Darwin Unhinged: The Bugs in Evolution

In a search for experimental confirmation of the hypothesis that there is a creative Mind in nature that fosters evolution it's interesting to look at the results of Lenski's long-term multigenerational attempt to demonstrate Darwinian evolution of a large total population of E. coli bacteria in the lab.

"The E. coli long-term evolution experiment (LTEE) is an ongoing study in experimental evolution led by Richard Lenski that has been tracking genetic changes in 12 initially identical populations of asexual Escherichia coli bacteria since 24 February 1988." (Wiki)

This experiment has been a failure as far as demonstrating evolution of any new innovative complicated or irreducibly complex designs. It has mostly been devolution - broken genes, that had an initial moderate fitness benefit at the cost of loss of genetic information and eventually a dramatically lower fitness, as predicted by Michael Behe. The only innovation of any kind was the development of aerobic citrate metabolism, but it involved little new information - it utilized the already existing genetic design for anaerobic citrate metabolism.

From https://evolutionnews.org/2020/06/citrate-death-spiral/, about a recent paper on this research:

"(In the development of aerobic citrate metabolism)...a region of the prodigious bacterium’s DNA that was close to a gene coding for a citrate transporter (that is, a protein whose job is to bring external, dissolved citrate into the cell; citrate is a common chemical that cells metabolize) had duplicated. The duplication mutation placed the control region of a different gene next to that of the citrate transporter.
...................................................
(The paper) reports on 2,500 generations of further evolution of the citrate mutant (since COVID), in nutrient media that contains either citrate alone or citrate plus glucose (as for earlier generations). As always with the Lenski lab, the research is well and thoroughly done. But the resulting E. coli is one sick puppy. Inside the paper they report that “The spectrum of mutations identified in evolved clones was dominated by structural variation, including insertions, deletions, and mobile element transpositions.” All of those are exceedingly likely to break or degrade genes. Dozens more genes were lost. The citrate mutant tossed genetic information with mindless abandon for short term advantage.

In a particularly telling result, the authors “serendipitously discovered evidence of substantial cell death in cultures of a Cit+ clone sampled from … the LTEE at 50,000 generations.” In other words, those initial random “beneficial” citrate mutations that had been seized on by natural selection tens of thousands of generations earlier had led to a death spiral. The death rate of the ancestor of the LTEE was ~10 percent; after 33,000 generations it was ~30 percent; after 50,000, ~40 percent. For the newer set of experiments, the death rate varied for different strains of cells in different media, but exceeded 50 percent for some cell lines in a citrate-only environment. Indeed, the authors identified a number of mutations — again, almost certainly degradative ones — in genes for fatty acid metabolism that, they write with admirable detachment, “suggest adaptation to scavenging on dead and dying cells.”

The degraded E. coli was eating its dead.

Lessons to Draw

Let me emphasize: the only result from the decades-long, 50,000-plus generation E. coli evolution experiment that even seemed at first blush like it had a bit of potential to yield a novel pathway in the bacterium has resulted instead in spectacular devolution."

It occurs to me that if there really were a Mind in nature that in response to environmental pressures to change, creatively designs and redesigns organisms for their survival, then Lenski's experiment would have yielded at least a couple of novel and innovative new designs. It didn't - it yielded mostly drastic genetic degradations. That certainly seems to falsify the above hypothesis. The experiment also falsifies neo-Darwinist processes at least in the area of innovative new designs as opposed to devolution.

Of course, the all-permeating Mind could have all sorts of additional powers such such as picking and choosing where and when it creates new designs, and accordingly realize that it would be pointless to innovate during a human experiment. But this is so ad hoc.

In a search for experimental confirmation of the hypothesis that there is a creative Mind in nature that fosters evolution it's interesting to look at the results of Lenski's long-term multigenerational attempt to demonstrate Darwinian evolution of a large total population of E. coli bacteria in the lab.

"The E. coli long-term evolution experiment (LTEE) is an ongoing study in experimental evolution led by Richard Lenski that has been tracking genetic changes in 12 initially identical populations of asexual Escherichia coli bacteria since 24 February 1988." (Wiki)

This experiment has been a failure as far as demonstrating evolution of any new innovative complicated or irreducibly complex designs. It has mostly been devolution - broken genes, that had an initial moderate fitness benefit at the cost of loss of genetic information and eventually a dramatically lower fitness, as predicted by Michael Behe. The only innovation of any kind was the development of aerobic citrate metabolism, but it involved little new information - it utilized the already existing genetic design for anaerobic citrate metabolism.

From https://evolutionnews.org/2020/06/citrate-death-spiral/, about a recent paper on this research:


It occurs to me that if there really were a Mind in nature that in response to environmental pressures to change, creatively designs and redesigns organisms for their survival, then Lenski's experiment would have yielded at least a couple of novel and innovative new designs. It didn't - it yielded mostly drastic genetic degradations. That certainly seems to falsify the above hypothesis. The experiment also falsifies neo-Darwinist processes at least in the area of innovative new designs as opposed to devolution.

