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Exoplanet Biosignatures Workshop-Without-Walls Review Papers - Discussion Forum

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Dear Colleagues,

Friday 9 June, 2017 was the last day of the official comment period for the NExSS Exoplanet Biosignatures review papers.  

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4. Exoplanet Biosignatures: Future Directions

  1. NExSS Manager

    Contact: Sara I. Walker, sara.i.walker*at*asu.edu
    Summary: We summarize novel concepts about planetary biosignatures that are just emerging in the literature, addressing the importance of environmental context and biology that may be very different from Earth.  Topics include evaluating:  the evolutionary trajectory of coupled systems to identify high- vs. low-probability outcomes; classification of biosignatures from process-based, multi-disciplinary perspectives;   laboratory and theoretical validation outside of Earth-like conditions.  We summarize the debates over these novel ideas, proposals from the community for developing them further, and consider modeling of observational discriminatory power, and set the stage for future instrument development requirements.

    (Note:  Equation formatting errors were caught on 6 June 2017.  Please download fixed PDF.)

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  2. Tanai Cardona

    Hi again, I wanted to comment in here on a few aspects regarding the evolution of oxygenic photosynthesis. I hope this is somewhat useful and constructive. I apologize in advance for the lengthy commentary.

    Some minor things first:
    Last sentence, page 5, typo: it says: "quantifying what is ‘life’ is."

    Page 6, line 6, typo: “I’ll know it when we I it”. 


    The interesting bits:
    Page 7, “However, O2 as a biosignature may be rare: for 85% of Earth’s history, life did not produce significant amounts of atmospheric O2, and understanding of the origins of oxygenic photosynthesis is still too limited to quantify expectations of its likelihood on other worlds.”

    This is the question that must be asked. What information is required on the evolution of oxygenic photosynthesis in order to quantify expectations of its likelihood on other worlds?

    How do you know that the information you seek for this quantification is not available yet?

    Some of the things that we know with good confidence about the evolution of oxygenic photosynthesis are the following (not an exhaustive list):

    1) On Earth there is one single form of oxygenic photosynthesis.
    2) The standard configuration of the photosynthetic machinery can be traced back to the last common ancestor of all cyanobacteria with photosynthesis.
    3) This last common ancestor, defined as the most recent ancestor between the earliest evolving clades (genus Gloeobacter) and all other cyanobacteria, already had a highly sophisticated version of oxygenic photosynthesis, including a standard form of Photosystem II able to oxidize water by a mechanism that is identical in all extant cyanobacteria and photosynthetic eukaryotes.
    4) Therefore, the evolution of oxygenic photosynthesis predates the last common ancestor of cyanobacteria. The evolution of the reaction center proteins provide further constraints on the evolution of oxygenic photosynthesis.
    5) Photosystem II today is a heterodimer of core reaction center proteins, named D1 and D2, with the OEC located in one of the monomers, D1. We know for certain that the ancestral photosystem capable of water oxidation had to be a homodimer, with two OEC positioned symmetrically on each side of the reaction center.
    6) Given the large evolutionary distance between D1 and D2, and the slow rates of evolution of reaction center proteins it can be concluded that a large diversity of bacteria capable of oxygenic photosynthesis must have existed before the last common ancestor of cyanobacteria (Cardona, 2016). How abundant was this diversity is a different issue. However, as I mentioned in point 1) only one lineage of oxygenic photosynthetic bacteria seemed to have survived. In addition, from the evolution of D1 and D2 it is also possible to conclude that oxygenic photosynthesis had been evolving for a long time before the last common ancestor of cyanobacteria (Cardona et al., 2017).
    7) More evidence of transitional stages in the evolution of oxygenic photosynthesis can be found in the diversity of D1 core proteins retained in the genomes of all known cyanobacteria, some of these have ancestral traits that are informative regarding the origin of water oxidation, see for example (Cardona et al., 2015).

    The point that I want to make again is… what exactly do you need to know about the origin of oxygenic photosynthesis to quantify exactly the likelihood of its evolution?


    Page 29, ”The photon energy is used to control the redox state of the oxygen evolving complex (OEC), a highly oxidizing molecule that then is used to oxidize water, thus generating oxygen.”

    This is an unusual way to talk about water oxidation in Photosystem II. I suggest something like this:

    ”The photon energy is used to oxidize the oxygen evolving complex (OEC) of Photosystem II, a metallocluster used to catalyze the oxidation of water, thus generating oxygen.”

