Michael J. Behe, ‘Experimental Evolution, Loss-Of-Function Mutations and “The First Rule Of Adaptive Evolution”’, The Quarterly Review Of Biology, Volume 85, No. 4, December 2010
A.C. McIntosh, ‘Information and Entropy — Top-Down or Bottom-Up Development in Living Systems?,’ International Journal of Design & Nature and Ecodynamics, Vol. 4(4):351-385 (2009)
William A. Dembski and Robert J. Marks II, ‘Bernoulli’s Principle of Insufficient Reason and Conservation of Information in Computer Search’, Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics, San Antonio, Texas (October 2009): 2647–2652
William A. Dembski and Robert J. Marks II, ‘Conservation of Information in Search: Measuring the Cost of Success,’ IEEE Transactions on Systems, Man and Cybernetics A, Systems & Humans, Vol. 39 (5):1051-1061 (September, 2009)
William A. Dembski and Robert J. Marks II, ‘The Search for a Search: Measuring the Information Cost of Higher Level Search,’ Journal of Advanced Computational Intelligence and Intelligent Informatics, Vol.14, No.5, 2010, pp. 475-486
Winston Ewert, George Montañez, William A. Dembski, Robert J. Marks II, ‘Efficient Per Query Information Extraction from a Hamming Oracle,’ Proceedings of the 42nd Meeting of the Southeastern Symposium on System Theory, IEEE, University of Texas at Tyler, March 7-9, 2010, pp.290-297
Winston Ewert, William A. Dembski and Robert J. Marks II, ‘Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism,’ Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics. San Antonio, TX, USA – October 2009, pp. 3047-3053
Montañez G, Ewert W, Dembski WA, Marks II RJ (2010), ‘A vivisection of the ev computer organism: Identifying sources of active information’, BIO-Complexity 2010(3):1-6. doi:10.5048/BIO-C.2010.3
The blog post on ID.Plus has links to all the papers.
First, remember that Behe’s peer-reviewed paper (PDF) was about whether evolutionary mechanisms were capable of creating any new information, that supports new functionality, that confers an evolutionary advantage.
Excerpt:
Losing information is one thing — like accidentally erasing a computer file (say, an embarrassing diplomatic cable) where, it turns out in retrospect, you’re better off now that’s it not there anymore. Gaining information, building it up slowly from nothing, is quite another and more impressive feat. Yet it’s not the loss of function, and the required underlying information, but its gain that Darwinian evolution is primarily challenged to account for.
That’s the paradox highlighted in Michael Behe’s new review essay in Quarterly Review of Biology (“Experimental Evolution, Loss-of-Function Mutations, and “The First Rule of Adaptive Evolution“). It’s one of those peer-reviewed, Darwin-doubting biology journal essays that, as we’re confidently assured by the likes of the aforesaid Jerry Coyne, don’t actually exist. Casey Luskin has been doing an excellent job in this space of detailing Michael Behe’s conclusions. Reviewing the expansive literature dealing with investigations of viral and bacterial evolution, Dr. Behe shows that adaptive instances of the “diminishment or elimination” of Functional Coding ElemenTs (FCTs) in the genome overwhelmingly outnumber “gain-of-FCT events.” Seemingly, under Darwinian assumptions, even as functionality is being painstakingly built up that’s of use to an organism in promoting survival, the same creature should, much faster, be impoverished of function to the point of being driven out of existence.
And then the Evolution News post has an interview with Ann Gauger, (whose peer-reviewed publications have been featured before on this blog).
Here’s one of the questions:
… In your own research with Dr. Seelke, you found that cells chose to “reduce or eliminate function.” But with vastly bigger populations and vastly more time, wouldn’t we be justified in expecting gene fixes too, even if far fewer in number?
And her reply in part:
For most organisms in the wild, the environment is constantly changing. Organisms rarely encounter prolonged and uniform selection in one direction. In turn, changing selection prevents most genetic variants from getting fixed in the population. In addition, most mutations that accumulate in populations are neutral or weakly deleterious, and most beneficial mutations are only weakly beneficial. This means that it takes a very long time, if ever, for a weakly beneficial mutation to spread throughout the population, or for harmful mutations to be eliminated. If more than one mutation is required to get a new function, the problem quickly becomes beyond reach. Evolutionary biologists have begun to realize the problem of getting complex adaptations, and are trying to find answers.
The problem is the level of complexity that is required, from the earliest stages of life. For example, just to modify one protein to perform a new function or interact with a new partner can require multiple mutations. Yet many specialized proteins, adapted to work together with specialized RNAs, are required to build a ribosome. And until you have ribosomes, you cannot translate genes into proteins. We haven’t a clue how this ability evolved.
