Macroevolutionary Progress Redefined: Can It Happen Without Gene Transfer? What'sNEW since 2002

A string of symbols constitutes information. The amount of information may be measured in more than one way. Three ways, introduced by abbreviations, are:

QI — The raw "quantity of information," simply the length of the string.
LAC — The "least algorithmic complexity" of the string, equivalent to the length of the most efficiently encoded version of it, with any redundancies and long repeats compressed — analogous to the "zipped" version of a computer file.
AM — The "amount of meaning" in the string, equivalent to the length of the LAC version after any meaningless portions have been removed.

Examples: strings of symbolsunitsQILACAM
A string of 100 identical bitsbits100< 10~ 0
A string of 100 random bitsbits100100~ 0
An efficient telegram of 100 characterscharacters100~ 100~ 100
A salamander's genomebase pairs>10^11~10^10?~10^9?

Micro- and Macroevolution in Terms of Genetic Meaning

Microevolution and macroevolution are familiar, embattled concepts. Here we redefine them in terms of genetic meaning in order to take a new look at macroevolutionary progress:

Microevolution — Genetic changes that do not increase or decrease (=) the amount of meaning (AM) in the genome, with phenotypic effects that may range from critical (examples 1 & 2) to none at all (example 5).
Macroevolution — Genetic changes that increase (+) or decrease (-) the amount of meaning (AM) in the genome, usually with major phenotypic effect (examples 6 - 10). Macroevolutionary progress, naturally, requires an increases in AM (8 - 10), just as new computer capabilities require new programs.

Examples of genetic changes QI LACAMm/M
1Mutations that cause amino acid substitutions in proteins such as viral coat proteins, temporarily evading the host's immune system===m
2Point mutations that reversibly activate or silence promoter or repressor subroutines===
3Gene or whole genome duplication only+==
4Gene duplication followed by irreversible silent or optimizing mutations in one copy++=
4.1Temporary loss of function by a reversible acquisition of a nonsense sequence++=
5Physical loss from the genome of nonfunctional, nonsense DNA --=
6Mutation to nonsense of a formerly functional gene==-M
7Physical loss from the genome of a formerly functional gene---
8Acquisition of a resistance plasmid by a bacterium+++
9Acquisition of mitochondria and plastids by cells+++
10First acquisition of genetic programs for methanogenesis, photosynthesis, oxygen metabolism, nitrogen fixation, multicellularity, cell specialization, meiosis, sexual reproduction, locomotion, digestive systems, circulatory systems, nervous systems, immune systems, woody stems, leaves, shells, gills, lungs, limbs, bones, teeth, scales, skin, hair, wings, eyes, ears, etc.+++


The full expression of a genotype may involve the generation of many mutations to completely explore. During this process, some evolutionary changes that would count as macroevolutionary progress under its more traditional definition would not qualify here. For example, if the relevant genetic programs are already present, a point mutation, as in examples 1 or 2, might trigger a significant increase in the size of an organ, even the brain.

De novo genes complicate the analysis. They are formerly silent, untranscribed sequences, which may become active, useful genes. Very many examples are being noticed. Since this is so, a given, silent sequence may not be "nonsense" after all. Three New Human Genes has examples and links.
For another example, related to item 4, in 1999, a team at University College London (Dulai et al.
*) deduced a plausible way for trichromatic vision in the howler monkey to have evolved from dichromatic vision by gene duplication and random mutation. If their surmise is correct, one of the howler's two opsin genes was duplicated, and a point mutation in one copy encoded a single amino acid substitution that altered the color sensitivity of the opsin protein. Subsequent deployment of this third protein made 3-color vision possible.

It may have happened that way. But if the genetic programs for gene duplication, and for enhanced mutations at the targeted location ("directed mutation") are already present, then the actual genetic steps just described may be considered as the execution of existing programs. The amino acid substitution by itself is not different from that in example 1, and one protein coat or color sensitivity range has no more meaning than another. This evolutionary mechanism is still quite remarkable, but it has not been shown to be capable of producing the new programs for any of the steps listed in examples 9-10.

Example 8, the acquisition of a resistance plasmid is debatable, because the sequence may have virtually no "meaning." For example, it may just provide the cell with the equivalent of a new passcode. Here, with a smaller "up" arrow, we suggest that acquiring a potentially useful one adds only a small increment of meaning. But the same effect (immunity) may also be reached by point mutations in an existing sequence, as in example 1, where no meaning is gained.

