I have argued that natural genetic engineering is the real creative process in evolutionary innovation. A central but undocumented feature of my argument is that cells can coordinate separate DNA-change events to produce functional new genome structures. How can experimentalists test this argument?
The experiments will probably involve microorganisms, such as bacteria or yeast. A standard procedure for measuring microbial DNA change (mutation) is to place the microbes in a petri dish where they cannot grow into colonies, count the number of cells deposited, incubate them for a period of time, and count the number of colonies that appear. Each colony arose from a mutational event that overcame whatever prevented growth (e.g., inability to utilize the nutrients provided or to synthesize a needed biochemical). The ratio of colonies to cells placed on the growth medium is the mutant frequency. We can measure how various treatments, such as UV irradiation, change this frequency.
Mutation experiments generally look for changes at a single location in the genome. With modern DNA-sequencing technology, the precise changes are easy to identify. Colonies typically appear two to three days after the appropriate DNA change has occurred. In most cases studied, suitable mutations occur in the population prior to plating. Examining the petri dishes after two or three days indicates the frequency of preexisting mutations.
Longer incubation of the selection plates often produces a large increase in the number of colonies. This indicates that mutations continue to occur under selection conditions. By counting these colonies and analyzing the population dynamics of the selected bacteria, we can determine whether selection affects the process of genome change.
When selection significantly stimulates mutations above prior levels, the process is called "adaptive mutation." Molecular geneticists agree that adaptive mutation (observed in different microorganisms) occurs when selective stress triggers natural genetic engineering activities that carry out DNA changes allowing mutated cells to form colonies.
In some cases, we know the consensus interpretation is correct. Together with my colleague Genevieve Maenhaut-Michel, I confirmed this. We studied an experimental situation where the required DNA change (a special type of coding sequence fusion) was never detected during normal growth but increased at least 100,000-fold after selection.
Other groups confirmed selection stress triggering natural genetic engineering by detecting evidence of "induced hypermutation" at various locations throughout the genome and by direct measurement of mutator function.
It is likely that more complex changes can be triggered by selection conditions. My colleague Bernhard Hauer worked for many years at the large German chemical company BASF. In order to produce certain specialty biochemicals, BASF used microbes. But often the good producer organisms would only grow on expensive nutrients. So Bernhard simply plated them on medium containing economic nutrients, waited for a month or so, and harvested the late-appearing colonies. Unfortunately, this was before the days of rapid sequencing, and we do not know what kinds of DNA changes occurred in the long time before the colonies finally appeared.
In order to look for coordinated natural genetic engineering at multiple locations, one approach is to repeat what Bernhard did but start with well-defined strains. We know that coding sequences that lack transcription signals can be activated by the upstream insertion of mobile elements in bacteria and yeast.
The strategy is to engineer strains that could only grow when multiple mobile element insertions activated several different coding sequences. For example, these sequences might encode proteins needed at various steps of a metabolic pathway (for nutrient utilization or for biosynthesis). Selection for activation of all the sequences together simply involves placing the microbes on a medium where the whole pathway is essential for growth, and then waiting for colonies to appear.
If the initial experiment was to prove successful and colonies did eventually appear, it would be essential to exclude alternative explanations and quantify the coordination. The most important control would be to show that no single activation event led to slow growth on the selection medium. Such growth could enable other activation events to occur independently later during proliferation.
Measuring the individual frequency of each single activating event over the time it took for the combined changes to appear helps quantify the degree of coordination. The expected frequency of truly independent changes would be the multiplied product of the individual frequencies. If the frequency of selecting all the changes at once turned out to be significantly higher than this multiple, there would be evidence for a coordinating process.
To learn how coordination operates, two standard approaches are applicable. One is to sequence the genomes of the individually and coordinately activated strains. Are the DNA changes the same or not? For example, if distinct mobile elements activated individual versus multiple coding sequences, we could conclude that different triggering processes occurred in the two cases.
