Chimpanzee Genome Published: Is There a Monkey in Your Genes?

Nature’s cover story September 1 is about the publication of the chimpanzee genome.  Evolutionists are digging through the data for evidence of human common ancestry.  Have they found it?  The results, as usual, are mixed: MSNBC News states the situation concisely: “Genome comparison reveals many similarities – and crucial differences.”  Here is the gist of seven articles and papers about the chimpanzee genome from Nature, with additional references to popular reports:

1. Introduction:  Chris Gunter and Ritu Dhand, “The Chimpanzee Genome,” Nature 437, 47 (1 September 2005) | doi: 10.1038/436047a.
   “Comparing the genetic code of humans and chimps will allow us to comb through each gene or regulatory region to find single changes that might have made a difference in evolution,” they say, but remind us that the oft-quoted 96%-similar-gene figure between chimps and humans must be seen in context: “At a conservative estimate we share about 88% of our genes with rodents and 60% with chickens.  Applying a more liberal definition of similarity, up to 80% of the sea-squirt’s genes are found in humans in some form.  So it’s no surprise that we are still asking, ‘What makes us human?’”
2. Overview:  Wen-Hsiung Li and Matthew A. Saunders, “The chimpanzee and us,” Nature 437, 50-51 (1 September 2005) | doi: 10.1038/437050a.
   After summarizing statistical similarities and differences in genes of chimps and humans, this article hastens to remind readers that a clear picture of evolution does not jump out of the mass of data.

   The question of what genetic changes make us human is far more complex.  Although the two genomes are very similar, there are about 35 million nucleotide differences, 5 million indels and many chromosomal rearrangements to take into account.  Most of these changes will have no significant biological effect, so identification of the genomic differences underlying such characteristics of ‘humanness’ as large cranial capacity, bipedalism and advanced brain development remains a daunting task. (Emphasis added in all quotes.)

3. Chimp Culture:  Andrew Whiten, “The second inheritance system of chimpanzees and humans,” Nature 437, 52-55 (1 September 2005) | doi: 10.1038/nature04023.
   A primate psychologist in Scotland, Andrew Whiten presents an overview of a study parallel the genome project, the attempt to understand chimpanzee culture and social inheritance.  He highlights a key difference:

   Ape culture may be particularly complex among non-human animals, yet it clearly falls far short of human culture.  An influential contemporary view is that the key difference lies in the human capacity for cumulative culture, whereby the achievements of successive generations have built on previous developments to create complex structures such as languages and technologies.  Chimpanzees have accumulated many traditions, but each remains sufficiently simple that there is little scope for it to have developed significant complexity compared to its original form.  Hints of cumulation exist, such as the refinement of using prop stones to stabilize stone anvils during nut-cracking, but these remain primitive and fleeting by human standards.  One possible explanation that has been offered for this human-chimpanzee difference lies in the social learning mechanisms available to each species, an issue that new genetic approaches based on the complete chimpanzee genome sequence may help to unravel.

   Actual studies of chimp social behavior are relatively recent.  Whatever the differences, Whiten seems to never doubt they are matters of degree, not kind.

4. Chimp Psychology:  Marc Hauser, “Our chimpanzee mind,” Nature 437, 60-63 (1 September 2005) | doi: 10.1038/nature03917.
   Marc Hauser (evolutionary psychologist, Harvard) is quick to justify his “preposterous” title, imagining the rage of Bishop Wilberforce at the suggestion humans have a developed chimpanzee mind.  He means to say that the entire animal kingdom shares mental relatedness:

   ….the bottom line at present is that for each psychological capacity explored, some other animal shares this ability with chimpanzees.  The reason why chimpanzees may be uniquely placed to enlighten human origins is due both to their phylogenetic proximity to humans as well as the extent to which they have accumulated a suite of psychological abilities in the service of solving social and ecological problems that were largely shared with those faced by our hominid hunter-gatherers.

   Based on observations of chimps, Hauser thinks humans share two things with chimpanzee mental powers: “folk mathematics” and “folk psychology.”  In his conclusion, he says, “At the genetic level, the publication of the chimpanzee genome will lead to increased capacity to pinpoint homologies.  However, we are woefully ignorant about how genes build brains, and how the electrical activity of the brain builds thoughts and emotions”, although the situation is more promising than it was five years ago, “owing to the convergence of three disciplines: comparative genomics, animal psychology and developmental neuropsychology.”  The gap between genomics and psychology is shrinking, he is thinking.

