A worksheet targeted for High School students proving once and for all that Photosynthesis is not “Irreducibly Complex”

Some present may remember an entertaining (not to mention illuminating (pun intended) ) blog by Professor Larry Moran:

http://sandwalk.blogspot.ca/2016/04/fun-and-games-with-otangelo-grasso.html

I am a high school Biology teacher and Professor Moran threw out some challenges which cut me to the quick.

Here is a very brief and incomplete summary:

The dual photosystems of Blue-Green Algae clearly evolved late from a combination of a type I reaction center in species like Heliobacter and green sulfur bacteria and a type II reaction center from species like purple bacteria and green filamentous bacteria. The oxygen evolving complex was a late addition.

Both photosystems employ Porphyrins and Carotenoids which are important in various metabolic processes (not just photosynthesis) meaning their evolutionary history may reflect many other functions only to be co-opted later for photosynthesis. Meanwhile both can be demonstrated to have abiogenic origins.

Meanwhile RuBisCO is found in non-photosynthetic species…

According to Professor Moran, many misconceptions are perpetuated when teaching according to textbook orthodoxy. Instead we should consider Photoreduction and Photophosphorylation as two stand-alone processes, and that the capture of light energy to produce carbohydrates is a highly specialized phenomenon; which, from an evolutionary point of view is not really (at least not originally) part of “photosynthesis” (i.e. carbohydrate anabolism).

Even Flowering Plants not only can, but in fact most of the time do, decouple ATP/NADPH production from Carbon fixation. Indeed, much of the ATP & NADPH generated by Photosystems II & I respectively are in fact redirected to immediate energy needs, even in flowering plants.

Meanwhile, I heartily agree with Larry Moran’s thesis that it is important (nay, let’s say instead imperative) to teach students that there’s more to life than just flowering plants and humans?

Larry Moran (in very unsubtle and less than gentle terms) “suggests” such strategies should apply to teaching of all biochemistry; i.e. from simple pathways to more complex pathways.

A recent “must-read” article inspired me to respond to Larry Moran’s challenge,

https://www.nature.com/articles/ncomms13924.pdf

… and I have cobbled together a worksheet, where I attempt to prove that photosynthesis is

1 – misunderstood (tis not really about Glucose and it’s not even about the Calvin Cycle) at least from a Biochemist’s evolutionary POV. Ecologists have justification to differ.
2 – NOT “irreducibly complex” but rather a hodge-podge cobbling by evolution over a long period of time. (cf https://embryo.asu.edu/pages/evolution-and-tinkering-1977-francois-jacob)

Larry Moran’s fingerprints are all over this work of mine, for which I really cannot claim any originality on my part.

I would be grateful for any constructive input and suggestions for improvement. Remember, the intended target audience remains high school students.

Thanks in advance and best regards,

Here it is:

https://drive.google.com/file/d/0By6ZKSkkTEG-QXFtWVhKOWNwREE/view

374 thoughts on “A worksheet targeted for High School students proving once and for all that Photosynthesis is not “Irreducibly Complex”

  1. OK OK… I get it. My worksheet may be a bit too elementary for most present. I still would appreciate feedback before inflicting it upon my cherubs in class.

    Thanks in advance

  2. Quantum coherence in photosynthesis for efficient solar-energy conversion

    http://www.nature.com/nphys/journal/v10/n9/full/nphys3017.html

    “…Quantum coherence describes how more than one molecule interacts with the same energy from one incoming photon at the same time. In essence, rather than the energy from a particular photon choosing one route to pass through the photosynthetic system, it travels through multiple channels simultaneously, allowing it to pick the quickest route. “The energy of the absorbed light is finding more than one pathway to move along at any one time,” explains physical chemist Greg Scholes of the University of Toronto, leader of the research group that highlighted the effect. “We can’t pinpoint the energy of that light. It’s shared in a very special way…”

    https://www.scientificamerican.com/article/shining-a-light-on-plants-quantum-secret/
    By adding Quantum Coherence should definitely help you to resolve the issue of irreducible complexity in photosynthesis…

  3. TomMueller,

    In the first paragraph you imply that the cell is nothing more then a chemical reaction chamber. This implies reaction like in a test tube versus enzymes inside living cells that are produced from DNA blue prints.

