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
You clearly missed my point! You are committing the identical ignoratio elenchi as Otangelo Grasso as described in the OP. Perhaps you should reread it.
I suggest you review some basic Biology at a high school level!
This is from an online high school level text :
C4 cells in C3 plants
The ability to use the C4 pathway has evolved repeatedly in different families of angiosperms — a remarkable example of convergent evolution. Perhaps the potential is in all angiosperms.
A report in the 24 January 2002 issue of Nature (by Julian M. Hibbard and W. Paul Quick) describes the discovery that tobacco, a C3 plant, has cells capable of fixing carbon dioxide by the C4 path. These cells are clustered around the veins (containing xylem and phloem) of the stems and also in the petioles of the leaves. In this location, they are far removed from the stomata that could provide atmospheric CO2. Instead, they get their CO2 and/or the 4-carbon malic acid in the sap that has been brought up in the xylem from the roots.
If this turns out to be true of many C3 plants, it would explain why it has been so easy for C4 plants to evolve from C3 ancestors.
http://www.biology-pages.info/C/C4plants.html
Quod erat demonstrandum!
No… No… No… that is exactly the opposite of what I am suggesting. You are presuming “irreducible complexity”! I am not! That is why I suggest the bits and pieces of the chloroplast biochemical machinery are independent stand-alone operations that can and do operate independently of each other, and were cobbled together by evolution over geological time. Take Cyclic Phosphorylation for example where PS I operates independently of PS II even in modern angiosperms (as just one example)
Damn – I wish you would study some High School Biology! My students all know that NOT ALL transcription factors are protein and that gene regulation is not all about transcription factors.
Allow me to cite another high school level source on the subject you should master before you pester me again! http://www.biology-pages.info/R/R.html#rna
Wow Sal… there you again! If you cannot dazzle anybody with brilliance, baffle them with BS! Could you please at least try to understand my comments before cutting and pasting diagrams you also clearly do not understand.
I will address the quantum rebuttal presently.
I agree with Nicolas Humphrey, Daniel Dennett and Richard Dawkins, Christopher Hitchens, Lawrence Krauss and countless others that Christian Jihadi (like yourself) who indoctrinate your children with anti-scientific Creationism are guilty of child abuse, but for different reasons than they suggest.
I discussed this with a pious Baptist pastor as we were both watching our children play water-polo and I suggested to him that he should embrace (Leviticus 19:14): “You shall not curse the deaf nor place a stumbling block before the blind…”
If children realize that Evolution is just as empirically valid as the Heliocentric Theory of the Solar System, these children may turn their back on faith entirely, and I consider that a bad thing (a view not unanimously held by many present, I understand.)
That Baptist pastor and I met on common ground and he no longer promulgates the nonsense you ascribe to.
You Mung – are a dangerous man who as many others here will cause scandal and outrage in innocent minds who should rather be taught Non-overlapping magisteria (NOMA) as espoused by Stephan Jay Gould, such that your young charges understand at the outset that faith cannot contradict science and vice versa.
… funny you should mention that…
I once suggested to a Catholic hard-line theologian that belief in the Nicean Creed was tantamount to belief in the Easter Bunny and Santa Claus.
You should read some Bart Ehrman. He too was once a born-again Christian who believed in Jesus’ divinity… until the scales fell off his eyes that is.
I have been reviewing a lot of Ehrman lately and delving into other authors’ analyses which are riveting
I could recommend some titles if you like.
J-Mac I am in your debt! Just like Mung before, you have inspired another worksheet!
I am amazed how naive Theists of the YEC-sort are quick to expound eloquently on the perfection of G-d’s creation only to be contradicted by how adaptations are rarely perfect (Panda’s thumb and all) and apparently jerry-rigged and cobbled together in less than perfect fashion coincidentally from parts already available.
Such silliness occurred on Larry Moran’s sandwalk.blogspot where a beleaguered mregnor “cried uncle” and declared that Intelligent Design did not ipso facto imply perfection!
