Friday, October 23, 2015

Nature publishes a misleading history of the discovery of DNA repair

The history of DNA repair is well-known. Here's a quote from "Early days of DNA repair: discovery of nucleotide excision repair and homology-dependent recombinational repair" by W.D. Rupp in 2013 (Rupp, 2013).
This article describes events related to the first papers published in the 1960s describing nucleotide excision repair (NER) and homology-dependent recombinational repair.
Here's are the relevant papers.
Setlow, R.B., and Carrier, W.L. (1964) The disappearance of thymine dimers from DNA: An error-correcting mechanism. Proc. Natl. Acad. Sci. (USA) 51:226–231. [Full Text]

Boyce, R.P., Howard-Flanders, P. (1964) Release of ultraviolet light-induced thymine dimers from DNA in E. coli K-12. Proc. Natl. Acad. Sci. (USA) 51:293–300. [Full Text]

Pettijohn, D, and Hanawalt, P. (1964) Evidence for repair-replication of ultraviolet damaged DNA in bacteria. J. Mol. Biol. 9:395–410. [PubMed]
Setlow, Howard-Flanders, Hanawalt and others are widely recognized as the scientists who discovered DNA repair in the early 1960s.

The recent Nobel Prize for DNA repair went to Tomas Lindahl, Paul Modrich, and Aziz Sancar and the citation implied that Tomas Lindahl discovered DNA repair.
In the early 1970s, scientists believed that DNA was an extremely stable molecule, but Tomas Lindahl demonstrated that DNA decays at a rate that ought to have made the development of life on Earth impossible. This insight led him to discover a molecular machinery, base excision repair, which constantly counteracts the collapse of our DNA. [Nobel Prize, Chemistry 2015]
It's simply not true to say that the rate of spontaneous decay of DNA makes the development of life on Earth impossible. If that were true, then DNA repair enzymes would have had to arise at the same time as DNA and that didn't happen. The Intelligent Design Creationists are making a big splash over statements like that because, if true, it strongly suggests intelligent design. It may be true to say that once large genomes evolved, DNA repair and accurate DNA replication became selectively advantageous but that's not what the Nobel citation says.

It's certainly not true that Tomas Lindahl was the first one to realize that DNA repair is important.

Let's look at how the leading science journal in the world covered this story in the issue of Oct. 7, 2015 [DNA repair sleuths win chemistry Nobel]. We expect Nature to do a much better job of getting the history right.
The 2015 Nobel Prize in Chemistry has been awarded to three researchers for their work on DNA repair.

Tomas Lindahl, Paul Modrich and Aziz Sancar “mapped, at a molecular level, how cells repair damaged DNA and safeguard the genetic information”, says the Royal Swedish Academy of Sciences in Stockholm, which awards the prize.

DNA is not a stable molecule, but slowly decays over time. For life to exist, as Lindahl first realised while working at the Karolinska Institute in Stockholm in the 1970s, there must be repair mechanisms that fight back against this process.
Tomas Lindahl was still a student when the first papers on DNA repair were published. By the 1970s it had already been known for a decade that DNA gets damaged over time and two mechanisms of repair had already bee reported in the scientific literature. This statement in Nature is very misleading.
Numerous scientists have since chronicled the many ways in which damaged DNA is patched up, says Stephen West, who works on DNA repair at the Francis Crick Institute in London, where Lindahl is now an emeritus group leader. “The DNA repair field is a large field,” he says. “Many of us thought a Nobel would not go to this field because there are so many people with a claim to the prize."

But the three repair mechanisms recognized with the Nobel prize "are probably the three most important and best understood mechanisms," West says, adding that the awards are "fantastically well deserved".
It's true that there are many scientists who have contributed to our understanding of DNA repair and it's true that there are many different mechanisms. The prize was given for discovering DNA repair mechanisms that are different from those published in the 1960s.

Fair enough. I might have made a different decision but that's not the point. The point is that having picked latecomers to the field, you still have to get the history correct. This article in Nature would have been the perfect place to give credit to those early workers who discovered DNA repair. Steve West could have made sure that the Nature reporter got it right.
Lindahl, who is regarded as one of the founders of the field, chronicled a process dubbed base excision repair, in which specific enzymes recognize, cut out, and patch up bases in the DNA molecule. Before his work, "I don’t think anybody really considered the idea that DNA requires active engagement by a set of housekeeping processes to keep it in a stable state," says Keith Caldecott, who studies DNA repair at the University of Sussex, UK, and did postdoctoral work with Lindahl.
... those ignorant of history are not condemned to repeat it; they are merely destined to be confused.

