In Six Days (A Biology PHD looks at Evolution)

In Six Days ^ | 02/17/05 | Timothy G. Standish, PHD biology

[DannyTN]

Timothy G. Standish, biology First published in In Six Days Science and origins testimony #9

Edited by John F. Ashton

Dr. Standish is associate professor of biology at Andrews University in Berrien Springs, Michigan. He holds a B.S. in zoology from Andrews University, an M.S. in biology from Andrews University, and a Ph.D. in biology and public policy from George Mason University (University of Virginia), Charlottesville, Virginia. He teaches genetics at Andrews University and is currently researching the genetics of cricket (Achita domesticus) behavior.

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Reading The Blind Watchmaker by Richard Dawkins was a pivotal experience for me. I had recently started my Ph.D. program at George Mason University and eagerly signed up for a class entitled “Problems in Evolutionary Theory.” The Blind Watchmaker was required reading, and with growing enthusiasm I noted glowing endorsements printed on the cover. According to The Economist, this book was “as readable and vigorous a defense of Darwinism as has been published since 1859.” Lee Dembart, writing for the Los Angeles Times, was even more effusive: “Every page rings of truth. It is one of the best science books—of the best of any books—I have ever read.” A book that was “Winner of the Royal Society of Literature’s Heinemann Prize, and the Los Angeles Times Book Award” must contain nothing but undistilled brilliance. I felt smug with confidence as I paid for the book and left the store, brimming with ebullience to start reading.

After wading through all the hyperbole, I was stunned by the ideas put forward by Dawkins in The Blind Watchmaker. Rhetoric burnished the arguments with a glittering sheen, briefly giving the impression that pebbles were gems. But once each metaphor was stripped aside, the core ideas did not support the idea that natural selection could account for the origin of life and the meaningful complexity of organisms. Most startling to me was the realization that, one of the book’s core theses, in fact, violated the principle of natural selection.

Dawkins wove two ideas together in supporting Darwinism. The first idea was that, given enough chances, the improbable becomes probable. For example, flipping a coin ten times in a row and getting heads each time is very unlikely; one would only expect it to happen about 1 in 1,024 tries. Most of us would not sit around flipping coins just to see it happen, but if we had a million people flipping coins, we would see it happen many times. This phenomenon is publicized in the newspapers when lottery winners are announced. Winning a million-dollar jackpot is unlikely, but with millions of people purchasing tickets, eventually someone wins.

Dawkins admits that the odds on life starting from a random collection of chemicals is very slim, but given an immense universe and the billions of years it has existed, the improbable becomes probable. In this is echoed the logic of Ernst Haeckel, who wrote in his book The Riddle of the Universe, published in 1900:

Many of the stars, the light of which has taken thousands of years to reach us, are certainly suns like our own mother-sun, and are girt about with planets and moons, just as in our solar system. We are justified in supposing that thousands of these planets are in a similar stage of development to that of our earth … and that from its nitrogenous compounds, protoplasm has been evolved—that wonderful substance which alone, as far as our knowledge goes, is the possessor of organic life.

Haeckel was optimistic about the presence of conditions that could support life on planets other than earth, and it is in this that one of the problems with Dawkins’ argument emerges. While the universe is immense, those places where life as we know it could survive, let alone come into being, seem to be few and far between. So far, only one place has been discovered where conditions for life are present, and we are already living on it. Thus, there is not much cause for optimism that the universe is teeming with planets bathed in a primordial soup from which life might evolve. Dawkins wrote glibly of the immensity of the universe and its age, but failed to provide one example, other than the earth, where the unlikely event of spontaneous generation of life might occur. Even if the universe were teeming with proto-earths, and the spans of time suggested by modern science were available, this is still not a great argument, as if something is impossible—in other words, the odds of it happening are zero—then it will never happen, not even in an infinite amount of time. For example, even if we had our million people flipping coins, each with ten flips in a row, the odds on any one of them flipping and getting 11 heads in ten tries is zero because the odds of getting 11 heads in ten tries with one person is zero. The bottom line is that the odds on life evolving from nonliving precursors is essentially zero. Ironically, this was the stronger of the two ideas, or arguments, presented by Dawkins.

The second argument was presented as an analogy: imagine a monkey typing on a typewriter with 27 keys, all the letters in the English alphabet and the space bar. How long would it take for the monkey to type something that made any sense? Dawkins suggests the sentence spoken by William Shakespeare’s Hamlet who, in describing a cloud, pronounces, “Methinks it is like a weasel.” It is not a long sentence and contains very little meaning, but it works for argument’s sake. How many attempts at typing this sentence would it take a monkey, which would presumably be hitting keys randomly, to type the sentence?