    To debunk irreducible complexity you need to explain the DNA sequences that “evolved” to create the electron transport chain which is a photo later in your presentation. Building that requires the organization of greater than 100000 nucleotides which have 4^100000 possible arrangements.

    Bottom line is that you have no experimental science to back up this claim and a huge challenge explaining the origin of the DNA sequence. I would shelve the desire to support evolution and just accurately describe the process. You are missing how the cell manufactures enzymes but maybe you have already explained this.

  4. colewd: Building that requires the organization of greater than 100000 nucleotides which have 4^100000 possible arrangements.

    I love it when Colewd talks dirty. 🙂

  5. colewd:
    TomMueller,

    In the first paragraph you imply that the cell is nothing more then a chemical reaction chamber.This implies reaction like in a test tube versus enzymes inside living cells that are produced from DNA blue prints.

    To debunk irreducible complexity you need to explain the DNA sequences that “evolved” to create the electron transport chain which is a photo later in your presentation.Building that requires the organization of greater than 100000 nucleotides which have 4^100000 possible arrangements.

    Bottom line is that you have no experimental science to back up this claim and a huge challenge explaining the origin of the DNA sequence.I would shelve the desire to support evolution and just accurately describe the process.You are missing how the cell manufactures enzymes but maybe you have already explained this.

    Thank you! That is just the kind of feedback I am looking for! You have no idea how perplexed some of my students can become when confronted with pseudo-science outside of the classroom by ignorant but well-intentioned pastors. I need just this kind of feedback to anticipate and prevent confusion.

    This reminds me of Mung’s earlier confusion regarding what he considered irreducibility of ATP (which I address in this worksheet).

    Yes of course, I address the importance of enzymes and their evolution in my own classroom, but this worksheet is going to evangelize the good word in other classrooms whose teachers may not have addressed just this sort of misconception in class.

    I remain in your debt…

  6. TomMueller: This reminds me of Mung’s earlier confusion regarding what he considered irreducibility of ATP (which I address in this worksheet).

    Please don’t make things up and attribute them to me.

    Thank you

  7. For a guy who made a grand announcement he was leaving J-Mac sure still posts a lot. Still low quality science free dreck too.

  8. Adapa,

    Thank you for reminding me that I should leave!

    I have been hoping for Joe and Tom to rip apart the quantum information conservation theory with their speculative genetics mixed with other nonsense… I guess it is not going to happen unless I leave for good…

  9. TomMueller,

    Tom
    In the paper you claim that life arose from inorganic chemicals. If a student asked how do you know this, what would your answer be?

  10. colewd:
    TomMueller,

    Tom
    In the paper you claim that life arose from inorganic chemicals.If a student asked how do you know this, what would your answer be?

    Colewd,

    I am eager to answer your question but am unable to do so until I am certain we are on the same wavelength.

    I take it you have no issues with the “standard” heliocentric model of our solar system.

    Yet according to Genesis, our flat planet is the centre of the universe (much less our solar system) which is covered by a dome-like “firmament” which holds back the primordial waters mentioned in creation.

    Apparently there are windows in this firmament which G-d opened when Noah’s flood happened.

    All the celestial bodies ; the sun the moon and the stars are embedded in this firmament, which rotates about a stationary Earth etc etc etc

    Explain to me how you know that this is not so, that astronaughts really did land on the moon according to the standard heliocentric model everyone agrees upon.

    You explain that to me and maybe then I will be in a position to answer your question…

  11. TomMueller,

    All the celestial bodies ; the sun the moon and the stars are embedded in this firmament, which rotates about a stationary Earth etc etc etc

    Explain to me how you know that this is not so, that astronaughts really did land on the moon according to the standard heliocentric model everyone agrees upon.

    The claim that the planets rotate around the sun is consistent with general relativity which is modeled and experimentally validated.

