Friday, 25 August 2017

How Molecular Clocks Are Refining Human Evolution's Timeline

How Molecular Clocks Are Refining Human Evolution's Timeline

By Bridget Alex and Priya Moorjani

This article was originally published at The Conversation and has been republished under Creative Commons.

DNA holds the story of our ancestry—how we’re related to the familiar faces at family reunions as well as more ancient affairs: how we’re related to our closest nonhuman relatives, chimpanzees; how Homo sapiens mated with Neanderthals; and how people migrated out of Africa, adapting to new environments and lifestyles along the way. And our DNA also holds clues about the timing of these key events in human evolution.

When scientists say that modern humans emerged in Africa about 200,000 years ago and began their global spread about 60,000 years ago, how do they come up with those dates? Traditionally researchers built timelines of human prehistory based on fossils and artifacts, which can be directly dated with methods such as radiocarbon dating and Potassium-argon dating. However, these methods require ancient remains to have certain elements or preservation conditions, and that is not always the case. Moreover, relevant fossils or artifacts have not been discovered for all milestones in human evolution.

Analyzing DNA from present-day and ancient genomes provides a complementary approach for dating evolutionary events. Because certain genetic changes occur at a steady rate per generation, they provide an estimate of the time elapsed. These changes accrue like the ticks on a stopwatch, providing a “molecular clock.” By comparing DNA sequences, geneticists can not only reconstruct relationships between different populations or species but also infer evolutionary history over deep timescales.

Molecular clocks are becoming more sophisticated, thanks to improved DNA sequencing, analytical tools, and a better understanding of the biological processes behind genetic changes. By applying these methods to the ever-growing database of DNA from diverse populations (both present-day and ancient), geneticists are helping to build a more refined timeline of human evolution.

Sunday, 23 July 2017

Nothing in Medicine Makes Sense Except in the Light of Evolution

The title of this post is a direct allusion to Theodosius Dobzhansky's famous 1973 article Nothing in Biology Makes Sense Except in the Light of Evolution [1] in which he outlined facts from areas such as ecology and molecular biology, and stated that "all these remarkable findings make sense in the light of evolution: they are nonsense otherwise." In a similar manner, aspects of human anatomy, developmental biology, physiology, and genetics which look bizarre, poorly designed, and otherwise defy rational description (not to mention difficult to memorise and store for quick recall) become perfectly understandable when understood in the light of an evolutionary origin for the human species. Examples include extra nipples along the milk line [2], the inverted retina [3], the multiple  pseudogenes, retrotransposons, and endogenous retroviral elements we share with primates [4], not to mention the presence of non-coding intronic DNA, which leads to mutations at intron-exon borders that "often disrupt premRNA splicing in ways that alter gene products and lead to countless genetic disabilities, including various cancers and other metabolic defects." [5]

I am not the first to allude to Dobzhansky in reflecting on the increasing importance evolution has for both understanding the basic clinical sciences on which medicine is based, and for the practice of medicine itself. Ajit Varki, Distinguished Professor of Medicine and Cellular & Molecular Medicine at the University of California,  San Diego wrote in 2012 a paper with the same title as this post where he states that the 'scientific aspects of medicine are rooted in understanding the biology of our species and those of other organisms that interact with us in health and disease. Thus, it is reasonable to paraphrase Dobzhansky, stating that, 'nothing in the biological aspects of medicine makes sense except in the light of evolution'" and proceeds to outline his experience in teaching evolution to medical students. [6] Given that there are more than 4.7 million hits in Google Scholar when searching for evolution and medicine, Varki's desire (and that of many other physician and scientists) to integrate evolutionary biology in the teaching of medicine is eminently sensible.

