%% BioMed_Central_Tex_Template_v1.06 %% % % bmc_article.tex ver: 1.06 % % % %%IMPORTANT: do not delete the first line of this template %%It must be present to enable the BMC Submission system to %%recognise this template!! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% LaTeX template for BioMed Central %% %% journal article submissions %% %% %% %% <8 June 2012> %% %% %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% For instructions on how to fill out this Tex template %% %% document please refer to Readme.html and the instructions for %% %% authors page on the biomed central website %% %% http://www.biomedcentral.com/info/authors/ %% %% %% %% Please do not use \input{...} to include other tex files. %% %% Submit your LaTeX manuscript as one .tex document. %% %% %% %% All additional figures and files should be attached %% %% separately and not embedded in the \TeX\ document itself. %% %% %% %% BioMed Central currently use the MikTex distribution of %% %% TeX for Windows) of TeX and LaTeX. 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Repeat \author command as much %% %% as required. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \author[ addressref={aff1}, % id's of addresses, e.g. {aff1,aff2} corref={aff1}, % id of corresponding address, if any % noteref={n1}, % id's of article notes, if any email={mlynch11@asu.edu} % email address ]{\inits{ML}\fnm{Michael} \snm{Lynch}} \author[ addressref={aff2}, % id's of addresses, e.g. {aff1,aff2} % corref={aff2}, % id of corresponding address, if any % noteref={n1}, % id's of article notes, if any email={marinovg@stanford.edu} % email address ]{\inits{GKM}\fnm{Georgi K.} \snm{Marinov}} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the authors' addresses here %% %% %% %% Repeat \address commands as much as %% %% required. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \address[id=aff1]{% % unique id \orgname{Biodesign Center for Mechanisms of Evolution, Arizona State University}, % university, etc % \street{Waterloo Road}, % \postcode{85287} % post or zip code \city{Tempe, AZ}, % city \cny{United States} % country } \address[id=aff2]{% % unique id \orgname{Department of Genetics, Stanford University School of Medicine}, % university, etc % \street{Waterloo Road}, % \postcode{94305} % post or zip code \city{Stanford, CA}, % city \cny{United States} % country } %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter short notes here %% %% %% %% Short notes will be after addresses %% %% on first page. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{artnotes} %\note{Sample of title note} % note to the article % \note[id=n1]{Equal contributor} % note, connected to author \end{artnotes} \end{fmbox}% comment this for two column layout %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The Abstract begins here %% %% %% %% Please refer to the Instructions for %% %% authors on http://www.biomedcentral.com %% %% and include the section headings %% %% accordingly for your article type. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % \begin{abstractbox} % \begin{abstract} % abstract % \parttitle{First part title} %if any % Text for this section. % \parttitle{Second part title} %if any % Text for this section. % \end{abstract} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The keywords begin here %% %% %% %% Put each keyword in separate \kwd{}. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % \begin{keyword} % \kwd{} % \kwd{} % \kwd{code} % \kwd{} % \kwd{} % \end{keyword} % MSC classifications codes, if any %\begin{keyword}[class=AMS] %\kwd[Primary ]{} %\kwd{} %\kwd[; secondary ]{} %\end{keyword} % \end{abstractbox} % % \end{fmbox}% uncomment this for twcolumn layout \end{frontmatter} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The Main Body begins here %% %% %% %% Please refer to the instructions for %% %% authors on: %% %% http://www.biomedcentral.com/info/authors%% %% and include the section headings %% %% accordingly for your article type. %% %% %% %% See the Results and Discussion section %% %% for details on how to create sub-sections%% %% %% %% use \cite{...