  12. Bill,

    I’m not sure why Tom is asking you the question, but you’re not answering it. You’re merely stating that the heliocentric model is consistent with GR.

    Tom is asking how you know the following is not true:

    Yet according to Genesis, our flat planet is the centre of the universe (much less our solar system) which is covered by a dome-like “firmament” which holds back the primordial waters mentioned in creation.

    Apparently there are windows in this firmament which G-d opened when Noah’s flood happened.

    All the celestial bodies ; the sun the moon and the stars are embedded in this firmament, which rotates about a stationary Earth etc etc etc

    Explain to me how you know that this is not so, that astronaughts really did land on the moon according to the standard heliocentric model everyone agrees upon.

    [Emphasis added]

  13. keiths,

    Tom is asking how you know the following is not true:

    Again, the claim is inconsistent with general relativity.

  14. colewd:

    Again, the claim is inconsistent with general relativity.

    Whence the ‘again’? You didn’t say that before. You said that heliocentrism was consistent with GR, which is different from saying that the biblical model is inconsistent with it.

    Anyway, I’m guessing that he will now ask you to explain how you know that the biblical model is inconsistent with GR.

  15. colewd:
    TomMueller,

    The claim that the planets rotate around the sun is consistent with general relativity which is modeled and experimentally validated.

    How do you know this? How do you know the empirically validated version of events is true and that Biblical exegesis is not?

  16. TomMueller: No really – Mung, you were my muse and I remain in your debt! I THANK YOU!

    So you took my question about ATP and turned it me making a claim that ATP is irreducibly complex?

    Mung: Do we have an evolutionary explanation yet for ATP?

    WoW. Please don’t do that.

  17. colewd: In the first paragraph you imply that the cell is nothing more then a chemical reaction chamber.

    I hope his students google the term.

  18. I don’t see where the paper even mentions irreducible complexity. Am I missing something here?

  19. TomMueller,

    How do you know this? How do you know the empirically validated version of events is true and that Biblical exegesis is not?

    You gain confidence through experiment of your hypothesis and its repeatable validation of the model. In the end all science is tentative.

  20. Mung: So you took my question about ATP and turned it me making a claim that ATP is irreducibly complex?

    Mung: Do we have an evolutionary explanation yet for ATP?

    WoW. Please don’t do that.

    uhmmm… please do not quote out of context, not even your own quotes.

    You made two statements and a rhetorical question in response to my statement about irreducible complexity. Here was the exchange:

    TomMueller: So, neither Chloroplasts nor the Biochemical details of Photosynthesis are indeed viable candidates for Irreducible Complexity or Intelligent Design.

    MungI never saw that coming. Pigment me devastated. 🙂

    Do we have an evolutionary explanation yet for ATP?

    So…. yes indeed your claim that your previous remarks had nothing to do with “irreducible complexity” is specious to say the least!

    Please “stop doing that” if indeed we are to continue any exchange. Your intellectual dishonesty is deplorable.

  21. Mung:
    I don’t see where the paper even mentions irreducible complexity. Am I missing something here?

    As I just demonstrated in the previous post:

    YES INDEED … you are missing much! Perhaps you should reread the paper, especially the last two pages.

  22. colewd:
    TomMueller,

    You gain confidence through experiment of your hypothesis and its repeatable validation of the model.In the end all science is tentative.

    Now you are delving into questions philosophical. Yes indeed, at a very fundamental level you are correct BECAUSE ALL KNOWLEDGE IS TENTATIVE

    Where is NeoKantian when we need him?

  23. This is great! I am going to use all this in the classroom! … especially the bit about … repeatable validation of the model!”

    Gentlemen,[sic] yet again I remain in your debt!

  24. TomMueller: Your intellectual dishonesty is deplorable.

    So you make things up about what I claimed and then accuse me of intellectual dishonesty. And you’re allowed to teach children. Did you vote for Trump?

  25. Mung: So you make things up about what I claimed and then accuse me of intellectual dishonesty. And you’re allowed to teach children. Did you vote for Trump?

