Being Emergence vs. Pattern Emergence: Complexity, Control, and Goal-Directedness in Biological Systems

Emergence is much discussed by both philosophers and scientists. But, as noted by Mitchell (2012), there is a significant gulf; philosophers and scientists talk past each other. We contend that this is because philosophers and scientists typically mean different things by emergence, leading us to distinguish being emergence and pattern emergence. While related to distinctions offered by others between, for example, strong/weak emergence or epistemic/ontological emergence (Clayton, 2004, pp. 9–11), we argue that the being vs. pattern distinction better captures what the two groups are addressing. In identifying pattern emergence as the central concern of scientists, however, we do not mean that pattern emergence is of no interest to philosophers. Rather, we argue that philosophers should attend to, and even contribute to, discussions of pattern emergence. But it is important that this discussion be distinguished, not conflated, with discussions of being emergence. In the following section we explicate the notion of being emergence and show how it has been the focus of many philosophical discussions, historical and contemporary. In section 3 we turn to pattern emergence, briefly presenting a few of the ways it figures in the discussions of scientists (and philosophers of science who contribute to these discussions in science). Finally, in sections 4 and 5, we consider the relevance of pattern emergence to several central topics in philosophy of biology: the emergence of complexity, of control, and of goal-directedness in biological systems

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA

Non-coding genomic regions in complex eukaryotes, including intergenic areas, introns, and untranslated segments of exons, are profoundly non-random in their nucleotide composition and consist of a complex mosaic of sequence patterns. These patterns include so-called Mid-Range Inhomogeneity (MRI) regions -- sequences 30-10000 nucleotides in length that are enriched by a particular base or combination of bases (e.g. (G+T)-rich, purine-rich, etc.). MRI regions are associated with unusual (non-B-form) DNA structures that are often involved in regulation of gene expression, recombination, and other genetic processes (Fedorova & Fedorov 2010). The existence of a strong fixation bias within MRI regions against mutations that tend to reduce their sequence inhomogeneity additionally supports the functionality and importance of these genomic sequences (Prakash et al. 2009)

Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures

<p>Abstract</p> <p>Background</p> <p>Genomes possess different levels of non-randomness, in particular, an inhomogeneity in their nucleotide composition. Inhomogeneity is manifest from the short-range where neighboring nucleotides influence the choice of base at a site, to the long-range, commonly known as isochores, where a particular base composition can span millions of nucleotides. A separate genomic issue that has yet to be thoroughly elucidated is the role that RNA secondary structure (SS) plays in gene expression.</p> <p>Results</p> <p>We present novel data and approaches that show that a mid-range inhomogeneity (~30 to 1000 nt) not only exists in mammalian genomes but is also significantly associated with strong RNA SS. A whole-genome bioinformatics investigation of local SS in a set of 11,315 non-redundant human pre-mRNA sequences has been carried out. Four distinct components of these molecules (5'-UTRs, exons, introns and 3'-UTRs) were considered separately, since they differ in overall nucleotide composition, sequence motifs and periodicities. For each pre-mRNA component, the abundance of strong local SS (< -25 kcal/mol) was a factor of two to ten greater than a random expectation model. The randomization process preserves the short-range inhomogeneity of the corresponding natural sequences, thus, eliminating short-range signals as possible contributors to any observed phenomena.</p> <p>Conclusion</p> <p>We demonstrate that the excess of strong local SS in pre-mRNAs is linked to the little explored phenomenon of genomic mid-range inhomogeneity (MRI). MRI is an interdependence between nucleotide choice and base composition over a distance of 20–1000 nt. Additionally, we have created a public computational resource to support further study of genomic MRI.</p

