For a summary of my group’s latest research on UK broadleaved trees, and a discussion of the positive interaction between my science and Christianity, listen to this week’s episode of the ECO Chamber podcast, from the ENDS Report. My interview starts 30 minutes in.
Category: Genomics
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Science moves closer to Adam and Eve?
Yesterday, the journal Science published a study providing evidence that humans are descended from very small population. The authors detect a bottleneck lasting about 100,000 years with an average effective population size of about 1280. They date this to about 813,000 to 930,000 years ago, placing it before the divergence of Neandertals and Denisovans from modern humans. This coincides with a large gap in the hominin fossil record. They suggest it is the period in which the human chromosome number of 23 originated.
Such a bottleneck has not been detected before. Effective population sizes did not fall below 10,000 in previous genome analyses. The authors of the new study provide simulations to show that their software is better at detecting bottlenecks than older software.
A few years ago, I was involved in an extensive discussion with other Christian biologists on whether the (then current) estimates, which never dropped below 10,000, disproved the hypothesis that human descend from a single couple. Representatives of the organisation Biologos argued that they did. I argued that they did not, because the methods used were simply unable to detect short sharp bottlenecks. Eventually, a measure of consensus emerged. We agreed that genomics does not rule out a single couple as the sole progenitors of humans. The organisation Biologos adopted a new position on the issue: that Adam and Eve are only ruled out in the last 500,000 years but not before that.
The methods used in the study published in Science yesterday are similar to the older methods in that they also cannot detect short sharp bottlenecks. They rely on the assumption that the human population size was stable over time windows lasting many generations, in order to calculate an effective population size for that time window. Thus, a bottleneck of two is not ruled out by their methods. In some ways, the single-couple hypothesis becomes more plausible given the new evidence for a prolonged bottleneck with an average effective population size of about 1280.
The new study, and the discussion going on around it, are also helpful reminders that no studies estimating past effective population sizes should be taken as absolute truth. The authors begin their study by saying “ancient population size history of the genus Homo during the Pleistocene is still poorly known” and “a new approach is needed to improve the inference accuracy of population size history.” This was of course true in 2018, when I was previously discussing this issue with Christian biologist. But this caveat was not as clearly stated in the scientific literature at that time, which made it hard to persuade some layperson onlookers that caution was needed. It is an unfortunate feature of the scientific literature that publicly accessible critiques of methods are often only available once a new improved replacement is found.
Christians must be cautious about how they interact with studies exploring past human effective population sizes from genomes. Such methods are not able to either prove or disprove the hypothesis of Adam and Eve. But none-the-less it is fascinating to see the science appearing to move towards, and not away from, this hypothesis.
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Public lecture “Trees of Life: Do they exist?”
In gave my inaugural lecture as Professor of Evolutionary Genomics at Queen Mary University of London on 16th November 2022, the film of which can be viewed below.
Inaugural lectures are a chance to give a personal view on one’s research field, at a level that will be understood by the whole university and the general public.
My Vice-Principal asked me to be more personal than usual in this inaugural, speaking about my Christian faith as well as my research as a biologist.
I decided to do this by placing side-by-side “tree-of-life” concepts from the Bible and from The Origin of Species. By comparing and contrasting the evidence for these very different trees of life, I tried to help the audience understand how I think through things as both a biologist and a Christian.
Whether or not this worked, you can judge for yourself.
The lecture drew on articles I have published in Nature Ecology and Evolution, Nature Plants, and American Journal of Botany. I describe work by others in Nature and Nature Communications. The Origin of Species provided my starting point on Darwin’s tree of life simile. The works of Richard Dawkins, especially The Greatest Show on Earth and The God Delusion, provided helpful material in both sections of the lecture. On the Biblical tree of life, I used an argument by Peter J. Williams, (whose research recently featured in Nature) developed in his book Can We Trust the Gospels? I also refer to research by Elizabeth Barnes on inclusion in the biological sciences.
I have been a full professor at Queen Mary for over four years now, but there is a back-log of inaugural lectures, and many never happen at all. So it was a great privilege to be invited to give this.
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Natural v. Artificial Selection
Last week I published a short article in Molecular Ecology on evidence for natural selection. It has proven difficult to show natural selection occurring in real time in wild populations. New approaches may help, and these are being pioneered in studies of Soay sheep. While commenting on these new approaches, I make several general points about the evidential case for natural selection.
