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Friday, July 27, 2012

High School Students Find LUCA!

What's Wrong with this Picture?

Biology New Net posted a press release today from the American Institute of Physics: Researchers dig through the gene bank to uncover the roots of the evolutionary tree. It advertises the work of William Duax and his colleagues, including some high school students who work in his lab on Fridays.
Ever since Darwin first published The Origin of the Species, scientists have been striving to identify a last universal common ancestor of all living species. Paleontological, biochemical, and genomic studies have produced conflicting versions of the evolutionary tree. Now a team of researchers, led by a professor at the State University of New York at Buffalo and including area high school students, has developed a novel method to search the vast archives of known gene sequences to identify and compare similar proteins across the many kingdoms of life. Using the comparisons to quantify the evolutionary closeness of different species, the researchers have identified Actinobacteria, a group of single membrane bacteria that include common soil and water life forms, as the base of the evolutionary tree. They will present their findings at the annual meeting of the American Crystallographic Association (ACA), held July 28 – Aug. 1 in Boston, Mass.
What they did was to identify all the S19 and S13 sequences they could find in GenBank. (S19 and S13 are relatively poorly conserved ribosomal proteins on the small subunit.) When they constructed a phylogenetic tree from these sequences they identified Actinobacteria as the probable last universal common ancestor (LUCA).

They will be presenting their results in Nature at a meeting of American crystallographers. Duax will be giving one presentation and a high school student will give the other (posters?).

It's too bad Duax and his students didn't come to Evolution Ottawa 2012 earlier this month. He and his students could have enjoyed a lively discussion of their results and the problems associated with constructing a universal tree of life. It would have been a real educational experience for the high school students and a real cultural experience as well. (They could have tried poutine and Beaver Tails. )

Duax has played a leading role in reaching out to high school students in the Buffalo area and I think he deserves a lot of praise for his efforts over the past two or three decades. However, there's something troubling about the science and I think he puts his finger on the problem in a recent interview [Dr. William Duax - Science Mentor].
Where would your research be without the aid of the students who have helped you over the years?

Because our goals are controversial and considered by a majority of biologists in the world to be impossible, I have no funding for the research program. I have received some support from friends and local charities for the training program. Those funds have been used to provide stipends to some of the high school students and college student mentors and programmers, and for computers and supplies.

I have been working on this project for about 14 years without support. In the past four years the students have generated the data needed to substantiate our conclusions and the students are writing manuscripts that we will submit to national and international journals.

What are some of the early findings you’ve achieved thanks to your work mapping the genetic code of bacteria?

We have a significant body of data that supports our conclusion that the bacterial phylum of Actinobacteria (which includes the bacteria causing tuberculosis and leprosy) includes the Last Universal Common Ancestor (LUCA). We can also demonstrate that at least six species in that phylum use only half of the coding system used in man. (The code used in man is erroneously called the universal genetic code.) We also have uncovered strong evidence that just four of the 20 common amino acids, Glycine (single letter code-G), Alanine (A), Arginine (R) and Proline (P) define and maintain protein shape and may have been the first amino acids to assemble into proteins. Because the single letter codes for these four amino acids spell GARP, we refer to our work as “Evolution According to GARP” with apologies to John Irving.
Lots of us scientists have lost their funding and most of them would be excellent high school mentors if they had a bit of money and a cheap research project. But let's not forget that sometimes there's a very good reason why scientists don't get funded; for example, their proposal might be "controverial" (i.e crazy).

Should universities/departments exercise some control over who mentors high school students?


  1. Not being all that familiar with this area, I'm sure I'm missing some of the problems with Daux's claims. The biggest issue to me is basing the claims on 2 ribosomal genes - as we've seen may time, the LUCA for one gene can be different than for other genes, even when both genes are found in the same organism. Not to mention all the issues that come along with horizontal gene transfer, etc.

    But, despite those problems, I think its great that he is exposing high school students to this sort of science. Yes, its simply database mining, and he's overstating his findings, but at least these students will be exposed to "real" science and have a bit of an understanding of how science works in the real world.

