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

Adam and Eve still a possibility?

Geneticist Richard Buggs, Reader in Evolutionary Genomics at Queen Mary University of London, has just written an intriguing article in Nature: Ecology and Evolution (28 October 2017), titled, Adam and Eve: a tested hypothesis? Comments on a recent book chapter. It appears that Buggs is unpersuaded that science has ruled out Adam and Eve. He thinks it’s still theoretically possible that the human race once passed through a short, sharp population bottleneck of just two individuals, followed by exponential population growth. Buggs disagrees with the assessment of Christian biologist Dennis Venema, professor of biology at Trinity Western University in Langley, British Columbia, who forthrightly declared in chapter 3 of his 2017 book Adam and the Genome that it is scientifically impossible that the human lineage ever passed through a bottleneck of two, and we can be as certain about this fact as we are about the truth of heliocentrism.

Here’s Buggs’ take-down of the three methods employed by Venema to discredit the possibility of a single primal couple. As a layperson, I have to say it looks as if Buggs has done his homework:

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The Cross: An embarrassment at the heart of Christianity

In a recent thread, I challenged Christians and other believers to explain why their supposedly loving God treats people so poorly. Toward the end of the thread, I commented:

We’re more than 1200 comments into this thread, and still none of the believers can explain why their “loving” God shits all over people, day after day.

If you loved someone, would you purposely trap them under the rubble of a collapsed building? Or drown them? Or drive them from their home and destroy their possessions? [Or stand by, doing nothing, while a maniac mowed them down using automatic weapons?]

Your supposedly loving God does that. Why?

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The Anti-Synthesis

Why we don’t want another “Synthesis”

High-level debates in evolutionary biology often treat the Modern Synthesis as a framework of population genetics, or as an intellectual lineage with a changing distribution of beliefs. Unfortunately, these flexible notions, used to negotiate decades of innovations, are now thoroughly detached from their historical roots in the original Modern Synthesis (OMS), a falsifiable scientific theory.

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Common Design vs. Common Descent

I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.

Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.

If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.

One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.
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It is time to say goodbye to J-Mac

As some on you have probably realized, the time comes for everyone to move on…
This time came for me…I believe it is in the best interests of everyone…without getting into any details.

I have learned a lot here. It was fun too…

For those who care, I have several time-consuming projects going both in my professional life and in my very rich life of the many hobbies… Interestingly, some of my hobbies became more that just that, and today pay many of my bills…I just hope that my new hobbies will not join the other side as there are only 24 hours in each given day.. 🙂

I wish you all well and please keep seeking the truth… wherever it leads you…

J-Mac

Five Proofs

of the Existence of God

Philosopher Edward Feser has a new book out in which he puts forth five arguments for the existence of God. These are not the “Five Ways” of Aquinas so it might be refreshing to discuss one or all of these. At the very least this OP may introduce readers to arguments for the existence of God which they had previously been unaware of.

The five proofs are:

  • The Aristotelian Proof
  • The Neo-Platonic Proof
  • The Augustinian Proof
  • The Thomistic Proof
  • The Rationalist Proof

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PVS patient regains consciousness after 15 years, thanks to nerve stimulation

From The Guardian (September 25, 2017): Nerve implant ‘restores consciousness’ to man in vegetative state by science correspondent Hannah Devlin:

A 35-year-old man who had been in a vegetative state for 15 years has shown signs of consciousness after receiving a pioneering therapy involving nerve stimulation.

The treatment challenges a widely-accepted view that there is no prospect of a patient recovering consciousness if they have been in a vegetative state for longer than 12 months.

Since sustaining severe brain injuries in a car accident, the man had been completely unaware of the world around him. But when fitted with an implant to stimulate the vagus nerve, which travels into the brain stem, the man appeared to flicker back into a state of consciousness.

He started to track objects with his eyes, began to stay awake while being read a story and his eyes opened wide in surprise when the examiner suddenly moved her face close to the patient’s. He could even respond to some simple requests, such as turning his head when asked – although this took about a minute…

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The Mystery of Evolution: 10. Falsifying the Evolution-The Experiment #1

I have promised that I will try to falsify the evolutionary theory by performing some simple experiments, as many of Darwin’s faithful on this blog have been really reluctant to do or even to suggest such an experiment…

However, one video was posted on TSZ suggesting that such an experiment has already been performed by Biologist Ken Dial in a study of how young birds use their developing wings that is supposed shed light on the evolution of flight in birds.

