The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.
Is junk DNA bunk? A critique of ENCODE
Open accessAbstract
Do data from the Encyclopedia Of DNA Elements (ENCODE) project render the notion of junk DNA obsolete? Here, I review older arguments for junk grounded in the C-value paradox and propose a thought experiment to challenge ENCODE’s ontology. Specifically, what would we expect for the number of functional elements (as ENCODE defines them) in genomes much larger than our own genome? If the number were to stay more or less constant, it would seem sensible to consider the rest of the DNA of larger genomes to be junk or, at least, assign it a different sort of role (structural rather than informational). If, however, the number of functional elements were to rise significantly with C-value then, ( i ) organisms with genomes larger than our genome are more complex phenotypically than we are, ( ii ) ENCODE’s definition of functional element identifies many sites that would not be considered functional or phenotype-determining by standard uses in biology, or ( iii ) the same phenotypic functions are often determined in a more diffuse fashion in larger-genomed organisms. Good cases can be made for propositions ii and iii . A larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon, is needed.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme
Gould, S. J., & Lewontin, R. C. (1979) · Proceedings of the Royal Society of London. Series B. Biological Sciences · doi:10.1098/rspb.1979.0086 · Cited by 7,770
Landscape of transcription in human cells
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187
Exaptation—a missing term in the science of form
Gould, S. J., & Vrba, E. S. (1982) · Paleobiology · doi:10.1017/s0094837300004310 · Cited by 5,136
The B73 Maize Genome: Complexity, Diversity, and Dynamics
Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., et al. (2009) · Science · doi:10.1126/science.1178534 · Cited by 4,046
Genome Regulation by Long Noncoding RNAs
Rinn, J. L., & Chang, H. Y. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-051410-092902 · Cited by 4,005
Selfish DNA: the ultimate parasite
Orgel, L. E., & Crick, F. H. C. (1980) · Nature · doi:10.1038/284604a0 · Cited by 2,156
Selfish genes, the phenotype paradigm and genome evolution
Doolittle, W. F., & Sapienza, C. (1980) · Nature · doi:10.1038/284601a0 · Cited by 1,829
Self-citationThe Origins of Genome Architecture
Abdel-Haleem, H. (2007) · Journal of Heredity · doi:10.1093/jhered/esm073 · Cited by 1,139
The origins of genome architecture
(2007) · Choice Reviews Online · doi:10.5860/choice.45-0862 · Cited by 953
Cited by
Ten things you should know about transposable elements
Bourque, G., Burns, K. H., Gehring, M., Gorbunova, V., Seluanov, A., Hammell, M., Imbeault, M., Izsvák, Z., Levin, H. L., Macfarlan, T. S., et al. (2018) · Genome Biology · doi:10.1186/s13059-018-1577-z · Cited by 1,430
The bioenergetic costs of a gene
Lynch, M., & Marinov, G. K. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1514974112 · Cited by 600
What Biological Functions Are and Why They Matter
Garson, J. (2019) · doi:10.1017/9781108560764 · Cited by 239
ORegAnno 3.0: a community-driven resource for curated regulatory annotation
Lesurf, R., Cotto, K. C., Wang, G., Griffith, M., Kasaian, K., Jones, S. J. M., Montgomery, S. B., Griffith, O. L., & The Open Regulatory Annotation Consortium (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1203 · Cited by 201
Genetic Changes Shaping the Human Brain
Bae, B.-I., Jayaraman, D., & Walsh, C. A. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.01.035 · Cited by 135
Metadata
- Authors
- Doolittle, W. F.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2013-03-11
- Volume
- 110
- Issue
- 14
- Pages
- 5294-5300
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2148964874
- Cited by
- 429
- References
- 54
- FWCI
- 61.34
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Is junk DNA bunk? A critique of ENCODE. https://app.cochat.ai/papers/10.1073/pnas.1221376110
- The paper
- Doolittle, W. F. (2013). Is junk DNA bunk? A critique of ENCODE. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1221376110
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
