"Scientific development depends in part on a process of non-incremental or revolutionary change...The usual prelude to changes of this sort is...the awareness of anomaly, of an occurrence or set of occurrences that does not fit existing ways of ordering phenomena. The changes that result therefore require 'putting on a different kind of thinking-cap'..." -- Thomas Kuhn
Conventional wisdom has it that the genetic changes underlying evolution are random accidents, each having a small chance of making incremental improvements in fitness. These ideas came about before we knew about DNA. Now that we have almost 60 years of DNA-based molecular genetics and genome sequencing behind us, a different picture has emerged. As I argue in my June 2011 book, molecular science reveals built-in cell systems for restructuring genomes in times of stress and challenge. The mobile genetic elements first discovered by Barbara McClintock have proved to be everywhere. Sometimes these are also called transposable elements (TEs) because they move ("transpose") from one site in the genome to new sites. They are part of an elaborate set of biochemical functions essential for making changes in DNA sequences (which do not happen without these functions). But the question still remains: does the evidence exist that these same functions are responsible for actual evolutionary change? A recent Nature paper (Lindblad-Toh, Garber et al. 2011) provides some answers.
Investigators from Harvard and MIT's Broad Institute carried out an exhaustive comparison of the human genome sequence with the sequences of 29 other eutherian mammals (the ones that have placenta and diverged from Marsupials). Using state-of-the-art bioinformatic tools, they searched for positively selected features in the human and other 29 genomes. The search identified genetic loci encoding approximately 4,400 out of 13,000 protein families as falling into the positively selected category and are, therefore, presumed adaptively useful throughout eutherian mammals' evolution. While this result was consistent with conventional expectations, the big surprise came when the researchers looked at so-called "non-coding" regions of the genome. These regions contain DNA sequence signals for essential functions, such as packaging the DNA within the nucleus, copying DNA into RNA, replicating the genome, and distributing the two genome copies equally to daughter cells at cell division. "Our data revealed >280,000 mobile element exaptations common to mammalian genomes covering ~7 Mb..., a considerable expansion from the ~10,000 previously recognized cases. Of the ~1.1 million constrained elements that arose during the 90 million years between the divergence from marsupials and the eutherian radiation, we can trace >19% to mobile element exaptations."
A detour will probably be helpful here to explain the term "exaptation" for readers not familiar with it. The word "exaptation" was invented by the late Stephen J. Gould and fellow paleontologist Elisabeth Vrba in 1982 to describe inherited adaptations that have acquired new functions in the course of evolutionary change (Gould and Vrba 1982). It denotes a fundamental aspect of evolution where the jobs encoded by one component of the genome can undergo alteration so that they meet a new adaptive need. Exaptations can occur at all levels of genome encoding, from essential recognition sites to protein coding sequences to entire networks of proteins and the DNA signals they recognize. For example, the same signaling cascade of proteins is used in various organisms to communicate information to the genome about oxidative stress, osmotic pressure, and the presence of suitable sex partners.
As the Broad Institute authors note, "Mobile elements provide an elegant mechanism for distributing a common sequence across the genome, which can then be retained in locations where it confers advantageous regulatory functions to the host -- a process termed exaptation." In other words, new DNA signals in the genome do not need to evolve independently by random mutation at each site where they play an important role. Different DNA signals can be distributed to many sites by the biochemical systems that mobilize defined segments of DNA (mobile genetic elements) to new locations. In this way, evolution of the DNA signals embedded in the genome resembles genetic engineering more than a mutational random walk. The fact is that only fairly recent exaptations can be identified because the traces of the original mobile genetic elements tend to disappear with sequence changes over time. Thus, the >280,000 cases of mobile genetic element exaptation identified in the Lindblad-Toh et al. paper represent the lower limit of genome formatting by a process I dubbed "natural genetic engineering" twenty years ago (Shapiro 1992). Although conventional evolutionists have tended to ignore the importance of mobile genetic elements in evolution -- calling them "junk DNA" (Orgel 1980) -- and treat the well-documented cases of mobile genetic element exaptation as minor and accidental exceptions, the weight of evidence revealed by this article cannot be dismissed so easily.
The idea that mobile genetic elements and natural genetic engineering are fundamental to genome evolution dates back to Barbara McClintock's work on what she called "controlling elements" (McClintock 1987). When she compared controlling elements to the recently discovered repressor-operator system of E. coli (McClintock 1961), her interpretation was widely rejected because DNA mobility was not considered important to the short-term regulation of protein synthesis and genome expression. This rejection notwithstanding, her "controlling elements" terminology now appears prescient in light of recent genomic discoveries. She considered mobile genetic elements as "controlling" elements in the genome because they altered the expression patterns of a particular genetic locus when they inserted into it. This is just what evolution needs to rewire genomic networks at times of evolutionary challenge, especially when similar changes have to occur at more than one locus (McClintock 1956).
