Arguing Against Intelligent Design

[Biochemist]

This thread is fantastic. Never has my understanding of the 'evolution of evolutionary theory' been clearer.

I think all the credit goes to Buff. She adds clarity wherever she steps.

 

She's probably a babe, too. Damn it.

[Biochemist]

When we do this (as has been done on Hypography several times, including here:

 

http://hypography.com/forums/biology/5505-statistical-probability-issues-speciation.html

 

The gist of this old thread is that the "random" model produces a statistical probability of about zero (give or take). Ergo, most folks who subscribe to the viability of a serial-mutation model concede that in order to this to work, something in the state of nature had to significantly reduce the odds.

At the risk of seeming incredibly ego-centric (by quoting myself!), I went back and read most of this short thread. It is not for the faint of heart, but it does walk through the introduction to the problem pretty well.

 

It is worth a read for any of you who want to get in on the debate.

[TheFaithfulStone]

From the old thread - I'm not a Biochemist...er... Biochemist, but I did notice that you at least one statement that is not strictly true - and at least one thing that doesn't seem logically sound.

 

First off

I am sure we have lots of examples of computer code with more than 30,000 routines. None run as cleanly as a cell.

 

Maybe, but there's only like 90 actual instruction mnemonics. This one I'm calling "factually innaccurate" since there may be more than 30,000 routines in a computer program - but they're nothing but shorthand for longer strings of those 90. And when you get right down to, there's really only ONE working thing in a computer, and that's a transistor. Switch or Amplify. Take your pick. So you can write things like Hypography by saying "Switch" or "Amplify" gazillions of times. That's like emergent complexity in that certain combinations do something, and certain combinations don't. You don't write EVERY combination in a computer program, just the ones that do something. You know what the rules for success are, and you work within those parameters.

 

Again, this model assume that there was an extant influence that erased the model farthest from the target sequence. This would only by applicable if the interim sequences were expressed, and favorably selected. We do not have any evidence of such. We do know that this occasionally happens (like my salamander) but not that it created new body plans.

 

I'm pretty sure that you're making an assumption that's not warranted, which is that interim sequences that DIDN'T work had to be selected AGAINST. That is, as Dawkins put it, that there "are many ways to be alive, but many more ways to be dead." That's not really true. We're not trying to make a particular sentence (which is where people always get hung up on the Weasel thing) we're trying to make ANY SENTENCE. Given that you know the basic rules of English, it's not that hard to write some English sentence.

 

For the sake of argument, say I want to spell a word. I start with "A". Well - I'm done. So "A" goes onto "AB" - which isn't a word. So I move on to "AC" - which isn't, and then onto "AD" which is. BUT I also move on to "B" which isn't and ALSO "ABA" which isn't. Until I get to "I" which is an "ABE" which is. So, it isn't like I stop trying chemical combinations - I just stack up every advance that I make, and also keep going back and trying the old stuff.

 

I'm not saying it would be a fast process - but it wouldn't take long to create a bunch of semi sensible sentences. Remember, until you've got LOTS of success, you don't punish failure, you reward success. As long as there are resources for the failures to consume, they continue on. That is - failures continue to try different things at the level they failed at.

 

Right now, there are thousands of self-organizing auto catalysts out there trying to create life. Everytime they get started though, thinking to their little protoplasmic selves "Dude, I could use some random proteins" something faster swims by and grabs the protein they wanted.

 

TFS

[InfiniteNow]

YouTube - Evolution IS a Blind Watchmaker http://www.youtube.com/watch?v=mcAq9bmCeR0

 

In this video I deconstruct the broken watch straw man argument used by creationist / ID supporters to attack evolution. I had to pack a ton of information into this video so you WILL need to pause it periodically.

 

The basic premise of the argument is that a bunch of parts will never randomly assemble into the correct arrangement to form a properly functioning complex. Once again, creationists / ID supporters miss the basic concept of evolution entirely. No biologists believes, nor is there any evidence that complex systems form spontaneously in one fell swoop. That would be creation. Systems evolve through many intermediates, one step at a time, slowly building up the complexity.

