for the interbreeding between early humans and Neanderthals. We’ve covered some of this data before, but it’s particularly compelling to hear it described by one of the scientists leading the field of study.</p>

<p>However, our goal at The BioLogos Foundation isn’t just to make the Church aware of the fascinating and convincing scientific evidence for gradual creation. As we have said <a href="http://biologos.org/blog/a-geneticists-journey">before</a>:</p>

<blockquote><p>BioLogos exists to help Christians think carefully about the ramifications of these new data in light of long-standing traditional ways of viewing human creation. We have some re-thinking to do, but it can be done and will be done within the context of a Christian faith that is fully orthodox and thoroughly evangelical. Any time we draw closer to truth, to God’s truth, we have nothing to fear. There is still much to learn, but we can look back at what we have learned with awe—absolute awe.</p></blockquote>

<p>It is truly amazing that we know so much now about our early days.  For example, Africans do not have DNA which is specifically derived from Neanderthals, whereas people in the rest of the world do carry a small amount.  This confirms the picture of human history derived from studying fossils.  Neanderthal bones have not been found in Africa, so it isn’t surprising that their DNA is not there either.  The fact that non-Africans have some of the DNA found in Neanderthal bones confirms that which geneticists knew from other studies: we have two distinct groups of human ancestors—those who left Africa in ancient times and those who stayed.</p>

<p>God chose to reveal himself and to begin working with a distinct sub-group of ancient  humans, those descended from Abraham and Sarah.   To Abraham, God made a marvelous promise.   Drawing his attention to the stars above, God said that someday Abraham’s descendents would outnumber the countable stars in the universe.  And so it came to be.  Indeed through our adoption into the family, we are all children of Abraham.  The God of Abraham is our God too and each one of us is one of those stars too numerous for Abraham to count.</p>

<p>Sometimes, it seems that we are uncomfortable with the notion that God made us through a gradual process that included apes in our family tree.  It is almost as though we would prefer dirt to apes.  Perhaps, in at least some cases, this is due to an inadequate appreciation for the fact that God loves, really loves, all of creation, not just us.  As special as we know we are, we can’t read Psalm 104, Genesis 1, Genesis 9 (where the covenant is not just with Noah but with all living creatures), or Job 38-41 without being reminded that <em>all</em> living creatures are God’s creation (see <a href="http://biologos.org/blog/creation-which-creation">here</a>).  The Neanderthals, the Denisovans, <em>Homo erectus</em>, and the australopithecines were God’s creation too!  Still, we modern humans have been singled out.  We’ve been <em>called</em> out.</p>

<p>True our family tree, as Pääbo shows here, is intriguing.  But let us never forget, that the most important thing about this tree is that God is the vine which exists at its core, and we are called to be the branches which bear fruit.  The fact that many of us have a small amount of Neanderthal DNA, some of us have Denisovan DNA, and others have neither is interesting, but it is really just a side issue for people of faith.  As a result of God’s visit to Abraham, followed eventually by God’s taking on flesh in the person of  Jesus of Nazareth, we can all know God as our heavenly Father.  We are children of God and as such, we are God’s representatives.  We are called to image God.  We are called to love God.  And we are called to love each other and to deeply respect all that he has made.</p>]]></content:encoded>
        <pubDate>Tue, 29 Nov 11 11:00:18 -0800</pubDate>
        <dc:creator>Darrel Falk, Mapes, Stephen</dc:creator>
        <!--<dc:date>Nov 29, 2011 11:00</dc:date>-->
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        <title>Series: Understanding Evolution</title>
        <link>http://biologos.org/blog/series/understanding&#45;evolution?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/series/understanding&#45;evolution?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>This blog series by Dennis Venema undertakes the task of clarifying numerous aspects of evolution that often become misconstrued by Christians. He first discusses the idea of speciation in a population over time, later applying it to the speciation process that occurred among hominids (human ancestors) which led to modern humans. He continues to support this idea by exploring so called “Mitochondrial Eve,”“Y Chromosome Adam” and other compositional clues of the human genome.</description>
        <content:encoded><![CDATA[<h3>Geographic isolation and reproductive barriers</h3>
<p>As we have seen, speciation (the events that lead to reproductive isolation between populations of organisms) can be a prolonged and complex process. Populations can become isolated geographically (e.g. through migration) and begin to accumulate genetic differences that may raise a barrier to reproduction between them. This barrier may only be a partial barrier, however. The stickleback populations we discussed previously are an example: the first event leading to speciation was physical separation when some marine fish colonized new freshwater habitats. Even after significant differences accumulated between the marine and freshwater forms, a second wave of colonization of fresh water by the marine form brought the two groups into contact again, leading to some genetic exchange even as the two groups remained largely distinct. At the point of the second colonization, whether one or two species is/are present is a point of discussion: the case can be made for either.  A scientist arguing for one species would point out that the two groups can still produce fertile offspring, whereas a colleague might argue for two based the distinct characteristics and ecological niches of the two populations, as well as the observation that the hybrids resulting from interbreeding are not as well adapted to either niche. The point is clear: speciation, as a slow process, is a <em>gradient</em>, and a clear line of demarcation cannot be drawn on a gradient. To return to our flip-book analogy, every adjacent page is only slightly different from the pages on either side. If we compare widely separated pages, the differences are clear. The point is that there is no single page in between them that we can identify as the point where the images “became different.”</p>

