Rubisco and Evolution

By: Matt

Ribulose-1,5-bisphosphate carboxylase oxygenase; more commonly known as “Rubisco” sounds like something you might find in the cookie aisle at the grocery store. In fact you find Rubisco almost everywhere you look. It is the most common protein in green plants, and is by and large responsible for life as we know it. Many of us have seen Chuck Missler’s misguided video “Peanut Butter-the Atheist’s Nightmare”. Missler argues that if evolutionary theory is correct, then occasionally life should spontaneously occur in a jar of peanut butter. He is missing the boat on more than one issue. First evolutionary theory doesn’t address the origin of life; it states only that over time the frequency of genes in a population will change. Secondly it’s extremely unlikely that a jar of Peter Pan® is going to be exposed to an atmosphere similar to earth’s 3 billion years ago. He has set up a straw man, hoping that an uneducated public wouldn’t notice, and then tried to knock him down. In this essay I would like to argue that Rubisco is, in effect, “the creationist’s nightmare”. Rather than set up an imaginary straw argument I will ask a legitimate question and hope for an honest discussion.

Like all proteins Rubicso has a function, its job is to grab carbon from CO2 early on in photosynthesis and make place it onto a 5 carbon sugar (Ribulose biphosphate) in order to create a pair of 3 carbon sugars. There are several more steps involved before the plant has converted Ribulose Biphosphate into the much more familiar glucose, but all that is for another day. If you really want to understand how it all works Google “Calvin Cycle” Figure 1 shows where Rubisco fits in the Calvin cycle.

But here’s the rub. Rubisco is painfully ineffective. Virtually all life as we know it depends on green plants ability to fix carbon from the atmosphere, but the enzyme that does it is barely functional. Unlike most enzymes, which do their task and turn over in hundreds or thousands of times every second, Rubisco can fix only three carbon atoms/second. Worse, it isn’t very selective about what molecules it grabs. 27% of the time (more than a quarter of all reactions) our beknighted enzyme grabs Oxygen instead of Carbon. When this happens the oxygenated Ribulose Biphosphate molecule travels along the Calvin cycle to its completion, thus wasting not only Rubisco’s efforts, but those of every other enzyme along the way, and then a further set of enzymes that are required to break down this faulty molecule. The term for this miscue is “photorespiration” and if you were a plant you’d really hate it. The reason Rubisco is so common in plants is that it is so ineffective. If it was as speedy and precise as the other enzymes in the photosynthetic pathway its numbers could be reduced by a factor of at least 100.

So how did this come about? Why are plants saddled with this weak enzyme? Of course we can’t know for sure, as gene sequences from the pre-Cambrian are not preserved, but it’s a reasonable guess that the Rubisco was one of the very first enzymes created by the earliest organisms on our planet. There are over 400 varieties of Rubisco, indicating that it has had plenty of time to evolve, and identifying the variety of Rubisco in a leaf is one way (albeit kind of an unnecessary one) to identify the species. On the way to becoming photosynthetic, a necessary early step would have been simply capturing carbon atoms and using them as building blocks. It is easy to imagine at the time this happened our atmosphere didn’t have any Oxygen, so photorespiration wouldn’t have been an issue. Unfortunately for plants evolution isn’t a magic bullet, and even though we can imagine better ways to fix carbon, none have evolved. It’s not for lack of trying. Several plants have modified the system somewhat through either the C4 pathway or the Crassulacean acid metabolism (CAM) pathway. Neither eliminated the need for Rubisco, but both found ways of having the enzyme do its work in a region of the leaf with either less Oxygen or more CO2.

I believe that if a thoughtful creator was involved the single most important enzyme for the pinnacle of His creation (presumably that’s us humans) would not have an error rate of 27% and a speed orders of magnitude slower than others. Without green plants we don’t exist, and without photosynthesis there are no green plants, and without Rubisco there is no photosynthesis. Clearly this doesn’t prove there is no creator. An idea that can’t be proved is equally hard to disprove, but to my way of thinking this is even more telling than the litany of other questions out there. Ones like: Why do whales have finger bones? How come the Panda’s thumb is made from a different bone than my thumb? Where did the T-Rex’s go? What is does prove is that if there is a creator, the creator was forced to work from a toolbox of available pieces and parts to put together life on our planet. And THAT flies in the face of a good many religious doctrines.

My feeling is that there was no creator involved, but it can’t be proved either way and isn’t arguable. However, “young earth creationism” is wrong on every level, and can be countered by looking at the ages of rocks, the ages of stars, the geology of the Hawaiian Islands and a host of other big ticket items. We can look at the inside of each and every leaf on the planet and see the truth that stares us in the face.

12 Comments on “Rubisco and Evolution”

  1. Very reasonable indeed.

    However, IMO, to think that reason and rationality could ever provide us an understanding of life is naive at best.

    First, “tell” me how reason and language were created. And then use that language + reason to tell me how the world was created.

    I don’t think we can reason out existence. It’s too abstract.

    No offense man. I realize you’re not actually claiming to know anything, and that’s the point. You couldn’t possibly know, ever.

    And I offer you an alternative theory derived from mythology.

    Apparently, a long time ago there were these men (and women) who were capable of extraordinary deeds. They were godlike.

    They say that these people had a different system of cognition than we do today.

