Beyond Darwinism describes efforts to go beyond the Modern Synthesis or "Neo-Darwinian" evolution developed in the early twentieth century by Julian Huxley, Theodosius Dobzhansky, Ernst Mayr, and others.

They include Evolutionary Development Biology or "Evo-Devo" theory, the Extended Evolutionary Synthesis, the Third Way of Evolution (TWE) project, and Evolution 2.0

Evolutionary developmental biology, informally known as evo-devo, grew from 19th-century beginnings, where embryology faced a mystery: zoologists did not know how embryonic development was controlled at the molecular level. Charles Darwin noted that having similar embryos implied common ancestry, but little progress was made until the 1970s. Then, recombinant DNA technology at last brought embryology together with molecular genetics.

One is deep homology, the finding that dissimilar organs such as the eyes of insects, vertebrates and cephalopod molluscs, long thought to have evolved separately, are controlled by similar genes such as pax-6, from the evo-devo gene toolkit. Another is deep homology, that dissimilar organs such as the eyes of insects, long thought to have evolved separately, are controlled by similar genes such as pax-6, from the evo-devo gene toolkit. Still another possibility is the neo-Lamarckian theory that epigenetic changes are being inherited along with changes in DNA.

In 1977, a revolution in thinking about evolution and developmental biology began, with the arrival of recombinant DNA technology in genetics, the book Ontogeny and Phylogeny by Stephen J. Gould and the paper "Evolution and Tinkering"[28] by François Jacob. Gould laid to rest Haeckel's interpretation of evolutionary embryology, while Jacob set out an alternative theory. This led to a second synthesis, at last including embryology as well as molecular genetics, phylogeny, and evolutionary biology to form evo-devo.

In 1978, Edward B. Lewis discovered homeotic (homeobox, HOX) genes that regulate embryonic development in Drosophila fruit flies, which like all insects are arthropods, one of the major phyla of invertebrate animals. There were evidently strong similarities in the genes that controlled development across all the eukaryotes.

In 2001, a seminar entitled "From Embryology to Evo-Devo" (Evolutionary Biology) was held at the Marine Biology Laboratory at Woods Hole MA.

This Evo-Devo theory should not be confused with the Evo Devo Universe community.

The Extended Evolutionary Synthesis (EES) augments the Modern Synthesis with additional causative factors. It includes multilevel selection, transgenerational epigenetic inheritance, niche construction, evolvability, and several concepts from evolutionary developmental biology

EES consists of a set of theoretical concepts argued to be more comprehensive than the earlier modern synthesis of evolutionary biology that took place between 1918 and 1942. The extended evolutionary synthesis was called for in the 1950s by C. H. Waddington, argued for on the basis of punctuated equilibrium by Stephen Jay Gould and Niles Eldredge in the 1980s.

EES was reconceptualized in 2007 by Gerd Müller and Massimo Pigliucci and their 2010 book Evolution: The Extended Synthesis, which is the current basis for work on the extended synthesis.

See the 2017 Royal Society article "Why an extended evolutionary synthesis is necessary" for further details.

Denis Noble and James A. Shapiro established The Third Way of Evolution (TWE) project in 2014. The TWE, which is also known as the "Integrated Synthesis," shares many similarities with the extended evolutionary synthesis but is more radical in its claims. The TWE consists of a group of researchers who provide a "Third Way" alternative to creationism and the modern synthesis. The TWE predicts that the modern synthesis will be replaced with an entirely new evolutionary framework. Similar to the extended evolutionary synthesis (EES), advocates cite examples of developmental bias, genetic assimilation, niche construction, non-genetic inheritance, phenotypic plasticity and other evolutionary processes. Shapiro's natural genetic engineering, a process described to account for novelty created in biological evolution is also important for the TWE.

The difference between the extended synthesis and the TWE is that TWE calls for an entire replacement of the modern synthesis rather than an extension.

Noble has proposed Ten Principles of Systems Biology:[

Biological functionality is multi-level

Transmission of information is not one way

DNA is not the sole transmitter of inheritance

The theory of biological relativity: there is no privileged level of causality

Gene ontology will fail without higher-level insight

There is no genetic program

There are no programs at any other level

There are no programs in the brain

The self is not an object

There are many more to be discovered; a genuine 'theory of biology' does not yet exist

Venn diagram of the Integrated Synthesis of TWE

James A. Shapiro has discovered regulatory networks that adapt to stress conditions to maximize the probability of survival.

All living cells sense and respond to changes in external or internal conditions. Without that cognitive capacity, they could not obtain nutrition essential for growth, survive inevitable ecological changes, or correct accidents in the complex processes of reproduction. Wherever examined, even the smallest living cells (prokaryotes) display sophisticated regulatory networks establishing appropriate adaptations to stress conditions that maximize the probability of survival. Supposedly “simple” prokaryotic organisms also display remarkable capabilities for intercellular signalling and multicellular coordination.

These observations indicate that all living cells are cognitive.

How life changes itself: The Read–Write (RW) genome. Physics of Life Reviews, Vol 10, Iss 3, September 2013, pp.287-383

Shapiro explicitly explains that this cognitive behavior is "purposeful"...

Rather than being the passive beneficiaries of random mutations and natural selection, all organisms play an active role in their hereditary variation and natural selection by activating transposable elements in response to ecological challenges.

"Evolutionary Change Is Naturally Biological and Purposeful", in Evolution on Purpose: Teleonomy in Living Systems, 2023, p.255, MIT Press

These "purposeful" internal regulatory networks may be invisible, but they complement the clearly visible and purposeful behaviors of the simplest prokaryotes like bacteria rotating their flagella counterclockwise when measurement along their cell surface signals better conditions ahead, but who rotate clockwise and tumble, then start off in a random direction in search of better conditions.

Denis Noble is also a major participant in an ambitious program called Evolution 2.0. Noble, Harvard geneticist George Church and advertising strategist Perry Marshall, are offering an incentive prize ten times the size of the Nobel – believed to be the largest single award ever in basic science – to the person or team solving the largest mystery in history: how genetic code inside cells got there, and how cells intentionally self-organize, communicate, then purposely adapt. This $10 million challenge, the Evolution 2.0 Prize can be found at herox.com/evolution2.0.

Evolutionary Developmental Biology or "Evo-Devo," the Extended Evolutionary Synthesis (EES), and the Third Way of Evolution (TWE) have all added new sources of variation in what gets inherited in the next generation.

But there is no change in Darwin's fundamental idea of natural selection, popularly known as "Survival of the Fittest." Indeed, Darwin knew nothing of DNA and the Genetic Code.

Many thinkers who want too get Beyond Darwinism oppose the random (chance) source of variation and are looking to find "purpose in the universe, even before the origin of life."

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