This is meant to be a thread on my paper, Measuring Active Information in Biological Systems.
Sorry I have not been participating in the initial conversation, but the conversation seemed like it was already generating more heat than light when I looked in on it. Additionally, I have spent the last month in a combination of finalizing my work at New Medio / ITX (where I have worked for almost 20 years) to start a new position on Monday, finalizing a new book on electronics, helping various organizations get connected digitally during this time, and it is the end of the school year for our homeschool co-op, so my time has been limited.
Anyway, I have been answering questions about the paper at The Skeptical Zone, but thought I would also stop by here to answer questions. I would like this thread to be dedicated to the content of the paper (and obviously related items). If there are questions that are outside of this, I would like those to be handled in a different thread. Note that the paper does not specifically mention Intelligent Design, or the paper’s relevance to Intelligent Design. While I think the paper does have relevance to Intelligent Design, I would like to separate that from the discussion of the paper itself. So, if people want to discuss that, we can open up a thread for that. However, I think the paper stands alone as a useful contribution, whether or not it can be linked to ID.
So, let me start with an overview of the paper and the background that it comes from. I have been arguing for a long time that mutations are indeed not random with respect to the needs of the organism. You can see a short, short video I did on this a long time ago, or a more in-depth one here, or an old BIO-Complexity paper about the subject here.
The problem I found was that, even though many of the facts of directed mutations were widely known. See for instance here for a conversation with Larry Moran which is pretty typical of the conversations I have. Despite agreeing that mutations are only occurring in the gene that needs to be modified, they don’t view this as being “directed”. Essentially, everyone has a preconceived notion in their mind about what “direction” should look like. If the mode of directionalization doesn’t match their particular pre-conceived notion, they simply state that the mutation is not directed.
Additionally, I found that there was no quantitative evidence that anyone could point to for mutations being random. This was simply being stated in the literature without justification. It might be true, but, lacking a mechanism for quantification, it would be impossible to know. On that note, I should point out that it is theoretically possible to agree with my paper almost wholeheartedly and not believe in directed mutations. That is, I could perhaps have come up with a correct way of quantifying it, but, when we actually apply that quantification to nature itself, it always comes up zero. This would mean both that my paper is correct, and that random mutations are the norm (note - I do have some examples of positive active information in my paper, but, in theory, these could wind up being total anomalies to the norm). Additionally, as mentioned earlier, one could also agree with my paper wholeheartedly, think that directed mutations occur, and not think it has anything at all to do with Intelligent Design.
Therefore, my goal with using active information was to find a way to quantify “directedness” which was independent of the actual mechanism used for directing. What active information does is that it measures what the effects of an actual randomized process will do, and it compares it to what is actually happening. So, we can compare and see if the process that is actually happening in biology is better than, equal to, or worse than random with respect to the fitness of the organism. Obviously there will be chemical bias in the mutation system. But, if that bias reliably points more in the direction of fitness than a non-biased process, then that is an effect that requires explanation. If the specific base pairs that are more likely to be mutated are more likely to be beneficial than other base pairs chosen at random, then that is an effect that requires explanation.
The way I actually envision active information being used, however, is the opposite. My hope is that people will use active information in order to tell when a mechanism for mutation should be searched for. It takes a lot of time, effort, and money to search for a biological mechanism for mutation (Zhang and Saier have done a lot of work on this, and, if you read their papers, it takes a lot of experiments to track this stuff down). Therefore, it would be good if, going in to the process, you knew there was something to find. My hope is that active information will be used like a metal detector. It is a simple way to find out whether or not there is something happening worth investigating. That way, time, effort, and funds can be directed to elucidating the systems most likely to be biologically interesting.
I also fully expect that, if people wind up agreeing with active information, they will eventually find it so obvious as to not be worth speaking about. I actually think that’s largely true, except for the fact that, as of this moment, people do have a mental block when thinking about directed mutations. My hope is that active information will remove this mental block. If that happens generally, then my guess is that shortly afterward, everyone will wonder what the hubbub was originally about, and why my paper was needed to begin with, since the concept was so obvious.
Additionally, my paper also notes that actually performing these experiments leaves a lot of questions, because there will always be intermixing between induced random mutations, and the mutations that the organism is already doing (whether they are random or not). The paper offers a statistical mechanism for separating these out in certain circumstances.
So, if you can take the time to read the paper, please do so, but I think that is enough to start a conversation. I don’t have time to just sit on the thread all day, but I will try to answer questions at least by the end of each day (though probably not Monday). If you would like a side topic addressed (i.e., something not relevant to this thread), just make a new topic and link to it here so it is findable.