Skip to main content
SpringerLink
Log in

Trashing life’s tree

  • Published:
Biology & Philosophy Aims and scope Submit manuscript

Abstract

The Tree of Life has traditionally been understood to represent the history of species lineages. However, recently researchers have suggested that it might be better interpreted as representing the history of cellular lineages, sometimes called the Tree of Cells. This paper examines and evaluates reasons offered against this cellular interpretation of the Tree of Life. It argues that some such reasons are bad reasons, based either on a false attribution of essentialism, on a misunderstanding of the problem of lineage identity, or on a limited view of scientific representation. I suggest that debate about the Tree of Cells and other successors to the traditional Tree of Life should be formulated in terms of the purposes these representations may serve. In pursuing this strategy, we see that the Tree of Cells cannot serve one purpose suggested for it: as an explanation for the hierarchical nature of taxonomy. We then explore whether, instead, the tree may play an important role in the dynamic modeling of evolution. As highly-integrated complex systems, cells may influence which lineage components can successfully transfer into them and how they change once integrated. Only if they do in fact have a substantial role to play in this process might the Tree of Cells have some claim to be the Tree of Life.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Notes

  1. One issue ignored here is the degree to which even the simple tree may be an approximately true description of life’s history (Godfrey-Smith 2009). If one could argue that the simple tree description were approximately true of life’s history, it would neither be necessary to refine the tree nor to discard it. Evaluating this claim is beyond the scope of the present paper and ultimately depends on what purpose we want the representation to serve. Those who emphasize the extent of LGT would likely press that LGT is so important in shaping cellular life that no serious biological purpose could be served by a representation which didn’t include it, even one that was in some respects “approximately true”.

  2. Some discussions of the TOL do not explicitly state what the tree is intended to represent. Furthermore, examining tree construction methods may not uncover this, as the signal used to reconstruct the tree may be different from the plausible representative aim of the tree. To use a simple example, a biologist may conduct a census of a panda population by counting panda droppings. Although she counts droppings, her aim is obviously to measure panda number. Similarly, some biologists constructing trees based on rRNA divergence may aim to construct a more substantive tree of life, not simply an rRNA gene tree. However, the nature of this “more substantive tree” is not always transparent.

  3. All cell-division events need not be represented as a bifurcation in the TOC, as a full interpretation of the tree could include some standard (e.g., ecological) for grouping cell lineages together. Important for our purposes here is that any split in those grouped lineages would correspond to some (set) of cell-division events.

  4. The TOC works most naturally as an interpretation of the tree of prokaryotes, not of the tree of sexually reproducing organisms. This paper focuses on challenges to the TOC from LGT, so it will suffice to see whether the history of prokaryotic life can be identified with the TOC. Although the history of sexually reproducing organisms can less easily be understood in terms of the TOC, the relative lack of LGT in those organisms means that we may be able to maintain a “simple” interpretation of the TOL, in terms of recursively bifurcating species, in that domain.

  5. Certain phenomena, such as endosymbiosis, can make even cellular history non-tree-like if two cells contribute equally to a progeny cell. For our purposes what matters is that a history of cells would still be dramatically more tree-like than would be full genomic histories, because the objections I consider against the TOC are based on the existence of LGT. Furthermore, endosymbiosis disrupts the cell tree primarily among eukaryotes, which are not the focus of this paper.

  6. It has been suggested that cell division may involve the transmission of “cytoplasmic structure” which can take different forms, contributing to the importance of the cellular lineage over particular gene lineages (Thaler 2009). If there is such heritable cytoplasmic structure, this would simply add one more kind of “fiber” to the rope that characterizes the cellular lineage.

  7. Recently, Doolittle (2009b) has coined the term “riboessentialist” in this connection.

  8. Doolittle (2004) pursues the metaphor further, suggesting that the old planks are then used to reconstruct a second ship. This does make the Ship of Theseus paradox more puzzling: Is the second, rebuilt ship really the original Ship of Theseus? But this particularly perplexing aspect of the problem has no close biological analogue – there is no other lineage in which all the parts of the first lineage are progressively integrated, eventually forming a genetically identical organism. Rather the “old planks” are incorporated into many different organisms.