The Origin of Flight–What Use is Half a Wing? | HHMI BioInteractive Video


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A Problem to Solve

Evolution is often presented as problem-solving. Genetic algorithms are often offered as proofs of evolution’s ability to solve problems. Genetic algorithms are as search algorithms.

As one book says:

Fundamentally, all evolutionary algorithms can be viewed as search algorithms which search through a set of possible solutions looking for the best – or “fittest” – solution.

Tom has asked me to specify a problem independently from the evolutionary process. Now I have to admit that I don’t really understand what that means. But I like Tom and I have a lot of respect for him, so I want to give it my best shot and see where it takes us. I’m also hoping this will shed some light on claims about how problem-solving genetic algorithms are designed to solve a particular problem.

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The Mystery of Christianity: 1. The Problem of Evil

Recently, we have been able to establish, reluctantly by some and without an official admission, that God could not have spared Adam and Eve from the consequences of their disobedience that led to sin, which resulted in aging, diseases, suffering, natural disasters outside of paradise and then eventually death… Continue reading

Purpose and Desire

Purpose and Desire: What Makes Something “Alive” and Why Modern Darwinism Has Failed to Explain It is the new book by physiologist J. Scott Turner, author of The Tinkerer’s Accomplice: How Design Emerges from Life Itself.

The book may make some “skeptics” uncomfortable, but maybe they should read it anyways.

From the book:

I have come to believe that there is something presently wrong with how we scientists think about life, its existence, its origins, and its evolution.

Without a coherent theory of life, whatever we think about life doesn’t hold water. This applies to the major contribution we claim that the modern science of life offers to the popular culture: Darwinism.

… there sits at the heart of modern Darwinism an unresolved tautology that undermines its validity.

… do we have a coherent theory of evolution? The firmly settled answer to this question is supposed to be “yes” …

I intend to argue in this book that the answer to my question might actually be “no.”

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The Idea of ‘Science’ “vs” “Religion’

There’s a rather good article recently published on Aeon, “Why religion is not going away and science will not destroy it“. Since we often circle around the question of the relationship between science and religion, and since most TSZ contributors seem to assume the conflict thesis — that science and religion tend to, and perhaps even must, conflict — I wanted to bring this article to your attention. Discuss — or not!

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The Mystery of Evolution: 9. I Origins by Richard Dawkins

Bumping around for millions of years without sight is not a problems for Richard Dawkins…Why would it be for evolution?

Question: Do not  ALL (systems involved in seeing and processing image) have to be working (fully functional) for the eye to receive and process vision? (or something like that)

Answer Richard Dawkins: It is a bit a fallacy because 1/4 of an eye or a100th of an eye is better than nothing…

Please watch the video as my keyboard can’t handle the rest of this Dawkins’ nonsense…

 

!8 mysteries to go…

Coevolutionary Algorithms

Coevolutionary algorithms approach problems for which no function for evaluating potential solutions is present or known. Instead, algorithms rely on the aggregation of outcomes from interactions among evolving entities in order to make selection decisions. Given the lack of an explicit yardstick, understanding the dynamics of coevolutionary algorithms, judging whether a given algorithm is progressing, and designing effective new algorithms present unique challenges unlike those faced by optimization or evolutionary algorithms. The purpose of this chapter is to provide a foundational understanding of coevolutionary algorithms and to highlight critical theoretical and empirical work done over the last two decades. This chapter outlines the ends and means of coevolutionary algorithms: what they are meant to find, and how they should find it.

Handbook of Natural Computing
Volume 2
p. 987
Chapter 31
Coevolutionary Principles

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Remedial education for colewd

In the thread FMM throws Jesus under the bus, I had the following exchange with colewd:

colewd:

Until you have an eye there is nothing to select for. You have 300k of nucleotides drifting toward a meaningless group of sequences. Until you find a group of sequences that can provide reproductive advantage (sight) it is drift drift drift.

keiths:

This is just a version of the “what good is half an eye” PRATT.

Seriously, Bill, how can you possibly have missed everything that’s been written on this subject, from Darwin onward?

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Intelligibility

One of the deeper questions that runs throughout philosophical speculation — Western, Eastern, and besides — is a kind of wonder or awe at the fact that the world does make any sense to us all. This awe can be expressed as itself an intellectual problem: why is the world intelligible? The question is sometimes put as: what is the source of the world’s intelligibility? Is the source of intelligibility itself intelligible? Or does a mystery remain after all explanations have had their say?

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