ID-Compatible Predictions: Foresighted Mechanisms Identified?
|June 20, 2008||Posted by Patrick under Evolution, Biology, Intelligent Design, Darwinism|
Core ID and ID-compatible hypotheses have various predictions. For example, there’s the confirmed predictions related to junk DNA and genetic nature of the platypus, the predictions about designer drugs, long-term preservation mechanisms for conserving information that is not currently implemented, and retroviruses being capable of being used to implement designed changes. At this time the scientific research we have so far does not provide conclusive positive evidence for some of these predictions, although there are tantalizing glimpses that such predictions may become known to be true. There’s also some types of observed changes that happen so rapidly and repeatedly that they would seem to defy being within the domain of strictly Darwinian processes. But such research is just beginning. (And Ken Miller claims that ID cannot make predictions and research cannot occur…)
But then there’s the predictions specific to ID-compatible hypotheses such as front-loading.
There are multiple variants of “front loading”:
1. Design was implemented in the universe itself. Everything is deterministic, and a plan rolled out from the initial implementation. Behe discussed this possibility briefly in EoE.
2. Design is not only in the universe and its laws but in the Origin Of Life (OOL). Darwinian mechanisms are taken into account by the Designer(s) and the architecture of life itself is configured to be modular, so that multi-functionality, gene duplication, cooption, and preadaptation, etc. are able to unmask secondary information.
Dembski’s recent work shows that in order to find the targets in search space active information is required. Besides “directed front-loading” there is the potential that ID only holds true in regards to the OOL. The front-loaded active information is the design of the system (modular components, plasticity in the language conventions, foresighted mechanisms, etc), which allows the “evolving holistic synthesis” to function without there being a directly embedded plan. I believe this is Mike Gene’s favored hypothesis?
Of course, this presumes that Darwinian mechanisms are capable of this task, for which we have no positive evidence at this time. I personally believe that given a system intelligently constructed in a modular fashion (the system is designed for self-modification via the influence of external triggers) that Darwinian processes may be capable of more than this. But that’s foresighted non-Darwinian evolution in any case, and even if there are foresighted mechanisms for macroevolution they might be limited in scope.
3. Similar to variant 2 except there is a specific plan encoded into the original life (a single LUCA) and Darwinian mechanisms play less of a role, only being capable of producing minor variation. This plan may or may not be self-terminating. John Davison is heavily in favor of the self-terminating variant, and I think he believes there may be multiple LUCAs.
4. Similar to variant 2 or 3 except that there are multiple instances of Design (multiple Origins Of Life, multiple LUCAs) occurring at the level of kingdom or phylum.
5. Essentially 2 – 4 except with the addition of Designer Intervention for certain information that is/was not modular but specific to a particular organism. I believe this is UD Jerry’s favored position?
This article will discuss recent evidence related to predictions made about foresighted mechanisms. The focus will be on variants 3-5 of front-loading.
Assuming intelligent evolution, for some types of Designed modifications the mechanism may not be self-contained within biology. If external mechanisms or direct modification is the case we may only find evidence for foresighted mechanisms that are limited in capability.
What are “foresighted mechanisms”? Allen MacNeill first raised the objection that the term “random mutations” is not precise enough, which I believe to be true. Although to be fair, when ID proponents refer to “random mutations” they usually mean it to encapsulate all currently known “engines of variation” (MacNeill’s favored term). For example, Behe did this in EoE. On one page I remember him listing the various things like gene duplication, etc. but in general he referenced them all as “random mutations”.
It is perhaps instructive to point out that Darwin never used the term “random mutation” (nor “random” anything, for that matter) in the Origin of Species. The concept of randomicity is a mostly 20th century concept (especially in biology), and one of dubious empirical merit IMHO.
More useful might be “non-foresighted”, as that describes more precisely the character of most (but not all) of the new variations that appear among the members of populations of living organisms.
Again, I would urge ID supporters to recognize that there is nothing intrinsic to evolutionary theory that would necessarily rule out design in nature. Indeed, as I have argued in several venues, nature is packed with design; that’s what a genome is – a design for an organism. So the question really is, where does the information in the genome come from, and how much does it contribute to the actual phenotypes of organisms? How much of the “design” of an organism is provided by its environment? And can any of this be shown to be foresighted? All good questions, and all answerable by empirical research. However, absent empirical support, none of them can be answered by theoretical speculation alone.