 

Here I deconstruct their straw man argument. Basically, I simulate clocks as living organisms. Selective pressure is focused on their ability to accurately tell time. NO goal is imposed on the design (you can tell this because every simulation ends with a differently constructed clock). And it works. Clocks evolve through a series of transitional forms: Pendulum, Proto-clock, 1-handed Clock, 2-handed Clock, 3-handed Clock, and 4-handed Clock. Gradually the complexity is built up.

 

These labels I have assigned to the transitional forms have nothing to do with the simulation itself. They are names I assigned so that we could analyze what the population was doing. The clocks are just clocks, living in their world, trying to tell time as accurately as possible.

 

One thing I wanted to address but didn't have time in the video is how rapid the transitional period can be. In some simulations the population goes from pendulums to 3-handed Clocks in a hundred or so generations. And the transitions between the transitional forms are even more rapid, happening in about ten generations. Chances are none or a very limited representation of that transition will be preserved in the fossil record.

 

One thing I should add. The program does not draw the clocks. It maintains, mates, and simulates them, but the drawing must be done manually from the genome matrix.

 

The program is written in MatLab.

 

The hand rotations that begin with 86 are 86,000 not 86.000. When YouTube compressed the video it becam hard to tell a comma from a period.

 

To download this video go to:

Evolution IS a Blind Watchmaker.wmv

 

To download the program go to:

Clock Evolution Functions.zip

 

Learn the facts, spread the truth, and most importantly, Think About It.

[Biochemist]

Good post, TFS. Thanks for going back to look at the old thread.

...there's only like 90 actual instruction mnemonics. This one I'm calling "factually innaccurate" since there may be more than 30,000 routines in a computer program - but they're nothing but shorthand for longer strings of those 90...

Well, at the risk of taking the analogy too far, the degree of complexity is not really based on the number of unique instructions, but more to the variances available in "program" behavior as the instructions are aggregated. For example, a really complex curve fitting programming algorithm may have a relatively small number of mathematical functions, but if it correctly identifies the "best" curve with the least variance from a complex data set, it is a complicated program indeed, and it is itself far more complex than the underlying instructions

 

Similarly, DNA is made entirely of (only) 4 nucleotides. Any set of 3 nucleotides will "code" for a specific single amino acid, out of a field of 20 (with very rare exceptions anywhere in any phylum). A typical protein has about 300 amino acids in it ("residues"). Typically if any more than 10 are changed, the protein is completely dysfunctional. Then there are about 100,000 proteins in a typical eukaryotic cell (this varies a bit by species). The physical arrangement of the 100,000 proteins is also exquisitely detailed, in that proteins do not float free in a bag of salt water. They are arranged in logical "bucket brigades," such that the output of one protein enzyme directly feeds as an input to another local, different enzyme to be used as a substrate.

 

Back to your point, suggesting that 4 DNA nucleotides are nothing but a "shorthand" for the 6 definitive proteins is a bit of a stretch. This is orders (and orders and orders) of magnitude more complex than suggesting our 26 arabic letters are "just shorthand" for a copy of Hamlet. It would be more like suggesting that the 26 letters are shorthand for a specifically sequenced set of all text on the planet. I suspect even that is too small a number. It is a little tough for me to get my head around numbers like 1 in 10^250. Think about 10^18 as the number of seconds since the Big Bang for a reference.

 

The math problem I was try to close on in the other thread was the theoretical problem of coding for 5-6 typical proteins where they did not preexist, and each protein has 200 unique amino acid residues.

I'm pretty sure that you're making an assumption that's not warranted, which is that interim sequences that DIDN'T work had to be selected AGAINST. That is, as Dawkins put it, that there "are many ways to be alive, but many more ways to be dead."

