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Common Descent (common ancestry) in Human Evolution?

The homepage for Human Evolution? — Science & Theology contains this subsection about Common Descent in Human Evolution:

    What happened in the history of human origins?  Most scientists who carefully examine the evidence agree with the following general outline:  There was a branching of our evolutionary family tree (with apes evolving in one way, and our ancestors in another way) about 8 million years ago;  during the next 2 million years the distance between these branches increased, as their differing sets of genes (and the associated physical & mental characteristics) continued to diverge;  in our branch of the tree about 6 million years ago, humans and chimpanzees still had the same common ancestor;  then humans and chimps evolved in different directions, with humans developing bipedalism (walking on two feet instead of four), plus opposable thumbs, larger brains, speech capabilities, and other distinctly human characteristics.
    This theory of human evolution with common descent (or common ancestry) is accepted by most scientists, both Christian and non-Christian, although there is debate about some details [like the unresolved questions in the "note" below] in the timings and shape of our family tree.  But common descent is theologically controversial in the Christian community, and is disputed by some scientists who are Christians.  This fascinating topic is examined in many of the pages below [in the homepage for Human Origins, and (with more detail) in [the page you're now reading].

• note:   Three other controversial questions ask, "Which model of evolution-and-migration — Single Origin (Out of Africa) or Multiregional — is more accurate for modern humans?" and "What is the genetic relationship between Neanderthals and Humans?" and "If small hobbit-like creatures were a separate species (Homo floresiensis), where do they fit into the family tree of modern humans?"

The rest of this page is incomplete, but it has significant content now and will have more later.

Topic Areas:
Pseudogenes (Vitamin C,...)
Fused Chromosomes in Humans
and More
(Genomes of Humans & Chimps, Human Genetic Diversity, Mitochondrial Eve,...);
Hominid Fossils as Evidence for Common Ancestry

Pseudogenes (Vitamin C,...) and other Genetic Markers are
shared by Humans & Other Primates (Chimps, Apes, Monkeys)

Most scientists think that genetics provides the most persuasive evidence for a common ancestry of humans and other primates.  In The Language of God, Francis Collins (who is a Christian, former director of the Human Genome Project, and current director of the National Institute of Health, NIH) says, "The study of genomes leads inexorably to the conclusion that we humans share a common ancestor with other living things."  The following introductory overviews explain some of the evidence-and-logic leading to this conclusion:
Genomic Organization, Introns, Pseudogenes & Genetic Similarities in Humans & Chimps by Deborah Haarsma & Loren Haarsma, who describe the evidence-and-logic that leads most scientists to accept human common ancestry: "The amount of similarity in genomic organization among humans, chimps, and apes goes beyond what would be expected from common function alone and is generally seen as evidence for common ancestry."
Basic Principles of Pseudogenes
• Michael Behe, a prominent advocate of Intelligent Design, thinks that pseudogenes provide strong scientific support for the common descent of humans: "Both humans and chimps have a broken [non-functional] copy of a gene that in other mammals helps make vitamin C. ... It's hard to imagine how there could be stronger evidence for common ancestry of chimps and humans. ...  [additional] compelling evidence for the shared ancestry of humans and other primates comes from... a broken hemoglobin gene. ...  If a common ancestor first sustained the mutational mistakes and subsequently gave rise to those two modern species, that would very readily account for why both species have them now." (quoted from The Edge of Evolution, published in 2007, pages 71-72)
Why I (a creationist) accept Common Ancestry (not Evolution) by Stephen Jones, explains why — mainly due to his logical evaluation of strong scientific evidence, especially the pseudogene for Vitamin C — he changed his position from opposing human common ancestry to accepting it, although he still rejects a fully naturalistic biological evolution.
Common Descent by RationalWiki, lists Powerful Evidence for Common Descent — in Anatomical Homologies, and shared genetics (RNA Code, Endogenous Retroviral Insertions, Pseudogenes) plus Chromosome Fusion, similar Embryology, and Convergence.  They describe the logic of non-functional pseudogenes:  "While it is possible that two independently evolved genes (or two genes created using a Common Design) might look the same because they both do the same thing, after an error invalidates a gene [converting the previously functional gene into a non-functional pseudogene] the sharing of this same error between two species is extremely strong evidence showing that both species derived from the same source where the error first appeared."  Scientists apply this logic to Gulonolactone Oxidase, "an enzyme that catalyzes the reactions needed to produce ascorbic acid (Vitamin C). ... All extant guinea pigs share the same inactivation mutation [in this gene], while all extant simians share a different mutation.  The likelihood of two different species sharing the same inactivation mutation is statistically impossible;  a better explanation is that the sharing is actually due to common inheritance. The most recent common ancestor of all extant guinea pigs developed one mutation in the gene, while a different mutation developed in the most recent common ancestor in simians."
Genome Comparisons of Humans and Other Primates by Graeme Finlay, who (on pages 104-108) explains how "shared genetic markers establish the fact that we and other creatures share common ancestry."  According to Francis Collins, the human genome has "virtually inescapable" implications showing the common ancestry of humans and other primates.  This genetic evidence is consistent with several theological views about Divine Guidance of Natural Process, and (before and after the science on 104-108) Finlay argues for one of these views.
The Human Genome and Human Evolution (in audio and accompanying slides) by Dennis Venema, shows why he thinks human evolution is the simplest (most parsimonious) explanation for a wide range of evidence — homology, redundancy, synteny, pseudogeny — when we compare the human genome with the genomes of other species.  From his talk at the 2009 Meeting of the American Scientific Affiliation.
• Evidence for Human Evolution — this will be available later from, according to an I.O.U. (up for a year, as of May 2010) at