Perhaps the more broadly interesting of these is a critique of the argument by analogy to natural selection. I suggest that, although widely used, the analogy has severe limitations. You can read this critique from the second to the seventh paragraph of my article, which is available open access here.
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Video: Adam, Eve and human genetic diversity
This video summarises my understanding of the current genetic evidence on whether or not humans could have passed through a bottleneck of a single couple at some point in our history.
It is a talk I gave in May 2020 for a group of scientists from across Europe who identify as Christians. This audience came from a range of different disciplines, so I tried to present at a level understandable to any educated layperson.
Everything I say here is preliminary and tentative. I welcome feedback and comments on this talk – especially from experts on human population genomics – especially if I say anything that is wrong. My box diagrams are of course simplifications, but I hope they convey the major concepts with clarity.
Since I gave this talk, a major paper has been published in Nature presenting high coverage genome sequences for populations across Africa. The key analyses mentioned in my video based on the 1000 genomes project need to be re-done on this new, much better dataset. I won’t have time to do that any time soon, but if someone else did, I would be delighted.
Christian viewers should not misunderstood me to be taking or recommending any particular scientific or exegetical position on a harmonisation between current science and the Bible. This talk has a much narrower focus than that. Much research has still to be done.
If you are interested in following the links I mention in the video, my slides can be downloaded as a PDF here.
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Adam and Eve our ghostly ancestors?
That a single couple could be the ancestors of all living humans is widely seen as an area of conflict between genetics and the Abrahamic religions. Though little detailed attention has been paid to this idea in the scientific literature (see ‘Adam and Eve: a tested hypothesis?’), current models of the history of genomic variation in African populations tend to forbid a bottleneck of two in the human lineage within the last five hundred thousand years (see ‘Adam and Eve: lessons learned’). Thus, belief in a literal pair of ancestors for all humans would entail an older date for Adam and Eve than believers had expected, or a revised understanding of human molecular evolution.
In a recent book, The Genealogical Adam and Eve, S. Joshua Swamidass, an Associate Professor at Washington University in St Louis, Missouri, seeks to resolve the dilemma faced by believers. He makes a major contribution to the debate, taking both sides seriously. Swamidass is a Christian himself, and a well-established scientist in chemical bioinformatics and drug metabolism. He has clearly read widely and deeply in evolutionary genetics. He outlines his ideas with caution and many references to the literature. He deserves a hearing by anyone who is interested in a better relationship between science and religion.
Dr S. Joshua Swamidass Swamidass suggests that Adam and Eve were a real pair who are present in the genealogical ancestry – but not necessarily the genetic ancestry – of all present-day humans. He draws on simulations published in Nature in 2004 by Douglas Rohde, Steve Olson and Joseph Chang showing that just a few thousand years ago many individuals must have existed who are genealogical ancestors of all present-day humans. Swamidass makes the simple suggestion that one pair of the shared ancestors of all living humans was “Adam and Eve”.
He also points out that not all of our ancestors contribute to our genomes. Those that do not are known as “ghost” ancestors. Thus, Swamidass’s “Adam and Eve” will have contributed nothing to the genomes of some, many, or perhaps even all, living humans. “Adam and Eve” are entirely untraceable using genetic information. Thus, believers can say all humans are descended from Adam and Eve, and no genetic evidence can falsify or confirm that belief.
From a purely genetical perspective, it seems hard to contradict this thesis. The findings of Rohde et al (2004) have been scrutinized and broadly confirmed by several papers that Swamidass cites and explains in his book. The fact that not all of our ancestors contribute to our genomes a simple corollary of Mendelian genetics. Swamidass notes that this view of Adam and Eve is (superficially at least) compatible with a diverse range of possible beliefs about when they lived, where they lived, and whether or not divine intervention was involved in their origin.
Swamidass argues that if his hypothesis is true, then there is “no evidence for or against Adam and Eve, ancestors of us all” (p. 81). Thus, he has an essentially unfalsifiable hypothesis regarding Adam and Eve. By doing this, he reaches something close to Stephen Jay Gould’s non-overlapping magisteria (NOMA) between science and religion, in an area where they have often been seen as making competing claims about reality. He hopes that this may be a way of making peace.