5. Brain Evolution:  Robert Sean Hill and Christopher A. Walsh, “Molecular insights into human brain evolution,” Nature 437, 64-67 (1 September 2005) | doi: 10.1038/nature04103.
   Noting that the human brain is twice the size of the chimp brain, Hill and Walsh attempt to explain the difference by evolutionary mechanisms.  The addition of whole new genes lacks support, but there appears to be evidence for changes in gene regulation or coding sequence.  Most studies focus on what goes wrong when a gene is mutated.  Anomalies in the FOXP2 gene, for instance, cause language disabilities in humans, and chimps and other animals exhibit sequence differences in that gene.  This, they feel, is evidence for positive selection toward language capability.  They admit, however, that “linkage of studies of gene function in humans with evolutionary analysis is just beginning,” and much work remains to be done.
6. Chimp Genome: The Chimpanzee Sequencing and Analysis Consortium, “Initial sequence of the chimpanzee genome and comparison with the human genome,” Nature 437, 69-87 (1 September 2005) | doi: 10.1038/nature04072.
   Here is the bulk of the genome report.  They start with Darwin:

   More than a century ago Darwin and Huxley posited that humans share recent common ancestors with the African great apes.  Modern molecular studies have spectacularly confirmed this prediction and have refined the relationships, showing that the common chimpanzee (Pan troglodytes) and bonobo (Pan paniscus or pygmy chimpanzee) are our closest living evolutionary relatives.  Chimpanzees are thus especially suited to teach us about ourselves, both in terms of their similarities and differences with human.  For example, Goodall’s pioneering studies on the common chimpanzee revealed startling behavioural similarities such as tool use and group aggression.  By contrast, other features are obviously specific to humans, including habitual bipedality, a greatly enlarged brain and complex language.  Important similarities and differences have also been noted for the incidence and severity of several major human diseases.

   The report highlights similarities but also large and surprising differences (summarized in #2, above).  Many of the differences occur in non-gene-coding regions.  Some sequence differences appear too great to have arisen by mutations since the time humans are said to have diverged from chimpanzees, considering that most mutations would be deleterious or, at best, neutral; in fact, it appears that mutation rates would have had to vary widely from gene to gene.  They indicate evidence for “selective sweeps” in the human lineage, in which all humans share mutations that have become “fixed”.  In short, “Our results confirm many earlier observations, but notably challenge some previous claims based on more limited data.”
       Their ending discussion asks the same question posed in the introduction, and reminds us that not all differences between species can be explained by genetic sequence differences:

   The hardest such question is: what makes us human?  The challenge lies in the fact that most evolutionary change is due to neutral drift.  Adaptive changes comprise only a small minority of the total genetic variation between two species.  As a result, the extent of phenotypic variation between organisms is not strictly related to the degree of sequence variation.  For example, gross phenotypic variation between human and chimpanzee is much greater than between the mouse species Mus musculus and Mus spretus, although the sequence difference in the two cases is similar.  On the other hand, dogs show considerable phenotypic variation despite having little overall sequence variation (0.15%).  Genomic comparison markedly narrows the search for the functionally important differences between species, but specific biological insights will be needed to sift the still-large list of candidates to separate adaptive changes from neutral background.

7. Comparison Study:  Ze Cheng et al., “A genome-wide comparison of recent chimpanzee and human segmental duplications,” Nature 437, 88-93 (1 September 2005) | doi: 10.1038/nature04000.
   A third of apparent segmental duplications in the human genome (defined by more than 94% sequence identity) are not found in the chimp genome.  This team compared the two genomes, and figured that this required a duplication rate of 4 to 5 million bases per million years since humans and chimps parted evolutionary ways.  Most of the changes, surprisingly, deal with chromosome structure.  No clear picture emerges for how or why these differences arose: “It is unknown whether slow rates of deletion, high rates of duplication or gene conversion are largely responsible for the evolutionary maintenance of these duplicates.”  A surprising conclusion is that “when compared to single-base-pair differences, which account for 1.2% genetic difference, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species.”

It’s interesting to notice how the news media differ on the emphasis given to these stories.  Some, like the BBC News focus on parts of the two genomes that are “99% identical,” while minimizing the “few differences.”  Others, like MSNBC, mention “many similarities – and crucial differences” up front.  One EurekAlert entry emphasizes right in the title the “big differences” in segmental duplications.  Another EurekAlert piece gives examples of the “dramatic genome alterations during primate evolution.”  National Geographic, though, shamelessly emphasized the similarities, practically venerating Darwin while putting humans in the chimp cage (08/29/2005) with this quote from a primate scientist at Emory University: “Darwin wasn’t just provocative in saying that we descend from the apes—he didn’t go far enough.  We are apes in every way, from our long arms and tailless bodies to our habits and temperament.”  And that, many would say, qualifies for Stupid Evolution Quote of the Week.