So foresighted mechanism would be one that self-modifies its information in response to external stimulus based upon preconceived design. Or in the case of higher creatures viruses may have once served as attached-but-still-external foresighted mechanisms. (Daydreaming: I wonder if I’ll ever be quoted in a biology book someday…)
The only negative to using the term Non-Foresighted Variation (NFV) is that it assumes Darwinism to be true if that term is used to encapsulate everything. For example, an intelligence may set conditions by which a pseudorandom function induces variation. So foresight would be involved in setting the conditions. NFV would be a subset of all mechanisms for variation, whatever that may be called.
I was about to express the same thought, except with a different interpretation. Engineers will often design functionality that goes unused unless particular stimuli causes a triggered event (a function that is generally unexpressed except under certain conditions triggered by other functions or changes in input/system). I believe that such observations could be an avenue for ID-oriented research: looking for foresighted mechanisms.
Just the other day I was discussing this very subject with a friend. A good Designer would program biology to be proactive, to respond to an ever-changing environment. I used the example of Pseudomonas aeruginosa and it’s nylon-eating capabilities within 9 days, which some ID proponents have inferred may implicate foresighted mechanisms. I do not believe that hypothesis has been adequately explored yet. Merely saying that the processes of the modern synthesis and chance cannot account for it is not enough in my estimation. I would prefer that someone try and determine exactly what is triggering the change. It may also be that the design of the system itself allows such rapid evolution and not externally-triggered mechanisms (sort of like how the designed shape of legos allows many configurations). In any case, the modern synthesis proves useless.
These Adriatic Lizards may be a similar avenue for ID research, although obviously a more difficult route. I think it’d be easier to observe bacteria.
But, really, in today’s environment I think the only way such research would be funded if any discovered foresighted mechanisms were glibly written to be a product of evolution (along the same lines as modularity, due its beneficial nature) via a disclaimer sentence.
The main point is that the existence of foresightedness entails intelligence. MacNeill recognizes this and although he never said so I would hope that finding such mechanisms would lead him to accepting ID (or at least some types of ID-compatible hypotheses).
I previously made the following prediction:
But let’s say we did find such foresighted mechanisms. Darwinists might argue that such mechanisms would be selected for without intelligence being involved. After all, being foresighted would allow proactive responses to a changing environment and thus increase survivability. It’s kind of like how they create a story for modularity.
My prediction has come to pass. Such foresighted mechanisms that modify genes have been empirically identified. And the reaction from Darwinists has been as expected.
Bill sent me an email a little over a week ago describing the research.
A new study by Princeton University researchers shows for the first time that bacteria don’t just react to changes in their surroundings — they anticipate and prepare for them.
What we have found is the first evidence that bacteria can use sensed cues from their environment to infer future events
The research team, which included biologists and engineers, used lab experiments to demonstrate this phenomenon in common bacteria. [Insert Disclaimer]They also turned to computer simulations to explain how a microbe species’ internal network of genes and proteins could evolve over time to produce such complex behavior.[/Insert Disclaimer]
In one part of the study, the researchers studied the behavior of E. coli, the ubiquitous bacterium that travels back and forth between the environment and the gut of warm-blooded vertebrates. They wanted to explain a long-standing question about the bug: How do its genes respond to the temperature and oxygen changes that occur when the bacterium enters the gut?
The conventional answer is that it reacts to the change — after sensing it — by switching from aerobic (oxygen) to anaerobic (oxygen-less) respiration. If this were true, however, the organism would be at a disadvantage during the time it needed to make the switch. “This kind of reflexive response would not be optimal,” Tavazoie said.
The researchers proposed a better strategy for the bug. During E. coli’s life cycle, oxygen level is not the only thing that changes — it also experiences a sharp rise in temperature when it enters an animal’s mouth. Could this sudden warmth cue the bacterium to prepare itself for the subsequent lack of oxygen?
To test this idea, the researchers exposed a population of E. coli to different temperatures and oxygen changes, and measured the gene responses in each case. The results were striking: An increase in temperature had nearly the same effect on the bacterium’s genes as a decrease in oxygen level. Indeed, upon transition to a higher temperature, many of the genes essential for aerobic respiration were practically turned off.
To prove that this is not just genetic coincidence[aka non-foresighted Darwinian mechanisms], the researchers then grew the bacteria in a biologically flipped environment where oxygen levels rose following an increase in temperature. Remarkably, within a few hundred generations the bugs partially adapted to this new regime, and no longer turned off the genes for aerobic respiration when the temperature rose.
And here’s where the predicted Darwinist interpretation takes place.