    1 – t’is you and not I, who is “making things up”. I will leave it for others to adjudicate.

    cf http://theskepticalzone.com/wp/remedial-education-for-colewd/comment-page-4/#comment-194258

    2 – better minds than yours consider that teaching creationism to children constitutes child-abuse. http://www.huffingtonpost.ca/entry/lawrence-krauss-physicist-creationism-taliban-child-abuse_n_2687808

    3 – I acknowledge and accept your ad hominems in the embittered spirit intended. Your obvious frustration indicates that I have you writhing in the talons of my inescapable logic and I gratefully receive your implicit (albeit less than gentlemanly) concession of defeat.

    Quod erat demonstrandum

    But please, let us not stop here! You continue to provide me excellent material for the classroom.

  26. TomMueller,

    YES INDEED … you are missing much! Perhaps you should reread the paper, especially the last two pages.

    The key thesis according to the op is that photosynthesis is not irreducibly complex. How would you argue the electron transport is not irreducibly complex? What do think would happen if you permanently knocked out cytochrome c in a mouse embryo?

    I don’t see your theme well supported as I don’t see your claim about abiogenesis well supported. Are you trying to use abiogenesis as a tool to support your argument against irreducible complexity?

  27. colewd: I don’t see your theme well supported as I don’t see your claim about abiogenesis well supported.

    Yet you are a design-proponent, despite the total and complete absense of any support for all ID-claims ever made.

    Astonishing hypocricy.

  28. TomMueller,

    Please “stop doing that” if indeed we are to continue any exchange. Your intellectual dishonesty is deplorable.

    I acknowledge and accept your ad hominems in the embittered spirit intended. Your obvious frustration indicates that I have you writhing in the talons of my inescapable logic and I gratefully receive your implicit (albeit less than gentlemanly) concession of defeat.

    You make an ad hominem argument then accuse Mung of one. Are you aware of this projecting you are doing? This is evidence of a lack of good faith, however I hope this is just a mistake on your part.

  29. The C4 version of photosynthesis evolved 40 times independently. Sonar also evolved independently in whales and bats.

    https://en.wikipedia.org/wiki/Convergent_evolution

    For instance, C4 photosynthesis, one of the three major carbon-fixing biochemical processes, has arisen independently up to 40 times.

    The “miracles” of evolution are endless. Not only did C4 photosynthesis evolve, it happened 40 times independently! Freaking amazing how random mutations will conspire to make the same thing over and over again.

    Look at all the other examples of convergent evolution too….

    PS
    The above are my sarcastic remarks.

  30. Rumraket,

    Yet you are a design-proponent, despite the total and complete absence of any support for all ID-claims ever made.

    Do you honestly believe this?

  31. colewd:

    Do you honestly believe this?

    Absolutely. Every last piece of “evidence” offered for ID-Creationism is of the negative form “natural processes can’t explain this to my satisfaction, therefore my specific GOD diddit!!” Every. Last. Piece.

    That false dichotomy doesn’t work in the scientific realm. In fact the God of the Gaps argument was rejected by science over 300 years ago.

  32. stcordova:

    The “miracles” of evolution are endless. Not only did C4 photosynthesis evolve, it happened 40 times independently!Freaking amazing how random mutations will conspire to make the same thing over and over again.

    Not so amazing is yet another time an, er, honest genius YEC ignores the feedback effect of selection in determining the results of evolutionary processes.

    PS
    The above post is sarcastic.

  33. …life had inorganic origins and all life forms continue to employ many of the same reactions that occurred in “proto-cells”, which were not yet “living”. Meanwhile, some bizarre modern cells have retained peculiar inorganic chemical reactions unique to the first “proto-cells” but occur nowhere else in Biology.

    Unlike today’s seas, the early ocean was acidic and rich in dissolved iron. When upwelling hydrothermal fluids reacted with this primordial seawater, they produced carbonate rocks riddled with tiny pores and a “foam” of iron-sulphur bubbles (the first proto-cells).