CLAIMS & RESPONSES (from the archive of Talk Origins)
Plagiarized Errors and Molecular Genetics by Edward Max, describes "another argument in the evolution-creation controversy." [his page contains links to all of the claim-and-response exchanges below]
Shared Errors in the DNA of Humans and Apes - David Plaisted (young-earth creationist)
      A Response to David Plaisted by Edward Max
Dr. Edward Max on Plagiarism & Shared Genetic Mistakes by afDave (creationist, on his blog, TruthMatters)
      A Response to AFDave by Edward Max
• Carl Wieland posted comments on the young-earth website of Answers In Genesis and then, after corresponding with Edward Max, removed them.
      A Response to Carl Wieland by Edward Max
Are pseudogenes ‘shared mistakes’ between primate genomes? by John Woodmorappe (young-earth creationist);  Edward Max says, "... Woodmorappe focuses on rare exceptions to the general principles outlined in my essay, while ignoring the vast amount of evidence supporting those principles. ... None of Woodmorappe's arguments make a convincing case against the conclusions of my essay.  Futhermore, despite his criticisms of almost every point I have made, Woodmorappe fails to offer an explicit alternative interpretation of the data I have discussed. ... I hope to respond to the Woodmorappe essay in more detail in a future rebuttal."

Adam and Eve, Vitamin C, and Pseudogenes by Daniel Criswell
Why the shared mutations in the Hominidae exon X GULO pseudogene are not evidence for common descent - by Royal Truman & Peter Borger

pages by proponents of INTELLIGENT DESIGN
• Uncommon Descent (in part of a page by 3 co-authors) responds to one of the Frequently Raised but Weak Arguments against Intelligent Design by explaining that Intelligent Design and Common Descent "are two separate theories about two different aspects of the problem, totally independent and totally compatible.  In other words, one can affirm Common Descent and Intelligent Design, Common Descent and Darwinian Evolution, or Intelligent Design and not Common Descent."   Above, Michael Behe (a prominent ID theorist) describes the strong genetic support for a common ancestry of humans and chimps.
A Primer on the Tree of Life by Casey Luskin (Intelligent Design) arguing against universal common descent, plus Design vs Descent

