Alternatives to Modern Evolutionary Theory


(John Harshman) #221

Are you suggesting that I don’t know how phylogenetic analysis is done? If you’re in doubt, you can read the methods section of any paper on the subject and tell me if they cluster based on overall similarity.

I’d like to see you try.

Now that’s an assertion. So far nobody has managed to demonstrate that it’s true.

We don’t quite know, but it’s the subject of lots of research; the field is called evo-devo. The reason it doesn’t produce garbage is that garbage is selected against.

(Timothy Horton) #222

Only if the Designer decided to produce a pattern which exactly mimicked biological common descent. In biological common descent offspring receive heritable traits from their parents. This produces a very specific branching pattern with even non-functional features like the pattern of ERV distribution in primates.

Designed objects do not have heritable traits. Every design is a separate entity with features included at the whim of a designer. A car can have a 8-track player one year, a cassette player the next, a CD player the next. It can change styles of wheels, engine size, etc. all at the Designer’s whim. There is no reason for Design to have a nested hierarchical pattern yet that is exactly what we see in the fossil and genetic records.

(John Harshman) #223

Note that these ERVs have no function within the organism. It’s like making a new car model with complete with the damage from a fender-bender that the previous model was in.

(S. Joshua Swamidass) #224

Careful @John_Harshman. A minority of them probably do have some function though this function could not explain the precise detailed placement of ERVs through the genome.

(John Harshman) #225

A tiny minority. I think I’m pretty safe in the present case.

(S. Joshua Swamidass) #226

Sure, but let’s not open ourselves up to a meaningless rebuttal that will be blown out of proportion as evidence against our main point. Just smidgen of precision in our language will prevent this.

(George) #227


Perfecto! ERVs are the great under-utilized resource for debates on Evolution!


I agree that the vehicle analogy is forced…but I know from experience that software is a better fit to a nested hierarchy.

Think of the development of Windows. It started with DOS (and technically before that CP/M). Originally, Widows was an awkward layer on top of DOS, and branched out into several concurrent variations that we would all rather forget. Then with Windows 95 (with the added bonus of “making everything you do being more fun”)…DOS was blended in and life got a little better.

Somewhere in there Windows NT branched off and the two kernels went along side by side. Windows 98 and Millennial edition were evolutionary dead ends. Windows 2000 brought a hybridization of the two lines again…then another devolution through Vista…an increase in function through Window 7 followed immediately by another dark time with Windows 8 and all the various attempts to regain evolutionary traction. Fitness increased again through Windows 10 and now is waning a bit again.

If it were possible to compare the binaries using a BLAST type tool you would find sections with identical sequence…you would see lots of homologous sections…you would see new features arrive and get persisted while others fade out and disappear…and you would likely find some junk bits that are no being called or used for anything just waiting for random mutation to stumble upon that killer new feature.

The images would be the easiest to pick out because of their correspondence with the output (protein coding regions), but the logic and control sections would be much harder to decipher and look, at least at first, like junk. Simple, but versatile code structures like loops, simple conditionals, parsing routines, and data validation code would appear all over from the early primitive versions to the latest and greatest, and even appear in viruses and other invaders.

I’m pretty sure no one at Microsoft is trying to trick us into thinking Windows evolved through a natural process, even though there are plenty of inherited traits, horizontal code transfers, and code drift.

It is not such a stretch to think that a designed information based system, especially something as intricate as life, could appear evolved to someone trying to reverse engineer it.

(Mikkel R.) #229

There is no data shown. Where is the character matrix?

In any case as explaind ad nauseam, that isn’t how you show that there is nesting hiearchical structure in the data by grouping by similarity. How many times does this need to be repeated?

(Mikkel R.) #230

Where is your character matrix?

I have linked this multiple times. You need to read it. Please just read this. Multiple times preferably.

