DNA enzyme far from ‘dumb machine’

Dr Santoso helped uncover a unique process in the DNA-replicating enzyme

Yusdi Santoso
Dr Yusdi Santoso with his son

With the discovery of a hidden computational component of the DNA-copying nano-machine, Dr Yusdi Santoso's experience in computer engineering and physics have proved useful in opening new biological pathways to solving genetic disorders.

During his Ph.D. study at Oxford University Yusdi studied DNA polymerase (illustrated at right), an enzyme best understood as a 'protein machine' that makes copies of DNA molecules for every new living cell.

In 2008 Yusdi and another lead researcher found that there is in fact an additional 'conformational transition' process that screens DNA bases (letters) for mistakes before the enzyme proof-reads and copies them.

Along with his studies at Oxford, Yusdi was surprised to discover a deep-seated emphasis on evolution and atheism at the core of the university's ethos.

This contrasted greatly with the views of his Catholic parents and the Islamic beliefs that surrounded him in his home country Indonesia. Here he had been taught Darwin's theory of evolution at school, but only as one view of origins, rather than as scientific fact.

"I didn't really think about evolution very much until going to Oxford," Yusdi explains.

He had specialized in bioinformatics in his computer engineering studies at Nanyang Technological University (NTU), but it was his deep interest in biophysics that earned him a scholarship from NTU for his Oxford Ph.D.

While at NTU, it was Yusdi's wife-to-be Jessica who brought a clearer understanding of life when she invited him to her Bible-believing church.

As he listened to the teachings of the Bible and Jessica's explanations of Christianity, he realized "I was religious, but going to church was [only] a cultural expectation. I came to see the Bible as God's revelation of Himself, which transcended any teaching of men. By reading it, I began to understand what God wants from us, and with this, God's peace came into my life."

With this understanding Yusdi remembers making the decision to surrender his life in obedience to Jesus Christ.

He later attended a church while at Oxford that affirmed the six days of Biblical creation, and curiously read the Biblical perspectives of 50 Ph.D. scientists in a book entitled In Six Days by John Ashton.

"I particularly appreciated the scientific depth of the arguments presented [in this book]," Yusdi says.

In Yusdi's view, the greatest difficulty with the theory of evolution is its improbability.

"The strength of evolution," he says, "is in the narration – it's a good story. However, when you look at the details it seems most unlikely."

As molecular biologist Francis Crick, one of the discoverers of the structure of DNA, admitted in his 1981 book Life Itself, "An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going."

Regarding the assumed evolutionary pathway of DNA polymerase, Yusdi comments, "None of my colleagues at Oxford can explain how a machine like this could have arisen through an evolutionary process."

The popular view among his colleagues, he explains, is that life began by RNA molecules forming self-reproducing systems – the 'RNA world hypothesis'.

However, he said, "nobody can show, in a way that's at all convincing, how a DNA polymerase machine made up of proteins could have evolved from RNA – and this would seem impossible to me.

"The intermediate forms would not function as well as the original forms, so they would be out-competed. The evolutionary explanations are just too simplistic and they ignore the details. To evolve a bicycle into a motorbike by adding an engine is a very big step, because engines are complex and need to be carefully designed. Similarly the differences between the different types of DNA polymerase would require much detailed design work at each stage."

Despite his interest in science, Yusdi has decided to pursue a career in business and software consulting because of rampant discrimination against Bible-affirming scientists.

DNA

He explains, "In many parts of the world, the scientific community discriminates against those who do not tow the party line on evolution. For example, it would have been very difficult for me to obtain funding for my work."

However, he is still glad he studied science because it enables him to "do something worthwhile."

"My discoveries were a step towards a greater understanding of DNA replication which could lead to the curing of some genetic disorders," he explains.

He says his research into DNA polymerase also showed him "just how complex life is".

"The Bible tells us that we are 'fearfully and wonderfully made' (Psalm 134: 19) and I saw this very clearly in much of my scientific work. All this speaks of an awesome Creator," he concludes.

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