<p>While this discussion might seem a little academic and uninteresting (perhaps because one might discount such events as mere ‘microevolution’ of sticklebacks), we have recently learned that similar events shaped human speciation. As far as we can tell, sticklebacks are not aware of, nor concerned about, the theological implications of how they came to be, but we certainly are for our own species (and perhaps even for sticklebacks). What was once an area of interest mainly for specialists is about to become a topic of intense discussion among evangelicals: we have only recently learned that a portion of the lineage leading to modern humans interbred with other hominid species they encountered as they migrated out of Africa ~50,000 years ago. In order to explain what happened, let’s pick up the tale at an earlier point, around 450,000 years earlier.</p>

<h3>Out of Africa, twice over</h3>
<p>Somewhere between 500,000 and 300,000 years ago, the ancestors of the Neanderthals (<em>Homo neanderthalensis</em>) left Africa and migrated into the Middle East region, and from there on to Europe and parts of Asia. (Recall that human ancestors, at this point, are all still in Africa, and will stay put until around 50,000 years ago). Neanderthals persisted in the Middle East and Europe until ~30,000 years ago, meaning there was a time where the humans leaving Africa about 50,000 years ago could have interbred with them before they went extinct. This remained an open question until techniques improved to recover and sequence ancient DNA. It is now possible to obtain and sequence DNA from Neanderthal remains, and the complete genome sequence of Neanderthals was published in early 2010. The results were fascinating: DNA sequence comparisons between the two species indicates that modern, non-African humans have about 1-4% Neanderthal DNA in their genomes. This variation, however, is not present in sub-Saharan Africans, since they are descended from humans that did not leave Africa and and thereby, because of geographical separation, never had the opportunity to interbreed with Neanderthals. We also know that the group that left Africa went through a reduction in population size to a about  1200 individuals (a genetic bottleneck), whereas those that stayed behind maintained a larger  population size (about 6000) over the same period.</p>

<h3>New details</h3>
<p>In addition to this information, we have recently discovered a new hominid species from Asia, as Darrel Falk recently <a href="http://biologos.org/blog/a-geneticists-journey">highlighted</a> here on BioLogos. This species, named the “Denisovans” is known to us only from a few bone fragments and one molar, but - wonder of wonders in this age of paleogenomics - this was enough for us to determine its complete genome sequence. The results were, again, fascinating: the Denisovans are relative of Neanderthals that split off from them after their common ancestor left Africa. The Neanderthals went west to Europe, and the Denisovans colonized Asia (and evidence suggests they were quite widespread). Even more interesting is that comparing Denisovan and human DNA indicates that some humans (modern Melanesians) have about 5% Denisovan DNA in their genomes. This variation is not found in Europeans or Africans.</p>