Of course, the all-permeating Mind could have all sorts of additional powers such as picking and choosing where and when it creates new designs, and accordingly realize that it would be pointless to innovate during a human experiment. But this is so ad hoc.

I read about this experiment in Behe's "Darwin Devolved". A couple of things occurred to me:

1) Since the environment was constant, there didn't seem to be a lot for evolution to do, and RM+NS could go wild throwing out genetic mechanisms that would not be needed in that particular environment. However, intelligent evolution couldn't do much either. A much more interesting experiment would have been to progressively change the food source to something that the original bugs could not metabolise.

2) In a model in which the evolutionary intelligence doesn't reside in the actual organisms, does one intelligence process multiple environments or does the intelligence split?

David

I read about this experiment in Behe's "Darwin Devolved". A couple of things occurred to me:

1)        Since the environment was constant, there didn't seem to be a lot for evolution to do, and RM+NS could go wild throwing out genetic mechanisms that would not be needed in that particular environment. However, intelligent evolution couldn't do much either. A much more interesting experiment would have been to progressively change the food source to something that the original bugs could not metabolise.

2)        In a model in which the evolutionary intelligence doesn't reside in the actual organisms, does one intelligence process multiple environments or does the intelligence split?

David

(1) I don't think a constant environment should prevent evolution, since at least the neo-Darwinistic processes are driven by the presence of environmental stress and mortality (regardless of its rate of change) and the potential for genetic changes to increase fitness by spreading these genetic changes into the population. 
I don't see why some sort of Mind permeating nature couldn't have detected the stress the E. coli were under (regardless of whether it came on suddenly at the commencement of the experiment or gradually thereafter). Then this Mind could have responded by creatively discerning or designing in perhaps one step a genetic modification that would yield aerobic citrate metabolism, while not breaking any genes in the process, adding it as a switchable option for the organism. Such a genetic change if necessary could be complicated, irreducibly complex, and might include originating an entirely new gene in the process. Of course we can imagine this might not be possible because E. coli already has an absolutely optimal design that can't be modified in any way without major problems, but this seems to be unlikely to me given the astronomical number of permutations and combinations of DNA changes that are possible.

(2) I think either is possible. One sufficiently high conscious intelligence could conceivably do it all, including simultaneous apparent battles between different organisms' evolution, such as predator-prey or parasite-host or food supply/habitat conflicts, etc. A much simplified human example could be the ability of some chess masters to simultaneously play multiple chess games against different opponents. 
A more common sense interpretation could be that because of inherent limitations the intelligence involved has had to be separate beings each controlling the evolution of individual species or groups of species. These evolutionary "arms races" make it look somewhat like that, where it looks like it may be a playful (from the beings' nonhuman perspective) competition between designers, with the separate different designers also having individually different aesthetic sensibilities and creativity.

[Laird]

In reading Bernardo Kastrup's thesis (the second one, a defence of idealism), subject matter relevant to this thread has arisen. Here, I quote from that thesis (footnotes elided), expecting that the relevance to this thread is obvious, particularly given the reference to Luciano Floridi:

As I elaborate in section 2.5, the “hard problem” is not merely hard, but fundamentally insoluble, arising as it does from the very failure to distinguish explanatory abstraction from empirical observation discussed in this paper. As such, it implies that we cannot, even in principle, explain mind in terms of matter. But because the contemporary cultural ethos entails the notion that mind and matter constitute a dichotomy, one may feel tempted to conclude that there should also be a symmetrical ‘hard problem of matter’—that is, that we should not, even in principle, be able to explain matter in terms of mind. The natural next step in this flawed line of reasoning is to look for more fundamental ontological ground preceding both mind and matter; a third substrate to which matter and mind could both be reduced.

A good example of this line of reasoning is brought by ontic pancomputationalism, which posits that ungrounded information processing is what makes up the universe at its most fundamental level (Fredkin 2003). As such, ontic pancomputationalism entails that computation precedes matter ontologically. But “if computations are not configurations of physical entities, the most obvious alternative is that computations are abstract, mathematical entities, like numbers and sets” (Piccinini 2015). According to ontic pancomputationalism, even mind itself—psyche, soul—is a derivative phenomenon of purely abstract information processing.

To gain a sense of the epistemic cost of this line of reasoning, consider the position of physicist Max Tegmark (2014). According to him, “protons, atoms, molecules, cells and stars” are all redundant “baggage”. Only the mathematical parameters used to describe the behaviour of matter are real. In other words, Tegmark posits that the universe consists purely of numbers— ungrounded information—but nothing to attach these numbers to. The universe supposedly is a “set of abstract entities with relations between them,” which “can be described in a baggage-independent way”. He attributes all ontological value to a description while—paradoxically—denying the existence of the very thing that is described in the first place.