… leaving him hoisted on the horns of a Popperian dilema
Again – I thank you just as I thanked Mung. You gentlemen [sic] are my muses and I shall return with another worksheet presently
TomMueller,
I was simplifying the “foundations” of matter and life for dazz’s sake as he clearly can’t think on quantum level…
If you really would like to expand your photosynthesis work sheet, you should consider going deeper; to the quantum level, as clearly photosynthesis operates on this level with almost 100% efficiency, where things are not only irreducibly complex but can also be in two places or more at the same time…or even beyond time…
If this subject is beyond your expertise, you can always as for help from two regular commentators here: Tom English and Joe Felsenstein.
Joe recently attempted to unify the general theory of relativity with quantum mechanics…as well as to apply the many different properties of water to an equation…
Tom, on the other hand, has been working on the math for quantum coherence in mutations…
Where are you going to get better expert support than here?
TomMueller,
This is from Larry’s blog. I made a small exchange with Larry but in the end I mostly agreed with his position.
So the problem I was trying to point out is your statement in the blog ” that you are going to prove once and for all the photosynthesis is not irreducibly complex” You can see that Larry disagrees with you.
Larry is making the statement that a claim that something could not possibly evolve is a statement of ignorance.
The same goes for your statement. You have positioned yourself to try and prove a negative which is very difficult.
Irreducible complexity was coined by Mike Behe to challenge Darwin’s claim that step by step processes can account for the diversity of life. Irreducible complexity is indeed a challenge to that claim.
No I am not disagreeing with Larry Moran. You are moving words around on a computer screen without attaching meaning to them
Larry specifically said Just because something is irreducibly complex by some strict definition doesn’t mean it could not have evolved.
I agree
What I am arguing (and Larry agrees) that any such strict definition of “irreducible complexity” does not apply to “photosynthesis” as Otangelo Grasso
wanted to maintain.
You really should reread the OP
And even more so to the claim that an imperceptible intelligence designed it.
Funny how IDists forget that, like, always.
Glen Davidson</a
TomMueller,
From Larry to Otangelo
Again Tom
Your paper does not support its thesis.
Your problem is the large difference between “remove any of the important proteins” and “step by step” evolution. If IC refers to the former only, then it doesn’t match reality. If it refers to the latter only, it isn’t a barrier to evolution. There are may possible steps other than the addition of invariant parts. Parts can change. A protein added originally to make a function work better can gradually assume the entire function and so become essential. That’s only one of many possible scenarios for gradual evolution of a system that has become IC.
John Harshman,
This is a hypothesis. Is it tested? Why would we assume that a protein for discrete function A could with 12 other proteins co opt to form an entirely new system like ATP synthase. How do you explain the DNA changes to get from A to B with a step by step process. Its hard to believe that random change could get a dozen discrete proteins to successfully bind together let alone form a complex function at the end.
Is there any evidence that self replication can occur without ATP synthase? If not we have no evidence that we can start the Darwinian process prior to this complexity. Behe’s argument is indeed challenging.
I try to make allowances for the fact that you have no idea what many of the words you say actually mean. When you say “tested”, for example, you presumably refer to evolving a complex system in the laboratory, which is quite unlikely and irrelevant to anything real. One can instead test by observation, in this case finding systems that are intermediate in some process of reaching IC. Consider, for example, the ribosome, a huge complex. Yet if you digest away all the proteins, leaving only the RNA, the ribosome is still capable of translation, though much less efficiently. I would consider that a good model. Note that this is quite different from a mass of random proteins spontaneously assembling into a new system.
A couple of points:
1- your rebuttal is irrelevant to my thesis
2- your rebuttal is wrong!
My thesis is a contradiction of Otangelo who claimed that the “miraculous” complexity of “photosynthesis” in its ENTIRETY means it is irreducible complex which Otangelo defined clearly: it could never have been cobbled together by available preexisting bits and pieces already available as stand alone operations.
In simple terms, Otangelo reiterated the “what’s the use of half an eye” as “what’s the use of half a chloroplast?”
My worksheet prompted students to understand that Photophosphorylation and Photoreduction and RuBisCo can and do operate independently in isolation, even today in modern ambassadors of ancient lineages still intimately associated with inorganic substrates in fashions which could not be too dissimilar to the earliest cells which evolved from abiotic protocells.
Your obtuse inability to immediately recognize the salient tenents of my thesis is telling!
Again I thank you and will rework my worksheet accordingly to make the logical progression more explicit and the conclusions yet more inescapable
THANK YOU! You too are my muse!