As it turns out, the odds can be easily calculated as the probability of getting each letter or space correct raised to the power of the number of positions at which they have to be correct. In this case, the probability of the monkey typing “m” at the first position of the sentence is 1/27 (we won’t worry about capitalization). The sentence has 28 characters in it, so the probability is (1/27)28 or 1.2 x 10–40. That is about one chance in 12,000 million million million million million million! You would want a lot of monkeys typing very fast for a long time if you ever wanted to see this happen!

To overcome this problem with probability, Dawkins proposed that natural selection could help by fixing each letter in place once it was correct and thus lowering the odds massively. In other words, as a monkey types away, it is not unlikely that at least one of the characters it types will be in the correct position on the first try. If this letter was then kept and the monkey was only allowed to type in the remaining letters until it finally had the correct letter at each position, the odds fall to the point that the average diligent monkey could probably finish the task in an afternoon and still have time to gather bananas and peanuts from admiring observers. Dawkins got his computer to do it in between 40 and 70 tries.

Luckily I had taken biochemistry before reading The Blind Watchmaker. Organisms are made of cells, and those cells are composed of little protein machines that do the work of the cell. Proteins can be thought of as sentences like “Methinks it is like a weasel,” the difference being that proteins are made up of 20 different subunits called amino acids instead of the 27 different characters in our example. The evolution of a functional protein would presumably start out as a random series of amino acids one or two of which would be in the right position to do the function the protein is designed to do. According to Dawkins’ theory, those amino acids in the right location in the protein would be fixed by natural selection, while those that needed to be modified would continue to change until they were correct, and a functional protein was produced in relatively short order. Unfortunately, this ascribes an attribute to natural selection that even its most ardent proponents would question, the ability to select one nonfunctional protein from a pool of millions of other nonfunctional proteins.

Changing even one amino acid in a protein can alter its function dramatically. A famous example of this is the mutation that causes sickle cell anemia in humans. This disease causes a multitude of symptoms, ranging from liver failure to tower skull syndrome. It is caused by the replacement of an amino acid called glutamate, normally at position number six, with another amino acid called valine. This single change causes a massive difference in how the alpha globin subunit of hemoglobin works. The ultimate sad consequence of this seemingly insignificant mutation in the protein causes premature death in thousands of individuals each year. In other proteins, mutations to some, but not all, areas can result in a complete loss of function. This is particularly true if the protein is an enzyme, and the mutation is in its active site.

What Dawkins is suggesting is that a very large group of proteins, none of which is functional, can be acted on by natural selection to select out a few that, while they do not quite do the job yet, with some modification via mutation, can do the job in the future. This suggests that natural selection has some direction or goal in mind, a great heresy to those who believe evolutionary theory.

This idea of natural selection fixing amino acids as it constructs functional proteins is also unsupported by the data. Cells do not churn out large pools of random proteins on which natural selection can then act. If anything, precisely the opposite is true. Cells only produce the proteins they need to make at that time. Making other proteins, even unneeded functional ones, would be a wasteful thing for cells to do, and in many cases, could destroy the ability of the cell to function. Most cells only make about 10% of the proteins they are capable of producing. This is what makes liver cells different from those in the skin or brain. If all proteins were expressed all the time, all cells would be identical.

In reality, the problem of evolving life is much more complex than generation of a single functional protein. In fact, a single protein is just the tip of the iceberg. A living organism must have many functional proteins, all of which work together in a coordinated way. In the course of my research, I frequently physically disrupt cells by grinding them in liquid nitrogen. Sometimes I do this to obtain functional proteins, but more often to get the nucleic acids RNA or DNA. In any case, I have yet to find that the protein or nucleic acid I was working on was not functional after being removed from the cell, and yet, even though all the cell components were present and functional following disruption, I have never observed a single cell start to function again as a living organism, or even part of a living organism. For natural selection to occur, all proteins on which it is to act must be part of a living organism composed of a host of other functional protein machines. In other words, the entire system must exist prior to selection occurring, not just a single protein.

“Problems in Evolutionary Theory” was a class that made me realize the difficulties those who discount the possibility of a Creator have with their own theories. The problems with evolutionary theory were real, and there were no simple convincing resolutions.

Progressing in my studies, I slowly realized that evolution survives as a paradigm only as long as the evidence is picked and chosen and the great pool of data that is accumulating on life is ignored. As the depth and breadth of human knowledge increases, it washes over us a flood of evidence deep and wide, all pointing to the conclusion that life is the result of design. Only a small subset of evidence, chosen carefully, may be used to construct a story of life evolving from nonliving precursors. Science does not work on the basis of picking and choosing data to suit a treasured theory. I chose the path of science which also happens to be the path of faith in the Creator.

