Front-loaded evolution
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Front-loading evolution[1] is the idea that the first organisms were designed for future states and contingencies. Front-loading ecompasses two related, yet logically distinct propositions. The first proposition is that life was designed to adapt to changing conditions, having been equipped with various mechanisms that facilitate evolution. The second proposition is that life was designed so as to make some specific event more likely, such as the evolution of multicellularity.
Rather than being an idea based strictly on the preservation of genetic information, front-loading explores dynamic processes such as extensibility, robustness, flexibility, modularity, constrained optimization, intrinsic control, prescribed information, compartmentalization, and pre-adaptation. Mike Gene and Krauze are among those exploring the concept, but Michael Behe, Michael Denton, Simon Conway Morris, and John A. Davison have also expressed ideas friendly to front-loading.
This topic is in the midst of a theoretical exploration, and as such, views presented would not have an all-encompassing reach. The approach is much more tentative, is an earnest effort to adhere closely to known data, and is motivated by curiosity about nature. The investigation currently revolves around reinterpretation research, which looks at current knowledge and looks for more explanations that could bring greater clarity to our scientific picture.
Front-loading includes investigating many levels of complexity: environments, ecologies, populations, organisms, organ systems, organs, tissues, cells, biomachines, informational structures, and all constituent parts of each of these levels.
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Evolution under intrinsic control
Taking a sober look into the rates of possible evolutionary change yields a view that seems discordant with current perspectives, including neo-Darwinism. It is widely acknowledged that most mutations are deleterious or neutral, and reliable statistics for the beneficial mutation rate are a hotly disputed issue. Another disputed area of research are controls on evolution. There are intrinsic and extrinsic controls at every level of complexity, including genetic controls like error correction, epigenetic controls like DNA methylation, developmental controls like ontogenetic depth, behavioral controls like phenotypic dependence, and extrinsic controls like environmental constraints.
This means that biological controls on evolution are the rule in biology. What do these controls mean for evolution?
Genetic controls
- Error correction
- LexA
- Mutations are "turned on" by the organism. "When E. coli cells are subjected to damage, they upregulate repair enzymes, which then go to work trying to fix the problem. If the damage persists, the cell upregulates recombination enzymes, which are tasked with recombining the DNA -- another way to repair it. And, says Romesberg, if the damage still persists, the cells upregulate enzymes whose sole task is to make mutations."[2]
"This important reference work, the result of a conference co-chaired with Nobel laureate Werner Arber, addresses the molecular strategies by which lineages of organisms respond to challenges and opportunities in their environment. It explores the notion that organisms have evolved the ability to modulate the rate, location, and extent of genetic variation. Jumps in efficiency, made possible by development of novel, efficient evolutionary strategies, could fuel rapid, saltatory expansion of species into novel niches as each innovation evolves."
"We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection."
Epigenetic controls
Developmental controls
Behavioral controls
Design-by-contract
Compartmentalization, extensibility
Predictions of front-loading
Misconceptions about front-loading
Misconception: "Front-loading is the idea that the designer put a copy of every gene into the first organism, programming the course of evolution."
As explained in "Misconceptions about front-loading", "[f]ront-loading does not claim that the first organism had a copy of every existing gene, and the phrase 'programmed evolution' makes it sound more deterministic than it really is." Just like the shape of the foundation of a house constrains the final shape of the house (without determining it), life was designed so as to make certain outcomes more likely, while leaving many details to the chance. For example, the designer might have equipped the first cells with proteins that could be easily co-opted to serve vital roles in multicellular organisms. This would make it likely that down the line, some organisms would evolve multicellularity, but the exact forms of these multicellular organisms could be determined by other factors.
Content to be merged ---> <---
- Quorum sensing and autoinducers
- Human brain result of 'extraordinarily fast' evolution
- Single-Celled Species' Genome As Complex As Ours? -- Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote [2] [3] [4]
- Gene switches and the Nervous system:
Genome size
This from the Wikipedia "Junk DNA" article Overall genome size, and by extension the amount of junk DNA, appears to have little relationship to organism complexity: the genome of the unicellular Amoeba dubia has been reported to contain more than 200 times the amount of DNA in humans"[1] [2].
The pufferfish Takifugu rubripes genome is only about one tenth the size of the human genome, yet seems to have a comparable number of genes. Most of the difference appears to lie in what is now known only as junk DNA. This puzzle is known as the "C-value enigma" or, more conventionally, the "C-value paradox"[3].
Cell-signaling controls
quorum sensing and these "autoinducers" are very interesting, perhaps something that could play into a front-loading scenario. See abstract below.
ACS Chem Biol. 2006 Aug 22;1(7):429-31.
Bacterial evolution by intelligent design.
Winans SC.
Department of Microbiology, 360A Wing Hall, Cornell University, Ithaca, New York 14853, USA. scw2@cornell.edu
Abstract: In a process called quorum sensing, bacteria produce and secrete certain signaling compounds (called autoinducers) that bind to receptors on other bacteria and activate transcription of certain genes. A clever genetic selection yields a new quorum-sensing transcriptional regulator that marches to the beat of a different drummer.
More front-loading links
http://telicthoughts.com/category/front-loading/
http://baraminology.blogspot.com/2006/04/luck-favors-prepared-darling.html
http://www.uncommondescent.com/archives/1567#comment-59378
http://www.uncommondescent.com/archives/1567#comment-59381
Unified physics theory explains animals’ running, flying and swimming
Prescribed Evolutionary Hypothesis (PEH) http://www.uvm.edu/~jdavison
http://www.uvm.edu/~jdavison/dpaper.html EVOLUTION AS A SELF-LIMITING PROCESS
Modular Selection Patterns W/ feed-forward loops
Note a description of transcriptional network motifs which "include feed-forward loops, single-input motifs, and multi-input motifs. A feed-forward loop describes a situation in which a transcription factor (TF) regulates a second TF, and these two TFs jointly regulate a common target gene." A metaphor to a manufacturing technique refers to protein complexes formed during the cell cycle which suggest "a general mechanism of “just-in-time-assembly,” where only some subunits of protein complexes are regulated during cell cycle progression and the synthesis of these subunits control the timing of complex assembly. “Just-in-time-assembly” may be a more efficient way of regulation compared with “just-in-time-synthesis,” in which case all subunits of protein complexes are regulated and synthesized at the same time during the cell cycle." http://telicthoughts.com/?p=1181 about: http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0020174
Horizontal gene transfer