  9. In contrast to its application here, the Ship of Theseus case is sometimes used to suggest that part substitution does not undermine ship identity (Danchin 2002).

  10. Although queasiness about these lineages seems pervasive, I don’t mean to suggest that everyone shares it. Boucher and Bapteste, for example, are clear that even after pervasive transfers “the lineages still exist” (2009, p. 532).

  11. This is assuming that the system is completely non-redundant, meaning that no aspect of its structure can be inferred from any other. Only in that case is it its own simplest description (Simon 1996).

  12. For different defenses of the value of prescinding from the details in explanatory contexts, see Batterman (2002), Kitcher (1999), and Strevens (2008).

  13. For an interesting history of the “stamp collector” jibe, see Johnson (2007).

  14. Metaphysically, there are more pragmatic and more realist ways of thinking about these aims, but we need not wade into such deep waters here. Very briefly though, a realist may think that nature “sets the agenda” for our inquiries, and that the Tree of Life would be real if it were helpful in carrying out that agenda. A pragmatist may deny that there is any naturally given agenda, and would judge the Tree (or other scientific representation) simply in terms of how it furthers our (possibly idiosyncratic) purposes. But on either approach, the TOC would be judged by its ability to help us carry out some scientific agenda.

  15. It has been suggested that immediate retention of genes through LGT requires not only neutral effects, but positive selection (Ochman et al. 2000). If so, this principle would have to be slightly modified.

  16. Carl Woese (2002, 2005) has also emphasized the importance of the cell and its organization in determining the likelihood of LGT. He writes that it is “the degree to which (and the way in which) the various componentry is integrated into a cell, the cell design, that determines what is and what is not horizontally transferred” (2005, p. 106). However, when it comes to describing this “cell design” and “organization” Woese focuses on a certain “core” of genes which he says constitutes cellular organization: the “design-defining genes”(2005, p. 111). He suggests that the organismal genealogy—and the TOC—is defined by those particular genes. This account of organismal lineages does fall prey to the essentialist critiques discussed in the previous section. It is counterintuitive to identify the organization of the cell with particular genes, since the total functioning of the cell is not determined by them alone. The enlightened TOC advocate should agree with Woese that cellular features control aspects of LGT, but should not reduce cellular organization to what Woese calls “a small cadre of genes”(2005, p. 111).

  17. It is sometimes suggested that word adoption rates are also affected by how similar the sounds of the potential adoptee are to the sounds in the adopting language. This is another dynamic principle in which the language governs which words enter it (McMahon 1994).

  18. For example, the cause of the “Great Vowel Shift” has not infrequently been called “mysterious” (Pinker 1994, p. 252).

  19. The terrain is too extensive to cover here, but there is no reason to think that the existence of cell or language-level principles has deeply emergentist implications. Following Loewer (2009) let us take emergentists to be those who deny that the laws of physics are dynamically complete. If they were incomplete, there might be nomological structure in the special sciences over and above that determined by the laws of physics. The principles I refer to here should not be identified with this sort of emergent law. Instead, they characterize dependence relations between the parts of a complex system. Some complex systems are organized such that the parts of the system do not have substantial effects on one another; others are tightly interconnected (Simon 1996). The existence of such principles would simply reflect the fact that cells and languages are instances of these highly interconnected systems.

  20. In the linguistic case, principles characterize change in a single language through time, while in the cellular case principles apply to changes in lineages. To appreciate the parallels, we can liken time-slices of a language to individual cells in a lineage.

  21. Ultimately, a certain level of contingency is compatible with the existence of many interesting cell-level generalizations governing dynamics. What matters for the explanatory relevance of cell-level generalizations is that they rule out some possibilities, not that they rule out all but one (leaving no contingency).

