Abstracts, and a Historical Note
on Publication Difficulties
IUBMB 2003 Abstract Template
In submitting an abstract and payment (if applicable), you certify that the paper is an original contribution that has not been presented or published elsewhere and give permission to the Congress Organizers to publish it on the Congress web site and in the Book of Abstracts. You further agree that if your abstract is accepted for poster presentation, you agree to be present at the Congress to present your research or arrange for its presentation.
8th IUBMB/ASBMB Abstract 2004
June Boston meeting FASEB.J (2004) 18, no. 8. page C27. Abstract 18.11.
The above abstracted work was judged complete in January 2003, and a paper entitled "Bacterial Genes as Microisochores" was prepared and submitted to Nature. The choice of this high-profile journal reflected the senior author's belief that the work presented a major advance. The Editors decided that it was "unlikely to succeed in the competition for limited space" and it was declined without being sent for external view. The title was then changed to "Genes as Microisochores" and the paper was submitted to a succession of journals (see Table below).
After much bizarre feedback from reviewers, the senior author hypothesized that the "isochore" buzzword might be leading editors to choose hostile external reviewers. So the title was changed in December 2003 to "Genomic conflict settled in favour of the species rather than of the gene at extreme GC% values." The proposed revision of the isochore concept was down-played. After a strange negative review by BMC Evolutionary Biology (e.g. "Reject because scientifically unsound"), the paper found sane and fertile ground in July 2004 in the form of the reviewers for the new New Zealand-based journal Applied Bioinformatics, a product of Open Mind Journals Ltd., which was in the process of being taken over by a larger publishing house (Adis Data Information BV).
While the above battle was ongoing, the senior author also attempted to get the work out in the formal literature by writing reviews. Attempts to get reviews in BioEssays and Trends in Genetics (Click Here) were unsuccessful, although in the latter case the editor did send the "letter," which he insisted must be brief, out to referees (Click Here). The editor finally replied:
Forsdyke Preservation more fundamental&
Once again I must apologise to you for the length of time this has taken, I had to approach nine referees before I would find two to look at it. I am afraid this is common with your papers - I am sure you find it as tiresome as I do.
This is not for us - the referees do not like it and neither do I - so as a result we are unable to publish it. I attach their comments.
However, happily, the Journal of Biological Systems (for which I happen to be an advisory editor) accepted a review entitled "Regions of relative GC% uniformity are recombinational isolators," without imposing any length limitations.
Another approach was to mention the work as part of a paper that the Journal of Theoretical Biology was not likely to decline, since it was a reply to a previous paper by some evolutionists who has questioned the senior author's hypothesis on the role of GC% in chromosomal speciation ("Chromosomal speciation: a reply").
The outcome of all this was that in the latter part of 2004 three papers giving different versions of the same message were scheduled to appear. This redundancy was forced on the senior author by defects in the peer-review process. Remarkably, the papers written after the original paper was written, appeared first.
From the viewpoint of the general scientific public, it can be noted that many scientists in the field had anonymous privileged access to the work (through acting, or being invited to act, as reviewers) for a year or two, prior to the public being able to access it. Whereas T. H. Huxley above implies adverse criticism fuelled by professional animosity, it seems likely in the present case that whatever merits the work had just were not recognizable in the intellectual climate prevailing among those asked to review papers in 2003-4. For example, the isochore community was preoccupied with defending itself against the strange assertion by E. S. Lander (International Human Genome Sequencing Consortium) that isochores did not exist at all (see Li et al. 2003. Comp. Biol. Chem. 27, 5-10)! Thank heavens for Open Mind Journals of Auckland! We lament that their life was so short, but are delighted that Applied Bioinformatics, while still "down-under", did not go-under so soon!
|Nature||20 Jan 03||27 Jan 03||No||F01428|
|26 Feb 03||18 Apr 03||Yes||013029|
|Nature Genetics||20 Apr 03||25 Apr 03||No||A12992|
|J. Theor. Biol.||30 Apr 03||24 Aug 03||4 Nov 03||Yes||JTBI-227|
|Mol. Biol. Evol.||6 Nov 03||2 Dec 03||Yes||03-0561|
|J. Mol. Evol||2 Dec 03||11 Dec 03||No||00180|
|BMC Evol. Biol.||13 Dec 03||3 Mar 04||Yes||12118208-
|Appl. Bioinform.||5 Mar 04||5 Jul 04||10 Jul 04||Yes|
For readers not familiar with scientific publication etiquette, please note that it is not permissible to submit to more than one journal at a time. Thus, authors must be in receipt of a rejection letter from journal A before submitting to journal B. The senior author had to get round this using the "salami" approach of separately submitting, as reviews, different aspects of the same basic message.
