Request and Question

[Chesterton]

I'd like to ask a favor. Would any TE care to critique the info on this webpage:

http://www.randommutation.com/darwinianevolution.htm

Also, one specific question from this page: the author says "What I am saying is that the Random Mutation Generator (and all evolutionary and genetic programs) demonstrate that evolution is an engineered process, not a random process. Evolution works the same way Genetic Algorithms do: by seeking pre-defined goals."

Do you, as a TE, think evolution is an engineered or a random process?

 

[gluadys]

I'd like to ask a favor. Would any TE care to critique the info on this webpage:

http://www.randommutation.com/darwinianevolution.htm

Also, one specific question from this page: the author says "What I am saying is that the Random Mutation Generator (and all evolutionary and genetic programs) demonstrate that evolution is an engineered process, not a random process. Evolution works the same way Genetic Algorithms do: by seeking pre-defined goals."

Do you, as a TE, think evolution is an engineered or a random process?

It will take me a while to go through it and some of it is technically over my head. But here is one problem with it.

He doesn't recognize one of the most essential differences between DNA and English (or any alphabetic) language. In English, a letter by letter substitution is very likely to result in gibberish, because there are many combinations of letters that are not words. But in the genetic code, no 3-base sequence is not a meaningful codon. So although a point substitution in DNA looks superficially like changing a letter in English, it should really be treated as changing the whole word. Changing a single base in one meaningful codon will always give you another meaningful codon---like changing "quick" to "fast" without any intervening steps.

More later when I have digested more of the article.

 

[gluadys]

This takes the cake!

For a whole sentence like

The quick brown fox jumped over the lazy dog

which has 44 characters, there are 5.8639153496314421699960747595891e+79 possible combinations.

That's about the same as the number of particles in the entire universe.

Now obviously there are many possible sentences that can be constructed with 44 characters, maybe billions. Maybe even trillions.

I guess. Actually if you don't count repetitions, there are only 28 "characters" in the sentence and two of them are a space and a period at the end of the sentence.

The very reason this sentence is used in typing classes is because it contains every single letter in the 26-letter English alphabet. Of course you can make billions, trillions of sentences with these characters. You can generate from these characters every single utterance in English past, present and future--including gibberish like Jabberwocky and words that haven't been invented yet.


I am not going any further into this. Basically he is saying that DNA does not work like English.

Well, no one ever claimed it did. Since his Random Mutation Generator is based on English, it is simply not applicable to DNA.

 

[Assyrian]

Maybe there is a closer parallel with Hebrew, where words often consist of three letters and there are no vowel in the original unpointed script. As a result you can rearrange the text, (pick every nth letter like the Bible Code) and you can get meaningful words coming out and a random message.

 

[Mallon]

Aye. The author's failure to understand the basic redundancy of the genetic code is what first jumped out at me, too. He needs to take high school biology again.

 

[shernren]

I don't know which is more painful, his ignorance or his arrogance.

The aspect that particularly grates with me is his ridiculous ignorance of the role of fitness functions. A fitness function is really just a big table listing each automaton and the "fitness" assigned to each. The only difference between "natural" fitness functions (e.g. Google ads) and "artificial" fitness functions is in implementation. Mathematically speaking they're one and the same.

Take "conformity to English spelling, grammar and syntax" as a fitness function. Our author clearly thinks it is a "natural" fitness function, unlike the "artificial" ones of Tierra and Avida. I would disagree: the rules of English seem very artificial and strange to many Chinese people. Spellcheckers, also, are "artificial" implementations of a "natural" fitness function. Indeed, natural fitness functions are less stringent, not more, than artificial ones (a "natural" fitness function for communication would include many non-verbal scenarios, whereas the author's imagined fitness function would exclude something as effective as a Spanish ad). On those grounds alone, the author's program clearly fails to invalidate evolution in nature.

Indeed, this analogy between artificial and natural implementations of fitness functions is exactly one of the most important examples Darwin gave in support of evolution (namely artificial breeding). The fact that our author does not understand it is clearly foundational to the fact that he does not accept evolution.

 

[shernren]

Do you, as a TE, think evolution is an engineered or a random process?

When you put ice into a drink (or down someone's shirt), you are clearly engineering a situation where that ice will melt and cool down the drink (or that person's unfortunate back).

And yet, the melting of ice is a random and disordered process. It is powered only by the simple fact that a situation in which energy is dispersed throughout the system is more likely than a situation in which there's a lot of energy concentrated in the drink (or the unfortunate person's skin) and very little concentrated in the ice. It's all mindless randomness and probability.

