Which, coincidentally or not, happens to also be the amount of information that Bio-Complexity (as it presently stands) has about likely beneficial additions to our knowledge of biology.
This is very poor communication I have to say. In trying to make sense of that sentence I get the impression that the author is trying to say that there is some degree to which the genome of an organism is likely to change in a beneficial way in some environment, and that this degree to which it is likely to do so, can be quantified and measured. And that the name of the unit of quantity is “active information”.
But isn’t that essentially just evolvability? Or maybe plasticity? So he’s sort of coming up with some sort of unit of measurement of evolvability?
OK, looking at equation (3), this is nearly the equation for a Likelihood Ratio statistic, differing only by a constant (~1.4). Bartlett goes on to do interpretation and whatnot, but he is still committing the equivalent of interpreting the magnitude of a p-value. Under the same assumption of randomness, equation (3) is a random variable is the same way a p-value is a random variable. No, a p-value does not have a “strength of difference” interpretation.
This might have a theoretical “non-centrality” interpretation, related to the statistical power to reject the null hypothesis of “non-centrality equals zero”. Measuring this quantity from data it only a way to restate the p-value of the test.
Other than that, he entirely ignores selection and the efficiency of genetic search, which is darned good, O[n*log(n)].
23 posts were merged into an existing topic: Side comments on Bartlett: Measuring Active Information
I’ve got the paper; will hold off until I get a chance to read it – quite busy today and tomorrow.
I don’t say any of them are wrong. It’s the swaggering “I know how evolution works, and I know this guy is wrong, as all ID proponents are wrong because they don’t know what they’re talking about” attitude that I object to – an attitude all too common on this site, which is why I hardly post here any more, or even read what’s posted here.
I haven’t analyzed Bartlett’s article yet, but I know him personally, and I know his qualifications, and he has advanced training in areas relevant to his article; whereas, based on Roy’s years of commenting here, I can’t see that he has training in anything at all, except studying opinions posted on blog sites that discuss evolution. I’m just asking for the grounds of Roy’s confidence that he knows what he’s talking about and Bartlett doesn’t. If he doesn’t want to answer, he doesn’t have to. Just registering that I don’t accept Roy as an authority on evolution, any more than I accept him as an authority on the history of ideas.
But then, very few people who post here are specialists in evolutionary theory (as opposed to biologists, biochemists, or other people with a keen layman’s interest in evolution) – I think you and Joe Felsenstein are the only two people posting here with Ph.D.s in the life sciences specializing in evolutionary theory. But you aren’t the only two who represent themselves as experts in it. In fact, Joe and you are less aggressive-sounding in the expression of your opinions than are a number of champions of evolution here with little to no formal training in the area. Why there has to be this swagger and bravado all the time is beyond me. Does it come automatically with the science training, or are we getting a non-representative sampling of scientists here, i.e., is it the case that only the angriest and most biased people with science training tend to argue on blog sites about evolution, and that the moderate and fair-minded ones aren’t usually found in such places?
Yes, it’s possible. But where that’s the case, the person usually sounds just as competent, both on matters of detail and on general exposition of the field, as the trained person. I have not found that with Roy’s posts, which strike me as pastiches of borrowed thought and arguments as opposed to an internalized mastery of first principles.
I’ve seen no evidence that Roy reads any of the literature; he repeats talking points.
I suppose that naked contradiction followed by “Bartlett doesn’t understand what he’s talking about” (the gist of Roy’s criticism) “makes sense”, but it isn’t much of an argument. It’s just nay-saying.
It my understanding that he has training in engineering, mathematics and computer science relevant to the various models he talks about and arguments he makes. He doesn’t have to be a master of every aspect of evolutionary theory to understand one small aspect of it well. The question is whether Roy has mastery of even one small aspect, or merely repeats the popularized defenses of the status quo against ID. I suspect it’s the latter, as I’ve seen nothing like personal mastery of any area of any science shown in any of his posts (as opposed to, say, your knowledge of animal classification, which appears to show intimate knowledge of the field).
I’ve answered you out of politeness, because you addressed me, but I have to get back to work now, so I’m exiting this thread.
Yep. The Blyth Institute is located in Johnny B’s home in Oklahoma, and he seems to be the only member. You’d think he could at least get a green screen shot of a science lab to match BIO-Complexity’s state-of-the-art ID research facility.
From Jonathan Bartlett’s, Technical Lead at ITX Corp, linkedin page listing for education, he has Union High School following with four years at Oklahoma Baptist University, with the (presumed) degree unspecified. From other articles, he also attended Phillips Theological Seminary, and has moved from an old earth to a young earth creationist camp.
Jonathan Bartlett … said he once made fun of people who believe in a young Earth, but now he is one.
