What Questions about Evolution Have Really Been Answered?

Post Author: Bill Pratt

Microbiologist James Shapiro, in his book Evolution: A View from the 21st Century, makes some common sense statements about the controversy over evolution. Remember that Shapiro is no young earth creationist. He is firmly entrenched as an important figure in the world of evolutionary science. Here is what Shapiro says:

General discussions of evolution, especially in the context of the “Intelligent Design” controversy, suffer from an unfortunate conflation in the minds of the lay public (and also of scientists) of three distinct questions:

• The origin of life

• The evidentiary basis for an evolutionary process

• The nature of evolutionary change

Almost universally, the term Darwinism is assumed to be synonymous with a scientific approach that has provided satisfactory answers to all three questions. It is to be hoped that, by now, you realize that these three questions are individually complex and that two of them are quite far from having coherent scientific explanations.

We have little solid science on the origin of life, in large part because there is virtually no physical record, but also because we still have gaps in our understanding of what constitute the fundamental principles of life.

As to the actual nature of evolutionary change processes, you have seen in Parts II and III [of his book] that cytogenetic observations, laboratory experiments, and, above all, molecular evidence about genome sequence changes tell us that the simplifying assumptions made in the 19th and early 20th Centuries are plainly wrong. They fail to account for the variety of cellular and genomic events we now know to have occurred. It should be emphasized that many change events have been quite rapid and have involved the whole genome—notably, symbiosis, interspecific hybridization, and whole genome doubling.

Shapiro goes on to say that he does believe that the second question has been answered.

The one issue that has effectively been settled in a convincing way is the evidence for a process of evolutionary change over the past three billion years. The reason the answer to this question is so solid is that every new technological development in biological investigation—from the earliest days of paleontology through light microscopy and cytogenetics up to our current molecular sequence methodologies—has told the same story: living organisms, past and present, are related to each other, share evolutionary inventions, and have changed dramatically over the history of the Earth.

However, little evidence fits unequivocally with the theory that evolution occurs through the gradual accumulation of “numerous, successive, slight modifications.” On the contrary, clear evidence exists for abrupt events of specific kinds at all levels of genome organization. These sudden changes range from horizontal transfers and the movement of transposable elements through chromosome rearrangements to whole genome duplications and cell fusions.

I can agree with Shapiro, on this last question, to a point. I don’t think we are clear on how all organisms are related, but we certainly understand how some organisms are related. We can also see that life forms have changed dramatically over the history of the earth. I would also agree that the second question is immensely more settled than the first and third questions.

Unfortunately, as Shapiro remarks, scientists tend to conflate all three of these questions as if they are one and the same. I am thankful that a biologist of Shapiro’s stature  has attempted to clear up this confusion.

  • “On the contrary, clear evidence exists for abrupt events of specific kinds at all levels of genome organization”

    Does he go into more detail as to what he means by “abrupt”? Are we talking about punctuated equilibrium?

  • It is true enough that many proponents of Darwinism strongly tend to overstate their success.

    “I can agree with Shapiro, on this last question, to a point. I don’t think we are clear on how all organisms are related, but we certainly understand how some organisms are related. – See more at: http://www.toughquestionsanswered.org/2013/10/11/what-questions-about-evolution-have-really-been-answered/#sthash.ioYjIaKl.dpuf

    If you were to become convinced that humans and apes share a common ancestor, would you give up your conservative Evangelical faith? Would you cease believing in Jesus?

  • Huntx011

    You have you have chosen an interesting source. Some of his reservations about evolution are based on his reservations, some would say rejection, of natural selection as one of the key processes underlying evolution. By largely restricting his analysis of evolution to the role played by genetic mutation alone he takes much of the support of the second and third questions off the table.

    If the full range of evolutionary processes is included the second and third questions have been, at least, well answered.