Regarding your distracting “essential protein” Shibboleth … John Harshman slew your non-argument better than I could manage, so I will dumb it down for you.
Yes, you can TODAY identify “essential proteins” whose function is essential in Chloroplasts TODAY!
You are begging the question again. I will not insult your intelligence by going any further.
See below
Oh wow… this like the movie Ground Hog Day
I see you are repeating the tactics of Otangelo!
You have moved the goal posts! It would appear you are implicitly conceding that “photosynthesis” is NOT IC but fathered cobbled together from pre-existing bits and pieces…
… obliging you to change tacts with the specious suggestion that the original bits & pieces themselves were I
Thank you… I agree that my next worksheet should follow just that train of thought!
BTW, ATP Synthase has commonalities with a DNA helicase with ATPase activity and H+ motors of Flagella
Not that it matters!
A modern Eukaryotes has demonstrated a reversion to ATP synthesis without the proton turbine found in Chloroplasts and Mitochondria
http://www.sciencemag.org/news/2016/05/first-eukaryotes-found-without-normal-cellular-power-supply
IOW not only is it possible to eliminate that “essential protein” you desperately invoked, it is even possible for a eukaryotes to forego an essential organelle
I realize now I failed to adequately answer this earlier question.
Otangelo Grasso went into ecstatic panegyrics extolling the miraculous complexity of “photosynthesis” and how it would be impossible to:
1 – separate the parts from each other by some sort of biochemical botanical vivisection and still keep a flowering plant alive
2 – meaning, the whole photosynthetic process of an angiosperm must be intelligently designed because something this marvelously complex could not arise spontaneously without divine intervention.
That is why Otangelo Grasso was disparagingly identified in mocking terms by others as an IDiot ( a term I myself would never use)
Yes of course, the complicated biochemistry of a chloroplast did not arise spontaneously all at once by natural processes. Everyone agrees on that.
That is why Scientists have identified the transitional and intermediate stand-alone processes which were cobbled together over geological time by Evolution.
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 (exactly like P. aestuarii mentioned in my worksheet) and a type II reaction center from species like purple bacteria and green filamentous bacteria.
The oxygen evolving complex was an even later 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… and is not integral to photosynthesis.
Maybe y’all should reread the OP again!
TomMueller,
I now understand you are attacking a strawman of Behe’s argument. The strawman is vulnerable yet you have come a very small way to address it. How does evolution “cobble anything together”?
How do you know there is enough time and population for known natural evolutionary processes to work?
How do you know they were “cobbled together”? Cobbled together implies a cobbler. Without a cobbler you are counting on serendipity to find functional advantage.
This is an assertion. I understand that most all papers on evolution make this assertion.
Co option is another evolutionary assertion. The reasoning is circular based on the a priori assumption of common descent.
Really? Any citations?
colewd
your comments are great! Keep them coming! Thank you!
This just the sort of dissimilitude some of my students are encountering outside of the classroom which requires remediation.
Hey, you borrowed this line from keiths!
Does your school encourage plagiarizing?
TomMueller,
I agree you made good arguments on this point. There is a long way from here to claiming that photosynthesis is not ” irreducibly complex”by Behe’s definition.
Ontagelo’s strawman is easier because he took an extreme position. I recommend you name your paper how to defeat an extreme creationist argument, which lowers your burden of proof and makes your evidence come alive.
John Harshman,
I mean to test directly the hypothesis. Observation is fine in formulating a hypothesis but it does not necessarily tell you if your model is repeatable.
So this observation starts a hypothesis. How do you test for the minimum configuration that will support cell replication reliably?
How have you tested ID?
Yeah, that’s what I thought.
Glen Davidson
That’s exactly what I thought you meant. I may have pointed out before that you have no idea how science works or what “test” means in science. This is a case in point.
I doubt you can, by your meaning of “test”. What the example does is to show that your idea is unwarranted and that plausible intermediates exist.
Let’s try something else. Do you think that the sun condensed from a gas cloud into a protostar, and that gravitational collapse led to the initiation of hydrogen fusion that gradually stabilized to put the sun on the main sequence? Or do you think that’s just an untested hypothesis, and we’ll never actually know until we can create a star by this process in the laboratory?
colewd, to TomMueller:
Tom,
Bill (colewd) isn’t right about much, but he did get this one right. Photosynthesis is irreducibly complex by Behe’s definition:
The IDers’ error is not in thinking that some biological systems are irreducibly complex; they are, by Behe’s definition. The error is in thinking that this renders them unevolvable.