The second standard approach is to ask if particular control functions are essential for coordinated change to occur. In the case of the starvation-induced coding sequence fusion that Genevieve and I studied in E. coli, we and others demonstrated the roles of regulatory proteases and transcription factors. To identify components of the control network is the first step to figuring out how it operates.
The approach I just suggested is relatively straightforward microbial molecular genetics. It would document cell capacity to generate an expression network by coordinated DNA changes at multiple locations in the genome. I feel confident that it will succeed. It would open a new chapter in experimental evolution.
If you look carefully, you'll see the experimental criteria for coordination spelled out: "Measuring the individual frequency of each single activating event over the time it took for the combined changes to appear helps quantify the degree of coordination. The expected frequency of truly independent changes would be the multiplied product of the individual frequencies. If the frequency of selecting all the changes at once turned out to be significantly higher than this multiple, there would be evidence for a coordinating process."
What continually amazes me is the argument that natural selection, by definition a post-variation process, can be invoked to explain how variation occurs. In the case I cited, the selection process imposes physiological stress on the microbes, and they respond with an elevated level of DNA change activity. Is that what you had in mind? If not, please clarify how natural selection could explain when and how frequently DNA changes occur.
I find your concerns about confirmational bias rather surprising. If Shapiro's goal was to experimentally determine the percentage of the observed mutations which were due to 'natural genetic engineering', your concern about confirmational bias might be appropriate . His goal is more modest: Are any of the observed mutational events due to natural genetic engineering? His suggested experiment where the frequency of observed three-fold mutations is to be compared with the likelihood of these three (assumed independent) mutations simultaneously occurring is indeed a good test of the roll of coordination in the genesis of these mutations.
I fully agree and take Hume's logical cautions quite seriously. All experimentalists can do is accumulate correlations so that theoreticians can connect them logically. That process continues until the logic breaks down, as it has with conventional evolution theory.
The only kind of "proof" we have in science is its development into technology, which permits us to manipulate the natural world in predictable ways. That technology is as successful as it has been is the strongest correlation of them all.
this is the kind of stuff you're looking for. Right?
in case you haven't seen this (yet):
Mei Nie, Maria S. Balda, and Karl Matter Stress- and Rho-activated ZO-1–associated nucleic acid binding protein binding to p21 mRNA mediates stabilization, translation, and cell survival
PNAS 2012 ; published ahead of print June 18, 2012, doi:10.1073/pnas.1118822109
http://www.pnas.org/content/early/2012/06/13/1118822109.full.pdf
..We thus identify a unique type of stress and Rho signaling activated pathway that drives mRNA stabilization and translation and links the cellular stress response to p21 expression and cell survival.
If the experiment you suggest is carried out, and the results you expect are confirmed, it will be hard to avoid the conclusion that cells are in some sense capable of teleological behavior in the modification of their genome. It would seem that the implications that this will have on the underlying mechanisms of evolution will be profound. The orthodox view of course is that all genome changes are random, that is, random in the sense that the changes are not biased in favor of mutations which would benefit the organism. Indeed, if the results you expect are confirmed, this concept of randomness underlying evolutionary genome changes would have to be if not abandoned, at last removed from its position of dominance and teleological based changes elevated to a position of prime importance.
You are by no means the only researcher pointing out a fundamental shift in our understanding of evolutionary mechanisms; an interesting review article pointing out concepts parallel to yours can be found here:
http://content.karger.com/produktedb/produkte.asp?typ=fulltext&file=000312910
From the abstract:
"This is especially important since some genes have spread in all domains of life and the exponential availability of eukaryotic genomes and metagenomic sequences will allow researchers to explore these genetic exchanges in a more comprehensive way, thus completely changing our perception of the evolutionary history of organisms."
If the experiment I suggested is successful, it will demonstrate a cell capacity to coordinate related useful changes in response to selective challenge. As I mentioned, careful controls will need to be done in order to show that the coordination is real and that the individual changes occur more frequently together than they would if occurring independently of each other.