Clearly, ontic pancomputationalism represents total commitment to abstract mathematical concepts as the foundation of existence. According to it, there are only numbers and sets. But what are numbers and sets without the mind or matter where they could reside? It is one thing to state in language that numbers and sets can exist without mind and matter, but it is another thing entirely to explicitly and coherently conceive of what—if anything—this may mean. By way of analogy, it is possible to write—as Lewis Carrol did—that the Cheshire Cat’s grin remains after the cat disappears, but it is another thing entirely to conceive explicitly and coherently of what this means.

Ontic pancomputationalism appeals to ungrounded information—pure numbers, mathematical descriptions—as ontological primitive, i.e., as the sole fundamental aspect of existence. But what exactly is information? Our intuitive understanding of the concept has been cogently captured and made explicit by Claude Shannon (1948): information is given by state differences discernible in a system. As such, it is a property of a system—associated with the system’s possible configurations—not an entity or ontological class unto itself. Under mainstream physicalism—that is, materialism—the system whose configurations constitute information is a material arrangement, such as a computer. Under idealism, it is mind, for experience entails different phenomenal states that can be qualitatively discerned from one another. Hence, information requires a mental or material substrate in order to be even conceived of explicitly and coherently. To say that information exists in and of itself is akin to speaking of spin without the top, of ripples without water, of a dance without the dancer, or of the Cheshire Cat’s grin without the cat. It is a grammatically valid statement devoid of any semantic value: a language game less meaningful than fantasy, for internally consistent fantasy can at least be explicitly and coherently conceived of and, thereby, known as such. But in what way can we know information uncouched in mind or matter?

One assumes that serious proponents of ontic pancomputationalism are well aware of this line of criticism. How do they then reconcile their position with it? A passage by Luciano Floridi—well-known advocate of information as ontological primitive—may provide a clue. In a section titled “The nature of information,” he states:
Information is notoriously a polymorphic phenomenon and a polysemantic concept so, as an explicandum, it can be associated with several explanations, depending on the level of abstraction adopted and the cluster of requirements and desiderata orientating a theory. ... Information remains an elusive concept. (Floridi 2008: 117, emphasis added)

Such ambiguity lends ontic pancomputationalism a kind of conceptual fluidity that renders it impossible to pin down. After all, if the choice of ontological primitive is given by “an elusive concept,” how can one definitely establish that the choice is wrong? In admitting the possibility that information may be “a network of logically interdependent but mutually irreducible concepts”, Floridi seems to suggest, even, that such elusiveness may be unresolvable.

While vagueness may be defensible in regard to natural entities conceivably beyond the human ability to apprehend, it is at least difficult to justify when it comes to a human concept such as information. We invented the concept, so we either specify clearly what we mean by it or our conceptualization remains too ambiguous to be ontologically meaningful. In the latter case, there is literally no sense in attributing ontological value to information and, hence, ontic pancomputationalism is—once again—strictly meaningless.

In reading Bernardo Kastrup's thesis (the second one, a defence of idealism), subject matter relevant to this thread has arisen. Here, I quote from that thesis (footnotes elided), expecting that the relevance to this thread is obvious, particularly given the reference to Luciano Floridi:

Kastrup gets credit for taking on these issues.  He presents admirable prowess for analysis.  I am not an Idealist, but appreciate his making of the case.

The argument in the above posted section from his thesis - is against ontic pancomputationalism.  It is another term for varieties of Digital Physics.

Both IR philosophers - Kenneth Sayre and Floridi - declare against  pancomputationalism/digital physics as the root of reality.  Bernardo is late to the party on that, but has a new perspective.  The Floridi quote, quite on point as a citation, is in the beginning of a paper by Floridi, where he spends most of the rest of it - trying to better define information and the science and logic that it currently includes.

Kastrup argues:

But what exactly is information? Our intuitive understanding of the concept has been cogently captured and made explicit by Claude Shannon (1948): information is given by state differences discernible in a system. As such, it is a property of a system—associated with the system’s possible configurations—not an entity or ontological class unto itself.

Wonderfully expressed by Kastrup and is a received viewpoint!  While the MTC (Shannon's Mathematical Theory of Communication) is not a class by itself, as it is abstractly separated from grounded realty by the heuristic requirement of the meaningfulness related to the data structures be ignored.

Physical outcomes are actual and unified (coherent), but we do understand meanings and decisions as having common ground with dispositions and propensities.  In the framework of measuring quantum events and MTC events, there is a common ground with seeing outcomes coming from environmental possibilities.   Bernardo's trained mind may see the framework of the MTC, as intuitive, it is similar to physics in that it's basic in probabilistic maths.  It may not be a easy perspective for the general public.