    The authors refer throughout the text to the OEC as a molecule, I think it is better to refer to it as a component of Photosystem II.


    Page 47, “The emergence of oxygenic photosynthesis involved conservation of photosystem structures that evolved in earlier organisms but also added a unique molecule, the oxygen evolving complex (OEC), which is responsible for oxidation of water but whose origin remains elusive, with no known precursors (Xiong and Bauer, 2002; Blankenship et al., 2007). Thus, the likelihood of another planet developing oxygenic photosynthesis, P(OP), is currently difficult to constrain.”

    This sounds quite odd. How can you say that the origin of the OEC remains elusive when citing papers that are 15 and 10 years old? Why do you think there's been no progress since then?

    I don’t think the origin of the OEC remains elusive: in fact, from the evolution of reaction center proteins a great amount of detail is available regarding the evolution of Photosystem II. The current understanding of the structure and function of Photosystem II far surpasses that of many other enzymes, and I am certain that today we can infer a great deal on the evolution of water oxidation catalysis.

    You mention that there are no known precursors, but it is not really quite like that. Perhaps, what you meant with "precursors" is not clear enough.

    There are many “precursor" states in the evolution of anoxygenic and oxygenic photosynthesis that can now be inferred from structural and phylogenetic data. I could count at least 7 or 8 precursors or transitional stages in the evolution of oxygenic photosynthesis starting from the ancestral homodimeric water oxidizing reaction centers before the evolution of the standard configuration of Photosystem II, and throughout the diversification of reaction center proteins and the heterodimerization of Photosystem II. See for example (Cardona et al., 2015). Another large number of precursors can be deduced from an analysis of the evolution of the chlorophyll and bacteriochlorophyll synthesis pathway.

    The literature on the evolution of photosynthesis has a lot of baggage. I understand that… I can imagine that it must be quite difficult (and tedious) to browse through all of that in order to seek the information the authors are looking for; and to weed out the speculation from the useful bits. However, I have attempted to do just that and my research for the past four years (since I became independent) has consisted on moving forward the understanding of the evolution of oxygenic photosynthesis... I have the advantage that I am a biologist and that I trained in biochemistry and biophysics labs that specialized in the study of the structure and function of Photosystem II. Although, I’m still pretty unknown, I must acknowledge that most of my work on the evolution of oxygenic photosynthesis is quite specialized and very recent, and I’m kind of arriving to the field as an underdog; so I understand if some of my "bold" claims seem unorthodox. Yet, if we want detailed insight into the origin of water oxidation chemistry to measure the probability of it emerging in an exoplanet, we will need a specialized understanding of photochemical reaction centers and Photosystem II structure and function, from an evolutionary perspective.


    Page 52, “The greatest challenge is P(OP), the origin of OP, due to unexplained origin of the key molecule in OP, the oxygen evolving complex (OEC).”

    I want to say that many aspects regarding the evolution of oxygenic photosynthesis that still today seem very mysterious or elusive, can now be resolved with confidence.

    What I think must be done here, perhaps at a future date in a different publication, is stating clearly what information regarding the evolution of oxygenic photosynthesis is needed to calculate P(OP). It is possible that such information is already available in the form of sequence data, structural and functional information of photochemical reaction centers, or contained within the known diversity of oxygenic photosynthetic organisms.


    Cardona, T. (2016). Reconstructing the origin of oxygenic photosynthesis: Do assembly and photoactivation recapitulate evolution? Frontiers in Plant Science, 7, 257. doi:10.3389/fpls.2016.00257
    Cardona, T., Murray, J. W., & Rutherford, A. W. (2015). Origin and evolution of water oxidation before the last common ancestor of the cyanobacteria. Mol Biol Evol, 32(5), 1310-1328. doi:DOI 10.1093/molbev/msv024
    Cardona, T., Sanchez-Baracaldo, P., Rutherford, A. W., & Larkum, A. W. D. (2017). Molecular evidence for the early evolution of photosynthetic water oxidation. BioRxiv, 109447. doi:https://doi.org/10.1101/109447

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  3. Nancy Kiang

    Posting for Ariel Anbar:

    "As albedo is a primary factor in a planet's energy balance but may be hard to measure remotely, is there a way to constrain the surface mineral albedo better, based on, e.g. star metallicity, orbital distance, some other formation factor?"