    The question of the origin of life is an important one and it is not clear if we will ever be able to prove exactly how life arose. However, the question of the origin of life is technically separate from questions about evolution – once life arose, evolution seeks to understand how these earliest organisms have changed over time and the processes that have propelled these changes to result in the richly varied biosphere we see today

  • anon

    I certainly gave up my “evangelical faith” when confronted with the facts of biology. I know many people with similar stories – probably one reason that so many people are moving to no or unaffiliated religious views in the US: the ideas behind evangelicalism are untenable.

    It took me two decades to get past my passive atheism: when I started to look at early Christianity from the apostolic era and classical theism, I realized that I was right to abandon evangelicalism but had far overstated the case against Christianity proper. Eventually I became an Orthodox Christian.

    One thing to be aware of is that many (not all) intellectuals in the really classical/apostolic Christian traditions accept both evolution as fact and theory. It appears to be a systematic conflict for fundamentalist-evangelicals primarily.

  • What facts of biology drove you to give up your “evangelical faith”? I know the facts of biology pretty darn well and I have seen no conflict with my faith.

  • I believe he is referring to changes that can occur in a single generation, but you should read his book for yourself. Again, it is pretty technically dense.

  • If I became convinced that humans and apes shared a common ancestor, i would not give up my conservative evangelical faith. At this point, the only thing I see that is non-negotiable about human origins is that there was a historical Adam and Eve. Common ancestry would still allow for this possibility.

    I don’t really see how that kind of evidence will ever be forthcoming, though, because of the fog of pre-history. Statements about direct genealogical ancestry are highly speculative and impossible to prove.

    Theories about human ancestry have changed numerous times over the last 100 years. It is hardly settled science, and I don’t see how it ever will be. Even a hard-core atheist paleontologist like Donald Prothero denies that we can derive human ancestry from fossil evidence.

  • That’s interesting!

    I would be glad to interact with you on my blog http://lotharlorraine.wordpress.com

    or entirely privately if you prefer: lotharlorraine@gmail.com

    2013/10/18 Disqus

  • Andrew Ryan

    Science shows Adam and Eve did not live at the same time.

  • sean

    “I don’t really see how that kind of evidence will ever be forthcoming,
    though, because of the fog of pre-history. Statements about direct
    genealogical ancestry are highly speculative and impossible to prove. ”


  • Care to expand on this?

  • How can genetics tell us anything about two specific people who lived tens of thousands of years ago? Answer: it cannot. Genetics only tells us about large populations of animals, and the further we go back in time, the larger the error bars get for those calculations.

  • Andrew Ryan

    To be fair, it looks like I might be behind the times. Up until very recently the idea of them living at the same time was seen as very unlikely, but when I looked just now for some of the articles on this, some of the more recent ones allow that they MAY actually have lived at the same time!

    The way the science works is this: “To trace the lineage of men, one must follow the Y chromosome back, and where mutations occur – this is where a branch in the heritage is. With the lineage of women it is different. For maternal lineage you follow the mitochondrial DNA instead. In previous studies, science had dated the earliest woman (our Eve) back to 190,000-200,000 years ago, with our earliest man (Adam) at only 50,000-115,000 years ago”


    “New studies place one of the earliest maternal ancestors (our Eve) now at 99,000-148,000 years ago where one of the earliest men (our possible Adam)now living in a similar time period at – 125,000-156,000 years ago, giving them at least some time overlap.”

    Bit of a wacky site that comes from (check out the last paragraph!), but the author of the piece wasn’t the one doing the actual research!


  • Andrew Ryan

    By looking at modern humans’ mitochondrial DNA and the Y chromosome. See my above link.

  • anon

    Biblical literalism, combined with an insistence that evolution doesn’t occur at all (or if it does it is only “within species”). Creationism in general as a dogma. While I am sure there are some evangelicals that have more nuanced views, I have met very few of them. Actually none in the flesh.

    In any case, if you look at the ante-nicene record, you will find a Faith for which virtually all the evangelical distinctives are absent – my view is that my extended period of atheism wound up being a blessing and led me out of American sectarianism and into Christianity proper.

  • anon

    For the early Christians, the Genesis narrative was primarily read in Christological terms (this is true for the Pauline writings for example). Adam is a type of Christ and more generally the hebrew “a’dam” refers to humanity – the prototype of us all.

