Did the judge in Dover make Intelligent Design swear to tell the truth and nothing be the truth? What did Intelligent Design say? I really truly like to know. Perhaps Patrick knows the answer. 
Henry,
The Judge determined that Intelligent Design is a RELIGIOUS exploration of nature … not a scientific one… because it presumes that there things that science will never explain.
While this is not technically incorrect (from a BioLogos viewpoint) … if it is RELIGIOUS … it isn’t allowed.
I believe even BioLogos accepts and promotes that position. BioLogos does not lobby school committees to have the idea that God GUIDED evolution taught in the classroom.
George
Have a Happy New Year!
This is an interesting question so let’s explore it a bit further.
First, it is important to define what is actually meant by the terms NeoDarwinism (ND) and Natural Selection (NS). Let’s say we start with some very simple (and admittedly incomplete) definitions of ND in the sense of genomic mutations being the means by which genomes are transformed (not just single nucleotide polymorphisms) and NS in the sense that the “fittest genomes” increase their relative proportion within the genomic diversity of a given species. Both of these can be modeled mathematically, at least in some instances. For example, BioLogos’s nice series on Lenski’s E.Coli Long Term Evolution Experiment (LTEE) is a great example where a) the genomic changes are know and can be modeled as mathematical transformations on nucleotide strings; b) the corresponding phenotypic gains in fitness can be measured because the function of the gene is known and the organism is available for measurements and c) the resulting reproductive fitness and fixation of the mutations can be measured by the increasing dominance of the genotype in LTEE’s controlled environment over a number of generations.
Now let’s say we wanted to go beyond just using this specific observation as evidence for the ND/NS hypothesis and we wanted to model the whole process mathematically. First we would need to model the different types of operations that can transform the genome and assign them probabilities according to their frequency in the LTEE environment (this would be a stochastic model, in the sense of our previous exchanges on randomness). Exhaustively exploring the space of all possible genomes resulting from just K<10 genome transformations may be borderline feasible for E.Coli on a supercomputer with enough memory, but let’s say we would model it using MCMC if exhaustive search is not feasible.
This would leave us with at least two challenges: a) how to model the phenotypic fitness of each possible genotype and b) determining how genotypic fitness (e.g., more efficient processing of a certain type of nutrient or resistance to given pathogen) translates into reproductive fitness. Neither of these is immediately obvious but the lack of an exhaustive genotype/phenotype mapping alone is reason enough why this type of model cannot progress very far at this stage of our biological knowledge.
So should we abandon the whole approach just because we cannot provide such comprehensive models today? I would argue we should not - if for no other reason, at least because we can very likely already train Markov Models on genomic transformations such that the observed outcomes would “emerge” with very high probabilities. It doesn’t yet make much sense to do that because a) the models would overfit the data given the large number of parameters and the (comparatively) small amount of data available to train them and b) the models would require gross genotype/phenotype “predictions” where current knowledge is lacking. However, what these models would show (and many biology papers show on a smaller scale) is that the ND transformations operating in NS environments do suffice to explain/support evolution on a smaller scale.
Now you might have been referring to ND/NS at a macro-evolution scale of animal and human evolution, in which case the models above are definitely way too simplistic to describe those systems. But given the history of this thread and the question’s focus on mathematical models, it seemed appropriate to at least consider how these models could be constructed at today’s more tractable scale.
Have a Happy New Year!
Have a Happy New Year!
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Thanks for a clear and well reasoned response -my first impression was to say that you have agreed with me, but in a positive manner. By this, I mean that you have considered experimental observations and have shown how some of these from simple models, may be shown to be consistent, or at least compatible, with the notions of ND, and by inference, NS. The other important point is that we agree on the limitations we may observe when ND is considered in some detail, even if it is through various modelling approaches.