<h3>Putting the story together</h3>
<p>Assembling all of this information reveals the following tale: the common ancestor of Neanderthals and Denisovans migrated from Africa to the Middle East between 500,000 and 300,000 years ago, leaving a population behind that would eventually become modern humans (at around 200,000 years ago). In the Middle East, the populations destined to become Neanderthals and Denisovans part ways, with their differences accumulating over the next several hundred thousand years to make them distinct species. When a population of modern humans leave Africa around 50,000 years ago, they encounter, and breed with, Neanderthals shortly after. This genetic exchange is small, since there are partial reproductive barriers in place, but a small fraction of Neanderthal DNA becomes established in this lineage. Groups from this population then part ways, with some migrating into Europe and others into Asia. This latter group then encounters the Denisovan hominids, interbreeds with them, and a fraction of Denisovan DNA takes hold as a result. This population goes on to colonize southeast Asia, Oceania and Australia, where we see this variation today in Melanesians.  Modern humans thus have different evolutionary trajectories: Melanesians have both Neanderthals and Denisovans in their lineage, Europeans have Neanderthals, and Africans have neither.</p>

<h3>New data, new questions</h3>
<p>Even as I stand amazed in what God has revealed to us about our origins through science,  I know that this new information will be difficult for some within the evangelical community to accept. Moreover, it is almost certain that some Christian groups, unfortunately, will misrepresent this data to their constituents (whether intentionally or not), and thus spread confusion that hinders the needed theological conversation. Still, I have reason for hope: God has seen it fit to reveal this information to us, and that suggests that He believes the evangelical Christian community is ready for this conversation to happen. As Darrel mentioned at the end of his <a href="http://biologos.org/blog/a-geneticists-journey">recent piece</a>, we at BioLogos want to assist our evangelical sisters and brothers in this conversation in any way we can, in full confidence that it can be done in an edifying way:</p>

<blockquote><p>BioLogos exists to help Christians think carefully about the ramifications of these new data in light of long-standing traditional ways of viewing human creation. We have some re-thinking to do, but it can be done and will be done within the context of a Christian faith that is fully orthodox and thoroughly evangelical. Any time we draw closer to truth, to God’s truth, we have nothing to fear. There is still much to learn, but we can look back at what we have learned with awe—absolute awe.</p></blockquote>]]></content:encoded>
        <pubDate>Fri, 28 Oct 11 08:25:23 -0700</pubDate>
        <dc:creator>Dennis Venema</dc:creator>
        <!--<dc:date>Oct 28, 2011 08:25</dc:date>-->
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        <title>Seeking a Signature</title>
        <link>http://biologos.org/essays/seeking&#45;a&#45;signature?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/essays/seeking&#45;a&#45;signature?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>In this article, Venema offers his review of Stephen Meyer&apos;s book Signature in the Cell.</description>
        <content:encoded><![CDATA[In this article, Venema offers his review of Stephen Meyer's book <em>Signature in the Cell</em>.]]></content:encoded>
        <pubDate>Wed, 19 Oct 11 15:14:01 -0700</pubDate>
        <dc:creator>Dennis Venema</dc:creator>
        <!--<dc:date>Oct 19, 2011 15:14</dc:date>-->
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        <title>Evolution and the Origin of Biological Information</title>
        <link>http://biologos.org/essays/evolution&#45;and&#45;the&#45;origin&#45;of&#45;biological&#45;information?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/essays/evolution&#45;and&#45;the&#45;origin&#45;of&#45;biological&#45;information?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>In this paper, Venema explores several examples in biology where random mutation and natural selection have indeed led to substantial increases in biological information. The question of how new specified information arises in DNA, far from being an “enigma”, is one of great interest to biologists.</description>
        <content:encoded><![CDATA[In this paper, Venema explores several examples in biology where random mutation and natural selection have indeed led to substantial increases in biological information. The question of how new specified information arises in DNA, far from being an “enigma”, is one of great interest to biologists. ]]></content:encoded>
        <pubDate>Wed, 19 Oct 11 14:48:05 -0700</pubDate>
        <dc:creator>Dennis Venema</dc:creator>
        <!--<dc:date>Oct 19, 2011 14:48</dc:date>-->
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        <title>From Intelligent Design to BioLogos</title>
        <link>http://biologos.org/essays/from&#45;intelligent&#45;design&#45;to&#45;biologos?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/essays/from&#45;intelligent&#45;design&#45;to&#45;biologos?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>In this paper, Venema tells the story of his transition from support of Intelligent Design to the view that God uses evolution as a creative mechanism.</description>
        <content:encoded><![CDATA[In this paper, Venema tells the story of his transition from support of Intelligent Design to the view that God uses evolution as a creative mechanism.]]></content:encoded>
        <pubDate>Wed, 19 Oct 11 14:17:25 -0700</pubDate>
        <dc:creator>Dennis Venema</dc:creator>
        <!--<dc:date>Oct 19, 2011 14:17</dc:date>-->
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        <title>C.S. Lewis on Evolution and Intelligent Design</title>
        <link>http://biologos.org/essays/c.s.&#45;lewis&#45;on&#45;evolution&#45;and&#45;intelligent&#45;design?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/essays/c.s.&#45;lewis&#45;on&#45;evolution&#45;and&#45;intelligent&#45;design?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>This article is a comprehensive study of the views of Christian author and apologist C. S. Lewis on the theory of evolution and the argument from intelligent design. It explains how he would distinguish expressly philosophical arguments for a Transcendent Mind from the current claims of the intelligent design (ID) movement to provide scientific evidence for such a reality.</description>
        <content:encoded><![CDATA[This article is a comprehensive study of the views of Christian author and apologist C. S. Lewis on the theory of evolution and the argument from intelligent design. It explains how he would distinguish expressly philosophical arguments for a Transcendent Mind from the current claims of the intelligent design (ID) movement to provide scientific evidence for such a reality.]]></content:encoded>
        <pubDate>Wed, 19 Oct 11 12:06:04 -0700</pubDate>
        <dc:creator>Michael L. Peterson</dc:creator>
        <!--<dc:date>Oct 19, 2011 12:06</dc:date>-->
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        <title>On Deciphering the Signature</title>
        <link>http://biologos.org/blog/on&#45;deciphering&#45;the&#45;signature?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</link>
        <guid>http://biologos.org/blog/on&#45;deciphering&#45;the&#45;signature?utm_source=RSS_Feed&amp;utm_medium=RSS&amp;utm_campaign=RSS_Syndication</guid>
        <description>The interesting thing about this is that Steve Meyer and I are probably really in almost the same exact position when it comes to our core beliefs. We differ primarily in one regard.</description>
        <content:encoded><![CDATA[<p>Steve Meyer has responded to Dennis Venema’s review<sup>1</sup> of his book <em>Signature in the Cell</em> in the September 2011 issue of <em>Perspectives on Science and the Christian Faith</em> (PSCF) (63:171-182).   Although, Dennis  has ably responded (63:183-192),  I would like to address one specific aspect of Meyer’s response, especially since it relates to the final paragraph of my initial <a href="http://biologos.org/blog/signature-in-the-cell">essay</a> regarding the book and  Dennis’s six part series on the BioLogos <a href="http://biologos.org/blog/evolution-and-the-origin-of-biological-information-part-6">website</a>.</p>