    These “energy-rich” “primitive co-enzymes” “drove” various reduction reactions in the formation of amino acids, the building blocks for proteins; and nucleotides, the building blocks for RNA and DNA.

    I see that you don’t limit making stuff up to the things that I write. Are you trying to teach your students or indoctrinate them?

  34. TomMueller: As I just demonstrated in the previous post:

    YES INDEED…you are missing much!Perhaps you should reread the paper, especially the last two pages.

    Nope. Nothing in there about irreducible complexity at all. Did you take out some pages?

    How can you not know what your own paper contains?

  35. colewd:
    Rumraket,

    Do you honestly believe this?

    Well, one could dispute whether every claim of IDists totally lacks support, but certainly the main positive claims are without any of the kind of support that should be required in science or in the judiciary. Especially, there is no definitive evidence for the design of life, even if one doesn’t especially fault a Newton or a Paley for thinking that their vague “evidence” pointed that way in their times. But many biologists knew even before Darwin that, while some aspects of life seemed quite well “designed,” others were rather different. “Homologies” were already identified as having affinities with “relatives,” and were not simply chosen to meet needs, a peculiar deviation from what we get from intelligent choices.

    This seems to be one of the issues that we have in communicating with creationists, who generally lack any real grasp of what counts as evidence in science. The problem is that the evidence needs to be much more specific than IDists/creationists seem to think that evidence is, and one doesn’t get to default to design just because one really prefers that “explanation.”

    Most importantly, reasonable ID is clearly falsified. Common design shouldn’t be limited to earlier “innovations” while lacking access to more recent (after divergence) ones, but that’s what we see. Bird wings have all of the evidence of having evolved from articulated terrestrial forelimbs (including the complexity of developing single structures from several bones to this day), and none of the evidence of knowledge of pterosaur wings or of bat wings–and vice versa. Makes total sense with unthinking evolutionary processes, no sense with “common design.”

    Thought possibilities simply aren’t limited to genealogy, while life’s possibilities are. That’s evidence, while all of the vague handwaving at how complex life is merely rests on unwarranted belief that, because we make complex functional things, a god must be responsible for complex functional things that we didn’t make. Because most creationists/IDists can’t think beyond that simplistic anthropomorphism, they never really even begin to evaluate the evidence in an analytic fashion.

    Glen Davidson

  36. Like a lot of Darwinists, Tom simplifies the complexity involves. He suggests just because proteins are pumped out that they will spontaneously assemble into photosynthetic structures. This is like arguing a frog will reassemble itself after being put in a blender because all the available proteins are there! HA!

    And Tom is a high school biology teacher. Has he learned yet transcription factors are proteins, not RNAs. Hehehe.

    But in any case, for those loving quantum mechanics, it plays out in the topic of solid state physics. We are taught in elementary theory about particles like electrons. Well there are quasi particles in quantum mechanics called EXITONS! A solid state substance, if properly assembled can allow exiton flow. Below is a schematic of one part of a photosynthetic system. It’s not quite as simple as Tom makes it out to be. You can see the parts have to be positioned properly to work. This involves developmental mechanisms.

    Click for larger image:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/11/exiton.png

    FIGURE 19–60 The supramolecular complex of PSI and its associated antenna chlorophylls. (a) Schematic drawing of the essential proteins and cofactors in a single unit of PSI. A large number of antenna chlorophylls surround the reaction center and convey to it (red arrows) the energy of absorbed photons. The result is excitation of the pair of chlorophyll molecules that constitute P700, greatly decreasing its reduction potential; P700 then passes an electron through two nearby chlorophylls to phylloquinone (QK; also called A1). Reduced phylloquinone is reoxidized as it passes two electrons, one at a time (blue arrows), to an Fe-S protein (FX) near the N side of the membrane. From FX, electrons move through two more Fe-S centers (FA and FB) to the Fe-S protein ferredoxin in the stroma. Ferredoxin then donates electrons to NADP (not shown), reducing it to NADPH, one of the forms in which the energy of photons is trapped in chloroplasts. (b) The trimeric structure (derived from PDB ID 1JBO), viewed from the thylakoid lumen perpendicular to the membrane, showing all protein subunits (gray) and cofactors. (c) A monomer of PSI with all the proteins omitted, revealing the antenna and reaction-center chlorophylls (green with dark green Mg2 ions in the center), carotenoids (yellow), and Fe-S centers of the reaction center (space-filling red and orange structures). The proteins in the complex hold the components rigidly in orientations that maximize efficient exciton transfers between excited antenna molecules and the reaction center.

