Educating an Intelligent Design Creationist: Pervasive Transcription

I'm replying to a post by andyjones (More and more) Function, the evolution-free gospel of ENCODE. This was the fourth post in a series and I'm working my way through five issues that Intelligentt Design Creationists need to understand.

Educating an Intelligent Design Creationist: Introduction

Pervasive Transcription

The idea that most of the human genome is transcribed dates back to the early 1970s. Workers isolated RNA from various sources and hybridized it to DNA (Rot analysis). They measured the amount of DNA that was complementary to this RNA and discovered two things:

1. Using highly purified messenger RNA (mRNA) the amount of DNA suggested that the genome had between 15,000 and 20,000 genes.
2. Using heterogeneous nuclear RNA (hnRNA) a much larger percentage of the genome was covered. This included the repetitive DNA fraction that we now know consist mostly of defective transposons.

These discoveries lead to intensive investigation of these non-coding DNA sequences and contributed to the discovery of introns and splicing. That accounted for a great deal of the mass of nuclear RNA that never made it into mature mRNA. Still, there was lots of RNA being synthesized that couldn't be accounted for. The data showed that this fraction was very complex (lot's of sequences) but that individual RNAs were not very abundant.

The main references quoted these days are Milcarek et al. (1974), Hugh et al. (1975), Holland et al. (1980), and Varley et al. (1980) but there were dozens of papers. The work was summarized in great detail in the first edition of Gene Expression by Benjamin Lewin. Most molecular biologists knew of these results.

Andyjones commented on this finding ...

... some people have known since the mid 70s that most DNA is transcribed into RNA, but sat on it because apparently they didn’t realise its significance ...

Now, to my mind the first point only underlines my original point about the cult of Darwinism (word defined according to the old-school, traditional and popular usage); that it can get in the way of the practice and dissemination of science, a dysteleological worldview which stagnates interest in trying to find function, something which has only recently been picked up again by ENCODE, and only then, Larry claims, because they don’t understand evolution.

It's true that most scientists were puzzled by this pervasive transcription but gradually they learned that a lot of it was introns and the rest was probably spurious transcription or junk RNA. They reached this conclusion because most of the transcripts were of very low abundance and were turned over (degraded) very rapidly.

I don't know where andyjones got the idea that scientist "sat on" the data. He seems to have made it up.

Andyjones says ....

The idea that (almost) everything gets transcribed sometimes but only by accident, is an explanation, but it is one that requires no investigation, and inspires no investigation. It is much more convincing to an already-convinced Darwinist than to anyone else. A Darwinist says, nah, there’s nothing here to be understood, stop looking. But to others, that would be a presumptuous ‘evolution-of-the-gaps’. Anyone who has reason to suspect teleology (meaning: engineering intent) is going to look just that little bit harder, and is going to see the importance of pervasive transcription just that little bit earlier.

Many scientists wanted to find a function for all of this RNA but they failed to do so. Meanwhile, other studies showed that much of our genome was probably junk DNA. This is about the time that scientists discovered pseudogenes (early 1980s) and discovered that half our genome was transposon pseudogenes (defective transposons). Experiments showed that a lot of pervasive transcription came from those regions of the genome suggesting that the transcripts were not functional.

It's simply not true to claim that the junk RNA explanation was not based on solid evidence and it's not true to claim that it stifled investigation. It's also ironic that andyjones thinks that the "Darwinists" would give up looking for an explanation when they (Darwinists) were doing the exact opposite! It's those who prefer natural selection (Darwinists) who most wanted there to be a function for this RNA. They still do.

I wonder if we should not be a little angry that this was not popularised in the 70s! My fiancee, who has a recent biology degree, is now annoyed that this fact was kept from her … The Darwinian establishment seem to have buried it, exactly the kind of thing I wanted to warn against.

The existence of hnRNA was widely known in the 1970s. It was discussed in graduate courses when I was a student. By the late 1970s we were teaching this material to undergraduates.

By 1990, the general consensus was that most of the rapidly degraded nuclear transcripts were probably introns although it was still an open question. That's the view that Benjamin Lewin popularized in his textbook Genes IV in 1990. The next decade showed that this was wrong because hundreds and hundreds of ESTs (expressed sequence tags) were being sequenced and most of them could not be assigned to a known gene.

---

Holland, C. A., Mayrand, S. & Pederson, T. (1980) Sequence complexity of nuclear and messenger RNA in HeLa cells. J. Mol. Biol. 138:755–778.

Hough, B. R., Smith, M. J., Britten, R. J. & Davidson, E. H. (1975) Sequence complexity of heterogeneous nuclear RNA in sea urchin embryos. Cell 5:291–299.

Milcarek, C., Price, R. & Penman, S. (1974) The metabolism of a poly(A) minus mRNA fraction in HeLa cells. Cell 3:1–10.

Varley, J. M., Macgregor, H. C. & Erba, H. P. (1980) Satellite DNA is transcribed on lampbrush chromosomes. Nature 283:686–688.