It sounds this problem of getting beneficial mutations and keeping them around is an intractable problem, at least on a naturalist worldview. It will be interesting to see how the naturalists respond to the peer-reviewed work by Behe and Gauger. The only way to know if Behe and Gauger are right is to let the naturalists talk back. It would be nice to see a formal debate on this evidence, wouldn’t it? I’m sure that the ID people would favor a debate, but the evolutionists probably wouldn’t, since they prefer to silence and expel anyone who disagrees with them.
Methodological materialism is the view that requires scientists to explain everything they observe in nature using material causes and never intelligent causes.
And now, from the Evangelical Philosophical Society blog, an article entitled “Is methodological materialism good for science?”. The article is written by Dr. Angus Menuge, whom I wrote about before.
Intro:
Should science by governed by methodological materialism? That is, should scientists assume that only undirected causes can figure in their theories and explanations? If the answer to these questions is yes, then there can be no such thing as teleological science or intelligent design. But is methodological materialism a defensible approach to science, or might it prevent scientists from discovering important truths about the natural world? In my contribution to The Waning of Materialism (OUP, 2010), edited by Robert Koons and George Bealer, I consider twelve of the most common arguments in favor of methodological materialism and show that none of them is convincing.
Of these arguments, perhaps the most prevalent is the “God of the gaps” charge, according to which invoking something other than a material cause is an argument from ignorance which, like a bad script writer, cites a deus ex machina to save our account from difficulty. Not only materialists, but also many Christian thinkers, like Francis Collins, worry that appeal to intelligent design commits the God of the gaps fallacy.
As I argue, however, not only is an inference to an intelligent cause not the same as an inference to the supernatural, it is a mistake to assume that all gap arguments are bad, or that only theists make them. If a gap argument is based solely on ignorance of what might explain some phenomenon, then indeed it is a bad argument. But there are many good gap arguments which are made both by scientific materialists and proponents of intelligent design.
So how do you make an argument like that?
As Stephen Meyer has argued in his Signature in the Cell, intelligent design argues in just the same way, claiming not merely that the material categories of chance and necessity (singly or in combination) are unable to explain the complex specified information in DNA, but also that in our experience, intelligent agents are the only known causes of such information. The argument is based on what we know about causal powers, not on what we do not know about them.
Since the inference is based on known causal powers, we learn that the cause is intelligent, but only further assumptions or data can tell us whether that intelligence is immanent in nature or supernatural. It is a serious mistake to confuse intelligent design with theistic science, and the argument that since some proponents of design believe that the designer is God, that is what they are claiming can be inferred from the data, is a sophomoric intensional fallacy.
Basically, you identify what material processes have been OBSERVED to be capable of, and then you show that the effect you are trying to explain is beyond the reach of those powers. For example, think of a Scrabble board left alone in a locked room with an open window from morning till evening. It’s summer, so the air conditioner is working hard all day. If you come home and enter the room and find a sentence on the Scrabble game board that says “IF YOU LEAVE YOUR WINDOWS OPEN THEN YOU PAY HIGHER ELECTRICITY BILLS” then does it make more sense to attribute that effect to the wind, or to an intelligent intruder?
If you are a materialist, then you can only appeal to matter, chance and time (and not much time, too). By ruling out intelligence, you are really confining yourself to an obviously wrong answer. But suppose you came home and found that that the tiles were scattered all over the board and on the floor and the only sequences spelled out “AN” and “ZYKDSFGOJD”. I think a better inference there is that the wind blew the bag open made a couple of nonsense sequences. Of course the idea that wind could blow open a bag of Scrabble letters at all is very unlikely, but if you rule out intelligence, that’s all you have left, no matter how strained the inference. You have to believe nonsense.
But what about the design theorist who can rule nonsense out as impossible? Well he hits on the correct explanation of the effect – intelligence.
As the fictional detective Sherlock Holmes says:
“When you have eliminated the impossible, whatever remains, however improbable, must be the truth.”
But if an intelligent design theorist comes along and rules out material causes as an explanation of the effect by showing that the effect is beyond the reach of matter, time and chance, then the explanation of intelligence must be, however improbably, true. The important thing is to rule out materialism by evaluating what material causes can do. We don’t want to rule it out by pre-supposition, because that’s what the naturalists do when they rule out intelligence as an explanation. Ruling things out by pre-supposition is how you get wrong answers to questions. Everything has to be on the table that we have experienced. And every human knows what it is to sequence Scrabble letters into meaningful words and phrases
By the way, the publisher of the book, OUP, is Oxford University Press. Angus Menuge doesn’t mess around.