I believe God provides evidence of His creative power for all to experience personally in our lives. To know the Creator does not require an advanced degree in science or theology. Each one of us has the opportunity to experience His creative power in re-creating His character within us, step by step, day by day.

This chapter from the book In Six Days, published and graciously provided at no charge to Answers in Genesis by Master Books, a division of New Leaf Press (Green Forest, Arkansas).

[DannyTN]

"Nehemiah 2:13 - And I went out by night by the gate of the valley, even before the dragon well, and to the dung port, and viewed the walls of Jerusalem, which were broken down, and the gates thereof were consumed with fire. "

As I said, I don't know what it means. It may have nothing to do with animals at all.

[Ichneumon]

One of the BIG ASSUMPTIONS for Carbon dating is that the modern value is only 1 out of every trillion or so carbon atoms is a Carbon 14. Therefore if the ratio was more or less in the past our dating can be way off. Say if the original ratio was 1 to ever 10 trillion atoms, then our assumption that the modern value was valid in the past, would give dates that are almost twice as old as real. Carbon-14's half life is 5700 years. Based on current values 1 in a trillion carbon atoms are Carbon 14. BIG ASSUMPTION is that ratio was the same thousands of years ago.

Sigh... So much creationist ignorance, so little time...

No, scientists do *NOT* just "assume" that past 14C concentrations were the same as today's -- you have only *ASSUMED* that they make such an assumption. They do not. They *know* that atmospheric concentrations likely varied to some degree over time, so they expend a lot of effort to FIND OUT what the past concentrations have been, and use those results to refine the radiocarbon dating methods.

Did you just make up that bit about them making a "BIG ASSUMPTION" of 14C constancy yourself, or did you just swallow and then parrot some creationist source's lie about it? Please answer.

Here's a post I wrote earlier in response to yet another person making the same WRONG assertion:

Yet can you answer with certainty the amount of carbon at any given time? As in, were the levels constant? The answer is no.

Very wrong. The answer is yes. There are many, many samples of known age (e.g. tree rings, arctic ice layers, lake bottom layers, etc.) which can be used to multiply and independently determine how much carbon-14 was in the atmosphere in any given year, and thus be used to calibrate Carbon-14 dating methods.

For a quick article on one such study, see http://more.abcnews.go.com/sections/science/dailynews/carbon0220.html

A much more technical treatment: Atmospheric Radiocarbon Calibration to 45,000 yr B.P.: Late Glacial Fluctuations and Cosmogenic Isotope Production

Such studies produce calibration results such as the following:

If the amount of Carbon-14 in the atmosphere had been exactly constant throughout time (and no one expects that it has been), then the results would fall on the straight diagonal line. Instead, the wiggly line indicates how much the actual amount of C-14 in the atmosphere deviated from the "base" amount, and from this we can know how much C-14 was actually present in any given year in the past 50,000 years.

Note that the above graph includes C-14 data from *two* completely independent sources (Lake Suigetsu varves, and ocean corals), and yet the results overlap beautifully, confirming each other. There is similar match from C-14 studies based on tree-ring data and other sources.

From this, we can build a Carbon-14 dating calibration or "correction" curve which can be used to confidently produce an accurate date from a given Carbon-14 measurement. These calibration curves look like this:

There are many databases available which are used to compile massive amounts of data to ensure the proper calibration of carbon-dating. For just one example, Marine Reservoir Correction Database.

Other methods are used to cross-check and calibrate other dating methods to ensure accuracy.

[Ichneumon]

If that is the same program I've seen before, it is invalid as it correlates a pseudo-random selection to the known content of a position and then fixes it and moves onward to the next position. That is not random by any definition or stretch of the imagination.

Please see my post #144 in this thread. Your impression of how the program proceeds is *not* accurate.

[D Rider]

Lesson: Even simple evolutionary processes are *incredibly* more efficient and effective than simple randomness alone. Evolution can *easily* accomplish things which would be *impossibly* improbable by purely random means.

All you need to add is information. (which is the point, silly)

[Ichneumon]

You'd swear those wings evolved, without any proof at all.

No, he'd swear they did, because of the huge amount of evidence that they had.

[Ichneumon]

All you need to add is information. (which is the point, silly)

Wrong, but thanks for playing.

[Alamo-Girl]

Thank you for your reply!

Your impression of how the program proceeds is *not* accurate.

It is somewhat different from the first one that was floating around the internet. But it is still not happenstance.