Then you need to build a character matrix like this (but bigger, that’s just a teaching example to get you to get the point) :

-but with more “species” of vehicles (at least 5 different bikes, at least 5 different cars, and so on), and with more character columns (in the link they use 29 different characters to infer a tree of echinoderms) and FROM THIS compilation of data infer the tree. What you’re doing it putting things on branches you sorta kinda feel like belong together.
But you’re not showing that an objective assessment of their characters actually does produce the result you think.

There’s a difference between FEELING that they should be grouped together, and SHOWING that they WILL group together under a systematic, objective assessment of their characters.

(Mikkel R.) #231

It’s not like biologists have been informing creationists of pseudogenes for decades. Probably the famous example is the defective vitamin C gene in the pathway for biosynthesis of vitamin C.

(George) #232


Yes, that is a classic one.

But in addition to that, there is the overall pattern, of thousands and thousands of ERV’s which very few people are bold enough to present as a really crushing argument - - in favor of Evolutionary processes!

This is an amazingly comprehensive thread on the topic back on BioLogos! @Pevaquark was an excellent “guide” through much of this thread!

(Mikkel R.) #233

It was not a search, but transitions are possible because of natural selection.

If there’s an organism born with defective limbs that couldn’t survive in it’s surrounding environment (it didn’t have the attributes it took to survive and pass on it’s genes), then it wouldn’t pass on it’s “garbage” mutation. Lots of individuals are born all the time, and among them are probably lots of developmentally defective limbs. And they are less successful at surviving and reproducing. It can’t swim fast enough, or hold it’s body weight, or run fast enough, or what have you. So just by the carriers of deleterious mutations being more likely to die, while carriers of mutations that are still able to support survival continue to the next generation, the average limb in the population changes incrementally over many generations.

How did humans breed these differet crops from their common ancestor without producing “garbage” during the transitions? By just discarding the garbage breeds they didn’t want. So mutation and genetic recombination resulted, literally just by chance, in phenotypic characteristics that human farmers like, and probably millions and millions of unwanted variants too that were discarded. And selection maintained a functional plant during the transition.


i know about this try by a creationist source:

Heavy truck Light truck Automobile 3-wheel motorcycle 2-wheel motorcycle Bicycle Unicycle
Horn 1 1 1 1 1 1 0
Manual steering 1 1 1 1 1 1 0
Multiple wheels 1 1 1 1 1 1 0
3 ln number wheels 9 7 4 3 2 2 0
Thick tyres 1 1 1 1 1 0 0
Motorization 1 1 1 1 1 0 0
Self stability 1 1 1 1 0 0 0
Backrest seating 1 1 1 1 0 0 0
Ln cargo capacity 5 3 1 0 0 0 0
Enclosed cabin 1 1 1 0 0 0 0
Steering wheel 1 1 1 0 0 0 0
Upward exhaust 1 1 0 0 0 0 0
Double wheels 1 1 0 0 0 0 0
Interior partition 1 1 0 0 0 0 0
Detachable units 1 0 0 0 0 0 0

(image from Walking whales, nested hierarchies, and chimeras: do they exist? -


its not intuitive but a fact that a bicycle is more similar to another bicycle then to a car. why its so hard to accept this simple fact?


are you sure about that? at least for ervs parts we know about large scale function:

“These data illustrate the potential of retroviral sequences to regulate human transcription on a large scale consistent with a substantial effect of ERVs on the function and evolution of the human genome.”

(John Harshman) #237

Nice. At least somebody has done the work you’re incapable of. But of course those characters and vehicles have been carefully chosen to generate the result the author wants. You can certainly create data like this for anything as long as you cherry-pick to fit that pre-conceived result. No argument there. But it’s not how the nested hierarchy of life works. Still, it’s better than anything you’ve tried before.

(John Harshman) #238

It’s as if you never even read that little conversation Joshua and I had.


The different DNA code for limb A and limb B is the genomes of the animals that have limb A and limb B. What stops genomes from becoming garbage is selection. This is why you see conservation of exons and other functional DNA when you compare genomes between species. Mutations will also produce neutral changes in non-functional or unneeded DNA where there is no selection.

(S. Joshua Swamidass) #240

Now expand this to include at least 10 different types or cars and twice as many features.