I do understand the point. But I accounted for this characteristic by only requiring that 200 of the amino acid resides had to work (which is low) and that the enzyme sequence was small, and that location did not matter. This is taking out a massive amount complexity in the real system. And I didn't care which 200 residues. So I probably artificially simplified the problem by something greater that 10^100 (!).

I'm not saying it would be a fast process - but it wouldn't take long to create a bunch of semi sensible sentences. Remember, until you've got LOTS of success, you don't punish failure, you reward success.

The other issue is that we can't ascertain that success was actually "rewarded." In the case of the Cambrian explosion, we cannot establish a trail where the precursor proteins had time to be selected. This is the crux of the problem.

[Moontanman]

.The other issue is that we can't ascertain that success was actually "rewarded." In the case of the Cambrian explosion, we cannot establish a trail where the precursor proteins had time to be selected. This is the crux of the problem.

 

I'm not going to pretend I totally understand most of the arguments this thread has "evolved into" but I do at least follow some of them. I would like to throw the proverbial monkey wrench into the discussion and ask how do we know there were only three phyla at the beginning of the Cambrian explosion? Fossils? Is it remotely possible that way before the explosion, before oxygen became abundant enough for large organisms, that there might have been many more phyla, evolved from protozoa type animals and although they had tissues, cells and such they were still so small due to lack of oxygen and soft due to ocean chemistry they simply didn't leave much in the way of fossils? Real fossils didn't commence until animals grew larger and evolved hard parts. Even though lack of evidence is a very bad way to start an idea, in this case it does at least seem to make sense. If many tiny but unicellular creatures existed pre explosion but are so far undetectable in the fossil record maybe we are discussing this with too little data. Just a thought, a contrary thought to be sure, but still it would explain a lot of things about the Cambrian explosion seeming to be so sudden. By the way, what were the three phyla? I'm thinking worms, jellyfish, and echinoderms, is this correct or way off?

[Biochemist]

......how do we know there were only three phyla at the beginning of the Cambrian explosion?...Is it remotely possible that...there might have been many more phyla...they simply didn't leave much in the way of fossils?

It is a good point, MM. Fundamentally, this issue falls one of two ways:

 

1) Gradualism- there were incremental changes that gradually accrued over a 250million year window

2) Punctuated Equilibrium- There were long periods of stasis, "punctuated" by sudden arrival of new body plans.

 

In the case of the Cambrian explosion, we are looking for a mechanism to explain either one. We had dramatic additions to body plans over this 250 million year window. Even if there were more phyla at the beginning, they would not likely have been the kind that were easily fossilized (i.e., those phyla with bones). Ergo whether there were more phyla pre-Cambrian, does not really matter. The issue is that there was a sudden increase in the complexity of body plans, and we don't have a good explanation.

 

The intent of the egregious math exercise was to find some way to support any model that decreases the probability of "random" changes to something palatable, maybe one in 10 billion. If we don't hypothesize some mechanism to "grease the skids" of the genetic alteration model, it looks like we would never have arrived.

 

I am pretty sure I am not a figment of my imagination.

[Moontanman]

It is a good point, MM. Fundamentally, this issue falls one of two ways:

 

1) Gradualism- there were incremental changes that gradually accrued over a 250million year window

2) Punctuated Equilibrium- There were long periods of stasis, "punctuated" by sudden arrival of new body plans.

 

In the case of the Cambrian explosion, we are looking for a mechanism to explain either one. We had dramatic additions to body plans over this 250 million year window. Even if there were more phyla at the beginning, they would not likely have been the kind that were easily fossilized (i.e., those phyla with bones). Ergo whether there were more phyla pre-Cambrian, does not really matter. The issue is that there was a sudden increase in the complexity of body plans, and we don't have a good explanation.

 

The intent of the egregious math exercise was to find some way to support any model that decreases the probability of "random" changes to something palatable, maybe one in 10 billion. If we don't hypothesize some mechanism to "grease the skids" of the genetic alteration model, it looks like we would never have arrived.

 

I am pretty sure I am not a figment of my imagination.