<p>BioLogos has dealt fairly extensively with what we thought was the basic premise of <em>Signature in the Cell</em>.   I had read the book carefully and I know Dennis did as well before we responded.  I sincerely thought that the heart of Meyer’s  argument is summarized in the following three quotes from the book:</p>

<blockquote><p>1. “So the discovery of the specified digital information in the DNA molecule provides strong grounds for inferring that intelligence played a role in the origin of DNA. <u>Indeed, whenever we find specified information and we know the causal story of how that information arose, we always find that it arose from an intelligent source</u>. It follows that the <u>best, most causally adequate explanation for the origin of the specified, digitally encoded information in DNA is that it too had an intelligent source</u>. Intelligent design best explains the DNA enigma” (p. 347, emphasis added).</p>

<p>2. “Since, as argued in Chapters 8 through 15, <u>intelligence is the only known cause of large amounts of specified information, the presence of such information in the cell points decisively back to the action of a designing intelligence</u>” (p. 382, emphasis added).</p>

<p>3. “Because we know intelligent agents can (and do) produce complex and functionally specified sequences of symbols and arrangements of matter, intelligent agency qualifies as an adequate causal explanation for the origin of this effect. <u>Since, in addition, materialistic theories have proven universally inadequate for explaining the origin of such information, intelligent design now stands as the only entity with the causal power known to produce this feature of living systems</u>.” (p. 386, emphasis added).</p></blockquote>

<p>So we at BioLogos have always thought that if mainstream science demonstrated an increase in “complex specified information” (CSI) without needing to invoke supernatural intervention, Meyer’s assertion that “intelligence is the only known source of such information in the cell” will have been refuted at the scientific level.  It sure seemed to me  that this is what he said in the above quotes.</p>