    I don’t see how to constrain it based on star metallicity - or at least I don’t think we know enough to do so. If it is a silicate rocky surface, the average albedo will depend on the balance of mafic vs. felsic rock. While those rock types reflect element abundances, the element abundances in these rocks depend on details of the melting of mantle material that leads to the magmas from which these rocks crystallize. Details like T, P, water content. The bulk element composition of the planet is of course a factor, but consider that the Moon and Mars both have large areas covered by mafic and felsic rocks. Then throw in oceans - very dark - as another variable, the abundance of which isn’t set by stellar metallicity… And the presence of highly reflective salt flats or ices, which again aren’t obviously constrained by metallicity, but rather by volatile inventories...

    We lack a theory of planetary evolution that would allow us to make this sort of prediction. One of my hobby-horses these days is that we lack such a theory and should set this as a community-wide, generational goal - in part because the sort of question you are asking is going to become more and more common as we get more exoplanet data.

    I'd be interested in other more informed thoughts from the remote sensing perspective."

     

     

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  4. Tanai Cardona

    I wanted to elaborate a bit more on the issue of calculating P(OP) and the lack of information regarding the origin of oxygenic photosynthesis and precursors to the OEC.

    Imagine the following hypothetical scenarios:

    1) The first form of photosynthesis is oxygenic. That is to say that photosynthesis evolve to oxidize water. Then anoxygenic photosynthesis evolved after that to avoid oxygen.

    2) Anoxygenic photosynthesis evolved first. 100 million years after the evolution of anoxygenic photosynthesis a mutation occurred that resulted in the oxidation of Mn and soon after in the oxidation of water.

    3) Same as 2) but instead of 100 million years, 1500 million years.

    4) Before the evolution of oxygenic photosynthesis, the first precursor oxidized Mn, then transitioned to peroxide, and then to water.

    5) Before the OEC, there was an Fe cluster, then after some selection it turned into a Mn cluster, with water oxidation emerging soon after.

    How any of these scenarios can be translated into a P(OP)? How is it that knowing the precursors of the OEC will help you calculate P(OP)?

    Perhaps a better approximation to P(OP) could come from estimating how quickly after the origin of life reaction centers evolved for the first time, and how quickly after the origin of reaction centers water oxidation emerged for the first time. If the answer is very quickly, then P(OP) may be high, if the answer is very slowly, then P(OP) may be low.

    I have been applying a Bayesian Framework, just like you’re proposing to do here, to the study of the evolution of water oxidation. I did this by studying the evolution of reaction center proteins (including those proteins that bind the OEC) as a function of time. Then I interrogated my data using Bayesian inference to understand what is more likely: that water oxidation emerged late in the history of life, right before the Great Oxidation Event (long after the evolution of photosynthesis); or that water oxidation evolved soon after the origin of photosynthesis (long before the Great Oxidation Event).

    I found out that the data is better explained if the origin of the OEC in Photosystem II emerged soon after the origin of photosynthesis and long before the Great Oxidation Event (Cardona et al., 2017). Thus, if photosynthesis emerged early in the evolutionary history of life, say 3.8 billion years ago (Nisbet & Fowler, 2014), then water oxidation must have emerged soon after that. Therefore, it may be that P(OP) is high.

    What I want to do now is to estimate the amount of time between the origin of life and the origin of photosynthesis from molecular data. This can be done now! The data is available because there are quite a few proteins of photosynthesis that can be traced back to the last universal common ancestor, like those involved in the synthesis of tetrapyrroles. I just need time and money!

    Cardona, T., Sanchez-Baracaldo, P., Rutherford, A. W., & Larkum, A. W. D. (2017). Molecular evidence for the early evolution of photosynthetic water oxidation. BioRxiv, 109447. doi:https://doi.org/10.1101/109447

    Nisbet, E. G., & Fowler, C. F. R. (2014). The early history of life. In K. D. M. & W. H. Schlesinger (Eds.), Treatise on geochemistry (2nd ed., Vol. 10, pp. 1-42). Amsterdam: Elsevier Science.

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  5. Nancy Kiang

    Thanks for all the brainstorming, Tanai!

    Regarding P(OP), besides using how quickly OP evolved on Earth as a metric, we would want also to know the geochemical context for the various molecules to arise, such as the Fe cluster prior to it becoming an Mn cluster.  Will look at your paper!

    The peroxide transition has been suggested in a few places, with thawing of Snowball Earth states releasing large amounts of peroxide in to the ocean. However, the Paleoproterozoic Makganyene glaciation occurred 2.3-2.2 Ga, a little more recent than the GOE at 2.4 Ga.  Maybe there were other localized frozen areas that might have released peroxide, but we need some paleoclimatologists to tell us the likely extent.

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