Bartlett was motivated to study biology and other disciplines after his first son was born with a rare genetic disorder and died a few years later. That study changed his mind about the age of the Earth.
As a graduate student at Oklahoma Baptist University and later a theology student at Phillips Theological Seminary in Tulsa, belief in an old Earth was his default position, Bartlett said.
But the more he studied it, he said, the more he came to believe that arguments for an ancient Earth were often circular; people in that camp had their model of what is true and tried to make the facts fit into it. Some fit nicely, others did not, he said.
“When I look at a larger-scale picture of geology, it supports young Earth creation,” he said.
I have created a side comments thread and moved a number of comments. It was not possible to completely separate comments I thought to be relevant from the squabbling, so I had to make a judgment call:
- Eddie’s personal experience with Bartlett is relevant.
- The origin/owner of the Blythe Institute is relevant.
The remaining personal attacks or snark should be disregarded, and I will police the thread to keep that from breaking out again. /fnord
ETA: There were a few comments moved that might be acceptable criticism, but such judgement calls are difficult. If you replied to an inappropriate comment it gets moved along with the rest - that’s all I have time to do.
The first thing that comes to my mind is “nature has already done these experiments”. The genomes of modern species are a record of accumulated random mutations, and I think they would be well served using that data. There’s tons of information on the human genome and human biology, and there are several other ape genomes to compare to.
Another problem I see is the different types of mutations. From the paper:
My gut reaction is that it may not be proper to compare the substitution rate with the indel rate. In the Lenski experiment, it was a recombination event that moved a promoter in front of the citrase gene. So how does one model that, and how was the recombination rate increased or decreased in different hypermutator lineages? What are the chances that a functional promoter that is active in aerobic conditions would find its way in front of the citrase gene?
Let me restore some relevant information that’s been excised:
Bartlett is a YEC with no expertise in evolutionary biology. The Blyth Institute is his personal project, apparently run from his house. And his writing is not very coherent. That is, it’s hard to figure out, based on his words, what he means, or in fact whether he means anything.
Can anyone explain what this means? How is active information measured? Why is information being compared to, apparently, mutation rate?
From what I can see, active information is the probability of getting a beneficial mutation. Per the usual, the major pitfalls are not knowing all possible beneficial mutations for a given selective pressure and the potential for committing the Sharpshooter fallacy.
The cit+ mutation in the Lenski experiment could be good example to work from. We simply don’t know all of the possible mutations that could have conferred the cit+ phenotype. There are probably many different promoters and recombination events that could have worked in this situation, not to mention the possibility of beneficial substitution mutations within the original promoter. I would also be curious to see how the E. coli SOS response could affect the results in this specific case.
The studies leading to the discovery of the SOS response are especially cogent to the overall thrust of Bartlett’s paper. Some of the earliest arguments for a possible mechanism of adaptive mutations was based on higher than expected lac+ revertants in E. coli. As it turned out, when starvation caused DNA damage this turned on several genes, including genes responsible for increasing the substitution and recombination mutation rates. The E. coli weren’t specifically creating mutations that fixed a broken lac gene, but were instead increasing their overall random mutation rate.
My understanding is that “active information” is the difference between the probability of getting a beneficial mutation completely randomly vs the probability of getting that same beneficial mutation in the presence of cellular corrective machinery and bias towards particular types of mutation.
I can give you an example of such “active information” in a genetic algorithm, if you like.
I suspect that ultimately Bartlett’s ideas are irrelevant, because even if he does manage to show that there is “active information” in genomes or cellular processes that lead to more beneficial mutations that would be expected by chance, that will do absolutely nothing to show that that “active information” isn’t the result of 4 billion years of evolution.
What do think has been done to show that active information is the result of 4 billion years of evolution?
Before that debate, it should be determined that the coined term “active information” is not an unhelpful misnomer. Does it clarify or obfuscate?
All of the “information” arguments from creationists are nonsense.
Information doesn’t actually exist. That is to say, it is not a natural kind in any reasonable sense. Information is a human abstraction, invented by humans for their own theorizing about the world.
If you see agency involved in the use of information, then that is correct. But it is human agency.
Evolution gave us biological creatures and causal processes. It did not give us information. That you see information in biology, is because we humans invented the idea of information and found it a useful way (useful for us) to study natural processes.
So yes, information comes from intelligent design – the intelligence is human, and the design is in designing ways for us to talk about the natural world.
A post was merged into an existing topic: Side comments on Bartlett: Measuring Active Information
And the same thing happens in somatic hypermutation in the antibody response. The side effect is that many lymphomas are started by its lack of specificity producing mutations in genes expressed at high levels at that point in B-cell maturation.