Monday, 17 July 2017

Endogenous Retroviruses and the Evidence for Common Descent


Common descent has not been an issue in the mainstream scientific community for over one hundred years. The case for common descent, which was considered solid in the early 20th century, has now become overwhelming based in no small part on the evidence from molecular genetics. The evidence is overwhelming when it comes to endogenous retroviral inclusions. ERVs are remnants of prior retroviral infections that have become integrated into the DNA of organisms. If they pass into the germline of an organism, its descendants can inherit them. Their presence is clear evidence of past infection in an ancestral organism.
Common descent would predict that the descendants of a species infected by a retrovirus, which subsequently became integrated into the germline, would inherit that retroviral inclusion at the same point in the DNA of the descendant organisms. We find evidence of this in organisms ranging from primates to sheep to crocodiles. It is difficult to imagine a more comprehensive demonstration of common descent, particularly when closely related species such as humans and chimpanzees share significant numbers of ERVs at the same point in their genome.
One analogy that should drive home this point is that of a mathematics teacher who receives ten exam papers that not only get the same questions wrong, but show the same errors in the working of the problem, and even share the same spelling errors at the same questions. Copying is the only reasonable conclusion, as it stretches credibility to assume that the ten students independently got the same questions wrong, made exactly the same mistakes in derivation and made the same spelling error. This is similar to what we see with closely related species with shared ERVs at exactly the same point in their genomes.
The following article should serve not only as an introduction to retrovirology for the layperson, but point out in detail the evidence for common descent from ERVs, examples where evolution has co-opted ERV components to perform new functions, and refutations of common evolution denialist arguments against the evidence for common descent from ERVs.
This review is large, but no apology is made for this. Shared ERV elements in related species is overwhelming evidence for common descent, which is why creationists, who are unable to refute this evidence raise objections which while superficially appealing to the layperson do not pass the critical scrutiny of the scientists whose professional life involves working with them. Dismissing the molecular evidence as “circumstantial evidence” is a merely an attempt to evade the burden of proof expected of anyone who opposes a consensus view. If one challenges a long-established position, one needs to understand what one us challenging intimately, and produce hard evidence for critical review by the scientific community. Otherwise, if that is not done, no one will take such attempted rebuttals seriously - and rightly so. No creationist refutation of this evidence from shared ERV elements exists - the consensus view that they support common descent remains unchallenged.

Thursday, 29 June 2017

Cancer, pain, and suffering before The Fall

Two things that YECs claim to be true, namely recent human creation and the absence of disease and suffering before Adam's sin are of course impossible to honestly defend given the overwhelming evidence against these assumptions. Further demonstration of this fact would not unreasonably be seen as redundant. However, given my medical background, a recent fossil discovery in South Africa of bone cancer in a 1.7 million year old hominin fossil caught my attention as a particularly powerful demonstration of facts of human antiquity and human suffering well before the earliest possible date for Adam in one powerful image.

Thursday, 4 May 2017

2017 BioLogos Conference Plenary Session Videos

When I shared notes from Heather Goodman's live blogging of the 2017 BioLogos Christ and Creation conference in Houston, Texas, I expressed my hope that a record of the conference would shortly be available. Thankfully, BioLogos have made available the plenary sessions so those unable to attend will be able to see leading scientists and Biblical scholars show how to understand Christianity in the light of the fact of evolution.

Friday, 14 April 2017

Galactic Archaeology - evidence of an ancient universe written in the stars

YECs are well aware that the evidence from the natural world overwhelmingly attests to an ancient universe, which is why they invest considerable effort in an attempt to explain away this data to preserve their hyperliteral reading of the creation narratives. Of course, this means advancing patently nonsensical ideas such as accelerated rates of radioactive decay and the creation of light in transit for objects more than 6000 light years away from the Earth. The former assertion is readily falsified when we realise that accelerated rates of radioactive decay would release enough heat to melt the crust of the earth, while the latter means what we see of the universe more than 6000 light years away is essentially a universe-sized special effect which may not have even happened. As Charles Kingsley put it when commenting negatively on Philip Gosse's book Omphalos in which he advanced creation with appearance of age as a means of explaining the evidence for an ancient natural history, "I cannot...believe that God has written on the rocks one enormous and superfluous lie for all mankind."

Sunday, 9 April 2017

More musings on monogenism (or why the human population was never as small as two people)

If every single human alive was exclusively descended from two people who lived around 6000 years ago, we would not expect the data from population genetics to show that the human population was never smaller than a few thousand individuals. Nor would we expect to see coalescent times for human genes in the hundreds of thousands of years. This is however exactly what we see, and it completely falsifies the anti-evolutionist position that the entire human race descended from six individuals approximately 4500 years ago and propagated away from Mt Ararat. What we see continues to show an African origin for the human race. As always, the problem here is simply one of choosing from an avalanche of papers that show this fact.