Before nature selects, gene networks steer a course for evolution

September 3, 2015 by Claudia Lutz, University of Illinois at Urbana-Champaign
Before nature selects, gene networks steer a course for evolution
The embryonic development of the buffy flower bat, Erophylla sezekorni, showing the progressive growth and formation of the wings. Credit: Courtesy of Karen Sears

Natural selection is a race to reproduce, a competition between individuals with varying traits that helps direct the evolution of a species. As scientists begin to explore the complex networks of genes that shape the form and function of each individual, they can ask a new question about evolution: How do the structures of these gene networks determine which individuals appear on the starting line, silently influencing evolution before competition has even begun?

University of Illinois researchers Karen Sears and Zoi Rapti, along with collaborators at Illinois and four other institutions, have addressed this question by exploring the gene network that guides limb development in mammals.

They found that during , when limbs are first forming, in this network varies little; later, when detailed limb structure is beginning to emerge, the network changes in structure, and gene activity varies more widely. This pattern may make it easier for evolution to tweak, rather than remodel, limb structure.

"When we look at the evolutionary record of animals, we find that there are some forms that have evolved repeatedly, and some that have never evolved," Sears said. "I want to know the role that development has in generating these patterns."

Sears, an associate professor of animal biology, and Rapti, an associate professor of mathematics, led the study, which was published in PLOS Genetics (DOI: 10.1371/journal.pgen.1005398). Sears is a member of the Carl R. Woese Institute for Genomic Biology (IGB).

Many genes encode proteins that influence or regulate each other's activity. These functional connections, and the genes that participate in them, can be imagined as the threads and intersections of a spider's web. Some of these interactions are stronger or weaker than others, and in the network they comprise, some genes have more connections than others. Computational models can mathematically describe this network structure.

Karen Sears, Associate Professor at the School of Integrative Biology and IGB faculty member, coauthored the new study. Credit: University of Illinois at Urbana-Champaign

Sears, Rapti, and colleagues wanted to know what happens when a chance event, like a mutation, changes the activity of one gene. How much will the whole network, and the resulting course of development, be affected?

Using published data on developmental gene interactions, they created a model of how genes interact during early and late stages of limb development. The model allowed them to pluck at the spider web of genes, and watch how much the rest of the web is disrupted.

The researchers found that in early limb development, the network resists the spread of change; even when one gene's activity is altered, the network as a whole continues to function almost as usual. Later in limb development, however, the architecture of the network is different, and a change in one gene's activity has a more widespread impact.

In addition, an empirical investigation of gene activity during limb develop in four different mammals—mice, bats, opossums, and pigs—showed that activity of developmental differs more in late development than in early development. This is true when comparing individuals of the same species, and also when comparing gene activity across species.

Together, these theoretical and empirical findings supported Sears' strongest initial hypothesis, that genomic mechanisms restrict the degree to which early limb development can vary in mammals. From an evolutionary perspective, this makes sense.

"If early development is disrupted, limb development will be severely disrupted, and it is very unlikely that the resulting limb structure will be selectively advantageous, said Sears. "Later development, which doesn't have as many downstream impacts, might be expected to be more free to vary because the consequences of that variation would be less dire."

Explore further: Evolution of a natural gene network explored by Yale researchers

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JVK
1.7 / 5 (6) Sep 05, 2015
The second law of thermodynamics is the first law of psychology: evolutionary developmental psychology and the theory of tandem, coordinated inheritances: comment on Lickliter and Honeycutt (2003) http://www.ncbi.n...14599284

Abstract excerpt:"Selection built anti-entropic mechanisms into organisms to orchestrate transactions with environments so that they have some chance of being organization-building and reproduction-enhancing rather than disordering."

Article excerpt: "...this view is very much natural selection centered, because it is natural selection that chooses some genes rather than others and in so doing orchestrates the interaction between the two inheritances so that high degrees of recurrent functional order can emerge and persist, such as eyes or maternal love."