Evolution of genomic sequence inhomogeneity at mid-range scales

<p>Abstract</p> <p>Background</p> <p>Mid-range inhomogeneity or MRI is the significant enrichment of particular nucleotides in genomic sequences extending from 30 up to several thousands of nucleotides. The best-known manifestation of MRI is CpG islands representing CG-rich regions. Recently it was demonstrated that MRI could be observed not only for G+C content but also for all other nucleotide pairings (e.g. A+G and G+T) as well as for individual bases. Various types of MRI regions are 4-20 times enriched in mammalian genomes compared to their occurrences in random models.</p> <p>Results</p> <p>This paper explores how different types of mutations change MRI regions. Human, chimpanzee and <it>Macaca mulatta </it>genomes were aligned to study the projected effects of substitutions and indels on human sequence evolution within both MRI regions and control regions of average nucleotide composition. Over 18.8 million fixed point substitutions, 3.9 million SNPs, and indels spanning 6.9 Mb were procured and evaluated in human. They include 1.8 Mb substitutions and 1.9 Mb indels within MRI regions. Ancestral and mutant (derived) alleles for substitutions have been determined. Substitutions were grouped according to their fixation within human populations: fixed substitutions (from the human-chimp-macaca alignment), major SNPs (> 80% mutant allele frequency within humans), medium SNPs (20% - 80% mutant allele frequency), minor SNPs (3% - 20%), and rare SNPs (<3%). Data on short (< 3 bp) and medium-length (3 - 50 bp) insertions and deletions within MRI regions and appropriate control regions were analyzed for the effect of indels on the expansion or diminution of such regions as well as on changing nucleotide composition.</p> <p>Conclusion</p> <p>MRI regions have comparable levels of de novo mutations to the control genomic sequences with average base composition. De novo substitutions rapidly erode MRI regions, bringing their nucleotide composition toward genome-average levels. However, those substitutions that favor the maintenance of MRI properties have a higher chance to spread through the entire population. Indels have a clear tendency to maintain MRI features yet they have a smaller impact than substitutions. All in all, the observed fixation bias for mutations helps to preserve MRI regions during evolution.</p

Calculation of Splicing Potential from the Alternative Splicing Mutation Database

© 2008 Bechtel et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Drude Conductivity of Dirac Fermions in Graphene

Electrons moving in graphene behave as massless Dirac fermions, and they exhibit fascinating low-frequency electrical transport phenomena. Their dynamic response, however, is little known at frequencies above one terahertz (THz). Such knowledge is important not only for a deeper understanding of the Dirac electron quantum transport, but also for graphene applications in ultrahigh speed THz electronics and IR optoelectronics. In this paper, we report the first measurement of high-frequency conductivity of graphene from THz to mid-IR at different carrier concentrations. The conductivity exhibits Drude-like frequency dependence and increases dramatically at THz frequencies, but its absolute strength is substantially lower than theoretical predictions. This anomalous reduction of free electron oscillator strength is corroborated by corresponding changes in graphene interband transitions, as required by the sum rule. Our surprising observation indicates that many-body effects and Dirac fermion-impurity interactions beyond current transport theories are important for Dirac fermion electrical response in graphene

The Grizzly, March 5, 1996

Airband Raises $5,000 • Borsdorf Appointed by Governor Ridge • All About Pledging • Opinions: A Feminist\u27s Point of View; My God ; The Role of the Soul in Evolution; Don\u27t Knock it Unless You\u27ve Tried it; Souls and Science: Where do we Draw the Line?; What it Really Means to be Left Wing; Money Rules the World • Women\u27s Art to be on Display at Berman • Groovy Hippies and Classical Style in Wismer • Faculty Spotlight: Dr. E. Diane Lyle-Smith • Alumna Spotlight: Elizabeth Buckenmyer • Blood Drive Winners • Ortman\u27s Wrestling Career Comes to a Close • Teams Finish Sixth at Conference Championships • Luka Returns as All-American • Team Ranked 10th in U.S.https://digitalcommons.ursinus.edu/grizzlynews/1377/thumbnail.jp

The Grizzly, February 13, 1996

Summer Research at Ursinus • Fairley Will Not Plead Insanity • Merck Announces HIV Drug Results • Faculty Spotlight: Dr. Lynn Thelen • Joe Clark, Gospel Choir Highlight Diversity Week • Information Superhighway Control • Captain Offender • In Search of Aristotle\u27s Prime Mover • An Entirely Warped Romantic Interlude • Hey Students, Take Some Initiative! • Do You Believe in Magic? • Take it Back, Captain Jack! • Not Slick Enough • Strike up the (String) Band! • Ursinus Handles Swarthmore, 70-39 • Ursinus Edges Washington, 64-62 • Swarthmore Sweeps UC Swim Teams • Gymnasts Victorious • Bears Regain Centennial Titlehttps://digitalcommons.ursinus.edu/grizzlynews/1374/thumbnail.jp

The Grizzly, February 27, 1996

Koestner Gives First-Hand Account of Date Rape • J-Board Charges Reimert Residents • Swastikas are Removed from Bomberger Hall • Buchanan Wins New Hampshire • The Skipped Diploma • Evolutionary Doubts • Fighting for Real Social Change • In Support of Healthier Relationships • Alan Morrison to Perform Recital • U.S.G.A. News • Faculty Spotlight: Dr. Peter Perreten • Staff Spotlight: Todd McKinney • Gymnasts End Season With a Win • Lacrosse Team Ranked 15th • Bears Compete at Indoor Championships • Lady Bears Fall in Conference Semishttps://digitalcommons.ursinus.edu/grizzlynews/1376/thumbnail.jp