Examples 9-10 list phenotypic changes resulting from genetic changes that increased AM, producing macroevolutionary progress as defined here, denoted by green "up" arrows in the AM column. The mechanism behind such a genetic change, in standard Darwinism, is generally believed to be mutation and recombination within an existing genome, as in example 4. But some advances, like mitochondria and plastids, were likely acquired by symbiosis. Apparently, a key component of the vertebrate immune system was acquired by gene transfer (Agrawal et al. *). Other examples of macroevolutionary progress are not supposed to require the acquisition of new programs by transfer, but transfer has not been ruled out as the ultimate source for any example. And closed-system experiments that would demonstrate macroevolutionary progress without transfer have not succeeded — neither in biology nor computer models.

Evolutionary biologists would agree that a change requiring a number of base changes, each of which is without value until all are present, cannot occur by natural selection. — John Maynard Smith *

At this point, macroevolutionary progress in a closed (quarantined) system has not been demonstrated. Without experimental evidence, one can reasonably ask whether macroevolutionary progress in a closed system is possible. Or, in the terms just introduced, can the amount of meaning in the genome of a species increase without the benefit of gene transfer from outside the species?

Postscript: Survival Advantage (SA)

What is the net phenotypic effect of the genetic changes listed in the chart? Darwinists would ask: Do they provide a Survival Advantage? (An "SA" column was not included.) For the macroevolutionary ones, examples 6-10, SA correlates well with AM. But for the microevolutionary ones, with no additional meaning, what correlates with SA? In example 1, SA for the virus and its host sums to zero. Examples 2 and 4 go both ways. Example 3 would only double the cost of maintening the genome. Example 5, a loss of DNA, would at least make genome maintenance easier.
Another theory, cosmic ancestry, accounts for macroevolutionary progress entirely by gene transfer in an open system. Its logic leads to the conclusion that highly evolved life has always existed. But the standard version of the big bang theory would preclude this version of panspermia, if the whole universe is a closed system that began without life. However, other versions of the big bang theory that do not preclude cosmic ancestry are consistent with the cosmological evidence. In any case, the lack of direct evidence for ongoing macroevolutionary progress in closed (quarantined) systems should not be ignored.