See for comparison: From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html
JVK
1.8 / 5 (6) Sep 05, 2015
See also: The significance and scope of evolutionary developmental biology: a vision for the 21st century http://dx.doi.org...de.12125

Excerpt: "Specifically, we need to understand the emergence, dynamics and interaction of evolutionarily conserved modules, how these modules interact to produce emergent properties in developmental networks, and how these networks result in phenotypic outcomes in specific environments through the process of evolution. This challenge will require both a systems-level
integration of information and a unification of central concepts across the broadest swath of biological levels, undertakings that evo-devo is uniquely poised to execute."

"...a systems-level integration of information..." links ecological variation to ecological adaptation without claims about EMERGENCE.
Captain Stumpy
4.3 / 5 (6) Sep 05, 2015
The second law of thermodynamics is the first law of psychology
no, it isn't

where is the link that supports this claim?
still spreading false information and then attempting to "interpret" studies with creationist dogma?

it has been pointed out that you have a 100% fail rate when interpreting actual science...
JVK
1.7 / 5 (6) Sep 05, 2015
The second law of thermodynamics is the first law of psychology: evolutionary developmental psychology and the theory of tandem, coordinated inheritances: comment on Lickliter and Honeycutt (2003). http://www.ncbi.n...14599284

Only a biologically uninformed science idiot would ask:
where is the link that supports this claim?
after I provided the link to the artcle with the title:The second law of thermodynamics is the first law of psychology: evolutionary developmental psychology and the theory of tandem, coordinated inheritances: comment on Lickliter and Honeycutt (2003)
AGreatWhopper
4.4 / 5 (7) Sep 05, 2015
This has seemed intuitively obvious for a long time. Look at Smilodon. The teeth grew long then short in cycles anywhere from 6-10 times during history but I'll bet they licked like cats that whole time. Certain traits don't seem to be as amenable to variation as others. There had to be a meta program for introducing variation under stress.

Shaddap ya inbred Georgia redneck troll, JVK! Takes some balls using your real initials considering how discredited and humiliated James V. Kohl is on so many websites. Finally found one that doesn't delete you on sight. Well, if you love troll spam so much, I guess you won't mind those fed up with your shit using your email on every spammy site they come across. jvkohl@bellsouth.net Might be nice to sign you up for a number of insurance quotes too. 706-455-7967
JVK
2 / 5 (4) Sep 05, 2015
http://www.scienc...15002415 Excerpt: "A species' range can be thought of as a manifestation of the ecological niche in space. Within a niche, evolution has resulted in traits that maximize fitness."

Any manifestation of an ecological niche is a manifestation that is nutrient-dependent and controlled by the physiology of reproduction. Ecological speciation is not the same as neo-Darwinian evolution because there is no such thing as an evolved niche.

Shaddap ya inbred Georgia redneck troll, JVK!


Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Excerpt: "...CHEMICAL ECOLOGY DRIVES ADAPTIVE EVOLUTION VIA: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction...."
Vietvet
5 / 5 (4) Sep 05, 2015
Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

http://www.ncbi.n...4049134/
JVK
2 / 5 (4) Sep 06, 2015
Every aspect of de novo gene creation is nutrient-dependent and the nutrient-dependent creation of new genes is required to prevent virus-driven entropic elasticity from becoming genomic entropy.

Nutrient-dependent RNA-mediated events link the epigenetic landscape to the physical landscape of DNA in the organized genomes of all species. The RNA-mediated amino acid substitutions exemplified in my 2013 review have protected all cell types of all individuals and all species from virus-driven pathology from the time of the creation of life on this planet.