  22. There may well be some less-enlightened TOL advocates who would deny even this, claiming that there is one unified, tree representation of life’s history which accounts for everything. As should be obvious, this view is too strong. However, it is not clear that there are many contemporary advocates of this strong view. Even many advocating something they call the tree of life say that there exist multiple representations of life’s history: “a web of life and a tree of Life are both useful representations of two different biological processes…A web of life illustrates the HGT component of genome evolution, whereas a tree of Life illustrates the history of cells” (Gribaldo and Brochier 2009, p. 515). Alternately, some tree advocates claim that “the organismal [cellular] phylogeny provides the backdrop” (Lerat et al. 2003, p. 101) on which we might represent LGT. As these tree-advocates suggest representing both cellular and genetic lineages, what is at stake is the relative importance of these patterns and whether the cell tree is a particularly interesting and explanatory one.

References

  • Andam CP, Williams D, Gogarten JP (2010) Natural taxonomy in light of horizontal gene transfer. Biol Philos. doi:10.1007/s10539-010-9212-8

  • Bapteste E, Boucher Y (2008) Lateral gene transfer challenges principles of microbial systematics. Cell 16:200–207

    Google Scholar 

  • Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF (2005) Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol 5:33. doi:10.1186/1471-2148-5-33

    Article  Google Scholar 

  • Bapteste E, Burian RM (2010) On the need for integrative phylogenomics: and some steps toward its creation. Biol Philos. doi:10.1007/s10539-010-9218-2

  • Batterman R (2002) The devil in the details. Oxford University Press, Oxford

    Google Scholar 

  • Beatty J (1995) The evolutionary contingency thesis. In: Wolters G, Lennox J (eds) Concepts, theories and rationality in the biological sciences. University of Pittsburgh Press, Pittsburgh

    Google Scholar 

  • Beiko RG (2010) Gene sharing and genome evolution: networks in trees and trees in networks. Biol Philos. doi:10.1007/s10539-010-9217-3

  • Beldade P, Koops K, Brakefield P (2002) Modularity, individuality, and evo-devo in butterfly wings. Proc Natl Acad Sci USA 99:14262–14267

    Article  Google Scholar 

  • Bouchard F (2010) Symbiosis, lateral function transfer and the (many) saplings of life. Biol Philos. doi:10.1007/s10539-010-9209-3

  • Boucher Y, Bapteste E (2009) Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective. BioEssays 31:526–536

    Article  Google Scholar 

  • Cairns-Smith AG (1985) Seven clues to the origin of life: a scientific detective story. Cambridge University Press, Cambridge

    Google Scholar 

  • Ciccarelli F, Doerks T, von Mering C, Creevey C, Snel B, Bork P (2006) Towards automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287

    Article  Google Scholar 

  • Coyne J (2009) Why evolution is true. Viking, New York

    Google Scholar 

  • Dagan T, Martin W (2006) The tree of one percent. Genome Biol 7(10):118. doi:10.1186/gb-2006-7-10-118

    Article  Google Scholar 

  • Dagan T, Martin W (2007) Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci USA 104:870–875

    Article  Google Scholar 

  • Dagan T, Artzy-Randrup Y, Martin W (2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci USA 105(29):10039–10044

    Article  Google Scholar 

  • Danchin A (2002) The Delphic boat. Harvard University Press, Cambridge

  • Darwin C (1859) The origin of species by means of natural selection, 1st edn. John Murray, London

    Google Scholar 

  • Doolittle WF (1996) At the core of the archae. Proc Natl Acad Sci USA 93:8797–8799

    Article  Google Scholar 

  • Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124–2128

    Article  Google Scholar 

  • Doolittle WF (2004) W. Ford Doolittle. Curr Biol 14:R176–R177

    Article  Google Scholar 

  • Doolittle WF (2005) If the tree of life fell, would we recognize the sound? In: Sapp J (ed) Microbial phylogeny and evolution: concepts and controversies. Oxford University Press, Oxford, pp 119–133