Stephen Jay Gould
Ontogeny and Phylogeny (1977)
I can't imagine what Keith Cladecott was thinking when he said that. Clearly he is wrong because lots of people knew about DNA repair enzymes before Lindahl. I started to work on DNA binding proteins in 1968 and I knew about repair enzymes back then. Lindahl did a lot of his graduate work with Jacques Fresco in the lab right above where I was working (he got his Ph.D. in 1967). I suspect he knew about the work of Setlow, Hanawalt, Howard-Flanders etc. because he hung out with the same people I did. (I don't recall if we overlapped.)

Surely an active worker in the field like Keith Caldecott knows the history? Maybe he thinks that the 1960s mechanisms don't count as "housekeeping"? (They do.)

I'm sorry if I come across and being an old fuddy-duddy about these things but it's one thing to ignore the past and quite another to misrepresent it. You can ignore it if you want but you don't have to lie about what really happened.

If you are ever tempted to write about the history of a field you're not familiar with, remember the famous saying by the Roman historian Pliny the Elder, "Google is your friend."1


1. The internet was down in Pompeii on August the 25th, AD 79. Otherwise Pliny the Elder would have known about toxic fumes and not died during the eruption of Vesuvius.

Rupp, W.D. (2103) Early days of DNA repair: discovery of nucleotide excision repair and homology-dependent recombinational repair. Yale J Biol Med. Dec 13;86(4):499-505. [Full Text]

12 comments :

  1. "It's simply not true to say that the rate of spontaneous decay of DNA makes the development of life on Earth impossible. If that were true, then DNA repair enzymes would have had to arise at the same time as DNA and that didn't happen."

    Didn't happen??? I think I will wait for your proof for this claim before I make any other comments about your post.

    ReplyDelete
    Replies
    1. it seems obvious to me you saying you don't have any proof to substantiate your claim.

      I recommend a text search for "Here's are the relevant papers." in the main post, and read the listed papers....

      Delete
    2. Imagine that! An IDiot who lies!

      Who would've guessed?

      Delete
    3. It seems quite strange that JoJo and Jack Jones are trying so hard to prove our stereotype of creations/IDiots to be correct. It also makes one wonder by Jonathan McLatchie et al. are not here, defending the "serious" ID positions from such outlandish behaviours.

      Delete
    4. We need to encourage people like Jonathan McLatchie and Vincent Torley as much as possible. ID will never be taken seriously as science as long as it embraces kooks and Young Earth Creationists. I think they know this.

      Torley is making a valliant attempt to educate IDiots about evolution over on Uncommon Descent where he is being accused of becoming a Darwinist. I admire him for doing that. I wish that people like Michael Behe and Michael Dentin would step up to the plate and purge the movement of all those IDiots who reject common descent.

      It is ridiculous that the entire ID movement claims to be scientific when many of its prominent voices think the Universe was created 6000 years ago.

      Delete
    5. Why would you want those people purged when they're the very best evidence that ID is a religious and political movement, not a scientific one? The fact that there are "scientists" who say that the age of the earth, the existence of a worldwide flood, and common descent are uninteresting questions on which they have no opinions is a priceless gift.

      Delete
    6. The Other Jim,

      "It seems quite strange that JoJo and Jack Jones are trying so hard to prove our stereotype of creations/IDiots to be correct."

      That's because JoJo and Jack Jones are classic trolls. They are not here to actually discuss science.

      Delete
    7. Those two were names as they were the only ones to comment on this post. Taking a look around, the ones trying to have actual discussions are quite few and far between.

      Back to my point. Where are the other ID proponents, keeping them in line? Why are they silent as these two, or ElShamah777, etc babble such embarrassing nonsense?

      Delete
  2. Jojo said " If that is the case, why would you even make such a claim to contradict scientific evidence presented by Nature and accuse them of publishing misleading history? How do you justify even to question it?"

    Professor Moran and his devotees are walking contradictions, These science fetishists who like to think of themselves as the defenders of reason reject how nature is known to operate when they reject the law of biogenesis.

    ReplyDelete
    Replies
    1. Really? How much do you understand about how that "law" was established. Think very carefully. Don't run into an answer that would only reveal your ignorance.

      While you think about it, I can tell you that I don't expect flies to magically appear on top of putrid meat, and that I don't expect bacteria to grow on culture medium without first innoculating the medium.

      (Leaving aside the stupidity of referring to people who disagree with your religious fantasies as "devotees" or "fetishists." Leaving also aside the hypocrisy, since you reject the law of biogenesis. You think that gods magically make fully formed adult humans out of dust.)

      Delete