Alternatives to Modern Evolutionary Theory



The hybridization you talk about would violate a nested hierarchy. Adaptations have to stay on their branch and not jump to other branches.

Can you show how these sequences produce a nested hierarchy?

It’s the massive amount of horizontal code transfer that would violate the tree.


Transcription is not a synonym for function. Non-functional DNA can be transcribed, especially when you put a viral promoter just upstream of the non-functional DNA. The 2,000 or so ERV’s that may affect gene regulation could be functional, but 2,000 is just 1% of the total ERV’s in the human genome.

However, function has nothing to do with the argument for common descent. Even if all ERV’s were functional they would still be evidence for common descent because of the distribution of orthologous ERV’s among species and because of sequence divergence.


Construct a tree with those characteristics. Once you do that, see if you get the same tree when you use engines as your characteristic. For example, here is a list of Toyota engines:

We could also look at the tree based on liquid or air cooling, fuel injection, type of fuel, and so on. Do you think you will get the same tree with these other features?


Maybe…I think there is a better chance that if it were large enough it would just cause people to assume there was another common ancestor.

I suppose it would be possible to write a “BLAST” for binary code…maybe if I get bored. :slight_smile:

I think to a degree it would depend on the specifics of the compiler, the encoding, and the degree of intentional obfuscation. I’m sure not all methods would be equally transparent. It would be a fun project…but non-trivial for someone with a day job.

(John Harshman) #245

BLAST does not test for nested hierarchy. It tests for similarity.


Granted…but it seems detecting similarity is where you would need to start. Do you have tool recommendations? It’s not a common exercise in the software world. It is much easier when you have the source code. :slight_smile:

(John Harshman) #247

No. Your problem is not so much detecting similarity as detecting and coding proposed homologies. Perhaps a modification of a sequence alignment program could produce a set of proposed homologous sequences that could be compared across versions. (Sequences of what? Binary code? Assembly language? High-level language instructions or strings?)

But I can see a point of sorts. The closer a human design process comes to common descent — using a prior object as template for modification, and using that object more than once for independent modifications — the more it will resemble a nested hierarchy. Two problems with that scenario: 1) I don’t think it’s going to get very close, even so, and 2) if that’s a model for God’s process, it makes him a very limited sort of designer.

(Mikkel R.) #248

Yep, and be sure to specify actual car, truck, van, motorcycle, and bike manufacturers and models. Anyone can just make up a data set.

(Bill Cole) #249

You need enough function to select. The empirical data does not support this hypothesis for many conserved proteins.

(John Harshman) #250

You will have to present that argument in more detail before it becomes intelligible.

(Matthew Pevarnik) #251

The point of ERV evidence for common descent is not really whether or not they do anything. Its their location in the genome across different species.

Ah its already been noted:

One of my favorites is Syncytin which there are a number of shared variants in lineages (we share at least two with other primates):


If we were trying to be as close as possible it would have to be the compiled code ready to be run.

It would be fun to find out. I think you might be surprised.

If the designed suite of applications were built using a high level of abstraction, took advantage of common code, leveraged good design patterns as often as possible, and were designed with algorithmic strategies to support diversification in support of the users requirements…it could be hard to tell the difference between shared design and common descent…especially after the applications were exposed to stochastic mutation for an indeterminate period of time. Theoretically… :slight_smile:

(Blogging Graduate Student) #253

Why do I get the feeling that you still haven’t read this paper?[0283:bonbpe];2

(John Harshman) #254

I did that exercise in 4th grade. It had a point, but only in retrospect: it showed how arbitrary classification of such objects is.

(Bill Cole) #255

I have pointed him to the work of Giuseppe Puccio at UD. Here is one piece. Vertebrates: An information analysis | Uncommon Descent

(John Harshman) #256

You will have to present that argument rather than nodding in the direction of someone else’s argument.

I don’t understand the main argument. He shows that animals more closely related to humans have proteins that are more similar to human proteins than animals more distantly related. So? There is the suggestion that much of the divergence of those proteins happened long ago. Again, so?

Note that Puccio seems to accept common descent, at a minimum of all animals. Why do you believe his results while rejecting the necessary assumptions?

(Bill Cole) #257

The argument is that preservation of sequences over deep time is evidence of limited functional space that can be selected for. I have already mentioned this to T. Gpuccio has a several articles showing this preservation.

(John Harshman) #258

Not much of an argument. But you have yet to make even that argument.

(Bill Cole) #259

Yes, I have John. In great detail at TSZ and here. Read Durston’s discussion with Joshua and side comments Durston Vertebrates: An information analysis | Uncommon Descent This is what has been discussed ad nauseam between Joe and gpuccio between UD and TSZ.

(Bill Cole) #260

I don’t reject his common descent working hypothesis in this case. If these animals were designed at different times the argument still works. The observation is lots of DNA changes however the amino acid sequences are preserved. All you need is time for this observation the origin of the animal is not critical to the hypothesis.