Lamarcks "denovo" genes at the "Bush of Life" verses Darwins Alchemy and Imaginations


"If "the sublime author of the universe" can create all the different species by separate acts of creation, he can so too, surely create one or two species to begin with, and confer upon them the power of evolving into the rest." - Jean Baptiste Lamarck, first proposed evolution 50 years before Darwin & father of epigenetics & Biology

The evolutionary "Bush of Life" or LECA (Last Eukaryotic Common Ancestor) is a model of evolution that suggests that all living things on Earth start at a "Bush" not Darwin's "Tree of Life." These ancestors are thought to have lived about 3.5 billion years ago, and it is from this ancestor that all of the diversity of life on Earth has arisen.


The LECA model is supported by a number of lines of evidence, including the fossil record, the genetic code, and the similarities between the body plans of different organisms.

However, there are some aspects of evolution that are not well-explained by the LECA model. For example, how do new genes arise? And how do organisms adapt to new environments so quickly?

One possible explanation for these phenomena is that they are due to the action of "orphan genes." Orphan genes are genes that do not seem to have any obvious function. As such they are not explained by NeoDarwinism. It has been suggested that they may play a role in processes such as speciation and adaptation.

Another possible explanation for these phenomena is that they are due to the action of "transposable elements" (TEs). TEs are DNA sequences that can move around within the genome. They have been implicated in a variety of processes, including speciation and adaptation.

It has also been suggested that epigenetics may play a role in evolution. Epigenetics is the study of how changes in gene expression can be inherited without changes in the DNA sequence as opposed to neo darwinism. It has been suggested that epigenetic changes may play a role in processes such as speciation and adaptation.

The LECA model is a powerful tool for understanding evolution. However, it is important to remember that it is just a model. There are still many things that we do not know about Lamarkian evolution, and the LECA model.

Here are some additional details:

  • TEs: Transposable elements are DNA sequences that can move around within the genome. They are often referred to as "jumping genes" or "transposons." TEs can be divided into two main types: retrotransposons and DNA transposons. Retrotransposons move by first being transcribed into RNA and then reverse transcribed back into DNA. DNA transposons move directly from one location to another in the genome. As they move as "chunks" the are not controlled by numerous random mutations by Darwin.

  • Epigenetics: Epigenetics is the study of how changes in gene expression can be inherited without changes in the DNA sequence per Darwin. Epigenetic changes are often caused by environmental factors such as diet, stress, and exposure to toxins. As such they "adapt" not "evolve" the organism rapidly without natural selections proposed environmental input. Epigenetic changes can have a profound impact on an organism's phenotype, or physical appearance.


Ants with the same genotype but vastly different phenotype.

  • HGT: Horizontal gene transfer (HGT) is the transfer of genetic material from one organism to another, not through reproduction. HGT is thought to be a common occurrence in the microbial world, but it has also been documented in eukaryotes, such as plants and animals. HGT can play a role in the evolution of new genes and the spread of antibiotic resistance.

These authors point out:

"The conventional wisdom has been that, in the emergence of novel genes, “natural selection is merely modified, while redundancy created.” In other words, new genes generally arise by the duplication of existing genes

de novo gene origins raise the question of how evolution by natural selection can produce functional genes from noncoding DNA

How could all of these pieces fall into place through the random processes of mutation, recombination, and neutral drift—or at least enough of these pieces to produce a protogene that was sufficiently useful for selection to take hold?

One can imagine a process by which short, simple genes periodically arise de novo, then gradually become more complex over time,"

Darwinian alchemy: Human genes from noncoding DNA

There you have it "imagine evolution." it's alchemy after all and we still study it.

But what about Darwins "Tree of Life."


Many point out there is no "Tree" rather a "Bush" of life. These scientists say it's a "tree of one percent,":

"Two significant evolutionary processes are fundamentally not tree-like in nature - lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes. To incorporate such processes into the bigger picture of early evolution, biologists need to depart from the preconceived notion that all genomes are related by a single bifurcating tree.

Evolutionary biologists like to think in terms of trees. Since Darwin, biologists have envisaged phylogeny as a tree-like process of lineage splittings. But Darwin was not concerned with the evolution of microbes, where lateral gene transfer (LGT; a distinctly non-treelike process) is an important mechanism of natural variation, as prokaryotic genome sequences attest

Evolutionary biologists are not debating whether LGT exists. But they are debating - and heatedly so - how much LGT actually goes on in evolution

These debates erupt most acutely over the concept of a tree of life. Here we consider how LGT and endosymbiosis bear on contemporary views of microbial evolution, most of which stem from the days before genome sequences were available.

Looking at the issue openly, the finding that, on average, only 0.1% to 1% of each genome fits the metaphor of a tree of life overwhelmingly supports the central pillar of the microbialist argument that a single bifurcating tree is an insufficient model to describe the microbial evolutionary process

If throwing out all non-universally distributed genes and all suspected cases of LGT in our search for the tree of life leaves us with a tree of one percent, then we should probably abandon the tree as a working hypothesis.

When chemists or physicists find that a given null hypothesis can account for only 1% of their data, they immediately start searching for a better hypothesis. Not so with microbial evolution, it seems, which is rather worrying. Could it be that many biologists have their heart set on finding a tree of life, regardless of what the data actually say?"

These are just a few examples of the many journal articles that have challenged the traditional view of the tree of life:

  • "Bushes in the Tree of Life" (2004) by Eric Bapteste and colleagues in PLOS Biology. This article discusses how the tree of life may be more accurately represented as a bush, due to the high frequency of hybridization and gene transfer between species.

  • "The tangled bank revisited: lateral gene transfer and the evolution of the tree of life" (2008) by W. Ford Doolittle in Nature Reviews Microbiology. This article argues that lateral gene transfer (the transfer of genes between unrelated species) is more common than previously thought, and that this has significant implications for our understanding of the tree of life.

  • "The tree of life is dead, long live the bush of life!" (2009) by Mark Pagel in Nature. This article provides a comprehensive overview of the evidence that the tree of life is not a realistic representation of evolutionary history.

  • The Biological Big Bang model for the major transitions in evolution

Eugene V Koonin

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity

No intermediate "grades" or intermediate forms between different types are detectable.

Here, I argue for a fundamentally different solution, i.e., that a single, uninterrupted TOL does not exist, although the evolution of large divisions of life for extended time intervals can be adequately described by trees

Molecular phylogeneticists will have failed to find the "true tree," not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.

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