    To read this as a historical narrative is an exercise in missing the point, but it is certainly in line with American fundamentalist readings.

    If you look at the Fathers of the Church, the ancient Liturgies – read
    the Scriptures with the Church and as Christ instructed as a
    revelation of Him – most of the science vs religion wars become substantially irrelevant to a reading of Genesis. That is why so many Orthodox and Roman Catholic philosophers, theologians and scientists fail to see as important the alleged conflicts/problems that preoccupy American evangelicals.

  • What exactly do you think biblical literalists take literally that they should be taking metaphorically?

    With regard to evolution, I would say the vast majority of Christians agree that plants and animals have changed over the last 3.5 bilion years on earth. There is a subset of evangelicals, young earth creationists, who deny this is the case, but they are a minority voice.

    I attend a very conservative Southern Baptist church and I would say that more than half of our church members believe the earth is old. I myself accept an old earth and the fact that some kind of evolution has occurred, but I think most of the scientific evidence only bears on the mechanisms of evolution that are within a species or genera. The mechanisms that cause large-scale changes in body plans are not at all agreed upon or understood.

    If you have not met evangelicals with more nuanced views, then you haven’t looked very hard! In fact, most evangelical scholars that I know are not young earth creationists.

  • As you said in your above link, mitochondrial DNA and the Y chromosome get us to populations of humans that lived during a very large range of time. And the latest, ever-changing evidence is that the male and female progenitors lived during the same rough period of time. I really don’t see science being able to do much better than this. Hence my doubt that there will ever be a scientifically ironclad case that Adam and Eve were not historical figures.

  • anon

    I went to an evangelical school and attended evangelical churches through my youth and occasionally with my family in adulthood. As an adult I was even more attentive in some respects. I’ve done post-seminary course work with evangelical texts. My wife’s family includes a number of people involved in full time pastoral, mission and ministerial roles in evangelical settings. I see them and listen to their ideas often. I will guess there are few people reading this blog that have met a broader range of evangelicals.

    Young earthism is just an extreme form of error – albeit shockingly common. Virtually none of them accept the basic premises of modern biology. Frankly, its disconcerting.

    I think the standard for reading the Scriptures is a) within the Church and b) with Christ as the lens. The idea of “history” as we conceive it didn’t exist when the Old Testament was being compiled, redacted, edited and copied. I’m quite confident the idea of “science” as we understand it wasn’t either. To be honest, this kind of thing is just not something I am worried about – in the Church, we spend our time exegeting Christ first and foremost.

    The Genesis narrative is a great example of how broken the evangelical approach to Scripture is: in the ancient Church, the creation account points to Christ’s Pascha. When Christ states “It is finished” it is understood as the completion of God’s creative act. Great and Holy Saturday is the Blessed Sabbath when God rests from all his works – in the tomb.

    At some level I think evangelicals are Christians and it is not for me to judge anyone. But I do think much of what goes on in that world is confused and I generally leave these kind of conversations somewhat saddened. Fighting against biological science seems like a pointless waste of time and effort.

  • I think it is pretty harsh to say that “At some level I think evangelicals are Christians,” as if they are some sort of sub-Christian cult.

    I have many friends who are eastern orthodox and Roman Catholic who would never say something like that. it seems that your bitterness runs deep.

    The way I define a Christian can be found here:


    I would also suggest you read this blog post about different Christian views on evolution:


  • anon

    I don’t have any bitterness nor did I meant that to be anything but a complement.

    All variants of what Harold Bloom called the “American religion” – mormonism, evangelicalism, jehovah’s witnesses, pentecostalism, have their roots in Christianity and evangelicalism is the one that has the closest family resemblance to the Biblical and historical faith. It’s major tenets and its understanding of the gospel differ significantly from the Apostolic teaching but I don’t believe it is the case that sincere evangelicals who want to follow Christ are “not Christian”. I would be surprised if any Roman Catholics or Orthodox believed that evangelicals “weren’t Christian”, but who knows. Anyway, this is rat holing a bit – apologies if I stepped over a line.