A more detailed scenario
Having established this basic claim that “Adam and Eve” are an undetectable pair hidden among our many shared ancestors, Swamidass cautiously builds up a more detailed scenario for our history. He seeks to maximise its appeal to as many believers as possible by bringing the narrative as close as possible to a literal reading of the Bible, without increasing its exposure to scientific falsification.
This leads Swamidass to posit a surprising scenario in which Adam and Eve were created de novo a few thousand years ago, essentially as carbon copies of pre-existing humans who had evolved from apes. Their offspring then freely mingled with the existing human population, and “like a drop of water in the ocean, Adam and Eve’s genome quickly disappeared” (p. 81). Confusingly, Swamidass describes his created Adam and Eve as “monophyletic” with evolved human beings, but by this he means “of the same biological type” (p. 85), rather than the more usual definition of “sharing common ancestry”.
Given that he invokes a miracle, one might assume that Swamidass includes within it some kind of biological, mental or spiritual (“ghostly”, to use an archaism) advance unique to Adam and Eve. He explicitly eschews such novelties. This shields his scenario from the possibility of scientific falsification (though not, of course, from philosophical arguments that miracles are anti-science), but makes the proposed divine intervention rather pointless and arbitrary.
To avoid the possibility of testing, Swamidass seeks to have no objective criteria external to the Bible that define Adam and Eve as distinct from other humans. He rejects terms like “philosophical humans” to describe them and instead prefers the term “textual humans” – in other words, what the Bible means by humans is what the Bible means by humans. Thus, he allows believers to define humans in a manner that is entirely decoupled from science, and concomitantly, irrelevant to science.
There are some features of this proposal that are attractive. It seemingly diffuses an area of tension between science and faith by allowing belief in a literal Adam and Eve who lived a few thousand years ago, seemingly without any conflict with current science. There are no doubt many theological objections to Swamidass’s ideas (see, for example, here). In terms of how his ideas interact with science, I see two areas of weakness.
1) Dating uncertainty
The appeal of Swamidass’s proposal rests on our beliefs about the certainty and age of three dates: (A) the most recent date at which all humans could have passed through a bottle-neck of two, giving a pair of universal genetic ancestors; (B) the most recent date at which all humans could share a pair of genealogical ancestors; (C) the date of Adam and Eve that seems to be implied by the Bible.
Diagrammatic Timeline: Joshua Swamidass’s proposal is at its strongest if there cannot have been a genetic bottleneck of two in the human lineage within the last few hundred thousand years (A), and if the most recent genealogical ancestors of all living humans (B) existed at a time close to dates for Adam and Eve inferred from the Bible (C). All of these dates are open to question. Swamidass’s proposal is most compelling if we believe with a high degree of certainty that (B) and (C) are the same and much smaller than (A). Swamidass argues that this is the case. But what if (C) was in fact uncertain, as many Christians argue? Or (B) was much higher than suggested by Rhode et al (2004)? Or (A) turned out to be smaller than we had imagined due to the presence of previously unaccounted for factors shaping the molecular evolution of African populations (such as a ghost lineage, or complex past metapopulation structure, for example)? In these cases, his scenario would be less attractive to believers.
Because the possibility of a real Adam and Eve is not a topic that the majority of geneticists are interested in, the literature on (A) and (B) is extremely limited, and the subject has not been fully explored. There may well be plausible scenarios in which (B) could become too large for an easy fit with (C) or by which (A) and (B) become close enough to one another for Swamidass’s scenario to lose much of its appeal.
For example, a more recent model than Rhode et al (2004) for estimating (B) was published by Kelleher, Etheridge, Véber and Barton (2016). This gives a much older date for the common genealogical ancestors of humans. Swamidass dismisses this study as (p. 59) “less relevant” because it “unrealistically” restricts migration to only a few kilometres. However, there is clearly room for debate, and future studies that include genetic data in order better to parameterise migration in genealogical models may give estimates that force Swamidass into a scenario that works less well than his current one.
2) The ghost in the machine
Another area of potential difficulty for Swamidass’ scenario is the origin of human consciousness: the “ghost in the machine”. Swamidass’ main focus is on reconciling Biblical and scientific dates for Adam and Eve. But for many believers, this issue may be peripheral compared to the conviction that the story of Adam and Eve is related in some sense (regardless of whether it is historical or mythological) to the origin of the soul. Previous attempts to reconcile Adam and Eve with evolution have tended to avoid a physical miracle but posit a non-physical divine intervention conferring human consciousness.