So, is icing a drink (or a person) engineered? Or random? Or neither? Or both?

I think that, whatever the answer is, it's not a scientific answer.

 

[Chesterton]

Thanks, folks. But about the general idea that random mutation is always seen to degrade organisms - don't all the random mutations we've observed result in weak, sickly, deformed or dead organisms? And isn't that even what we should expect given the incredible complexity of arranged information which comprises a normal/healthy living thing?

It's all mindless randomness and probability.

But is it to omniscience?

I think that, whatever the answer is, it's not a scientific answer.

Yeah, agreed.

 

[Mallon]

Thanks, folks. But about the general idea that random mutation is always seen to degrade organisms - don't all the random mutations we've observed result in weak, sickly, deformed or dead organisms?

Nope. Certainly, many of them do. But most mutations result in no phenotypic change at all. Again, this is due to the redundancy of the genetic code that the author of your article failed to appreciate.
And then again, some mutations are beneficial in that the "deformed" phenotypes they produce give great advantage in new environments. Don't forget, although mutations are generally random (though technically not entirely so), they are filtered through the very non-random process of natural selection. (Also don't forget that the Bible tells us God acts even through seemingly random processes, like the casting of a die, so there's really nothing atheistic about allowing for randomness in creation.)

 

[Chesterton]

Nope. Certainly, many of them do. But most mutations result in no phenotypic change at all.

I'm confused. Wouldn't "mutation" by definition be a change to the phenotype?

And then again, some mutations are beneficial in that the "deformed" phenotypes they produce give great advantage in new environments.

Can you cite an observed example (as opposed to to a historic supposed example)?

Don't forget, although mutations are generally random (though technically not entirely so), they are filtered through the very non-random process of natural selection.

I know, but in order for natural selection to do its work, the critter has to be normal/healthy enough to live awhile. And (according to evolution) the females prefer to reproduce with the healthiest males, right? So a fruit fly with a leg growing out of its eye socket will have even less chance of hooking up than I did at my high school dances, no?

(Also don't forget that the Bible tells us God acts even through seemingly random processes, like the casting of a die, so there's really nothing atheistic about allowing for randomness in creation.)

That's a very good point. In the marital act, millions of sperm will vie to reach the egg, and only one gets the prize. Is it a Divine special delivery, or random? I guess it's an interesting question, but like shernren said previously, not a scientific question.

 

[Mallon]

I'm confused. Wouldn't "mutation" by definition be a change to the phenotype?

I guess it depends on how you want to define the word. In biology, the word mutation simply refers to a change in DNA base pairs. And as was just explained, base pair mutations don't usually lead to a change in phenotype at all (again, because of the redundancy of the genetic code).

Can you cite an observed example (as opposed to to a historic supposed example)?

Nylon-eating bacteria.

I know, but in order for natural selection to do its work, the critter has to be normal/healthy enough to live awhile. And (according to evolution) the females prefer to reproduce with the healthiest males, right? So a fruit fly with a leg growing out of its eye socket will have even less chance of hooking up than I did at my high school dances, no?

Sure, sexual selection occurs, but it is not a hard and fast rule of evolution. It occurs in some species and not at all in others. And again, in some instances, mutations can lead to increased fitness, which would be strongly selected for in species practicing sexual selection.

 

[shernren]

I'm confused. Wouldn't "mutation" by definition be a change to the phenotype?

Only if you're a Marvel Comics writer.

In real life we're all mutants of some kind or another, compared to our parents. Now isn't that cool?

 

[hedrick]

I'm not a biologist, but I don't think the mutations in evolution are typically a random change of one codon. I believe they commonly involve moving around larger units. And of course some of the changes either have no effect or make things worse. There's a lot of time for evolution, so it can survive lots of unhelpful changes. I'm pretty sure there are good models for the kinds of changes that actually occur, and that they fit reality. I believe that web page reflects a model of change that isn't the one actually used. You really need some people who understand biology. E.g. try asking in talk.origins.

 

[gluadys]

I'm not a biologist, but I don't think the mutations in evolution are typically a random change of one codon. I believe they commonly involve moving around larger units. And of course some of the changes either have no effect or make things worse. There's a lot of time for evolution, so it can survive lots of unhelpful changes. I'm pretty sure there are good models for the kinds of changes that actually occur, and that they fit reality. I believe that web page reflects a model of change that isn't the one actually used. You really need some people who understand biology. E.g. try asking in talk.origins.

My understanding is that the most frequent type of mutation is a single-nucleotide polymorphism (SNP) i.e. a change (insertion, deletion, substitution, duplication) of one nucleotide. But mutations which affect longer sequences are not rare either.