Can Evolution be possible if Entropy is true; or rather, is Evolution possible because Entropy is true!

So what is Entropy?

To follow in the tradition of Maimonides. Entropy is NOT a tendency to disorder! I need to thank Joe Felsenstein for directing me to Frank L. Lambert’s insights on a previous thread probably best left alone. Here is a great site to elucidate Lambert’s insights:

http://entropysite.oxy.edu/

What about Evolution? Can complex systems arise naturally and spontaneously into higher tiers of complexity and order and opportunity—according to the Second Law of Thermodynamics— and all without divine intervention commonly described as Intelligent Design or Irreducible Complexity?

Sean Carroll has much to offer on this question:

Entropy and Complexity, Cause and Effect, Life and Time

Participants should refrain from arc-reflex boiler-plate diatribes echoing previously held opinion and first examine what Carroll has to say. Failure to do so will merit cyber-smack downs.

A corrected worksheet targeted for High School students proving that even if Photosynthesis were IC – it would still be evolvable.

This is my second kick at the can and a follow up to my last OP called:

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

In deference to Keiths, I have changed the title.

I want to thank participants for their insightful suggestions… yes that includes you Sal. I even included your frog metaphor.

Special thanks go to Mung and to Bill!

A very deep bow and tip of the hat goes to Keiths.

NEW LINK

I would appreciate any feedback and suggestions for improvement before I finalize it and submit to the Biology Teachers’ cyber-community for their perusal.

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

According to Michael Skinner; Darwin’s theory that natural selection drives evolution is incomplete without input from evolution’s anti-hero: Lamarck… Really now?!

Let’s just call this my random act of mischief for the day!                   😉

Michael Skinner, professor of biological science at Washington State University just came out with the following in the popular press:

Unified theory of evolution Darwin’s theory that natural selection drives evolution is incomplete without input from evolution’s anti-hero: Lamarck

Is it indeed time to revise the theory of evolution?  Or… Is Skinner in error and invoking a common misconceived textbook caricature of Lamarck?  IMHO: Short answers = NO! & YES!

I urge any and all to read Mark Ptashne’s insights before weighing in the discussion.

Bottom Line: Nucleosome modifications may be necessary for epigenetic responses, but they are not sufficient.

To quote PZ Myers, who cuts to the chase:

We say epigenetics is really important in development and in physiological adaptation — it’s good to know more about it, and is essential for understanding the state of the organism. But evolution? Meh. Acquiring the process of semi-permanently modifying the cell state is something that was a key innovation (OK, many innovations) in EVOLUTION [emphasis mine], but it’s been overhyped as an information transfer process on evolutionary timescales…

So who got the epigenetics story right? PZ Myers & Mark Ptashne?… or Michael Skinner?…

Competing Origin of Life Hypotheses – Fantastic Summary by the BBC

This article by Michael Marshall on the The Secret of How Life on Earth Began is probably the best summary on the topic I have read to date. I compiled a quick glossary below.

It’s not just about the “smoker” vs “souper” debate (sometimes referred to as the Metabolism First vs RNA World Brouhaha).  This article also examines other disparate competing hypotheses regarding the origin of life and even suggests that a unifying grand hypothesis may be possible.

A great read!

oparin haldane charles darwin atp tree of life chemiosmosis rna world franklin hershey chase peter mitchell cyanide nick lane alkaline vents hydrothermal vents clay meteorites geothermal pond volcanic pond ultraviolet compartmentalisation first lipid world genetics first montmorillonite citrate magnesium copper lipid precursors hodge podge world metal ion core deborah kelley lost city william martin luca last universal common ancestor origin of life reactor pier luigi luisi glycol nucleic acid günter wächtershäuser jack corliss michael russell pyrite david bartel philipp holliger gerald joyce peter nielsen polyamide nucleic acid pna albert eschenmoser threose nucleic acid tna eric meggers miller urey watson crick orgel john sutherland thomas cech walter gilbert thomas steitz jack szostak ribozyme rna enzymes ring of life vitalism trofim lysenko alexander oparin j. b. s. haldane armen mulkidjanian jillian f. banfield friedrich wöhler benjamin moore biotic energy warm little pond

Biology as viewed through 19th Century Lenses

Most modern readers have difficulty appreciating the resilience of spiritual or metaphysical overtones to 19th Century scientific thought, alternatively referred to as “vitalism” & “teleology”. At this point, a quick historical digression is in order.