} to cite references %% %% \cite{koon} and %% %% \cite{oreg,khar,zvai,xjon,schn,pond} %% %% \nocite{smith,marg,hunn,advi,koha,mouse}%% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%% start of article main body % %%%%%%%%%%%%%%%% %% Background %% %% Gerlitz et al. \cite{Gerlitz2018} were aware that three months prior to their note we published a reevaluation and more thorough annotation of the data sources to which they refer \cite{LynchMarinov2018}. Prior to embarking on their mission, they could have sought clarification by communicating directly with us, but did not do so. Our reanalysis lead to a slightly improved statistical fit of the ribosome number -- cell volume scaling relationship, although not significantly so. Contrary to the claims of Gerlitz et al., there were no systematic errors. The senior author of the comment to which we are responding (WFM) has argued that the establishment of the mitochondrion endowed eukaryotes with extraordinary energetic capacity, without which the complexity of eukaryotic cells would be impossible \cite{LaneMartin2010,LaneMartin2015,LaneMartin2016,Martin2017}. Our work suggests otherwise \cite{LynchMarinov2015,LynchMarinov2017}. This is not to say that mitochondrial endosymbiosis was not a watershed event in eukaryotic evolution, but a diversity of analyses consistently indicate that there is no quantum leap in the energetic capacity of eukaryotes relative to prokaryotes, but instead continuity of allometric scaling within and between phylogenetic groups. To put things into context, our initial interest in cellular bioenergetics was motivated by the unsolved problem of the amount of energy required to build a cell and to run its various genes \cite{LynchMarinov2015}. While performing our analyses, we realized that the data failed to support the hypothesis of Lane and Martin \cite{LaneMartin2010} that the mitochondrion precipitated a bioenergetic revolution said to enable a 200,000-fold increase in gene number (the source of this factor remains unclear). Lane and Martin \cite{LaneMartin2016} objected, raising the point that we had neglected ribosomes in ways that would somehow affect the legitimacy of our conclusions. We addressed the ribosome issue in Lynch and Marinov \cite{LynchMarinov2017,LynchMarinov2018}, showing that it in no way alters our prior conclusions. Motivated by ideas generated in our previous response to Lane and Martin \cite{LynchMarinov2016}, we also considered the substantial investment that eukaryotes make in lipid bilayers, as well as the relevant matter of the incidence of ATP synthase per cell. These newer analyses support our contention that the mitochondrion has not endowed eukaryotes with extraordinary energetic capacity, contrary to the conclusions in Lane and Martin (2010) \cite{LaneMartin2010}. Rather than providing scientific arguments relevant to the debate about mitochondria and the limitations of eukaryotic bioenergetics, Gerlitz et al. question the existence of the data upon which our analyses were based. Their contention is that many of the cell-volume data in Lynch and Marinov \cite{LynchMarinov2017} do not exist. Confusion was caused by our failure to note that the citations for these data were contained in tables other than the specific one that Gerlitz et al. focused on, which pertained to ribosome content. These issues are clarified in Lynch and Marinov (2018) \cite{LynchMarinov2018}. Two additional points of concern in Gerlitz et al. merit comment. First, they note that the cellular / physiological data from bacteria and eukaryotes are not drawn from the same distribution. No one has ever argued otherwise. What we have emphasized is the continuity in the scaling relationships of such data with cell size (Figures 1a, 2, and 4 in Lynch and Marinov (2015) \cite{LynchMarinov2015}; Figures 1 and 2 in Lynch and Marinov (2017) \cite{LynchMarinov2017}). Continuity in scaling refers to the absence of a discontinuous shift in an allometric relationship between two measures, which does not depend on complete continuity in distribution. Second, Gerlitz et al. again assert that we have misinterpreted the bioenergetics claims in Lane and Martin (2010) \cite{LaneMartin2010}. However, direct quotes from the latter show that this is not the case (Lynch and Marinov 2016 \cite{LynchMarinov2016}; see also the quotes in the Response to Reviewers in Lynch and Marinov (2017) \cite{LynchMarinov2017}). Lane and Martin’s definition of energetic capacity, the ratio of the total energy assimilated per number of genes, has no meaningful connection with energetics or evolution. Their metric is analogous to judging the fuel economy of car by dividing the volume of the gas tank by the number of parts. Under this view, an embellished vehicle with so many power-demanding bells and whistles that no fuel remains for generating mileage would nonetheless be regarded as superior. Martin's current attention to detail is welcome. In the primary paper of contention \cite{LaneMartin2010}, which Martin views as established fact, it is stated that ``There is an appreciable range of uncertainty in measurement for both cell mass and metabolic rates for microbes: values differing by one or two orders of magnitude might not be meaningfully different.'' Yet, in a recent paper attempting to bolster the original claims of Lane and Martin \cite{LaneMartin2010}, Martin \cite{Martin2017} states that ``In evolution there are no facts, there are only observations and their interpretation.'' The goal of evolutionary biology, as in all sciences, is to establish the material basis of facts and to settle disagreements via rational debate rather than through unsubstantiated accusations. In performing our analyses, it has been essential to rely on data from various sources, presumably with various levels of accuracy, and wherever possible we have attempted to use average observations over independent studies. The strong scaling relationships presented in Lynch and Marinov (2015, 2017) \cite{LynchMarinov2015,LynchMarinov2017} are inconsistent with a substantial error component in the data analyses, as this would greatly reduce the significance of the regressions and diminish the allometric coefficients relative to expectations under isometry. Indeed, the analysis of Gerlitz et al., based on a highly reduced data, set strongly supports our contention that there is no quantum leap in translational capacity in the bridge between prokaryotes and eukaryotes. We thank the authors for their supportive analyses. \begin{backmatter} % \section*{Abbreviations} % \section*{Competing interests} % The authors declare no competing interests. % \section*{Author's contributions} % G.K.M. conceived and designed the study. G.K.M. analyzed the data. G.K.M. and ML wrote the manuscript. Both authors read and approved the final manuscript. % \section*{Acknowledgements} % Support was provided by National Science Foundation awards MCB-1050161 and NSFMCB-1518060. This material is also based upon work supported by the National Science Foundation grant CNS-0521433. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% The Bibliography %% %% %% %% Bmc_mathpys.bst will be used to %% %% create a .BBL file for submission. %% %% After submission of the .TEX file, %% %% you will be prompted to submit your .BBL file. %% %% %% %% %% %% Note that the displayed Bibliography will not %% %% necessarily be rendered by Latex exactly as specified %% %% in the online Instructions for Authors. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % if your bibliography is in bibtex format, use those commands: \bibliographystyle{bmc-mathphys} % Style BST file (bmc-mathphys, vancouver, spbasic). \bibliography{bmc_article} % Bibliography file (usually '*.bib' ) % for author-year bibliography (bmc-mathphys or spbasic) % a) write to bib file (bmc-mathphys only) % @settings{label, options="nameyear"} % b) uncomment next line %\nocite{label} % or include bibliography directly: \begin{thebibliography}{100} \bibitem{Gerlitz2018}Gerlitz M, Knopp M, Kapust N, Xavier JC, Martin WF. Elusive data underlying debate at the prokaryote-eukaryote divide. Biology Direct. 2018; 13:21. \bibitem{LaneMartin2010}Lane N, Martin W. The energetics of genome complexity. Nature. 2010; 467:929--934. \bibitem{LaneMartin2015}Lane N, Martin WF. Eukaryotes really are special, and mitochondria are why. Proc Natl Acad Sci USA. 2015; 112:E4823. \bibitem{LaneMartin2016}Lane N, Martin WF. Mitochondria, complexity, and evolutionary deficit spending. Proc Natl Acad Sci USA. 2016; 113:E666. \bibitem{LynchMarinov2015}Lynch M, Marinov GK. The bioenergetic costs of a gene. Proc Natl Acad Sci USA. 2015; 112:15690--15695. \bibitem{LynchMarinov2016}Lynch M, Marinov GK. Reply to Lane and Martin: Mitochondria do not boost the bioenergetic capacity of eukaryotic cells. Proc Natl Acad Sci USA. 2016; 113:E667--E668. \bibitem{LynchMarinov2017}Lynch M, Marinov GK. Membranes, energetics, and evolution across the prokaryote-eukaryote divide. 2017; ELife. 6. pii: e20437. \bibitem{LynchMarinov2018}Lynch M, Marinov GK. Correction: membranes, energetics, and evolution across the prokaryote-eukaryote divide. 2018; Elife. 7. pii: e35006. \bibitem{Martin2017}Martin WF. Symbiogenesis, gradualism, and mitochondrial energy in eukaryote evolution. Periodicum Biologorum. 2017; 119:141--158. \end{thebibliography} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Figures %% %% %% %% NB: this is for captions and %% %% Titles. 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