It is not unreasonable for someone with a prior belief in God to think that the origin of human consciousness might involve more than just physical processes. The difficulties of explaining consciousness in terms of material processes and Darwinian evolution have been recently explored by the atheist philosopher Thomas Nagel in his book Mind and Cosmos. Christian philosopher Richard Swinburne argues something similar in his book The Evolution of the Soul. In chapter 4 of his book The God Delusion Richard Dawkins suggests that the origin of consciousness is “even more momentous, difficult and statistically improbable step than the origin of life”. It is not surprising therefore that theists would tend to see fingerprints of the divine in the origin of consciousness, and especially human consciousness. That Christian theists should associate the latter with Adam and Eve is understandable, as St Paul writes: “The first man Adam became a living soul” (1 Corinthians 15:45).
Superficially it might appear that such a spiritual intervention could easily be combined with Swamidass’s view, but as he works through his detailed scenario in the latter half of his book it becomes clear that such a combination would be highly problematic. If his genealogical Adam and Eve were the first to have human consciousness they would be objectively differentiated from evolved humans. This could open up his scenario to scientific testing and could also imply that some members of Homo sapiens were sub-human; both of these possibilities he wishes to avoid. Therefore, he concludes that, long before Adam and Eve, people had “minds and souls” and “science legitimately tells us the story of how they arose” (page 175). Believers may find this decoupling of Adam and Eve from the origin of the soul more questionable than an ancient date for an Adam and Eve who could be universal genetic ancestors of all humans with “minds and souls”.
Concluding thoughts
Given the surprisingly recent date at which shared genealogical ancestors arise in populations, it was well worth exploring how this might fit with the age-old belief in Adam and Eve. Joshua Swamidass does this in a highly detailed and truly inter-disciplinary manner. He shows respect for all sides, sincerely wanting to find a way forward that can defuse an area of conflict. It is to be hoped that this book will motivate the more sophisticated modelling of the human population history. It may also make believers ask questions about their hierarchy of beliefs about Adam and Eve. Is the most important thing about them the time in which they existed, or something that made them objectively unique? Are they genetic ghosts, or ghostly ancestors? The book has less to say to the atheist or agnostic reader, except perhaps to convince them that Christian views of Adam and Eve could be irrelevant to objective reality, and to persuade them that there are reputable scientists who take both science and religion seriously. No doubt Joshua Swamidass will be on this year’s shortlist for the Templeton Prize.
This blog was first posted at Nature Ecology & Evolution Community on 4 March 2020
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Lost elms of Kent
Mature elm trees in the English landscape are something I and many other have never seen. Dutch Elm Disease killed them all in the 1960s. Only the older generation can remember what we have lost. Browsing through some local photos from the 1930s this weekend, my eyes were opened to the size and grace of the elms that once existed. Here are some of those photos, from Capel, Kent. Beneath each one I show a picture of what the scenes look like today.
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How similar are human and chimpanzee genomes?
I recently participated in a discussion on the Biologos forum on the degree of similarity between the human and chimpanzee genomes. I was asked for my current view on this issue by Dennis Venema, who had found a old quote online from a newspaper article that I had written in 2008 on this issue. In 2008, in a couple of newspaper articles, I did some simple calculations based on the 2005 Chimpanzee genome paper. On the basis of these, I had come to the surprising conclusion that these data suggested that the human and chimpanzee genomes in their entirety could be only 70% identical. Dennis Venema asked me if this was still my view. You can read the whole discussion here. It is rather long, with lots of tangential contributions. If you want a quick summary of my perspective, here is my final closing statement (which I originally posted here):
“How similar are the human and chimpanzee genomes?” is a relatively straightforward scientific question. We are hindered by the still somewhat incomplete nature of both the human and the chimpanzee reference genome assemblies, but we can make this clear in our assessments and allow for the uncertainties that it raises.
The best way to assess the similarity of two genomes is to take complete genome assemblies of both species, that have been assembled independently, and align them together. The alignment process involves searching the contents of the two genomes against each other. (more…)
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Adam and Eve: lessons learned
This blog was first posted at Nature Ecology & Evolution Community on 14 April 2018
Preliminary conclusions about the possibility of a short, sharp human bottleneck
A few months ago I asked this community if modern genome science had tested an “Adam and Eve” hypothesis that the human lineage has passed through short, sharp bottleneck of two at some point in its history. While this question may sound bizarre to some, it is one that is often asked by those with a background in Abrahamic faiths. My post has therefore been taken up and discussed extensively on the Skeptical Zone and Biologos Forum over the past few months, as well as by various blogs.