What exactly is life?”! Traditional education systems were well-grounded in the classics, and many 19th Century naturalists could relate to an ancient Greek philosopher named Aristotle who was convinced no real boundary existed between “living” and “non-living”. According to Aristotle, non-living matter could give rise to living things because our universe possesses some vital life force or soul, “anima”, which could “animate” non-living matter. In Aristotle’s view: the universe, as a whole, had its own soul. In modern terms the universe could be considered as some giant fractal and we are all but elements therein. Even today, various mystical traditions hold similar ideas.

Continue reading

What did Lamarck and Darwin really say?

Historically and conceptually, modern Genetics and modern Evolutionary Theory are closely intertwined. Mendel and Darwin both published their masterpieces in the mid-1800s and both were promptly misunderstood and discounted for half a century. Both theories required several more “kicks at the can” before final acceptance. Put simply: the Theory of Evolution itself evolved in response to an emerging understanding of Genetics.

Some quick questions:

Question: Name the scientist that first suggested “the effects of use and disuse” were passed from one generation to the next?

Answer: Charles Darwin and NOT Jean-Baptiste Lamarck who actually had a somewhat different theory.

Question: Name the scientist who first to employed the term evolve/evolution while also suggesting human beings had “evolved” from apes?

Answer: That would be Jean-Baptiste Lamarck. (Lamarck in fact invented the word “evolution”, a word which never appeared in Darwin’s Book “Origin of the Species”). Continue reading

CRISPR goes retro: Bacteria can also take ‘RNA mug shots’ of threatening RNA-viruses.

The emergence of life for the first time on this planet constitutes the classic question of what came first; the chicken or the egg?!  Did a self-replicating DNA system occur before transcription or translation evolved (the DNA World) or did a self-replicating RNA system first emerge (the RNA world) or did self-replicating protein system first emerge (the Protein World)…or … let’s just leave it there for now. Continue reading

Hopelessly frustrated – most likely confused regarding latest on Xenoturbella

I would be grateful if somebody could help me out here as Bioinformatics is not my strong card.

Regarding the recent Nature publication

New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

I query the authors’ explanation; to wit…

The sister group relationship between Nephrozoa and

Xenacoelomorpha supported by our phylogenomic analyses implies that the last common ancestor of bilaterians was probably a benthic, ciliated acoelomate worm with a single opening into an epithelial gut, and that excretory organs, coelomic cavities, and nerve cords evolved after xenacoelomorphs separated from the stem lineage of Nephrozoa.

 

My problem arises with their placement of Ctenophora on their own phylogenetic tree as the “more primitive out-group” (for lack of better words on the spur of a rushed moment).  Myself, I always considered Ctenophora as bilateral – in this case more primitively bilateral which IMHO should root the bilateran tree… which of course begs more than one question upon rereading their analysis.

Forget Ctenophores – what about Cnidarians!?  Some taxonomists argue that Cnidarians are descendents of ancient bilateral coelomates and not the other way around. Biologists have known since the 1920s that Cnideria had a directive axis which gave them right and left-hand sides.  Volker Schmidt goes on to argue that non-radially organized hydrozoan larvae have an anterior concentration of sensory and ganglionic nerve elements, suggesting that a fundamental genetic toolkit for the establishment of bilateral and polarized anatomies was already present before the Cnidaria-Bilateria divergence.  Volker Schmidt goes so far as to suggest that diploblastic status of adult Cniderians is derived and that true mesoderm can be even be detected during Cniderian embryogenesis.  OK – I concede that last argument is particularly contentious… but you get my drift.

I am partial to the notion the UrBilateran that subsequently gave rise to “Protostomes” & Deuterostomes and was itself coelomate with possessed a dorsal nerve chord.  Any subsequent acoelomy and pseudocoelomy was derived… ditto ventral nerve chords.  But hey…  now I am being really contentious!