    The world they perceived around them was different than ours. Their description and perception of existence was quite unlike what we know today. For them, this state of being, this place we call reality was nothing more than a dream.

    And they were aware that it was a dream.

    Nobody knew exactly who had dreamt this dream first, or when. They also didn’t know if time (and space) even existed outside of this dream. What they did know was that they had been here for quite a while.

    Before they came here there was only darkness. A dreamless sleep.

    And they knew that one day they would return to the darkness.

    IMO, A good creation myth should have power, not reason.

    -f

  2. @Sh, I really like that, it is the universality of your “dream of creation” that rings, from Ancient Persian/Eastern stories to Incas they all have something similar. There must be something to that right?

  3. Sorry sh, but I have trouble believing that this world is the result of any kind of intelligence at all – all I see at work are the mindless, amoral forces of cause and effect constantly creating and destroying things.

    And such things as language are pretty easy to understand once one realizes that its creation is really not as complex as it first appears – begin with a few basic vocalizations that an animal would ascribe meaning to by instinct (such as a dog’s territorial bark or a squirrel’s danger call), add a capacity for cleverness (such as a means to develop advanced tools) and throw in a heap of socialization and viola: we have an animal that will inevitably develop a spoken language as it turns its capacity to vocalize into a tool to express ideas because it resides in an environment that requires greater levels of communication than a solitary animal would have.

  4. Azazel,

    No need to apologize bro.

    What I’m concerned with is what do these arguments bring you? What is the power in believing that everything is random and meaningless?

    The clock is ticking my friend. We are heading towards the darkness.

    I take that which brings me power and I discard everything else.

    It’s really not a matter of being right or wrong. We are all wrong no matter what.

    And I hate to be contrary, but to think that we can explain how language came to be by using language is like a dog chasing it’s tail.

    -f

  5. [Quote=sh]What I’m concerned with is what do these arguments bring you? What is the power in believing that everything is random and meaningless?[/quote]

    Now that you ask, there actually is a very significant amount power in such a realization – if all the universe is without any inherent purpose or meaning, then *we* (the sentient beings within the universe) are the arbiters of such things: existence becomes as meaningful as we want it to be as the world is a “morally” blank canvas upon which we can exercise the Will to Power – projecting our will onto reality and making it conform to us!

    In short, such a paradigm that rejects teleological interpretations of existence sets the stage for the individual to be a sovereign entity – and with this new-found power he might subvert the conventional wisdom promoted by the present order, possibly even destroy it altogether if there are enough individuals out there willing and able to act as sovereigns rather than as slaves to the established power structure.

  6. Then go ahead and claim that power my friend.

    What does it matter how we describe the world as long it brings us joy and hope?

    The world is ours. This is our moment before the dream ends.

    -f

  7. about Rubisco evolution

    Rubisco evolution is a fascinating subject.
    Yes, that enzyme “Rubisco is painfully ineffective” However, it succeed to feed all the biosphere by grabbing traces of carbon dioxide as low as 0.04 % of the present atmosphere!

    Yes, Oxygen disturbs that grabbing but it is 600 times more concentrated than Carbon dioxide.

    The energetic cost of the negative oxygen effect by photorespiration is not 27 % but more than 50 % at the beginning of the industrial era. See two papers online at Science Direct:

    Article titles:
    Modelling 18O2 and 16O2 unidirectional fluxes in plants – I. Regulation
    of pre-industrial atmosphere

    Modelling 18O2 and 16O2 unidirectional fluxes in plants – II. Analysis
    of Rubisco evolution

    http://dx.doi.org/10.1016/j.biosystems.2010.10.003

    The last one shows that, if plant evolution (and, of course, the Rubisco evolution) was directed by the gain of carbon, the gain was not as large as possible, because the negative effect of oxygen was used and developped as protective mechanism against the lag of carbon dioxide. For that, we demonstrate that the maximum velocity of oxygenase reaction of Rubisco was increased faster than the maximum velocity of carboxylase, the most useful for carbon gain. That is an example of compromise between safety and richness. Photorespiration could be considred as a costly insurance.

    Another aspect of Rubisco evolution is developped in
    Nisbet et al., 2011. The regulation of the air: a hypothesis. Solid Earth Discussion, 3, 769-788.
    with discussions en open access:
    http://www.solid-earth-discuss.net/3/769/2011/sed-3-769-2011.html
    where it is question of the role of the tail of dog…

  8. “from Ancient Persian/Eastern stories to Incas they all have something similar. There must be something to that right?”

    Or not.

    Anthropologists have long held that human development is similar, and hence human mythologies will be similar, as well. The study of parallel sociocultural development is not new; obvious structural examples are the pyramids of Egypt and the pyramids of Mexico; cultural examples of this parallelism abound.

    If there’s a similarity, it’s not because everything is ‘mystically connected’; it’s because we are truly alike, all over.

  9. I’ve got nothing more to add, except I think Anthropologists are totally clueless of what it means to be human.

    -f

  10. @W.D.-“it’s because we are truly alike, all over.”

    I agree, and it’s this ideal that causes me to believe there is importance in the stories globally.

    I didn’t mean in a “mystical” way but rather in a”spiritual” way which I view as something different.

    But hey, Tomato-Tomato.

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