What you’re trying to show in this thread is that photosynthesis is evolvable, not that it isn’t irreducibly complex.
John Harshman,
You can develop a model and test this because the parameters are measurable and repeatable such as masses gravitational effects and atomic forces.
You cannot predictably model random changes in DNA or model when reproductive advantage occurs.
You can make a probabilistic model of the length of time to fix a mutation in a population (Lynch). You can observe and measure cell replication which allows for testing a reduced ribosome.
Really? Where is the laboratory test of solar formation? I don’t recall one.
You don’t have to. Nor can you predictably model which particles formed the sun, but that doesn’t stop you.
Whatever do you think you’re talking about here? How does any of that allow for testing a reduced ribosome? And of course any model of solar formation can only be probabilistic. So, you’re an OEC, not a YEC?
Hi Keiths
I think we understand each other but I fear our gainsayers do not.
Behe indeed parses his terms far more carefully than those who quote him as already explained in this here:
http://tinyurl.com/y9fqjuv5
The issue is that even Behe is prone to conflating IC with “non-evolvability”
Behe: Demonstration that a system is irreducibly complex is not a proof that there is absolutely no gradual route to its production. Although an irreducibly complex system can’t be produced directly, one can’t definitively rule out the possibility of an indirect, circuitous route. (Behe, 1996, speech delivered to the Discovery Institute)
But Behe goes on to say that “as the complexity of an interacting system increases, the likelihood of such an indirect route drops precipitously.”
Excellent discussion here: http://content.csbs.utah.edu/~rogers/evidevolcrs/ircomp/index.html
Otangelo Grasso and others have suggested “photosynthesis” would be a paradigm of just such a conflation of IC with “non-evolvability”
Behe apparently has backed away from photosynthesis as a paradigm as colewd himself has himself just conceded above.
I am reminded of the apocraphyl story of Huxley supposedly whispering to Sir Benjamin Brodie: ‘the Lord hath delivered him unto my hand’ before replying to Bishop Wilberforce:
http://www.oum.ox.ac.uk/learning/htmls/debate.htm
The concession on colewd’s part has pulled the rug from under the creationists and John Harshman is running in for the kill, even as we speak.
I am bemused to note that colewd has been abandoned by his erstwhile allies and is standing alone in his defense of the undefendable.
John Harshman,
The causes have been tested. Einsteins model of general relativity was tested in 1918 by the eclipse experiment that validated his model that predicted space time curvature. The experiment has been repeated several times. This is the model used in cosmology and predicts star formation and ultimately black hole formation.
You do have to because evolution is driven by changes to DNA. The location of a given hydrogen atom in star formation is not relevant, however in DNA the order of the 4 types of nucleotides is critical to the specific life form.
If we were to start to knock out protein coding genes for ribosomes in e coli I could find out if we can grow a population with a reduced ribosome. Evolution as a concept requires self replication.
As far as YEC vs OEC I think the arguments of the OEC is more convincing. Michael Behe in particular.
colewd,
Behe accepts common descent. Does that cause any cognitive dissonance for you?
TomMueller:
Sure, but that’s no reason for you to do the same.
The lesson for your students should be “Yes, there are IC systems in biology, but that’s not a barrier to their evolution.”
keiths,
Behe does not chose to engage in debate on common descent and I don’t have a problem with that decision.
colewd,
That isn’t what I asked.
keiths,
Irreducibility complexity creates a problem for the standard evolutionary model especially with the discovery of DNA a sequence dependent blue print. If Tom is honest he will admit there are problems with text book evolutionary theory.
keiths,
I am trying to correct you because you think Behe believes in common descent. The reality is Behe does not think common descent is important and choses not to engage. Behe’s strategy is to attack Darwin’s mechanism which is really the backbone of his theory. I have been wondering when you guys are going to wake and smell the coffee 🙂
Your ability to self-delude without examining the evidence extends to Behe’s opinions too. Here are some quotes from Behe’s book The Edge of Evolution (taken from a creationist poster who’s angry about them):
“Evolution from a common ancestor, via DNA changes, is very well supported” (p. 12).