“This reprogramming clearly indicates that shutting down aerobic respiration following a temperature increase is not essential to E. coli’s survival,” said Tavazoie. “On the contrary, it appears that the bacterium has “learned” this response by associating specific temperatures with specific oxygen levels over the course of its evolution.” Lacking a brain or even a primitive nervous system, how is a single-celled bacterium able to pull off this feat? While higher animals can learn new behavior within a single lifetime, bacterial learning takes place over many generations and on an evolutionary time scale, Tavazoie explained. To gain a deeper understanding of this phenomenon, his team developed a virtual microbial ecosystem, called “Evolution in Variable Environment.” Each microbe in this novel computational framework is represented as a network of interacting genes and proteins. An evolving population of these virtual bugs competes for limited resources within a changing environment, mimicking the behavior of bacteria in the real world.
To implement this framework, the researchers had to deal with the sheer scale and complexity of simulating any realistic biological system. They had to keep track of hundreds of genes, proteins and other biological factors in the microbial population, and observe them as they varied over millions of time points. “Simulations at this scale and complexity would have been impossible in the past,” said Tagkopoulos. Even with the vast number crunching power the supercomputers provided by the University’s computational science and engineering support group, their experiments took nearly 18 months to run, said Tagkopoulos.
In this virtual world, microbes are more likely to survive if they conserve energy by mostly turning off the biological processes that allow them to eat. The challenge they face then is to anticipate the arrival of food and turn up their metabolism just in time. To help them along, the researchers gave the bugs cues before feeding them, but the cues had to appear in just the right pattern to indicate that food was on its way. [This sentence is vague, but are they intelligently helping them along in the same manner as AVIDA was helped along for evolving the EQU program?]
“To predict mealtimes accurately, the microbes would have to solve logic problems,” said Tagkopoulos, a fifth-year graduate student in electrical engineering and the principal architect of the Evolution in Variable Environment framework.
And sure enough, after a few thousand generations, an ecologically fit strain of microbe emerged which did exactly that. This happened for every pattern of cues that the researchers tried. The feeding response of these gastronomically savvy bugs peaked just when food was offered, said Tagkopoulos.
When the researchers examined a number of fit virtual bugs, they could at first make little sense out of them. “Their biochemical networks were filled with seemingly unnecessary components,” said Tagkopoulos. “That is not how an engineer would design logic-solving networks.” Pared down to their essential elements, however, the networks revealed a simple and elegant structure. The researchers could now trace the different sequences of gene and protein interactions organisms used in order to respond to cues and anticipate mealtimes. “It gave us insights into how simple organisms such as bacteria can process information from the environment to anticipate future events,” said Tagkopoulos.
The researchers said that their findings open up many exciting avenues of research. They are planning to use similar methods to study how bacteria exchange genes with one another (horizontal gene transfer), how tissues and organs develop (morphogenesis), how viral infections spread and other core problems in biology.
So now the solution to “core problems in biology” are foresighted mechanisms…NOT non-foresighted Darwinian mechanisms. Yet somehow this idea is twisted to fit into a Darwinian worldview. The sad part is that I predicted this reaction.
How many times have we noticed evidence of changes that have occurred faster than what should be capable of RV+NS (non-foresighted mechanisms)? Darwinists did not look for foresighted mechanisms since they would not expect them. Now they have found them, but due to their beliefs they’re determined to turn evidence on its head.
I’d be lying if I said that the ID movement has all its ducks in a row. The relatively low amount of ID research is one of them. It’s a real problem even if there are a real life reasons such as persecution and the need to maintain day jobs that usually don’t provide the opportunity for ID research. But increasing the amount of ID research is fixable, given enough support.
This is one aspect of this news that casts some gloom on the otherwise sunny outlook. This is exactly the type of research that Darwinists have effectively prevented ID proponents from undertaking. ID proponents have been talking about looking for such mechanisms for years. But how do you do research when they run you out of labs and universities and deny you funding?
Personally I’d love to see Darwinists and ID proponents working together. The major problem is procuring funding. I hate to see it when Darwinists are demanding that ID proponents produce more research and then at the same time advocating closing any potential avenues for this research to take place. If they want to be consistent and if they take these questions seriously they should be helping ID proponents receive a decent level of funding even if they do believe in general that ID is incorrect. At the very least these research projects may discover the limitations of certain mechanisms and in the process discover information that could advance medical technology. Who knows, maybe it would be an ID proponent who does the actual gruntwork and manages to find positive evidence for some Darwinian mechanisms being capable of producing CSI.