10 Jul 2023: Germline mutations are the proximate source of genomic innovation...?
"Evolution of a minimal cell" by R.Z. Moger-Reischer, J.I. Glass, K.S. Wise etal., doi:10.1038/s41586-023-06288-x, Nature, 05 Jul 2023. Microevolution, but that's not clear from the title.
20 Jan 2022: Mutation is not random.
Flying Fish and Aquarium Pets Yield Secrets of Evolution by Viviane Callier, Quanta Magazine, 05 Jan 2022. A single point mutation in some cases can give you really, really big fins.
13 Feb 2021: How did the human brain evolve?
...brain protein-coding genes under positive selection during primate evolution... by Guillaume Dumas et al., doi:10.1101/gr.262113.120, Genome Res., online 13 Jan 2021. We confirm that genes encoding brain-related proteins are among the most strongly conserved protein-coding genes in the human genome. ...Conversely, [indirect evidence suggests that] positive selection and might have played a role in human brain size expansion during primate evolution.
Overcoming the loss of blue sensitivity through opsin duplication in the largest animal group, beetles by Camilla R. Sharkey et al., doi:10.1038/s41598-017-00061-7, Sci Rep, 31 Jan 2017. Strong support for Example 4.
04 Dec 2019: ...plant cell wall-degrading enzymes obtained from bacteria and fungi via horizontal gene transfers...
11 May 2019: beetles acquire and optimize GH45 gene
18 Dec 2018: Horizontal Gene Transfer (HGT) is the only source for all of the evolutionary innovations observed among all of the bacterial clades examined.
16 Jan 2017: Scientists at the University of Chicago.... describes a new way to study microevolution.
02 Dec 2016: The textbox about De novo genes and the paragraph beginning Example 8 have been added.
11 Nov 2016: George Church says Prove it.
21 Aug 2016: Can antagonistic evolution compose de novo genes? — pertains to Example 8.
Huai Wang et al., "Evidence that the Origin of Naked Kernels During Maize Domestication Was Caused by a Single Amino Acid Substitution in tga1" [abstract], doi:10.1534/genetics.115.175752, Genetics, online 4 May 2015.
19 Nov 2014: We can find no extant organism that displays the gradual acquisition.... — Luis P. Villarreal
The Rainbow Connection by Kerry Grens, The Scientist, 1 Oct 2014. "Color vision as we know it resulted from one fortuitous genetic event after another."
18 Apr 2013: Earth was seeded by panspermia. (Points to an article that quantifies biological complexity.)
10 May 2012: The definition of life and speculations about its origin(s)... by Gerald Joyce of the Scripps Research Institute.
V.G.Gurzadyan, "Kolmogorov Complexity, String Information, Panspermia and the Fermi Paradox" [abstract | pdf], arXiv:physics/0508010v2 [physics.gen-ph]; and p352-355 v125, The Observatory [text], 2005. "The Fermi paradox 'Where is Everybody?' can be viewed under in the light of such information panspermia, i.e. a Universe full of traveling life streams."
9 Mar 2012: ...Fundamental elements of the C4 pathway ...were acquired via a minimum of four independent lateral gene transfers....
23 Feb 2012: Experimenters with a virus and its bacterial host in a quarantined system report a breakthrough.
10 Jan 2012: The mechanisms for this increase in complexity are incredibly simple, common occurrences — Geneticist Joe Thornton
29 Apr 2011: Biochemist Michael Behe uses a classification system similar to ours.
25 Nov 2009: Butterflies and caterpillars were once separate species, brought together by hybridization?
29 Oct 2009: 40,000 generations of E. Coli have been monitored in a long-term experiment.
"Language: Disputed definitions" [text], doi:10.1038/4551023a, p 1023-1028 v 455, Nature, 23 Oct 2008. Search for "Complexity", by M. Mitchell Waldrop.
20 Sep 2008: Woodstock of evolution?
19 Nov 2007: Ancient retroviruses spurred evolution of gene regulatory networks in humans and other primates.
Michael Hopkin, "Chimps lead evolutionary race" [text], doi:10.1038/446841a, p 841 v 446, Nature, online 16 Apr 2007. "It is possible that the genetic changes underlying brain size are very few." (Text and title ammended after first online publication.)
1 Dec 2006: Evolutionary Dynamics, by Martin Nowak, Belknap Press, 2006.
12 Nov 2006: The Making of the Fittest, by geneticist Sean B. Carroll, W. W. Norton, 2006.
14 Feb 2006: Researchers evolve a complex genetic trait in the laboratory?
28 Jan 2006: Important aspects of the history of life are replicable and predictable.
30 Sep 2005: The chimp genome has been sequenced. At least seventeen human genes contain exons missing in chimps.
26 Nov 2004: The evolution of a new fruitfly gene...
14 Apr 2004: "Can we ever hope to pin down the genetic changes that underlie the big steps in evolution?"
15 Jan 2004: Are normal microevolutionary processes sufficient to account for human origins?
2003, August 8: Gene transfer, wholesale?
Jack W. Szostak, "Functional information: Molecular messages" [text], doi:10.1038/423689a, p 689 v 423 Nature, 12 June 2003. "A new measure of information — functional information — is required...."
2003, April 7: Stephen Jay Gould's account of macroevolution, in a new Encyclopedia of Evolution....
2003, February 4: The latest results from a closed-system biological experiment.
A Reply from Aaron Kennedy prompts a discussion of issues related to this page, 26 Oct 2002.
A Reply from Susan Lindquist pertains to issues on this page, 24 Oct 2000.


+ Alka Agrawal, Quinn M. Eastman and David G. Schatz, "Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system" [
abstract], doi:10.1038/29457, p 744-751 v 394, Nature, 20 August 1998.
+ K.S. Dulai, M. von Dornum, J.D. Mollon and D.M. Hunt, "The evolution of trichromatic color vision by opsin gene duplication in New World and Old World primates" [abstract], doi:10.1101/gr.9.7.629, p 629-638 v 9 n 7, Genome Research, July 1999.
+ Maynard Smith, John, "Population genetics revisited," Nature, 10 Feb 2000.
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