    Google Scholar 

  • Doolittle WF (2009a) The practice of classification and the theory of evolution, and what the demise of Charles Darwin’s tree of life hypothesis means for both of them. Philos Trans R Soc Lond B Biol Sci 364:2221–2228

    Article  Google Scholar 

  • Doolittle WF (2009b) Eradicating typological thinking in prokaryotic systematics and evolution. Cold Spring Harb Symp Quant Biol doi:10.1101/sqb.2009.74.002

  • Doolittle WF, Bapteste E (2007) Pattern pluralism and the tree of life hypothesis. Proc Acad Nat Sci USA 104:2043–2049

    Article  Google Scholar 

  • Doolittle WF (2010) The attempt on the life of the tree of life: science, philosophy and politics. Biol Philos. doi:10.1007/s10539-010-9210-x

  • Forgacs G, Newman S (2005) Biological physics of the developing embryo. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Fournier G, Huang J, Gogarten JP (2009) Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Philos Trans R Soc Lond B Biol Sci 364:2229–2239

    Article  Google Scholar 

  • Franklin LR (2007) Bacteria, sex and systematics. Philos Sci 74:69–95

    Article  Google Scholar 

  • Galtier N, Daubin V (2008) Dealing with incongruence in phylogenetic analyses. Philos Trans R Soc Lond B Biol Sci 363:4023–4029

    Article  Google Scholar 

  • Godfrey-Smith P (2009) Darwinian populations and natural selection. Oxford University Press, Oxford

    Google Scholar 

  • Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19:2226–2238

    Google Scholar 

  • Gould SJ (1989) Wonderful life: the burgess shale and the nature of history. W. W. Norton & Company, New York

    Google Scholar 

  • Gribaldo S, Brochier C (2009) Phylogeny of prokaryotes: does it exist and why should we care? Res Microbiol 160:513–521

    Article  Google Scholar 

  • Hacker J, Kaper JB (2000) Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 54:641–679

    Article  Google Scholar 

  • Jain R, Rivera M, Lake J (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801–3806

    Article  Google Scholar 

  • Johnson K (2007) Natural history as stamp collecting: a brief history. Arch Nat Hist 34:244–258

    Article  Google Scholar 

  • Kitcher P (1999) The hegemony of molecular biology. Biol Philos 14:195–210

    Article  Google Scholar 

  • Kitcher P (2001) Science, truth, and democracy. Oxford University Press, Oxford

    Book  Google Scholar 

  • Labov W (1994) Principles of linguistic change, vol. 1: internal factors. Blackwell, Oxford

    Google Scholar 

  • Lake J, Moore J, Simonson A, Rivera M (2005) Fulfilling Darwin’s dream. In: Sapp J (ed) Microbial phylogeny and evolution: concepts and controversies. Oxford University Press, Oxford, pp 184–206

    Google Scholar 

  • Lawton G (2009) Uprooting Darwin’s tree. New Sci 201:36–40

    Article  Google Scholar 

  • Lerat E, Daubin V, Moran NA (2003) From gene trees to organismal phylogeny in prokaryotes: the case of the g-proteobacteria. PLoS Biol 1:101–109

    Article  Google Scholar 

  • Lienae EK, DeSalle R (2009) Is the microbial tree of life verificationist? Cladisics 25:1–7

    Article  Google Scholar 

  • Loewer B (2009) Why is there anything except physics? Synthese 170:217–273

    Article  Google Scholar 

  • Lopez P, Bapteste P (2009) Molecular phylogeny: reconstructing the forest. C R Biologist 332:171–182

    Article  Google Scholar 

  • Malkiel Y (1967) Every word has its own history. Glossa 1:137–149

    Google Scholar 

  • McMahon A (1994) Understanding language change. Cambridge University Press, Cambridge

    Google Scholar 

  • Michod R (1999) Darwinian dynamics. Princeton University Press, Princeton

    Google Scholar 

  • Nowak M (2006) Evolutionary dynamics: exploring the equations of life. Harvard University Press, Cambridge