It should also be noted that, in the senior author's experience, the struggle described here is not unusual. If every paper included in these web-pages were accompanied by an account of the corresponding publication saga, sometimes enduring over several years, their lengths would be prohibitive.
Although most papers of the senior author have eventually found a journal, this is largely due to his persistence. The tragedy is that many authors, especially young authors, are likely to be discouraged by the frequent incompetence, and sometimes ferocity, of peer-review, and so have given up on science altogether. Some cannot afford the luxury of persistence since their careers are at a stage where rejection means end of career. For more on this please see Forsdyke's peer-review web-pages.
Submission to Journal of Molecular Evolution
Subject: JME-2003-00181 Date: Thu, 11 Dec 2003
Dear Dr. Forsdyke,
Thank you for submitting your manuscript entitled, "Genes as Microisochores" to the Journal of Molecular Evolution.
Unfortunately, we cannot consider your submission for publication in JME. Generally we return manuscripts if the results presented are not novel. I have published a fair amount on base composition and on codon bias, and after reading this paper I don't think it adds anything that is unknown. One of our Associate Editors, who has expertise on genome base composition also recommends returning the manuscript.
I hope that you will continue to consider JME for publication of your work.
Submission to Trends in Genetics
TIGA2403 Submitted as a brief "Letter" 9 March 2004
Thank you for agreeing to consider my proposal as a letter. I include as email attachment the text condensed down to 819 words plus 26 references. Hope this length will be OK. There are no figures or tables.
Donald Forsdyke, Department of Biochemistry,
Queen's University, Canada
Preservation more fundamental than function: GC% preserves both selfish genes and genomes
Donald R. Forsdyke
decades have passed since William Hamilton and George Williams presented
a concept popularized as the “selfish gene”. Seeming to argue
that preservation was more fundamental than function, Williams 
proposed that a gene be defined by its property of remaining intact as
it passes from generation to generation. For Williams, “gene” meant
any DNA segment that has the potential to persist for enough generations
to serve as a unit of natural selection.
“Socrates’ genes may be with us yet, but not his genotype, because meiosis and recombination destroy genotypes as surely as death. … I use the term gene to mean ‘that which segregates and recombines with appreciable frequency’. … A gene is one of a multitude of meiotically dissociable units that make up the genotypic message.”
reproduction is as old as life, in that the most primitive living
systems were capable of fusion and combination and recombination of
their autocatalytic particles. Modern organisms have evolved elaborate
mechanisms for regulating this primitive power of recombination and for
maximizing the benefits to be derived from it.”
for Williams, the ultimate agency was “natural selection of
alternative alleles.” No other agency facilitated the preservation of
genes. His seminal text Adaptation and Natural Selection made a
compelling case for natural selection (i.e. function) “as the primary
or exclusive creative force” in evolution . The controversial
“higher levels of selection” that later won the advocacy of Stephen
Jay Gould, were “impotent and not an appreciable factor in the
production and maintenance of adaptation.” This view of the power of
natural selection was shared by those whom Gould came to characterize as
“ultraDarwinists” . The conflict between Darwinists and
supporters of hierarchical levels of selection  did not fade with the
Gould’s death in 2002. Although neither Williams nor Gould were aware
of it, over four decades a potential preserving agency, internal to the
organism, had been fleshed out in chemical terms as a component of the
base composition of DNA – GC%.
works of Akiyoshi Wada were prominent among those suggesting a link
between GC% and recombination [6-13]. Recombination between two
sequences usually follows a successful search for similarity. Allelic
genes can recombine because they have homologous sequences. More than
sequence non-similarity per se, Wada proposed that GC%
non-similarity would prevent genes blending by recombination, thus
losing their individualities. Indeed, bioinformatic analyses revealed a
mechanism by which GC% differences could impair the initial similarity
GC% has the potential to protect not
only genes from blending with allied genes in the same genome (so
facilitating an origin of genes), but also genomes from blending with
allied genomes in the same phylogenetic group (so facilitating an origin
of species; [15-17]). Thus, individual genes within a genome and
individual species within a phylogenetic group should be preserved, both
by virtue of functions (the classical phenotype), and by a distinct
agency, GC% (the genome phenotype).