Data are gems.  The critique that follows is in no way a criticism of the valiant effort to sequence the chimp genome, the human genome, or any other genome.  Like dreams, speculations inhabit the sleep of data darkness.  Data make a good alarm clock to jolt visionaries out of their slumbers and remind them it’s time to go to work.
    You can see how the same data can motivate vastly different interpretations, depending on one’s world view.  The evolutionists are grasping at the similarities, while the creationists are emphasizing the differences.  One thing stands out of these reports: the data are so complex and convoluted, anyone can spin the story almost any way they want.  Yes, there are phenomenal similarities, but there are also profound differences.  There are so many differences, in fact, that it stretches credulity to believe that millions upon millions of base pair substitutions and segmental duplications could have occurred in the time assumed by evolutionists that humans and chimps went their separate ways (see Alan Grey’s blog thoughts on this).  Clearly there is no clear discernible evolutionary trail linking the two as evolutionists had hoped.  That being the case, keep in mind several key points before going data mining:

• Epigenetics:  Genes cannot be telling the whole story.  There’s a lot more going on to make us human than just DNA.  If two mice species that look similar have just as much genetic difference (4%) as humans and chimps, and if dogs, from great danes to chihuahuas, have far less genetic difference (0.15%), then clearly phenotypic difference (outward appearance) is not a linear function of genotypic distance.  Mining just the genome for explanations is an exercise in reductionism.
• Inconsequential Differences:  Why should genes differ so widely that are only concerned with chromosome structure?  Why should there be so many segmented duplication differences, and “neutral” differences?  Evolutionists wanted to find clear evidence of positive selection leading to upright posture, language and culture.  Although such studies are just beginning, they only have a paltry few to suggest so far, and those are ambiguous.  They admit that the picture looks far more complex than expected.
• Phenotypic Revolutions:  Humans exhibit several profound anatomical differences shared by no other primate: upright posture, ability to do long-distance running (11/18/2004), naked skin with thermoregulatory function, prolonged maturation, vocal apparatus suited for language, a very large brain relative to body size, and much more.  Could this much interrelated change occur by undirected, accidental mutations over a few “short” millions of years?  Consider just all the bodily adaptations for endurance running mentioned in the highly-informative and interesting 11/18/2004 story.  It would seem that mutations to multiple systems would have had to conspire together for the end result of producing a marathon runner – but where is the evidence for strong positive selection in the DNA?  This underscores the point that genomics cannot provide a full answer.
• Social Revolutions:  Despite the antics about chimpanzee culture and mind, there is really no comparison with humans.  Take a luxury cruise, enter a national research laboratory, go to the symphony, fly a supersonic jet, run an advanced software program, carry on a discussion about algebra, read a philosophy book – then watch chimps screech and groom and break nuts with a rock.  Impressed?  Can such profound differences be accounted for by segmented duplications, ALU repeats and base substitutions alone?