“[O]ne leg of Darwin’s theory—common descent—is correct” (p. 65).
“The bottom line is this: Common descent is true” (p. 72).
“Despite some remaining puzzles, there’s no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives” (p. 72, emp. added).
Now is that choosing not to engage?
colewd,
He does, Bill. And it’s clearly causing you pain.
Behe, from The Edge of Evolution, p. 65:
No it doesn’t. And there’s no “standard evolutionary model” for which your argument applies.
Irreducibly complex functions and structures routinely evolve. A thing so simply as a potentiating neutral mutation that has to happen first, in order to yield a new function in conjuction with a beneifical mutation through an epistatic interaction, is an example of an irreducibly complex function that evolved.
The discovery of DNA and the sequence information it contains was a colossal confirmation of the reality of historically inferred evolutionary relationships. Reality is diametrically opposite to what you mindlessly repeat here.
From Theobald’s 29+ Evidences for macroevolution:
“It will be determined to what extent the phylogenetic tree, as derived from molecular data in complete independence from the results of organismal biology, coincides with the phylogenetic tree constructed on the basis of organismal biology. If the two phylogenetic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished. Indeed, only the theory of evolution, combined with the realization that events at any supramolecular level are consistent with molecular events, could reasonably account for such a congruence between lines of evidence obtained independently, namely amino acid sequences of homologous polypeptide chains on the one hand, and the finds of organismal taxonomy and paleontology on the other hand. Besides offering an intellectual satisfaction to some, the advertising of such evidence would of course amount to beating a dead horse. Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life.” – Emile Zuckerkandl and Linus Pauling, discussing the possibility of the twin nested hierarchy before the first molecular phylogenies had been made.
(1965) “Evolutionary Divergence and Convergence in Proteins.” in Evolving Genes and Proteins, p. 101.
Yes, he, no more than you, actually bothers to come up with any evidence for design.
Instantly revealing the pseudoscientific core of his project.
Glen Davidson
Behe, from The Edge of Evolution, p. 71:
Ouch, Bill.
And the causes of evolution haven’t been? Actually, we stick with the tested causes of evolution, mainly because they have been tested.
What’s not been tested in any manner is design by unpercieved being.
Yes, that’s the beauty of evolution, it sticks with physics, not poofery. IOW, while evolution isn’t intimately tied to GR, it’s what is compatible with it, while energy/matter coming from outside of the system via miracle is not.
In some sense, though, it is true that stellar and planetary accretion are relatively predictable, if not down to the most minute details. What isn’t predictable (not way before the event, anyhow), say, is the geology of terrane accretion on the west coast of North America.
Or language evolution. How would anyone predict the vowel shift of English? Or, in Justinian’s day, who could predict the evolution of English after the Norman Conquest? Some things are just too complex to predict, while many of the causes can be sorted out after the fact–as in language evolution and biologic evolution.
Of course you don’t. It would be nice if you could, but many things are irreducibly complex (butterfly effect), yet they can be understood by science to a fair degree.
When are you going to be able to predict anything at all using design?
Why don’t we need to replicate language evolution in order to recognize it and its main causes?
You have yet to make any convincing argument for either.
Glen Davidson
keiths,
Here is a video that is years after the edge was published with a conversation between me and Mike Behe. It starts at 1hr 23 min in. Salvador is also on the call.
colewd,
What does is say that you want anyone to know? Does it contradict the claims about common descent in his various books?
Rumraket,
Can you back up this claim with experimental evidence that irreducibly complex functions routinely evolve. Lenski is at 60000 generations or more. What irreducibly complex features evolved there? Gene duplication and the expression of an existing gene?
John Harshman,
It will show what I am claiming came from a direct conversation about common descent and not some quote from a book.
colewd,
I watched that segment and nothing in it contradicts what Behe wrote in The Edge of Evolution.
Behe accepts common descent. Deal with it.
What in there contradicts the quotes from the book? Behe admits universal common descent but says he isn’t very interested in the subject. That’s all.
Behe says something like: “I think the evidence for common descent is strong, it explains the similarities, design explains the differences”
keiths,
If thats what you got out of the video it explains a lot.