 

Ok, I'm back on track. I see where you want to go, I wish I could add to it intelligently but my only Idea is maybe the explosion of hard body parts occurred then because it couldn't have earlier due to as I have said lack of oxygen and ocean chemistry that didn't allow for deposition of hard parts. I've been looking into Precambrian life and I've seen fossils that are very suggestive of some of the animals that later had hard body parts for what it's worth. Possibly the mechanism was simply the environment, before the Cambrian explosion it simply wasn't possible due to environmental conditions. Since we really can't know the genetic make up of those early organisms are it possible the complexity of genetic material was already there, expressing a complexity it couldn't completely exploit in the then current environment? BTW, thanks for simplifying this for me, I was trying to wrap my mind around things I wasn't really ready for. Still doesn't keep me from thinking the wrong way though so let me know if I am still not on track.

[Moontanman]

I have found there were several things that could have promoted the Cambrian explosion or delayed it. One thing is that stromatolites declined drastically about one billion years ago. Many think this is due to tiny complex animals began to feed on them at that time. Genetic material used as a clock put the origin of complex animals at about 750 million to 1.5 billion years ago. One billion is a good compromise. After that the Earth experienced several complete glaciation events from about 800 million or about 600 million years ago. during this time the Earth was frozen over completely to the equator. this caused life to retreat to the volcanic vents in the ocean. This allowed for isolated populations which also promoted speciation. After this the oceans which had been filled with metals released from the undersea vents was stirred up by some type of movement of the continents. The continents moved around all the way from the poles to the equator in just a few million years. Some think the earths crust as disengaged from the core and actually moved 90 degrees from it's original place. This along with blooms of algae fueled by the metal content of the water allowed oxygen to rise to high levels and mixed nutrients into the water column that had been sequestered in deep sea sediments. The oxygen allowed for the deposition of calcium and formation of hard body parts and large body plans. To me it was like building a bomb, all the parts were assembled long before it was detonated.

[TheFaithfulStone]

Back to your point, suggesting that 4 DNA nucleotides are nothing but a "shorthand" for the 6 definitive proteins is a bit of a stretch. This is orders (and orders and orders) of magnitude more complex than suggesting our 26 arabic letters are "just shorthand" for a copy of Hamlet. It would be more like suggesting that the 26 letters are shorthand for a specifically sequenced set of all text on the planet. I suspect even that is too small a number. It is a little tough for me to get my head around numbers like 1 in 10^250. Think about 10^18 as the number of seconds since the Big Bang for a reference.

 

That's actually just about the OPPOSITE of the point I was trying to make, and it's also kind of confuses the issue a little. Hamlet is a "product" (like an animal, or a finished program.) - the rules of the English language are the "shorthand" - the "shorthand" lets you do ultra complex things in far fewer steps. A "sort of" phonological rule in English for instance, is that words tend to alternate between consonant sounds and vowel sounds (that's SUPER simplified, but you get the idea.) You know almost before you start, that you don't have to try combinations like CCC - it can't possibly spell anything. That's what I'm talking about - it's easy to create ludicrously complicated things from just a few simple rules. Have you ever played with cellular automata? It's a 2D grid. Three neighbors gets your born. Less than two and you die, more than three and you die. You can make pictures of airplanes appear depending on your initial set up.

 

Watch the clock video though, and you see what I'm talking about. Most mutations are totally neutral - and it's not until you have kind of a "critical mass" that you get ACTUAL competition for resources. Until then you just have a bunch of random parts floating around. You could have a bunch of random mutations that do nothing, but then one MORE random mutation could do a whole LOT.

 

So - parts with affinities until WHAMMO - pendulums. Then Pendulums with extra parts until WHAMMO clocks with hands. Then, WHAM, WHAM WHAM - clocks with four hands. That's as high as the clock-sim goes - but if you were to keep changing the rules of the game ever-so-subtly - you could make it do ALL KINDS of crazy stuff. What if you didn't put a lower resolution on the timing mechanism, for instance? I bet you'd have millisecond clocks before long.