These points challenge the Darwinian story, but creationists have a challenge, too, to explain the similarities. Some evolutionists are convinced this is a crippling blow to creationism, and establishes evolution as the only explanation (despite their own challenges).  Really?  Let’s attempt a creationist explanation of the similarities between the human and chimpanzee genomes, because clearly the vast majority of the DNA is essentially identical.  First off, lest we overplay these similarities, remember that both human and chimp genomes share many commonalities with mice and even with sea squirts, worms and chickens.  The whole living world is built on the same genetic code and basic toolkit.  But why would a Creator make things similar, especially humans, who were supposedly created to be the stewards of the earth?
    A good first reply to a “why?” question is to ask: “why not?”  A wise king doesn’t send a complete foreigner as ambassador, but chooses one from among their own.  The Old Testament prophets, too, were men, not angels or aliens in spaceships.  Even the Lord God incarnate was born of a woman, laid in a manger as a human baby.  He grew up to live, eat, sleep, and speak as fully man though, according to Hebrews 1:1-2, he was an exact representation of God’s divine nature.  It is a non-sequitur to assume that humans, in order to serve a special God-given role in the world, must be completely genetically distinct from other living organisms in their embassy.
    Human beings, in the image of God, have to inhabit the same biosphere with chimps.  We are creatures as much as they are.  We breathe the same air, require the same bodily functions, eat much of the same food (e.g., bananas), have the same senses and share the same world.  Evolutionists often knock down a straw man by insisting that a divine Creator would have created every species separately and distinct from each other one.  Why so?  If a protozoan needs a peptidyl transferase enzyme, why should the human analog be utterly and completely different, designed de novo from scratch out of other materials?  Why would it not be a good design feature to provide redundancy of basic functions and parts, like subroutines and modules of a complex software suite, mixed and matched for a variety of environments and purposes?  Homology does not prove common ancestry without first assuming it does – a circular argument, as Jonathan Wells demonstrates in his book Icons of Evolution (see “Homology for Dummies,” 05/05/2004).  The nested hierarchy of animal forms, resulting in similarities and differences between groups at all levels, can be employed as an argument for design.  In his thought-provoking book The Biotic Message, Walter ReMine argues that there is enough commonality to falsify polytheism, but enough difference to falsify evolution.
    Look at the new data for a moment through Biblical creation glasses.  This is nearly impossible for Darwinists, and for those steeped in Darwinian education, it requires a painful removal of many ingrained assumptions.  In the beginning, God created a perfect world, filled with animals and plants made to reproduce after their kind.  This does not imply fixity of species, because God would have programmed in variability for robustness against perturbations (see 03/14/2005, 01/26/2005 and 09/22/2004 entries).  Nor does it predict a lack of similarity, because everything came from a common designer.  The creation of man by the hand of God from the dust of the ground does not imply utter and complete distinction from chimpanzees – because it’s not the raw materials that made Adam and Eve distinct, but the genetic program – the intelligent design – that organized the material into the human form.  This program evidently shared many if not most of the “subroutines” and modules God previously used in apes, mice and sea squirts.
    Then, God breathed into the man’s nostrils the breath of life, and man became a living soul.  This is fodder for theologians, not biologists, but most certainly included the spiritual, social, emotional, moral, lingual and intellectual faculties that so distinguish humans from all other animals: we alone were made in the image of God.  We are, as Wernher von Braun worded it, souls cast in animal bodies.  Our physical, material nature had much in common with the animal world, but the human pair alone walked and talked with God in the original “very good” creation.  But that’s not the whole story.
    The world was cursed when man sinned.  The fall is critical to the creation explanation.  Darwin lost his faith in Christianity primarily from two things: (1) Lyell’s persuasion that the earth was millions of years old, too old for Genesis, and (2) the problem of evil.  Natural theology was strong in the early 1800s.  Powerful as its arguments were, it had no answer to the suffering and evil we see in the world around us.  Darwinists gleefully knock down the straw god of the beneficent artificer deity by pointing to evil and suffering, when the Bible presents a God of wrath who judges sin and punishes disobedience – but then offers salvation to the rebels through his own grace.  Only the Biblical picture of creation, fall and redemption gives a logically self-consistent picture of why the world is both beautiful and ugly, both sublime and painful.  (The Darwinians solve the problem by denying the existence of evil – “whatever is, is right” – but our consciences know better.)  There’s still more to the creation explanation.
    A world-wide Flood happened.  The antediluvian world, cursed and decaying, endured possibly thousands of years of human violence and genetic decay.  Humans and many other animals could have varied substantially and, while living in the same times and places, experienced the same genetic pressures and changes.  Then, only 8 human representatives and 2 of each animal survived the Deluge aboard the Ark.  This would have resulted in genetic sweeps and bottlenecks and, again, subjected the animals to similar gene-altering pressures.  After the Flood, a vastly different environment opened up to the survivors.  They have undergone additional variation and genomic pressures ever since.  The varieties of finches, hummingbirds, dogs, cats and human “races” did not require millions of years, only thousands.  These changes are (1) conservative, to maintain the species, and (2) horizontal, not adding new genetic information but just shuffling what was already present (more or less melanin, more or less fur, longer or shorter beaks on birds, accentuated markings on insect wings, etc.).  Since dispersal was not uniform, the differences between created kinds (not species, but groups able to vary within limits) led to the biogeographical differences seen today, including those on the Galápagos Islands that so impressed Darwin.
    Whether you find this account plausible depends on many presuppositions you trust.  It does have two forensic advantages over the evolution just-so storytelling method, though: (1) sufficient causal agency (intelligence) for the spectacular complexity observed in the genomes (10/27/2004, 06/14/2005), and (2) an eyewitness testimony (by the Creator himself).  In challenging Darwinists, we cannot stress that first point enough (they ignore the second one, but cannot ignore the first).  Evolutionists play marbles with diamonds when playing their storytelling games with genes and DNA.  The human and chimp genomes, and all others, are incredibly, stupendously complex, such that we should humbly stand in awe of these evidences of intelligent design.  Remember the complexity of a nose (06/27/2005), or a tiny roundworm (06/25/2005) or fruit fly? (12/08/2003).  If even Richard Dawkins is stupefied by the wonders around him (09/12/2004), it would seem that building on a foundation of intelligent design at least, if not (better) trusting the Word of the designer, is the best starting point for interpreting any vast library of information.
    See Apologetics Press for an initial creationist response to announcements about the chimp genome by Dr. Brad Harrub, co-author of The Truth About Human Origins (2003, 526pp).