Guangzhou Researcher Debunks 'Duon' Discovery of Stamatoyannopoulos

Dr. John Stamatoyannopoulos, who receives University of Washington Alumni Early Achievement Award for his ENCODE ‘discoveries’ surprised the world again in late 2013 by discovering second genetic code and publishing in a glam journal.

Not-at-all glam journal Molecular Biology and Evolution reports (emphasis ours) -

Reassessing the Duon Hypothesis of Protein Evolution

There are two distinct types of DNA sequences, namely coding sequences and regulatory sequences, in a genome. A recent study of the occupancy of transcription factors (TFs) in human cells suggested that protein-coding sequences also serve as the codes of TF occupancy, and proposed a duon hypothesis in which up to 15% of codons of human protein genes are constrained by the additional coding requirements that regulate gene expression. This hypothesis challenges our basic understanding on the human genome. We reanalyzed the data and found that the previous study was confounded by ascertainment bias related to base composition. Using an unbiased comparison in which G/C and A/T sites are considered separately, we reveal a similar level of conservation between TF-bound codons and TF-depleted codons, suggesting largely no extra purifying selection provided by the TF occupancy on the codons of human genes. Given the generally short binding motifs of TFs and the open chromatin structure during transcription, we argue that the occupancy of TFs on protein-coding sequences is mostly passive and evolutionarily neutral, with to-be-determined functions in the regulation of gene expression.

Observations -

1. ‘Not at all glam’ equals ‘respected’, when it comes to science and journals. Molecular Biology and Evolution was founded by Walter Fitch and Masatoshi Nei, two well-respected evolutionary biologists, and continues to publish serious papers.

2. The only ‘press release’ this debunking received is a mention in Dan Graur’s blog. Duon ‘discovery’ was covered by all major media including Times, Forbes and possibly even Playboy.

3. The debunkers work at a Chinese university in the state located right across the border from Hong Kong. Guangzhou is the capital of Guandong, which used to be one of the poorest provinces of China 25 years back. Then the economic liberalization made it the fastest growing manufacturing center, and now the place is focusing on building a knowledge economy. Shenzhen is the more well-known city of the province.

4. Professor Xionglei He, the senior author of the paper, did his PhD at University of Michigan with Jiangzhi Zhang, who himself was a PhD student of Masatoshi Nei. Masatoshi Nei is a colleague of Ken Weiss at Penn State University and supervised Dan Graur’s PhD thesis in the 80s. So, you can clearly see the pattern that USA/UK are sending away highly trained scientists to China, while feeding the clowns like Birney and Stamatoyannopoulos. Rinse and repeat for a few years and you get -

Homolog.us Reports from Asia Will Hong Kong be the Bioinformatics Capital of the World?

5. We bring back the obligatory video that is reserved for Dr. Stamatoyannopoulos.