I would humbly argue back, that when meaningfulness is restored to the abstract bits, we can measure the evolution of information objects, just like we can physical objects.  The action of information comes from these real-world meanings - embedded in the nexus of information structures.  Those probabilities are substance, which are detectable as outcomes.  These outcomes are the structure within systems and are measured as order and organization.

While not arguing for a ontological view for the information sciences, I do argue for (two or more) environments to observe and record.  A separation from physics/chemistry is needed, in the sense that the units of measure are pragmatically measuring different levels of activity in realty.  Information sciences are a parallel track to he physical sciences.  This is best seen in Biology, where bioinformatics is a skyrocketing field.

[Laird]

I am not an Idealist

This is a useful disavowal, especially given that I have never been able to figure out just exactly what you are! All I know is that you are something of an "informational realist", but now that you've also disavowed (by proxy) pancomputationalism/digital physics, I have to ask: what's left?! Informational realism alone is not adequate as a comprehensive ontology, especially in the context of a disavowal of pancomputationalism. You remain, to me, Stephenw, an enigma.

While the MTC (Shannon's Mathematical Theory of Communication) is not a class by itself, as it is abstractly separated from grounded realty by the heuristic requirement of the meaningfulness related to the data structures be ignored.

I think what you're saying here (although I had to work hard to parse and interpret this sentence!) is that although information in the sense defined by Claude Shannon is a valid concept, it ignores any meaning which information-prone agents might attach to that information. Have I understood correctly?

I would humbly argue back, that when meaningfulness is restored to the abstract bits, we can measure the evolution of information objects, just like we can physical objects.

With the aim of "figuring you out", I think the most useful question I can ask at this point is: do you believe in free will? If so, how do you see it as applying at the level of "information objects"? Is it (at least in part) that conscious entities are "free" to choose the meaning that they attach to "information objects", and how they act on that meaning?

Informational realism alone is not adequate as a comprehensive ontology, especially in the context of a disavowal of pancomputationalism.

I think what you're saying here (although I had to work hard to parse and interpret this sentence!) is that although information in the sense defined by Claude Shannon is a valid concept, it ignores any meaning which information-prone agents might attach to that information. Have I understood correctly?

Thanks for probing my post.  Answering the question of Free-Will, yes it a selection made by a personal mind.  In the debate here, my stance was to point to degrees of freedom in physics and point to objective measuring of will, as outcomes expressing motivation, intent and purposeful design.  Living things select behavior using mind, mind defined as information processing.

We got taught the fundamentals of physics in grade school.  We - the general public - had no exposure to the simple facts of information science.  You have me understood me.  It is a starting point and fundamental fact of how it works, bits measures structure - as symbols and code - and not meaning.  http://philsci-archive.pitt.edu/10911/1/...mation.pdf

 Nevertheless, it is traditionally agreed that the seminal work for the mathematical view of information is the paper where Claude Shannon (1948) introduces a precise formalism designed to solve certain specific technological problems in communication engineering (see also Shannon and Weaver 1949). Roughly speaking, Shannon entropy is concerned with the statistical properties of a given system and the correlations between the states of two systems, independently of the meaning and any semantic content of those states. 

Untangling this and putting the meaningful substance - "fire" - back into the equations is the mission for me.  The pathway is the ecology and evolution of information objects, where the structuring and transformation of one level of reality takes place.

[Laird]

Answering the question of Free-Will, yes it a selection made by a personal mind.  In the debate here, my stance was to point to degrees of freedom in physics and point to objective measuring of will, as outcomes expressing motivation, intent and purposeful design.  Living things select behavior using mind

OK, no problem. I understand so far. However, this...

mind defined as information processing.

...doesn't seem to me to be a valid definition of mind. In particular, it seems to be equally subject to the critique levelled by Bernardo against unanchored information, except that here we have unanchored information processing. It seems to me that similarly to why information cannot be the basis of reality in that it (information) only makes sense in that context when embodied (i.e., as information *about* some tangible thing), nor can information processing be the basis of a mind in that it only makes sense in that context when treated as a process of mind. Thus, mind precedes (its) information processing, and cannot be reduced to it. At least, this is how it seems to me.

Moreover, I don't see how defining mind as information processing explains subjectivity (awareness). Subjective awareness is not entailed by information processing as we well know given the electronic devices with which we're communicating: they are processing information, but they are (presumably) not aware. Thus, again, there must be something more to mind than information processing.

Finally, I don't see how defining mind as information processing encompasses the free will of, and meaningfulness chosen by, mind, both of which you affirm.

[Laird]

A little note to readers who weren't aware: Stephenw responded to my above post and continued this dialogue in a new thread Mind in action. As I wrote in that thread, I think that this was a useful choice.