From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

Viral proteins may regulate human embryonic development http://phys.org/n...tml#nRlv

Viral Genome Junk Is Bunk http://www.icr.or...cle/8661

"The Darwin Code: Intelligent Design without God" http://rna-mediat...eg-bear/
Captain Stumpy
3.7 / 5 (3) Sep 06, 2015
Only a biologically uninformed science idiot would ask
@jk
if you would please open the link, you will find that the author info states
Evolutionary Psychology, Department of Anthropology
this is a specialised field and is NOT general (or ALL) psychology, so your statement is false because you didn't specify particulars

also note, the paper is paywalled, and it can't be validated that the author substantiates this claim for all/general psychology, but in the context of evolution & anthropology, it makes sense because
In a natural thermodynamic process, the sum of the entropies of the interacting thermodynamic systems increases
Any actual college student learns this... perhaps you didn't get the chance before failing out?

perhaps you would like to "interpret" what the author meant and fill everyone in?
or is your dogma getting in your way?
Captain Stumpy
3.7 / 5 (3) Sep 06, 2015
Was looking at research that a colleague was doing on various types of science deniers and the #1 reason that white people in the SE USA deny evolution is not a literal interpretation of the Bible, as they claim, but because they refuse to accept that they are not superior to blacks. Evolution really undercuts that. It means we're all the same under the skin. THAT is what they're rejecting, not science.
@jim_x
I would like to see that paper if you can forward the links... i have some serious doubts, IMHO... mostly because the bible belt is focused highly in the SE of the US, and that there are more fundamentalist religious orders in the SE USA than i've seen elsewhere (but that is anecdotal, not published in a study)

thanks for the links and info... appreciate it
Captain Stumpy
4 / 5 (4) Sep 06, 2015
"The Darwin Code: Intelligent Design without God" ...rna-mediat...eg-bear/
PSEUDOSCIENCE and PHISHING SITE

when you accept religious dogma or creationist claims as legitimate, then your site is NOT A SCIENCE SITE, it is a RELIGIOUS ONE

therefore, you promote PSEUDOSCIENCE

reported

also note: and ARTICLE is not equivalent to a STUDY... and a single STUDY is NOT EQUIVALENT to a VALIDATED STUDY

please stick with facts, NOT PSEUDOSCIENCE or conjecture
JVK
2 / 5 (4) Sep 06, 2015
See: Viral and Cellular Genomes Activate Distinct DNA Damage Responses
http://www.cell.c...l%3Dtrue

Excerpt: "...γH2AX foci discriminate "self" and "non-self" genomes and determine whether a localized anti-viral or global ATM response is appropriate. This provides an elegant mechanism to neutralize viral genomes without jeopardizing cellular viability."

Reported as: http://phys.org/n...nts.html

See also: From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html "...three additional topics shall be considered...: genomic sexual dimorphisms, neurosteroids, and immunological factors." My comment: All three factors are nutrient-dependent and RNA-mediated.
Vietvet
5 / 5 (3) Sep 06, 2015
"Evolution by natural selection is one of the best substantiated theories in the history of science, supported by evidence from a wide variety of scientific disciplines, including paleontology, geology, genetics and developmental biology"
http://www.livesc...rks.html

@verkle

It's hilarious you gave JVK a "5" when you have no clue about what he wrote. One idiot young earth creationist supporting a delusional young earth creationist.
JVK
1 / 5 (3) Sep 06, 2015
The Surprising Origins of Evolutionary Complexity http://phenomena....man-dna/

Excerpt:

"Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed "the blind watchmaker." To some extent, it just happens."

Evolution by natural selection is not supported by any experimental evidence of biologically-based cause and effect, which is why only biologically uninformed science idiots believe in it.
Vietvet
5 / 5 (1) Sep 07, 2015
The Surprising Origins of Evolutionary Complexity http://phenomena....man-dna/

Excerpt:

"Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed "the blind watchmaker." To some extent, it just happens"

http://phenomena....man-dna/ leads to An Ancient, Mysterious Scrap of Human DNA.

You are so addled you can't match an excerpt to the correct URL. Good link though, more support for evolutionary theory.

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