 

Anyway, you've now talked enough math and statistics that I'm confused as to what you're even saying - so you might want to break it down again - but here's the deal.

 

1) Simple rules can result in nearly unbounded complexity, left to "themselves"

2) You reward success but don't punish failure.

3) The definitions of "success" and "failure" can be arbitrary.

 

Now, there's evidence to support all of those assertions. What exactly is your evidence that proteins and amino acids cannot be created by the process of additive change and emergent complexity?

 

TFS

[Biochemist]

That's actually just about the OPPOSITE of the point I was trying to make....A "sort of" phonological rule in English for instance, is that words tend to alternate between consonant sounds and vowel sounds (that's SUPER simplified, but you get the idea.)...

 

1) Simple rules can result in nearly unbounded complexity, left to "themselves"

2) You reward success but don't punish failure.

3) The definitions of "success" and "failure" can be arbitrary.

I do think I understand your point. I am sorry I got lost in your analogy. The issue on the table is how did the "rules" themselves surface in biological systems.

Now, there's evidence to support all of those assertions. What exactly is your evidence that proteins and amino acids cannot be created by the process of additive change and emergent complexity?

This question seems a little backwards. The more important question is where is the evidence they can. There is little doubt that some DNA configurations and some genomic alterations (mutations or not) are more common than others. But the rules themselves would have to be emergent. And the probabilities against the rules themselves emerging appear high. The rules certainly exist, but how did they get there?

 

And there are several large "gotchas" precluding significant mutative change. Whenever trash substrates (that is, dysfunctional substrates) are produce within a cell (at least, within eukaryotic cells) there are sophisticated systems (lysosomes mostly) that digest the non-functional substrates. Essentially, unwanted proteins get tagged with ubiquitin (I don't think anyone knows how the targets are identified). The lysosomes recognize the ubiquitin tags, and the nonfunctional proteins get broken down by the lysosomes. Ergo, there are not significant amounts (in fact, nearly none) of non-functional proteins sitting around in a cell. The protein has to be functional immediately, or it is trashed.

 

Hence for a significant, new protein that has not yet appeared phylogenetically, we need to figure out how to get the probability of arrival down below (1/20)^200 or so for each protein in a 5 or 6 protein set (a typical enzyme system). I don't think your "watchmaker" metaphor has a lot of applicability where each watch piece in the bag is eradicated before the second piece can enter the bag.

[TheFaithfulStone]

Biochemist, I'm not sure you're looking "deep enough" at this.

 

I've I've got 2 H's and and O - I'm going to end up with water.

 

It's still basic chemistry that nets you stuff like amino acids. How do you end up with a cell that destroys "trash" proteins? The cells that developed this mechanism did better than cells that didn't have it. If you suppose (and I don't think it's unwarranted) that a mechanism like this is necessary to develop multicellular life, then it's really no surprise that eukaryotic cells all have this mechanism.

 

The difference between life and clock-simulation is that life can actually make up it's own rules as it goes along.

 

I think that there's not an issue here. Emergent complexity can handle the question. We may not be able to fully appreciate HOW the complexity emerges, but I don't think it's necessary to posit further mechanisms. It seems like less of a distance to me from "biochemicals randomly drifting around" to "biochemicals drifting around with the purpose of eating other biochemicals" than does "bacteria" to "humans."

 

TFS

[Biochemist]

It's still basic chemistry that nets you stuff like amino acids. How do you end up with a cell that destroys "trash" proteins? The cells that developed this mechanism did better than cells that didn't have it.

I don't have any problem with this "faith" position.

If you suppose (and I don't think it's unwarranted) that a mechanism like this is necessary to develop multicellular life, then it's really no surprise that eukaryotic cells all have this mechanism.

I don't have any problem with this "faith" position either.

The difference between life and clock-simulation is that life can actually make up it's own rules as it goes along.

 

I think that there's not an issue here. Emergent complexity can handle the question. We may not be able to fully appreciate HOW the complexity emerges, but I don't think it's necessary to posit further mechanisms.