    Should universities/departments exercise some control over who mentors high school students
    Probably, but I'm not convinced that over-stating findings automatically means Daux is a bad mentor. Using these students as cheap labour, though, may be...

    Are you planning a post on McGuinties plan to balance the budget by screwing over kids too young to vote - err, I mean cutting back bachelors degrees to three years and focusing on on-line learning?

    PS: no strike-through in comments?

    1. The biggest issue is expecting a currently existing clade of eubacteria, a highly derived one to make it even worse, to be the last common ancestor of all life(!). And all of this derived from data of just 2 poorly conserved genes...

      Database mining is fine, the problem is that the whole study had oversized goals, shoddy execution and unbelievable conclusions. Not exactly a very good experience for high schoolers interested in science, really.

    2. It seems really strange that a group that causes disease in Man would also contain the last common universal ancestor. Isn't that a fairly derived/advanced attribute?

  2. We also have uncovered strong evidence that just four of the 20 common amino acids, Glycine (single letter code-G), Alanine (A), Arginine (R) and Proline (P) define and maintain protein shape

    Coming from a crystallographer, this is either crazy or irresponsible or horribly worded statement. If I had to pick, crazy would be my choice.

  3. "Ever since Darwin first published The Origin of the Species..."

  4. I am by no means an expert in getting grant money, but my understanding is there are many possible reasons why a given proposal might not get funded:
    - it could be crazy
    - it could be a basically good idea, but poorly written
    - it could be poorly organized, for example the reviewers might be unconvinced that the timeline is realistic, or that all of the necessary controls and QA/QC measures are in place
    - it might be excellent, but not aligned with the funding agency's main goals
    - etc.

    As far as departmental control over mentoring high school students, certainly some basic oversight seems reasonable to prevent neglect or undue exploitation (e.g. cheap labour for boring, repetitive tasks).

    In Dr. Duax's case, 14 years without a successful grant seems rather extreme. Regarding the science he's talking about, the biggest red flag for me is the idea that LUCA is a contemporary organism. Presumably Duax is not actually trying to state that some cell line has remained completely unchanged for several billion years, but it kind of comes across that way. And I don't understand the last part about only four amino acids being responsible for protein shape. Have Duax and his students made a revolutionary discovery in the field of protein folding?

  5. Casting impressionable high school students (likely their first exposure to science) in the role of outsider in the scientific community does them no favors. It could actually stymie their development.

    1. What about casting them as misunderstood rebels?

      "They laughed at Galileo, after all."

  6. 14 years without a successful grant seems rather extreme.

    This is an idiotic comment coming from someone who's obviously never applied for a meaningful grant in times of devastatingly competitive paylines.

    1. Tons of very good grants never get funded - true. But it's not idiotic in a sense that anyone who happened, for whatever reason, to have 14 year of no research funding is going to be effectively dead in term of original experimental research. Your competitors with funding are going to do 99% of research you were ever going to. Research today is expensive - you've got to have money to stay competitive.

    2. Yah...but Duax has 137 (17 in the last 5 years) published papers and a signifcant number of first author publications on bacterial evolution and phylogenetics, so it would seem that he has no touble doing research and getting it published. I question the inpugning of his research program based on the lack of publically funded grants.

    3. Michael M.

      I think you missed the point.

      True, he has published some work on the evolution of proteins and the genetic code but most of it is published in journals that do not have expert reviewers in those fields.

      Note that he and his student are presenting their work at a crystallography conference and not an evolution conference.

    4. DK,

      I haven't had a research grant for 19 years but during that time I've mentored about 20 undergraduates doing projects with me on molecular evolution.

      I think I did a pretty good job. Quite a few of them now have Ph.D.'s in biochemistry and molecular biology [see The Evolution of the HSP70 Gene Family].

    5. Larry, I was talking about research, not training undergrads. And I was talking about experimental research, not database digging.

    6. Larry, have you looked up the journals that Duax has published his phylogentic research to seen if they lack staff qualified to evalute such manuscripts?