So much is step one of an experimental evolution program. Hopefully, confirmation of my prediction would stimulate more and increasingly ambitious attempts to document the generation of evolutionary novelty in real time.
Drawing teleological conclusions would only be appropriate once we had further evidence on the nature of the coordinating process. Presumably, it would come in the form of identifying cell molecules needed for coordinating the positive changes at distinct locations. Figuring out how they work will be a big challenge.
I prefer describing the conclusions in this step-by-step manner to making large generalizations.
The DNA sequence evidence for the action of natural genetic engineering in real genome evolution is in the link I gave to John Kowk at the bottom of the comments. Now we have to transform evolution science from historical and inferential to experimental.
I am not saying that there aren't certain regions more prone to change, or that there are mechanisms to bear with stress through change, but there's still problems with differentiating cause and effect.
There you go again, refusing to believe what is plainly set out for you.
In the case I studied with Genevieve and other colleagues, there is no doubt that aerobic starvation activates the mutations. Recall, the mutations were completely undetectable without starvation (http://www.ncbi.nlm.nih.gov/pubmed/6233472), and their frequency increased by an enormous five orders of magnitude.
In addition, the mutations can be recovered without ever undergoing direct selection, as you can read for yourself (http://www.ncbi.nlm.nih.gov/pubmed/7957088). Moreover, the changes require a specific transposase protein (http://www.ncbi.nlm.nih.gov/pubmed/2174011) as well as regulatory factors shown to activate its expresssion under the starvation stress conditions (http://www.ncbi.nlm.nih.gov/pubmed/10231489).
If you continue to deny direct evidence of cause and effect, I would have to conclude that you are dedicated to obfuscation rather than understanding. I can understand that from a character like Jerry Coyne, who claims to have "all the facts on my side." But I had the impression you were open to empirical demonstrations. What more do you need?
more prone to change, or that there are mechanisms to bear with stress
through change, but there's still problems with differentiating cause
and effect.
Let me restate, this is what I meant:
http://genome.cshlp.org/content/15/10/1365.short
How long does it take for a low-probability process that leads to an exponential growth to observability to cross the threshold for some examples to be found? How likely is that to happen? Under such circumstances 100,000 is certainly not an `enormous factor'.
You simply ignore the question asked and incoherently list a bundle of your 20-year-old papers.
Charles never claimed to be original - and he certainly was not. Natural selection refers to the 'end process' of evolution - after the variation has occurred. The causations of variation is the key to understanding evolution. And it appears to be much more than simple mutation.
If you haven't seen it, you might find my earlier blog on this same point to be of interest (http://www.huffingtonpost.com/james-a-shapiro/what-is-the-key-to-a-real_b_1280685.html).
Please don't forget to give us the symbiogenesis link. I, for one, want to be sure I know about the case you cited. Thanks.
I recommend you view this:
http://www.amnh.org/exhibitons/darwin
By 1842, Darwin had come up with Natural Selection and had coined the term; in 1858, Wallace derived it independently of him.
However - Lamarck was still wrong. The changes acquired during a lifetime of an organism happen in cases that Lamarck himself could not have possibly observed. Moreover, Lamarck postulated such changes in cases when clearly they do not exist.
There is a great concept paper about it from E. Koonin and Y. Wolf - "Is evolution Darwinian or/and Lamarckian?".
Literally over night.
This is not really about Lamarck vs. Darwin. They actually had rather similar views about the inheritance of acquired characteristics.
Lamarck, being French, often argued from general principles. As Samuel Butler pointed out (http://www.gutenberg.org/ebooks/23427), Lamarck's emphasis on the conditions of life could be interpreted as rather similar to Darwin's ideas abut the struggle for existence.
Today we can actually do experiments to test very specific ideas about how genomes change. My point in this blog concerns the ability of cells to generate functional networks in their genomes. If that can be established experimentally, then the next step will be to investigate what influence sensory inputs have on the process.