Two Ape-Chromosomes are fused into One Human-Chromosome
If the great apes (chimpanzees, gorillas, orangutans) have 48 chromosomes, but humans have 46 chromosomes, how could apes and humans have the same common ancestor?
Two Fused Ape-Chromosomes in Humans is explained in a brief Background Essay (3 k), and a 3-minute video by Ken Miller
How can two chromosomes fuse into one? (and survive natural selection) by Monica Rodriguez
Comparison of the Human and Great Ape Chromosomes as Evidence for Common Ancestry from the Evolution Evidence Page (Robert Williams);  this page is 44% main body, plus 56% references.
Human Chromosome 2 is a fusion of two ancestral chromosomes by Alec MacAndrew, and
      Human Chromosome 2 - a Creationist Response by Luke Plant (14% is blog, 86% is comments)
Ken Miller's Cold (Chromosomal) Fusion by Casey Luskin (Intelligent Design), and
     response to Luskin from The Questionable Authority
      criticism of Ken Miller by Jean Lightner (for young-earth Answers in Genesis)
      indirect reply from Ken Miller as part of the blog of Created and Rational

The following areas of study provide support for common ancestry, and examine specific aspects of it.

Genomes of Humans and Chimpanzees — Similarities & Differences
Comparing DNA of Humans & Chimps — an overview from the National Institute of Health in 2005
Comparisons of Human & Chimpanzee Genomes - abstracts from three review articles in 2008
A New View of Human-Chimpanzee Genome Differences from Howard Hughes Medical Institute in 2005
Genome Differences in Non-Coding Parts of Genome & Differences Between Human and Chimp Genomes from Science Daily, plus analysis of a more-distant cousin in a comparison of genomes for Humans & Rhesus Monkey

Chimp genome sequence very different from man by David DeWitt
      response from Talk Origins

Genetic Diversity (re: timing of species branching, and size of population bottlenecks)
Genetic Diversity Within Species — basic principles, by Deborah Haarsma & Loren Haarsma.

Mitochondrial Eve
This idea is based on analysis of mitochondrial DNA (mtDNA) that is inherited from a mother but not father:
Genetic Adam & Mitochondrial Eve by Deborah Haarsma & Loren Haarsma, explains "why scientists don't believe that all humans descended from these two individuals."
Mitochondrial Eve and Y-Chromosome Adam from Biologos (Francis Collins, Karl Giberson, Darrell Falk,...)
Have scientists traced humanity back to Eve? from Talk Origins (then click link for "Next Claim: CB621.1")
      Young-Earth Response from CreationWiki in their Encyclopedia of Creation Science
Human Migration & Mitochondrial Eve from CreationWiki (plus 3 bottom-of-page links in "See Also")
What, if anything, is a Mitochondrial Eve? by Krishna Kunchithapadam
Mitochondrial Eve by Wikipedia — principles, misconceptions, and relation to "Out of Africa" migration

Generalized Common Descent — for all of life, not just humans
Probably we'll have another page for this, and there will be some overlap between it and this page, with its focus on questions about the common descent of humans with other animals.  For a "general links-page" here are a few candidate-pages:
• Common Descent: It's All or Nothing (summary and full page) by Gert Korthof, is about a general "full common descent," not just common descent for humans.

Hominid Fossils and Common Descent
Scientists have discovered hundreds of human-like fossils.  When an age is assigned to each fossil, based on radiometric dating plus geological dating of the rock formation where the fossil is found, we observe that fossil anatomy and brain size gradually change from primitive hominids (5 million years ago) to anatomically modern humans (beginning around 100-200 thousand years ago) who moved into Europe and East Asia about 40,000 years ago.
Fossil Hominids: The Evidence for Human Evolution — a links-page by Jim Foley, for TalkOrigins
Human Origins and Intelligent Design by Casey Luskin (Intelligent Design) is mainly about hominid fossils

I.O.U. — There will be more about fossils (and genetics) later.