On a deeper level, I think we would have to ask ourselves, what we mean by a law of biology, a hypothesis, and a semantic treatment, in our discussions on ND and NS. I have looked at the Lenski papers, and noted that a key feature of these experiments was (from memory) attempts to quench his samples at various times so as to “map” the sequence of events - unless I have misread this, he did not get clear data, but a series of results that he used to infer his conclusions. But perhaps more interesting is other work that attempted to find a correlation using meta-analysis (I have posted these some time ago, and I cannot recall anyone challenging my remarks) to establish a statistically valid correlation between measurements and a “law” of NS. These attempts failed to provide such a clear correlation.
I need to add that I am not implying work in this area is invalid, or that evolutionary biologists are not doing good work - far from it. But I am making the observation that if an ubiquitous law of nature is at work, termed natural selection, such work would have clarified this by now and provided a quantitative treatment, from “first principles” as some of us physical scientists are fond of saying. I am making an important distinction between semantics, in which some observations may be rationalised within such statements, and a rigorous law of science, on which we would base our thinking and treatments of the science in question. In the context of our discussions on theology and science, and the wider question of harmony between faith and science, such a distinction imo is of great importance. Since NS does not meet the required criteria, I place such thinking into the speculation category (you may prefer a theory or work in progress).
On your remarks on the utility of models and stochastic treatments, I am in complete agreement - I recall a major University provided a molecular mechanics model of a virus (I think it was this) after expending a huge effort - although at a low level, requiring super computers and a team of experts, this achievement is nonetheless to be admired and encouraged. Further progress may take place in such areas, and this is to be encouraged. The wider discussion on faith and science however, has not progress beyond a clock type universe vs a pointless universe, and imo will not progress, until people are willing to reconsider a dogmatic view of ND and NS - I wish it would go beyond this.
You include “etc” as though you assert that nobody lobbies schools to teach religious topics.
And yet we all know that YECs of one stripe or another certainly do lobby school systems to teach religious ideas…
George
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You should edit your address… it is currently addressed to “johnZ”.
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This is the problem with abbreviations like ID or YEC… there is just too much overlap.
I consider YEC to be a legitimate part of the Intelligent Design camp. And so does the YEC camp!!!
They push for Intelligent Design to be taught in schools… so that the camel’s nose can get into the classroom…
George
You are an odd combination of total pessimism about the work of BioLogos …
and yet total optimism that YEC and ID are not to be confused.
And yet the truer estimate would be:
BioLogos will continue to find success in getting its message to new generations of Evangelicals…
and YEC’s will continue to muddy the waters between Young Earth Creationism and Intelligent Design - - forever.
Oh @Eddie … goodness gracious …
Try to have a splendid 2016!
P.S. In order to reduce my post count, I will add this note here.
Just to clarify, again, let me explicitly say I have no doubt you are correct about Discovery and the groups you name.
My problem was in your use of “ETC”. But didn’t I already state this?! Your use of “Etc” when discussing Intelligent Design can EASILY include Young Earth Creationists.
And THEY are the problem. They are working very hard to get that camel nose under the
school tent… And I would have expected you to be the first one to suspect their motivations!
Indeed I think we are in agreement on pretty much all counts. I too agree that it is useful to distinguish between different levels of NS claims - on the one hand it is clear that humans are exposed to NS (e.g., non-viable zygotic genomes or in response to epidemics) but on the other hand it is imprecise to not have a rigorous mathematical definition of NS’s survival or reproductive fitness.
FOXP2 is a good example of a gene that illustrates these modeling difficulties. This is one of the genes in which both Homo Sapiens and Neanderthal differ from other primates and it is thought to be significant even though the difference is in only 2 amino acids out of 715 (T303N and N325S). A major reason why it’s thought to be significant is that it was shown in Lai et al, Nature 2001 that even just one mutation (R553H) on this gene in the KE family can result in significant physical (rigid lower half of the face), cognitive (lower IQ) and language impairments (difficulty pronouncing words). The reasoning then goes that the human version of the gene could have resulted in substantial gains in language and cognition and thus be an important factor in the biological underpinning of human phenotypes. But how can this be tested? Konopka et al, Nature 2009 approached this problem by substituting the chimpanzee version of FOXP2 for the human version in human cell lines and measuring the immediate effects in terms of gene expression and observed molecular/cellular phenotypes (which I suppose is not unlike the other references you were alluding to in your post). However, it is easy to see that the ultimate organism-level phenotypic impact of even just one mutation on just one gene can be very difficult to determine - it is simple to measure neurons’ mobility, axon growth, synapses, etc but those measurements are orders of magnitude removed from the ultimate cognitive impairments resulting from just this one mutation. To make things even more complicated for NS, it is not at all clear that the cognitive impairments resulted in any decrease in reproductive fitness - according to Lai et al, Nature 2001, every single member of the KE family with the mutated version of the gene actually had more children than the one couple that was homozygous for the non-mutated version of the gene.