    Google Scholar 

  • Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304

    Google Scholar 

  • O’Malley M, Dupré J (2007) Size doesn’t matter: towards a more inclusive philosophy of biology. Biol Philos 22:155–191

    Article  Google Scholar 

  • Philippe H, Douady C (2003) Horizontal gene transfer and phylogenetics. Curr Opin Microbiol 6:498–505

    Article  Google Scholar 

  • Phillips B (2006) Word frequency and lexical diffusion. Palgrave Macmillan, England

    Google Scholar 

  • Pinker S (1994) The language instinct: how the mind creates language. HarperCollins, New York

    Google Scholar 

  • Planet P (2002) Reexamining microbial evolution through the lens of horizontal transfer. In: DeSalle R, Giribet G, Wheeler W (eds) Molecular systematics and evolution: theory and practice. Birkhauser, Basel

    Google Scholar 

  • Puigbò P, Wolf YI, Koonin E (2009) Search for a ‘tree of life’ in the thicket of the phylogenetic forest. J Biol 8:59. doi:10.1186/jbiol159

    Article  Google Scholar 

  • Raff R (1996) The shape of life: genes. development, and the evolution of animal form. University of Chicago Press, Chicago

    Google Scholar 

  • Shapiro J, Dworkin M (1997) Bacteria as multicellular organisms. Oxford University Press, New York

    Google Scholar 

  • Simon H (1996) The sciences of the artificial, 3rd edn. MIT Press, Cambridge

    Google Scholar 

  • Sterelny K, Griffiths P (1999) Sex and death. University of Chicago Press, Chicago

    Google Scholar 

  • Strevens M (2008) Depth: an account of scientific explanation. Harvard University Press, Cambridge

  • Thaler D (2009) The cytoplasmic structure hypothesis for ribosome assembly, veritcal inheritance, and phylogeny. BioEssays 31:774–783

    Article  Google Scholar 

  • Toulmin S (1953) The philosophy of science: an introduction. Hutchinson’s University Library, London

    Google Scholar 

  • Wilson EO (1994) Naturalist. Grand Central Publishing, New York

    Google Scholar 

  • Wilson J (1999) Biological individuality: the identity and persistence of living entities. Cambridge University Press, Cambridge

    Google Scholar 

  • Wilson R (2005) Genes and the agents of life: the individual in the fragile sciences. Cambridge University Press, Cambridge

  • Woese C (2002) On the evolution of cells. Proc Natl Acad Sci USA 99:8742–8747

    Article  Google Scholar 

  • Woese C (2005) Evolving biological organization. In: Sapp J (ed) Microbial phylogeny and evolution: concepts and controversies. Oxford University Press, Oxford, pp 99–118

    Google Scholar 

  • Yates T, Salazar-Bravo J, Dragoo J (2004) The importance of the tree of life to society. In: Cracraft J, Donoghue M (eds) Assembling the tree of life. Oxford University Press, Oxford, pp 7–17

    Google Scholar 

  • Zhaxybayeva O, Gogarten JP (2004) Cladogenesis, coalescence and the evolution of the three domains of life. Trends Genet 20:182–187

    Article  Google Scholar 

  • Zhaxybayeva O, Lapierre P, Gogarten JP (2004) Genome mosaicism and organismal lineages. Trends Genet 20:254–260

    Article  Google Scholar 

Download references

Acknowledgments

I would like to thank John Dupré and Maureen O’Malley for their work on this issue and for establishing and running the Question the Tree of Life research project. I am particularly indebted to my referees and to Maureen O’Malley for helpful suggestions on this paper.

Author information

Authors and Affiliations

  1. New York University, New York, NY, 10003, USA

    L. R. Franklin-Hall

Authors
  1. L. R. Franklin-Hall
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to L. R. Franklin-Hall.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Franklin-Hall, L.R. Trashing life’s tree. Biol Philos 25, 689–709 (2010). https://doi.org/10.1007/s10539-010-9219-1

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10539-010-9219-1

Keywords

Search

Navigation