<p>With that in mind, we’ve put a great deal of effort into showing a number of cases in the lab and in nature where scientific data have provided very strong evidence for increased CSI which is entirely consistent with how we scientists would define “natural explanations.”  All this time, starting with my first essay almost two years ago,  we sincerely thought we were engaging Meyer’s book on Meyer’s  terms.</p>

<p>But now, in his <em>PSCF</em> article, Meyer states that arguments based on examples of increased CSI  don’t count if they occur after life began on Earth. </p>

<blockquote><p>“<em>Signature in the Cell</em> argues, first that no purely undirected physical or chemical process—whether those based upon chance, law-like necessity, or the combination of the two—has provided an adequate causal explanation for the ultimate origin of the functionally specified biological information.  <u>In making that claim, I specifically stipulate that I am  talking about undirected physical and chemical processes, not processes (such as random genetic mutation and natural selection) that commence only once life has begun</u>.  Clearly material processes that only commence once life has begun cannot be invoked to explain the origin of information necessary to produce life in the first place) (pp. 173-174, <em>Perspectives on Science and Christian Faith</em>, Sept. 2011, emphasis added).</p></blockquote>

<p>Since I had read the book very carefully, and have gone over it many times since, I was amazed that I could have missed this stipulation.  Again, he says: “<u>I specifically stipulate that I am [not] talking about … processes (such as random genetic mutation and natural selection) that commence only once life has begun</u>.”</p>

<p>Did he really specifically stipulate that?   Have we been barking up the wrong tree all this time?   While we knew the main focus of Meyer's book was the origin of life (not mechanisms of evolution), his argument clearly stated, we  thought, that no large increase in CSI (Complex Specified Information) had ever been demonstrated without the need to invoke intelligence.  Period. </p>

<p>I went back through my well-marked up copy of the book again, re-examining each section in which he wrote about increased CSI.    Despite my best efforts, I could not find the stipulation he mentions in the<en> PSCF</em> article. Still, thinking I had missed it, I spent $15 for an electronic version of the book—one that would allow me to identify every time the word “mutation,” or natural selection” appeared—anything that would help me find his stipulation.  I couldn’t find it.</p>

<p>Actually I thought Meyer was pretty clear and highly specific in his book.  Consider this scientific challenge on page 429:</p>

<blockquote><p>If, for example, someone successfully demonstrated that "large amounts of functionally specified information do arise from purely chemical and physical antecedents," then my design hypothesis, with its strong claim to be the best (clearly superior) explanation of such phenomena, would fail.</p></blockquote>

<p>Find a case where a large amount of CSI has accumulated without needing to invoke intelligence, and his argument, Meyer said, fails.  This is a strong statement, clearly worded, and there is no hint of Meyer’s stipulation that it doesn’t count if life has already begun.  In Dennis Venema's BioLogos blog series, he showed many cases where there were large increases in CSI (whole genome <a href="http://biologos.org/blog/evolution-and-the-origin-of-biological-information-part-5">duplication</a>, for example) without needing to invoke that supernatural intervention was necessary to create it.  Chromosomes, the cell division machinery, and nucleotides  <em><u>are</u></em> “purely chemical and physical antecedents.”  The information content in the genome, Venema showed, quadrupled early in vertebrate history through material processes that we know and understand well.  Did this not meet the scientific criteria that Meyer specifically called for?</p>

<p>I don’t know how misunderstandings like this happen.  I believe that Stephen Meyer, who I consider to be a friend and colleague, thinks the stipulation exists in his book and that he worded it clearly.   I assume he thinks it was implied in some overarching statement that I have not been able to find. I also think he believes he was clear.  Unfortunately, clear he was not.  I’ve looked thoroughly and I have not been able to find his stipulation.</p>

<p>In post after post, we have set out to demonstrate the scientific case we thought Meyer called for.  Then in the end, it sure seems to us, that the rules changed, even though Steve feels they were written in his book all the way along.</p>

<p>Still, let’s move on.  Let’s play by the new rule and let’s define it carefully.</p>

<p>So here’s the rule as I now understand it:  If large increases in CSI can be demonstrated without the need to invoke an external intelligence, “then [Meyer’s] design hypothesis with its strong claim to be the best (clearly superior) explanation of such phenomena, would fail.”</p>