Evidence on how an agency could affect preservation independently of function came from many quarters, and included studies of base compositions at different codon positions. Third positions of codons play little role in the encoding of amino acids, and so are freer to vary than first and second codon positions. Thus, a third codon position difference between potentially recombining alleles should, without affecting protein function, serve to impair a similarity search and so militate against recombination. However, differences in GC% being a major factor in the impairment of a search , it is not just any third codon position difference, but a difference that changes GC%, that is likely to be important. Indeed, early differences in third codon position GC% precede the functional differences that characterize duplicating genes [18-22]. Early differences in third codon position GC% are observed when prokaryotes, which when so inclined can engage in sexual recombination , duplicate into two species [24-25]. There is much, albeit indirect, evidence that this also applies to eukaryotes [15-17]. Studies of hybrid sterility could provide critical evidence . Indeed, while not envisaging a role for GC% differences, Horacio Naviera and Xulio Maside found the results of such studies “unexpected” and suggested that “a new paradigm is emerging, which will force us … to revise many conclusions of past studies” .
J. R. Mortimer for Perl programs, and S.-J. Lee for bioinformatic
analyses. Queen’s University hosts my web-pages where full text
versions of several of the cited references may be found (http://post.queensu.ca/~forsdyke/homepage.htm).
1. Lehninger, A. L. et al. (1993) In Principles of Biochemistry, 2nd Edition, pp. 789. Worth Publishers, New York
2. Dawkins, R. (1976) The Selfish Gene, Oxford University Press
3. Williams, G. C. (1966) Adaptation and Natural Selection, pp. 1, 8, 22-24, 56, 138. Princeton University Press
4. Gould, S. J. (2002) The Structure of Evolutionary Theory, pp. 595-744. Harvard University Press, Cambridge, MA
5. Morris, R. (2001) The Evolutionists. W. W. Norton, New York
6. Skalka, A. et al. (1968) Segmental distribution of nucleotides in the DNA of bacteriophage lambda. J. Mol. Biol. 34, 1-16
7. Vizard, D. L. and Ansevin, A. T. (1976) High resolution thermal denaturation of DNA thermalites of bacteriophage DNA. Biochemistry 15, 741-750
8. Wada, A. et al. (1976) Long-range homogeneity of physical stability in double-stranded DNA. Nature 263, 439-440
9. Bibb, M. J. et al. (1984) The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences. Gene 30, 157-166
10. Wada, A. and Suyama, A. (1985) Third letters in codons counterbalance the (G + C) content of their first and second letters. FEBS Lett. 188, 291-294
11. Suyama, A. and Wada, A. (1983) Correlation between thermal stability maps and genetic maps of double-stranded DNAs. J. Theor. Biol. 105, 133-145
12. Wada, A. and Suyama, A. (1986) Local stability of DNA and RNA secondary structure and its relation to biological functions. Prog. Biophys. Mol. Biol. 47, 113-157
13. Forsdyke, D. R. (2004) Regions of relative GC% uniformity are recombinational isolators. J. Biol. Sys. (in press)
14. Forsdyke, D. R. (1998) An alternative way of thinking about stem-loops in DNA. J. Theor. Biol. 192, 489-504
15. Forsdyke, D. R. and Mortimer, J. R. (2000) Chargaff’s legacy. Gene 261, 127-137
16. Forsdyke, D. R. (2001) The Origin of Species, Revisited. McGill-Queen’s University Press, Montreal
17. Forsdyke, D. R. (2003) William Bateson, Richard Goldschmidt, and non-genic modes of speciation. J. Biol. Sys.11, 341-350
18. Matsuo, K. et al. (1994) Short introns interrupting the Oct-2 POU domain may prevent recombination between the POU family genes without interfering with potential POU domain ‘shuffling’ in evolution. Biol. Chem. Hoppe-Seyler 375, 675-683
19. Zhang, Z. et al. (2003) Evolutionary history and mode of the amylase multigene family in Drosophila. J. Mol. Evol. 57, 702-709
20. Zhang, Z. and Kishino, H. (2004) Genomic background drives the divergence of duplicated amylase genes at synonymous sites in Drosophila. Mol. Biol. Evol. 21, 222-227
21. Montoya-Burgos, J. I. et al. (2003) Recombination explains isochores in mammalian genomes. Trends Genet. 19, 128-130
22. Iwase, M. et al. (2003) The amelogenin loci span an ancient pseudoautosomal boundary in diverse mammalian species. Proc. Natl. Acad. Sci. USA 100, 5258-5263
23. Gratia, J. P. and Thiry, M. (2003) Spontaneous zygogenesis in Escherichia coli, a form of true sexuality in prokaryotes," Microbiology 149, 2571-2584
24. Belgard, M. and Gojobori, T. (1999) Inferring the direction of evolutionary changes in genomic base composition. Trends Genet. 15, 254-256
25. Belgard, M. et al. (2001) Early detection of G + C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. J. Mol. Evol. 53, 465-468
26. Naveira, H. F. and Maside, X. R. (1998) The genetics of hybrid male sterility in Drosophila. In Endless Forms. Species and Speciation, pp. 330-338. Oxford University Press
A Reviewer's Comments
This is a strange paper. The form is very attractive. The manuscript is clear, well-written, concise, and addresses a fundamental issue that has to do with major paradigms of genetics and evolution. The content of the paper, unfortunately, seems to me highly criticable. The author argues that variation in GC-content between genes/genomes is selected to prevent recombination and allow functional divergence/speciation. There are several reasons why I think this should not be published in TIG (or in any journal, to tell the truth).