There are many eye-opening consequences of the basic role that natural genetic engineering plays in the evolutionary process. We will explore these conceptual changes in future blogs. For the moment, it is deeply satisfying to note that intense genome sequence analysis has validated the work of McClintock and her many followers in the field of mobile genetic elements.
REFERENCES
Gould, S. J. and E. S. Vrba (1982). "Exaptation--a missing term in the science of form." Paleobiology 8(1): 4-15. http://www.jstor.org/stable/2400563 .
Lindblad-Toh, K., M. Garber, et al. (2011). "A high-resolution map of human evolutionary constraint using 29 mammals." Nature 478(7370): 476-482. http://www.ncbi.nlm.nih.gov/pubmed/21993624.
McClintock, B. (1956). "Intranuclear systems controlling gene action and mutation." Brookhaven Symp Biol(8): 58-74. http://www.ncbi.nlm.nih.gov/pubmed/13293421.
McClintock, B. (1961). "Some parallels between gene control systems in maize and in bacteria." American Naturalist 95: 265-277. http://www.jstor.org/stable/2458651.
McClintock, B. (1987). Discovery And Characterization of Transposable Elements: The Collected Papers of Barbara McClintock New York, Garland. ISBN 978-0824013912.
Orgel, L., Crick, FH (1980). "Selfish DNA: the ultimate parasite." Nature 284: 604-607. http://www.ncbi.nlm.nih.gov/pubmed/7366731.
Shapiro, J. A. (1992). "Natural genetic engineering in evolution." Genetica 86(1-3): 99-111. http://www.ncbi.nlm.nih.gov/pubmed/1334920.
As for the article, I have to admit it makes a lot of sense: I don't know what portion of a cell's metabolism is involved in copying and maintaining the so-called "junk" portions of the genome, but I do know that keeping useless segments of DNA around seems rather a waste of resources. Knowing that it serves a purpose--especially such an elegant one--is a neat discovery.
Thank you for taking the time to share it with us.
Sorry for the liberal use of quotation marks but viewed this way the words enclosed in quotation marks cannot be viewed by the common definitions. If my synopsis is correct than perhaps this is the very reason that the explanation above is so obtuse...
Did I interpret this correctly?
I must also ask: With the continued discovery of variants of the four basic amino acids that we once thought where the sole components of DNA, is it conceivable that the DNA "repeats" have subtle differences that effectively record information of prior periods of environmental stress that are specific to a single variable?
I look forward to future articles.
Life changes as the result of genetic engineering, an intelligently directed, purposeful process, rather than by “natural selection” doing something (???) to random mutations. (genetic accidents).
If that is what the article claims, it is in dramatic opposition to current biological orthodoxy, which insists that purposeful change, or intelligent design, cannot be an aspect of living processes. They even appealed to the courts to ban intelligent design from being mentioned in the classroom. Certainly any form of engineering is by definition a purposeful process, whether the engineer is a deity or some natural intelligence innate to living systems. This has long been a question of bitter controversy, with the defenders of RM&NS accusing anyone question their orthodoxy of being “ignorant biblical creationists”. I’ve been a fan of Dr. Shapiro’s, but I’d hate to see his genetic engineering quietly accepted as a minor alteration in the details of Darwinian evolution. Life is either a mechanical process or it is not. Evolution, defined as descent with modification, was accepted before Darwin. Natural Selection and random mutations were Darwin’s unique contribution.
A Few Autistic Questions about Freud, Marx and Darwin
http://30145.myauthorsite.com/
The insight here is that cells ALSO have internal mechanisms which guide non-random genetic changes, and more astonishing, distribute them broadly to multiple loci, where the (potential) advantage can be rapidly adopted, even for dissimilar processes.
That does not suggest 'intelligence', I'm afraid, or design, if by design we mean a known goal or outcome was purposefully intended.
But it does suggest that life is more capable of responsive adaptation for survival than we'd previously assumed, and not just a passive reliance on chance.
This isn't unusual as a general idea - if you consider the mammalian diving reflex, for example - there are many abilities that creatures possess that are only invoked during certain conditions. But I don't think it's usually applied to the altering of DNA itself.
It has been long believed that many parts of human DNA are "doing nothing" or vestigially carried over, without any particular purpose in forming the person. This is the idea of Junk DNA.
I think this article is not suggesting that random mutation doesn't exist, but that other controlling factors within the DNA can also change it.
(PS - We need to carefully look for a downside to this, if only among a limited segment of the population. Trust me, "downsides" happen very frequently, and can really sneak up on you from behind.) - RC
Its great that you list the references, and I hope this will be common practice on Huffpost Science. Too many science news articles fail to give anything beyond an author's name. Ou, the names on this article. I obviously don't look at alot of big science papers because this is the first time I've ever seen something like "Baylor College of Medicine Human Genome Sequencing Center Sequencing Team" listed as an author.
Happy reading, Jim.
And he seems to do it over and over again.
What a kidder
I recently asked a good evangelical friend to explain fossils.
She said it was easy “God put them there”
Well, you can’t argue with that.