• Dr. Timothy Smith

How AI Can Unlock the Secrets of Human History


Photo Source: PxFuel



Fossil records suggest that humans or Homo sapiens, as a distinct species from other early human-like species, first appeared in Africa around 300,000 years ago. Further evidence indicates that about 90,000 years ago, some humans left Africa and began spreading across Europe, Asia, and Oceana, which includes Australia and the Pacific Islands. Fossils such as footprints, bones, and tools give clues to the early life of humans, but our DNA also contains living evidence of where we came from and who our ancestors were. With the development of artificial intelligence and genetic sequencing, researchers, can for the first time, use computers to analyze genetic information for clues other human-like species or “hominins” with whom early humans encountered, interacted, and interbred.


The humans leaving Africa ninety thousand years ago did not find the continents of Europe and Asia devoid of human-like species. They encountered other hominins such as the now-extinct Neanderthals in Europe and Asia and Denisovans in Asia. The Neanderthal and Denisovans represent ancient relatives of the modern human. Researchers believe that humans diverged from the Neanderthal around 706,000 years ago. (science.com) The Denisovans only recently came to light following the discovery and genetic sequencing of a finger bone fossil found in Denisova cave in Siberia, Russia, in 2010. (newscientist.com) Comparing the DNA sequences of modern humans and Neanderthals reveals that they are 99.5% identical to each other.


DNA provides the information or code needed for all living things to grow, reproduce, and survive in their environments. Changes in DNA called mutations alter the genetic code in ways that can lead to evolutionary events but not always. For example, some mutations can damage the DNA, resulting in cancer or death, but other mutations may improve the information stored in the DNA leading to an advantage over other species in their environment. Additionally, during reproduction, genetic information does some swapping or recombination between the DNA from the mother and the father—recombination results in children with traits from each parent as well as some new traits. You can think of recombination like having two nearly identical recipe books coming together and swapping some pages here and there. Some of the recipes will stay the same, but others can be different. This recombination process leads to genetic diversity and adaptability, and when it changes enough, a new species can evolve.


The modern human came out of Africa to populate the rest of the world. Following the fossil discovery of Neanderthals and Denisovans, researchers have pondered how humans interacted with these now-extinct hominins. Advances in the genetic sequencing of fossil bones now permit the human genome's direct comparison and extinct hominins. The results show that humans in Eurasia and Oceana had contact with the other hominins, interbred, and produced hybrid children. Genetic sequencing reveals that Neanderthals contributed 1-4% of the modern human genome, with people of European ancestry carrying around 1-2% Neanderthal DNA and East Asian DNA holding slightly more. Additionally, humans of Asia and Oceana have from 0.2-5% Denisovan DNA, with the highest found in Melanesia, including Papua New Guinea and Fiji. (medlineplus.gov)


Genetic information evolves through mutation and recombination, and scientists have found that such changes follow some predictable patterns over time. Through living in different environments, humans across the world have achieved a high level of genetic diversity. Based on the genetic diversity in modern humans and information from Neanderthal and Denisovan DNA, scientists can build models that predict when and for how long humans interbred with other hominins. Researchers from Estonia and Spain used the power of artificial intelligence to study the genetic history of humans and their extinct hominins. In their article in Nature Communications, Mayuk Mondal and others demonstrated that humans had multiple episodes throughout history when they blended or introgressed with the other hominins. (nature.com) Using statistical methods and a type of AI that discovers patterns called deep learning, the researchers developed a system to look at the human genome today and back-calculate how it could have gotten there. Their calculations support multiple times in history the Eurasian humans intermixed with the Neanderthal and Denisovans. Moreover, the data suggest another undiscovered hominin, different from the Neanderthal or Denisovans, that also contributed to human genetic diversity.


Today's modern humans emerged as a new species about three hundred thousand years ago, successfully expanded beyond Africa, and began to populate the rest of the world. In their expansion into Eurasia, humans encountered other human-like species such as the Neanderthal, who had been living there already for over forty thousand years. Even though scientists believe that humans separated genetically from them over 706,000 years ago, the evidence of Neanderthal DNA in Eurasian but not African humans indicates that the different species interbred. The recent discovery of another extinct hominin called the Denisovans led to the discovery that interbred with humans in Asia and Oceana. Research into the complex evolution of the human genome suggests that there was another hominin too that left a legacy in the human genome. Such a discovery opens up more questions about who we are and how our ancestors interacted with other hominins.




Dr. Smith’s career in scientific and information research spans the areas of bioinformatics, artificial intelligence, toxicology, and chemistry. He has published a number of peer-reviewed scientific papers. He has worked over the past seventeen years developing advanced analytics, machine learning, and knowledge management tools to enable research and support high level decision making. Tim completed his Ph.D. in Toxicology at Cornell University and a Bachelor of Science in chemistry from the University of Washington.



You can buy his book on Amazon in paperback and in kindle format here.