First, this hypothesis is not supported. The bibliographic survey about base composition variation and gene/genome divergence is fragmentary, and highly biased toward examples that might, anecdotally, appear to be in accordance with the proposed scenario (but are actually not, see below). It should be noted that none of the cited references (18-26), but those from the author himself, even refer to the hypothesis of a selected divergence of base composition. It should also be noted that these few examples in which duplicated genes (or diverging genomes) undergo an early divergence of GC-content are in no way the general case, as it is spuriously suggested in the manuscript.
Let us go for a rapid review of the actual content of these papers - at least the ones I know. Zhang found that the amylase gene was duplicated independently in two Drosophila lineages, and that, in the two lineages, one duplicate used to undergo a decrease in GC-content (19), apparently in agreement with the author's hypothesis. But Zhang then published (ref. 20) that this GC-decay was explained by the genomic context: in the two lineages, the GC-decreasing duplicate is located near the centromere, in a little-recombining region (there is a well-known correlation between local recombination rate and GC-content in many species). Not any selection for diverging GC here. The same explanation applies to the Fxy gene in the mouse (ref 21), who moved from the little recombining X chromosome to the highly recombining pseudoautosomal region. This (not selection) resulted in a rapid increase of GC%, as everybody agrees (Perry & Ashworth 1999 Curr Biol, Yi et al 2004 Genome Res). Iwase et al (ref 22) finally, did not even comment on variations in GC-content in their paper (which, by the way, has very little to do with speciation or duplication). Marais & Galtier (2004, Curr Biol), commenting on this paper, showed how it illustrates the role of local recombination as a force driving GC-content evolution.
The main message of these papers, therefore, is that recombination determines GC-content evolution, not the reverse - a scenario for which there is a compelling body of evidence not cited in the manuscript.
Secondly, this hypothesis is highly dubious on general grounds. Speciation often occurs between populations/subspecies showing a relatively low level of sequence divergence (eg less than 1%), and virtually the same base composition. Recombination between such taxa is possible, and actually occurs in hybrids. What prevents gene flow between subspecies are a relatively low number of loci that confer a reduced survival/fertility on hybrids. GC-content has just nothing to do with speciation, at least in plants and animals, as any searcher in the field, I am sure, would agree. About duplications and functional divergence, I could imagine that a duplicate quickly departing by chance the GC-content of the ancestral copy would have an increased probability of achieving functional divergence - although I don't know of any empirical evidence for this process. Even if it was proved, this hypothesis is weaker than the scenario proposed in this ms, where GC divergence is selected (not just a favourable contingency) for preventing recombination.
The only merit I see in this manuscript is to point out the challenging result of Bellgard et al (ref 25), who detected an emerging shift in the GC-content of a group of genes from two recently separated bacterial strains. Although I agree that this result deserves an explanation, it can certainly not be considered as a support for the very ambitious hypothesis proposed here.
In short, I recommend rejection because of biased and spurious bibliographic survey, and unsupported and implausible claim.
Anonymous Reviewer for TIG
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The above abstracts of conference posters were placed in these web-pages on 11 June 2004. This page was last edited 27 Nov 2010. The text of neither abstract was changed from the form as originally submitted. The type of the 2004 abstract has been enhanced. DRF