<p>Having stated the rule, we have to make two exceptions (Meyer himself made Exception #1 clear in Chapter 13; Exception #2 is the new stipulation we've been discussing):</p>

<blockquote><p>Exception 1.  We can’t count large increases in CSI which develop as a result of computer programs because minds designthe program parameters.</p>

<p>Exception 2.  We can’t count large increases in CSI which develop in the history of life, because DNA was necessary to set those processes in motion.</p></blockquote>

<p>So what can we count?  Until he clarified the existence of Exception #2, I thought any general increases in CSI  would count.  However, it is now very hard for me to imagine any increase in information that would not be categorized within either Exception 1 or Exception 2<sup>2</sup>.  The only thing left that doesn’t fit into one of these two exceptions is the origin of life itself.  The point of the book, I thought, was to bring other examples of increased CSI  to bear on this very question.</p>

<p>With Meyer’s exceptions and the inability to bring general CSI increases  to bear on the origin of life question, we also no longer have “<strong>positive</strong><sup>3</sup> experiments [which] provide causal adequacy of intelligent design” (p. 335, emphasis added).</p>

<p>So what are we left with?  Are we not simply left with the question of whether the origin of life experiments show that information-rich molecules will arise in a test tube from chemicals off the shelf?   Dr. Meyer, I think, says no, for reasons that are no longer clear to me other than that he’s given up on the science.  I, on the other hand say, “Wait a while.  Let the science play itself out before a scientifically based decision is made.”  To be frank though, I am a little concerned that even if the right mix of materials is found to produce molecules that can spontaneously assemble in a manner that gives rise to complex specified information,  Dr. Meyer or those who follow him will  say, “Sorry, you can’t  count that because it took a mind to create the conditions and it took a mind to mix them together in a test tube.”   And with that we’ll have a new stipulation which most likely was in some manner implied in <em>Signature in the Cell</em> to begin with.<sup>4</sup></p>

<p>The interesting thing about this is that Steve Meyer and I are probably really in almost the same exact position when it comes to our core beliefs.   Obviously as  fellow Christians, we both believe that there is a Mind behind the process.  We both think that the history of life with its constant increase in complex specified information is a product of the activity of God.  We both stand amazed at the majesty of creation and our love for the Creator who is personally involved not only in our own individual lives but those of our families and faith communities as well.  We differ primarily in one regard.  Steve thinks he has shown through scientific analysis that this Mind we both believe in must have been present and supernaturally active in the creation of information.    I think the Mind (God) was present, but I can’t put the existence of God into a scientific experiment to  demonstrate God's activity.  Furthermore, unlike Steve, I have no pre-conceived ideas about whether God's,<em>super</em>natural activity was necessary for creation of information.  God, as I see it, may have chosen to create information bearing molecules <em>indirectly</em> through God’s natural activity in a manner that is analogous to the development of a baby or the growth of a tree from a seed.</p>

<p>In the end, our difference is simple, he thinks that the test tubes won’t ever deliver information rich molecules and I think it is too early to say.  He has declared the matter more or less settled on the basis of scientific analysis.   I consider the matter fully unsettled.  But the most important thing of all has been settled and on this we both agree.  This Mind we speak of is God’s Mind--God's Holy Spirit.  That Spirit not only fills all of creation, but more specifically  that Spirit fills us with his Presence and envelopes us in his love.  This is cause for celebration and, with "sandals off,"  we each bow our heads in humble worship.   Truly, we--all of us--are standing on holy ground.</p>

<h3>Notes</h3>
<p class="date">1. Perspectives in Science and Christian Faith 62:276<br />
2. Note to Steve:  Does not the human brain count within Exception #2?   After all, it arose in the history of life and its development depends upon DNA.   If so, you might need an exception to the exception.<br />
3. The term “positive” is used 21 times in the book.  It is clearly important to the author that the evidence for intelligence associated with the origin of DNA be viewed not as absence of contrary evidence, but rather a piece of convincingly <em>positive </em>evidence that hinges upon the fact that CSI in general, can’t be built without a mind.<br />
4. I’m really not trying to be facetious here.  I really do think that’s what would happen. I can almost draft the stipulation now.</p>
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        <pubDate>Sat, 10 Sep 11 15:00:11 -0700</pubDate>
        <dc:creator>Darrel Falk</dc:creator>
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