Yes, you can measure it but you have to know the function of the sequence your are measuring, the protein it codes for and the preservation of the amino acid sequence. The above sequence if it codes for a preserved functional protein is greater the 500 bits of functional information. Certainly enough to infer design.
This does not say anything about the cause of the differences that create new features. Which of those mechanisms produce new gene families?
Again we donāt need this as we donāt need that method to determine that you came from your parents. We know the common ancestors and the descendants that directly came from those ancestors because the events were directly observed.
Where you need to assume common descent to form your tree the computer example does not.
No one is claiming human beings designed all life. H nice the trees will not be identical in nature. Besides living organisms are far more complex than cars. However you will find the same features.
Some traits that are common only in clades.
Some features which are common across clades with minor differences.
Yes, so what?.. if we know biological systems as well as cars, we might the able to put parts of an unrelated organism in another organism and get it to work.
You are really jumping on trivialities here.
You can plug it into any open reading frame webtool, such as this one:
It will give you all 6 reading frames and the possible peptides found in each.
I already listed the mechanisms: substitution, insertion, deletion, genetic recombination, and transposition. This is an incomplete list, but a good start.
Last I checked, computers donāt reproduce. Therefore, they did not evolve through common ancestry.
If you donāt have a tree, then you canāt claim that these designs fall into a tree. It is that simple.
The point is that those features fit into a noisy tree where life is concerned. You donāt find numerous and major violations in the tree of life like you do with objects humans design. It is trivially easy to find two cars within the same model who have different engines and a car and truck that have the same engine. The features in automobiles are mixed and matched with no adherence to a tree-like structure.
So why couldnāt another designer do the same thing with life?
None of those tools have been demonstrated to create novel functional features like an eye, muscle, flight feather, new brain function etc. Your just throwing stuff against the wall and hope something sticks. I agree with you that Shapiro is doing the same thing.
These new features are required for the hierarchal structure. Ancestry alone does not explain evolution. At this point we are without a real theory of lifeās diversity.
I think for now I have shown that we can indirectly measure functional information through preserved proteins.
Like I said the categories are same.
As to models, itās possible in nature to see very similar organisms with one being a marsupial and other being a mammal.
What you are pointing out are differences in degrees. Not to mention you are citing a totally subjective measure.
Again, you are confusing mechanism with history. There are proposed mechanisms for the differences in genomes, contrary to your claims. You are trying to claim that there are no proposed mechanisms for genetic change, and this is clearly false.
So why canāt the proposed mechanisms of mutation produce proteins that are then conserved through selection?
EDIT: I am adding the original question to which I am responding.
@Swamidass>> I have yet to see a design argument that does not include theological premises. Every one I have looked at is burdened with theological premises.
@Eddie>Examples, please, Joshua, from the books I mentioned, with page numbers indicating where the theological premises are inserted into the scientific discussion in such a way as to be essential to the argument for design? [emphasis added]
The common argument that āevolution is so improbable as to be impossibleā, and leading to any conclusion that might include God includes a tacit theological premise, or simple a tactic premise otherwise.
By way of example I characterize this argument as āThe odds of XXX occuring by random chance is 10^{-234}, which is less that the 10^{-150} probability bound, therefore the cause must be YYYā. This statement āThe odds of XXXā is generally presented in the same form and interpretation as a Bayes Factor (a Bayes Factor is a ratio of two probabilities). However, if/when I can dissect any real calculation out of this, the odds ā10^{-234}ā are actually a probability rather than a ratio.
To get the odds ratio interpretation of a Bayes factor we need something like this:
Odds = P[X|Design] \over P[X|evolution]
But we have only one number to plug in here, which is being interpreted as both probability and odds:
10^{-234} = P[X|Design] \over 10^{-234 }
ā¦ and solving for P[X|Design] leads to ā¦
P[X|Design] = 10^{-234 } \over 10^{-234 } = 1.0
ā¦ which reveals the tacit prior assumption that āDesignā is the only possible conclusion. Such arguments can only conclude the tacit assumption. If the designer is asserted to be God, this qualifies as a theological assumption, otherwise itās just a circular argument.
I confess to playing fast and loose with the math here, but I contend that any attempt to formalize the statement āevolution is so improbable as to be impossibleā will lead to revelation of a similar tacit assumption.
I am claiming the proposed mechanisms have not been successfully demonstrated.
Why would you expect mutation to produce a set of proteins and novel cells that product functional complex features?
Design can produce a sequence without trial and error so independent of probability.
Hi Bill 
@colewd
Design can produce a sequence without trial and error so independent of probability.
Can you please expand on that statement? I see several problems with it, but I think it would be best for you to clarify what you mean, rather than my pointing out things you did not intend. In turn, I will try to catch up on the previous discussion, since I just joined here. Thanks.
Hi Dan
Lets try this simple example. If I set up a computer search for your 10 digit phone number and it stops when it hears your voice we would expect this to take 10^10 searches and a while depending on the time required to make each call. There is no determined end to the search.
With a conscious intelligent being the task is simply finding your phone number with directory search thus eliminating probability from the process. There is a determined end to the search.
And
If nested hierarchies were only falsified by crocoducks, then youād have no theory worth a toss: only turtles with flowers would cause problems. If you donāt regard the groups with which turtles have even recently been linked as only distantly related - pareiasaurs, procolophonids (Parareptilia); captorhinomorphs (Eureptilia); lepidosauromorphs or archosauromorphs (Diapsida) - then you know even less zoology than I do. To quote Rieppel in last yearās publication:
Although sophisticated computer algorithms are being used in the search for turtle sister-group relationships, the situation still rembles the oneā¦ in the early twentieth century: there is hardly any major reptile group with which turtles have not been at least tentatively allied, even on the basis of cladistic analysis. This is remarkable, as cladistics has been touted to be a nonauthoritarian, objective method with which to reconstruct evolutionary relationships.
The new (2018) discovery is said by Rieppel to establish the Diapsid origins, which still leaves us choosing between the lizards and the crocodiles/birds - so in theory, feathers are still not completely off the agenda.
No, sorry, but that makes no sense in the context of tacit assumptions.
How did you arrive at a probability of design? My claim is this process has no measurable probability attached to it. If you think it does please support the claim.
In what way? We have seen all of these types of mutations happening in the lab and in the wild.
Answer my question, and I will answer yours.
So why canāt the proposed mechanisms of mutation produce proteins that are then conserved through selection?
Your testing standards are very low. A mutation occurring and a mutation or group of mutations creating an innovative feature are different things.
Proteins require a sequence capable of a fold and then a function often interacting with several other proteins. There are an enormous number of ways to produce a non functional sequence and less ways to produce a functional one. Where does this functional sequence come from if random change and selection is the driving mechanism? How would you predict this could reliably find function?
Where is the model that shows how a complex set of functional interdependent proteins evolve through this process? For a scientific hypothesis you need:
Thank you - now I understand you, but I think you do not understand my statement.
In Bayesian statistics we assign a prior probability distribution to an estimate or hypothesis. If that prior is āflatā or non-informative then we reach the same result as with frequentist statistical methods. In my example about tacit assumptions, I showed how this type of claim is equivalent to a Bayes Factor with a prior assumption that P_{prior}[X|Design] =1.0, for which the conclusion will always be āDesignā regardless of the data. IOW: This can only conclude that which was tacitly assumed. It might be a theological assumption if one asserts the designer is God, otherwise itās just a circular argument; concluding the assumption.
This has nothing to do with the probability of any particular design process, but reveals the tacit assumption which is present in this form of argument.
I will edit my response to include the question I was responding to - that might help. Try re-reading it now. Link