Circling back to the question on whether NS should be a law or a hypothesis, it would seem to me that it can be both but we must be clearer as to what is being claimed. While it would seem simple and uncontroversial to claim a law-type sense in that genotypes can fall bellow the survivability bar and be “naturally selected out” (e.g., non-viable zygotic genomes or in response to epidemics), it is also true that a lot is missing in being able to predict the phenotypic fitness of an organism so we can’t yet show whether NS’s reproductive fitness suffices to determine which genotypes survive and which don’t (more of a hypothesis in that sense, even though it’s overwhelmingly more supported by experimental data than any other approach).
A possible analogy that may be helpful here is that Copernicus and Galileo were right that Earth orbited the Sun way before Newton, Kepler and later Einstein and others figured out a lot more details on the math, planetary orbits and the nature of gravity itself. Earlier models were imperfect and did not explain all the observations but they were still accepted as valid theories and laws of physics even though they were “work in progress” for centuries. As with the rest of science, the key aspect of these models was that they made testable/falsifiable predictions that were mostly confirmed by experimental observations, similarly to what we see for ND/NS if we are careful in defining the scope of the claims.
All in all, it may well be that the major theological implications of genomics/evolution at this stage are the concepts of common ancestry and minimum populations sizes (as it relates to literal readings of Adam and Eve or Noah’s genealogies). Compared to these, it would seem to me that the impact of God creating and guiding using ND/NS versus using ID or teleology is relatively minimal, but that may be just me.
As this may be our last exchange of the year 
, I wish you and yours a blessed and happy 2016.
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Thanks for your good wishes and I too wish you a prosperous, healthy and happy 2016.
I suspect there is a vast area waiting for biologists and related disciplines to study, and to quote our current Prime Minister, this is an exciting time (for the bio-sciences). A major reason why I am reluctant to accept anything but the vaguest generalisations for ND and NS is the ethical implications associated with the phrase “evolution is how God created”. As computers, automation and instrumentation advances occur at a dizzying pace, I feel that we may soon reach the stage where human beings will think nothing is beyond us, and we should now build a bigger and better tower to reach unto the Almighty Himself. On this ethical front, I suspect chimps and other primates are way ahead of us (and may resent the notion of common descent) 
and it will be a long time before humanity can exist as an ethical race dedicated to the well being and goodness for us and this planet. History has written this truth in blood, tears and suffering, and we see it all around us nowadays.
We have indeed a very serious test ahead of us as a species - as we understand more and more about the phenotypic implications of human genetics it will be become progressively harder to resist the temptation to a) stop death and b) “self improve” intelligence, strength, looks, etc. The dangers of “human-designed humans” may not be immediately upon us but it would seem to me that it is more a matter of “when” than “if”. That will definitely be the most tempting and ambitious tower in human history and we can only pray that our society will be discerning enough to use such powerful revealed knowledge as Jesus has taught us to handle all power and riches - to glorify the Almighty and gleefully share with those in need.
Just to add a thought - we would glorify God in the best way if we sought and brought peace to the world, fed the hungry, protected the poor and frail, and all in all, aspire to ‘put on’ the attributes of Christ as a human race. The Creation points us to God as the Creator, but the acts of Christ and the Apostles shows us what we all need to do and become. Science is not a means to power, but rather an additional means to serve and provide what is good. While I am optimistic that God will grant us wisdom and guidance, I am also aware that we humans can find endless ways to do what is wrong.
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