    Nelson, David L.; Cox, Michael M.. Lehninger Principles of Biochemistry (Page 781). W.H. Freeman. Kindle Edition.
    Nelson, David L.; Cox, Michael M.. Lehninger Principles of Biochemistry (Page 781). W.H. Freeman. Kindle Edition.

    So we see some serious solid state engineering at the quatum level. Quasi particles are familiar to those in the transistor and computer chip industry as quasiparticles are the order of the day. The Designer levererages quasiparticle technology.

  37. Tom, what biology textbook are your students using and does it tell a different story for the origin of life than tale you tell in your paper? How do you plan to explain that to them?

    Do you also tell them that the entire earth and it’s atmosphere is also just a huge chemical reaction chamber? Heck, the entire universe is nothing but a massive chemical reaction chamber!

    Your students are nothing more than a conglomeration of chemical reaction chambers inside another chemical reaction chamber inside yet another chemical reaction chamber. Be sure to tell them that.

    Be sure to tell them how you are merely a collection of chemical reaction chambers emitting ‘information packets” that will infect their own chemical reaction chambers with your doctrines and that they should be taken with a grain of NaCl.

  38. I love how theists constantly argue that a wonderful, extremely intricate and complex universe (or life) like ours points to the existence of God, and also that without God the universe (and life) is just “a bunch of chemicals”

  39. Regarding the EXITONS in the diagram above for certain classes of photo synthesis.

    https://en.wikipedia.org/wiki/Exciton

    When a molecule absorbs a quantum of energy that corresponds to a transition from one molecular orbital to another molecular orbital, the resulting electronic excited state is also properly described as an exciton. An electron is said to be found in the lowest unoccupied orbital and an electron hole in the highest occupied molecular orbital, and since they are found within the same molecular orbital manifold, the electron-hole state is said to be bound. Molecular excitons typically have characteristic lifetimes on the order of nanoseconds, after which the ground electronic state is restored and the molecule undergoes photon or phonon emission. Molecular excitons have several interesting properties, one of which is energy transfer (see Förster resonance energy transfer) whereby if a molecular exciton has proper energetic matching to a second molecule’s spectral absorbance, then an exciton may transfer (hop) from one molecule to another. The process is strongly dependent on intermolecular distance between the species in solution, and so the process has found application in sensing and molecular rulers.

    Freaking amazing what random mutation can do (NOT!). Or mixing proteins in a blender (NOT!).

  40. Mung:

    …just a huge chemical reaction chamber….
    …nothing but a massive chemical reaction chamber!…
    … nothing more than….
    … you are merely a ….

    Even YOU should tire of this strawman built from false dichotomies.

  41. dazz: I love how theists…

    I love how Tom calls a “foam” of iron-sulphur bubbles the first proto-cells.

    He may as well be teaching his kids about Santa, the Tooth Fairy and the Easter Bunny.

  42. dazz:
    I love how theists constantly argue that a wonderful, extremely intricate and complex universe (or life) like ours points to the existence of God, and also that without God the universe (and life) is just “a bunch of chemicals”

    More precisely a bunch of subparticles…
    Arrangement of them into life is the tricky part…unless you know how to do it?

  43. J-Mac: More precisely a bunch of subparticles…
    Arrangement of them into life is the tricky part…unless you know how to do it?

    Begging the question 101
    Also, you missed my point entirely

  44. dazz: Begging the question 101

    Right! I forgot that you don’t know how to arrange the chemicals into life either but dumb luck dose… That explains the intelligence part…

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