The claim that genomic methods have been used to test and reject an “Adam and Eve” hypothesis was central to the recent book Adam and the Genome. My post, which critiqued the arguments made in that book, has received a broad level of explicit or tacit agreement in subsequent online discussions. More adequate ways of testing the hypothesis have been suggested, and preliminary results have been obtained.
Here I will share some of the lessons I have learned from these discussions and from further reading. These are somewhat tentative, and not all are based on published peer reviewed literature. In a short blog I cannot do not do full justice to all the contributions that have been made by various scientists within the online fora, so as far as possible I will try to provide direct links to the contributions of others.
Here are the lessons I have learned so far:
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Responding to Felsenstein, Schaffner and Harshman at The Skeptical Zone
Here is the text of a comment I posted at The Skeptical Zone in response to comments by Joe Felsenstein, Steve Schaffner and John Harshman on my Nature Ecology and Evolution blog on human bottlenecks:
Thank you all for interacting with my Nature Ecology and Evolution Community blog, and thanks to Vincent Torley for posting here. Vincent kindly sent me a personal email pointing out this thread to me and asking me to specifically interact with comments made by Steve Schaffner and Joe Felsenstein. I will also comment on John Harshman’s comments as he is making the strongest case against a bottleneck of two, which was not mentioned explicitly by Dennis Venema in his book chapter. (more…)
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Adam and Eve: a tested hypothesis?
Does genomic evidence make it scientifically impossible that the human lineage could have ever passed through a population bottleneck of just two individuals? This is a question I am asked semi-frequently by religious friends. With my current understanding of the genetic evidence, I can’t state categorically that it’s impossible. In this view, I find I differ from a recent book chapter on the topic. I’m writing this blog to run my thoughts past other biologists, and check I am not missing something. (more…)
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“Abundant bioactivity” of random DNA sequences?
This blog was written for the Nature Ecology and Evolution Community where it is posted here.
Probing the claims of a recent study
Readers of this blog will be aware of the recent Nature Ecology and Evolution paper entitled “Random sequences are an abundant source of bioactive RNAs or peptides”. Rafik Neme, the first author, posted an engaging Behind the Paper blog here.
On a quick look, I thought the study might be the beginnings of the solution to the mystery of orphan genes. (I posted about orphan genes here a few months ago.) The paper appears to demonstrate that an unexpectedly high percentage of random 150 base-pair DNA sequences are functional when expressed in E. coli. If true, this would suggest that de novo gene evolution could occur easily from junk DNA. (more…)
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The evolutionary mystery of orphan genes
Every newly sequenced genome contains genes with no traceable evolutionary descent – the ash genome was no exception
This week in Nature I and my co-authors published the ash tree genome. Within it we found 38,852 protein-coding genes. Of these one quarter (9,604) were unique to ash. On the basis of our research so far, I cannot suggest shared evolutionary ancestry for these genes with those in ten other plants we compared ash to: coffee, grape, loblolly pine, monkey flower, poplar, tomato, Amborella, Arabidopsis, barrel medic, and bladderwort. This is despite the fact that monkey flower and bladderwort are in the same taxonomic order (Lamiales) as ash. (more…)
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Ash tree genomics in response to ash dieback
The ash tree genome project published in Nature today began, for me, with a lunchtime conversation with Andrew Leitch in the SCR bar at Queen Mary University of London in early November 2012. Ash dieback had been found in natural woodland in England for in late October. Such was the seriousness of the likely environmental impact of the disease that the Prime Minister had convened the emergency COBRA committee to discuss the government’s response. (more…)
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Telegraph article: British woodlands need diversity from around the world
This article was written for The Daily Telegraph and is published online here.
Foreign tree species are needed to help preserve Britain’s woodlands from disease, argues Dr Richard Buggs.
Trees in Britain do not have enough genetic diversity to cope with a global influx of pathogens.
As global trade introduces new pests and diseases, we face ecological and economic disaster as one after another tree species succumb to imported diseases. (more…)