Hmmm. I thought the topic of this thread is "how" the complexity occurs. We can postulate or hypothesize any number of solutions. But this thread was discussing the "how".

It seems like less of a distance to me from "biochemicals randomly drifting around" to "biochemicals drifting around with the purpose of eating other biochemicals" than does "bacteria" to "humans."

I don't agree. Nearly all of the intracellular machinery was extant with the first eukaryote (in fact even with the first prokaryote): the 4 DNA nucleotides, the 20 amino acids, the fundamental replication schema, the fundamental transcription schema, and then the lysosome scavenger model (only in eukaryotes). It would be reasonable to argue that bacteria and humans are much closer than source chemicals and bacteria.

[TheFaithfulStone]

Hmmm. I thought the topic of this thread is "how" the complexity occurs. We can postulate or hypothesize any number of solutions. But this thread was discussing the "how".

 

Emergent complexity is a how. It's the mechanism. Where is it lacking? When I say we don't understand "HOW" the complexity emerges, I mean we can't recreate the conditions and watch it play over again. The same goes for Conway's Life. It's impossible to play it in reverse and figure out what the starting condition was.

 

Also why would prokaryotes and eukaryotes be the first "living" things? It would be difficult (at best) to have preserved semi-alive molecules (that you would actually KNOW are preserved and not just... well chemicals.)

 

TFS

[Biochemist]

Emergent complexity is a how.

Wait a minute. "Emergent complexity" is a name for an idea. The topic of this thread is fundamentally "how could complexity emerge if the building blocks for such complexity are insufficient to achieve the end complexity that we actually observe?" If I understand your answer, you are saying "because it does".

When I say we don't understand "HOW" the complexity emerges, I mean we can't recreate the conditions and watch it play over again.

Understood. But what I am suggesting is that there are a number of data points that are difficult to explain: The 250 million year window before the Cambrian explosion did not (apparently) allow enough time for the degree of complexity that we see fossilized in the Cambrian explosion to arrive.

..why would prokaryotes and eukaryotes be the first "living" things?

This is the general definition of life. If you are going to contend that DNA is "life" that is a bit of an outlier point of view. But changing the definitions does not change the problem. I am asking about the time window from prokaryotes to the Cambrian explosion. It looks like an awful lot of complexity arrived awfully quickly.

[Thunderbird]

Wait a minute. "Emergent complexity" is a name for an idea. The topic of this thread is fundamentally "how could complexity emerge if the building blocks for such complexity are insufficient to achieve the end complexity that we actually observe?" If I understand your answer, you are saying "because it does". Understood. But what I am suggesting is that there are a number of data points that are difficult to explain: The 250 million year window before the Cambrian explosion did not (apparently) allow enough time for the degree of complexity that we see fossilized in the Cambrian explosion to arrive.This is the general definition of life. If you are going to contend that DNA is "life" that is a bit of an outlier point of view. But changing the definitions does not change the problem. I am asking about the time window from prokaryotes to the Cambrian explosion. It looks like an awful lot of complexity arrived awfully quickly.

 

 

We can see a result of complexity in the morphology of fossils animals. What we cannot see is the genetic complexity of the single cell eukaryote...We always assume that simple morphology proceeds complex morphology, why is it that we do not acknowledge a clear bifurcation took place were one system reached a threshold in the micro-world and then literally exploded onto the landscape of the macro-world in a non-linear event.

[Biochemist]

We can see a result of complexity in the morphology of fossils animals. What we cannot see is the genetic complexity of the single cell eukaryote...

True. We are pretty much assuming that the ancient eukaryotes had about the same complexity as the current ones. Could be an incorrect assumption.

..why is it that we do not acknowledge a clear bifurcation took place...in the micro-world and then literally exploded onto the landscape of the macro-world in a non-linear event.

I think we are agreeing this happened. This issue it how? My argument is that it is difficult to argue (from the data) that it was gradual, serial mutation.