Rutherford, who is half Indian, was born in Ipswich in the East of England and attended Ipswich School.
He was admitted to the medical school at University College London, but transferred to a degree in evolutionary genetics, including a project under Steve Jones studying stalk-eyed flies. He completed a Ph.D. in genetics at UCL Institute of Child Health at Great Ormond Street Hospital in 2002. His PhD thesis subject was the role of a specific gene (CHX10) on eye development, with focus on the effect of mutations in this gene on the development of eye disorders.
Rutherford's other academic research was also on genetic causes of eye disorders, including the relation of retinoschisin to retinoschisis, the role of mutations of the gene CRX in retinal dystrophy, and the role of the gene CHX10 in microphthalmia in humans and mice.
Rutherford published a book on the topic of the creation of life. The United Kingdom printing has been called "two books in one", since Creation: The Origin of Life and Creation: The Future of Life are printed back-to-back so that one can read the book from either end. Among its topics, the first part of the book argues in support of the theory, first proposed by Thomas Gold, that life emerged not in primordial warm ponds, but in extremophile conditions in the deep ocean, while the second part discusses "synthetic biology" – the use of genetic modification to create new organisms. In the United States this book is published in a more conventional format with the title, Creation: How Science Is Reinventing Life Itself. He was also one of the authors whose works are included in the compilation The Atheist's Guide to Christmas.
Rutherford was the Podcast Editor and the audio-video editor for the journal Nature until 2013, responsible for all the publication's published audio, video, and podcasts. He also published audio interviews with notable personalities, including Paul Bettany on his role playing Charles Darwin in the movie Creation, and David Attenborough on his documentary Charles Darwin and the Tree of Life. He wrote editorials on other diverse topics ranging from the overlap of Art and Science to reviews of science-themed movies.
Rutherford is a frequent contributor to The Guardian, writing primarily on science topics. He wrote a blog series covering his thoughts and analysis while re-reading Darwin's On the Origin of Species, and has written articles supporting the teaching of evolution in schools, and criticizing the teaching of creationism as science.
He also writes on religion, notably a 10-part series on his experience participating in the Alpha course, and on New Age themes and alternative medicine, including a review critical of Rupert Sheldrake's A New Science of Life, and criticism of the lack of controls on advertising claims for homeopathy.
As a guest writer, he published an article in Wired on the possibility of using DNA for information storage.
Rutherford frequently appears on BBC science programmes, on both radio and television. Since 2013 he has been the host of the program Inside Science on BBC Radio 4. In 2012 he was featured on the series Horizon on BBC Two television in the documentary Playing God, which covered synthetic biology using the example of the "Spider Goat", a goat genetically modified to produce spider silk in its milk. In 2011 he presented, on BBC Four, The Gene Code, a two-part series on the implications of the decoding of the human genome, and his documentary, Science Betrayed, detailed the story of the discredited link between the MMR vaccine and Autism. In 2010, The Cell, his 3-part series on the discovery of cells and the development of cell biology, presented on BBC Four, was included in the Daily Telegraph's list of "10 classic science programmes". In 2006, Discovery Science produced the six-episode TV series, Men in White, in which three scientists, Rutherford, Basil Singer, and Jem Stansfield applied science to the solution of everyday problems.
He also appeared in BBC Radio 4's The Infinite Monkey Cage, with physicist Brian Cox, physician and science writer Ben Goldacre, author Simon Singh, musician Tim Minchin, and comedians Helen Arney and Robin Ince, and with The Infinite Monkey Cage Tour, the live show based on the programme. Rutherford is a frequent guest on the Little Atoms radio chat show, and he has also acted as a science advisor on programmes such as The Cat in the Hat Knows a Lot About That!, and the film World War Z. In 2011 he conceived and directed Space Shuttles United, a video and musical tribute to all the space shuttle missions.
Rutherford is a frequent speaker at scientific and academic events.
In 2013 he was an invited speaker at the QED conference in Manchester and at the 2013 North East Postgraduate Conference, and he delivered the 11th Douglas Adams Memorial Lecture at the Royal Geographical Society in London for Save the Rhino International. In 2012 he delivered the annual Darwin Day Lecture for the British Humanist Association.
Rutherford was a judge and host of the award ceremonies for the 2012 and 2013 Google Science Fairs. He is also a frequent guest at local science and sceptical events, such as Skeptics in the Pub.2014 Wellcome Book Prize shortlist for Creation: The Origin of Life
Because of his scientific, film, and musical experience, Rutherford has an Erdos-Bacon-Sabbath number of 15.