Here is the source code: Source Code Java Script.

Of particular import is the subroutine String repl(String s1, String s2, int start, int end) which replaces a segment of the string.

That is more like the Schneider model - it is not however, happenstance in that it applies boundaries at each iteration.

It also has a starting configuration and rules (an algorithm if you'll recall our discussion on another thread). Thus both this applet and the Schneider model are more supportive of Intelligent Design than Evolution by happenstance.

Remove the "happenstance" from evolution theory and either model could support either ID or Evolution.

[DannyTN]

"No, he'd swear they did, because of the huge amount of evidence that they had."

ROFLMAO. Yes you are right. That's exactly what he would claim.

[Ichneumon]

It is somewhat different from the first one that was floating around the internet.

No, I don't believe that it is.

But it is still not happenstance.

Yes it is.

Here is the source code: Source Code Java Script. Of particular import is the subroutine String repl(String s1, String s2, int start, int end) which replaces a segment of the string. That is more like the Schneider model - it is not however, happenstance in that it applies boundaries at each iteration.

What you're misunderstanding is that the "boundaries" (the range of replacement) is COMPLETELY RANDOM. Here is where the "repl" function is invoked:

    // Return the result of breeding myself with the supplied
    // (Weasel)Critter.  This is a simple crossover technique.
public Critter breedWith(Critter c_)
    {
        WeaselCritter c = (WeaselCritter) c_;
        return new WeaselCritter(repl(rep, c.rep, randomPos(), randomPos()));
    }

As the comment implies, this is just mimicking what happens to DNA during sexual reproduction -- paired strands of DNA have sequences "swapped" at random locations. It's called "crossover". See for example: Crossing Over and Genetic Recombination in Meiosis. But if including *random* crossover bothers you for some reason, it can be removed and the model will still converge upon the solution via evolution (it will just do so in the manner of asexual reproduction instead of sexual reproduction).

It also has a starting configuration

The "starting configuration" is COMPLETELY RANDOM. Here's the relevant section of the code:

        // Use our prototype Critter to randomly create a population
        // of Critters.  Since this is often slow, show our progress
        // as we go.
        population = new Critter[nCritters];
        for (int i = 0; i < population.length; ++i)
        {
            population[i] = prototype.spawn();
            if ((i % 10) == 0)
                reporter.progress(i, population.length);
        }
[...]
    // Return a randomly generated (Weasel)Critter.
public Critter spawn()
    {
        return new WeaselCritter(randomStringOfLength(rep.length()));
    }

and rules (an algorithm if you'll recall our discussion on another thread).

The only "rules" are the bare requirements of the process of evolution: Reproduction, (random)variation, and selection (the "warmer/colder" rating, which grants the "warmer" individuals in the population a higher probability of producing offspring in the next generation).

Thus both this applet and the Schneider model are more supportive of Intelligent Design than Evolution by happenstance.

Nonsense. The fact that the applet itself is "designed" is no more an indication that the modeled process "requires" design than does the fact that Galileo purposely built ramps in order to study the effects of gravity upon rolling objects indicates that "intelligent design" must be involved for objects to roll down inclines.

Remove the "happenstance" from evolution theory and either model could support either ID or Evolution.

False. Remove the "happenstance" (random variation) from the "Weasel" applet, and the endpoint will never be achieved.

[bondserv]

My question, then, is why would God try to trick us like that? Seems a bit cruel to me, and conflicts with my understanding of a God who loves those he created in his image.

It is about perspective.

Adam was created as a mature adult. God describes stretching the heavens like a curtain. When He stretched the light waves across space instantaneously He wasn't trying to trick us. He explained how He did it.

Isa 40:22 [It is] he that sitteth upon the circle of the earth, and the inhabitants thereof [are] as grasshoppers; that stretcheth out the heavens as a curtain, and spreadeth them out as a tent to dwell in:

In this scientific passage God describes how the earth is a sphere, and that from His enormous capacity the living things on the earth are insignificant. Letting us understand that creating a universe is no more difficult for Him, than stretching out a curtain would be for us. Billions of light years instantly. Hurling galaxies 200,000 miles per hour, like a Nolan Ryan fastball.

Why limit His capacity when He says otherwise.

[Alamo-Girl]

Thank you for your reply and for your replies over the last few days. They have been very instructive, revealing some things about your approach which I had not previously considered.

You are notorious for large posts and exhaustive research and sources - a property we share.

But the debate needs to be constructive:

I said: Remove the "happenstance" from evolution theory and either model could support either ID or Evolution.

You replied: False. Remove the "happenstance" (random variation) from the "Weasel" applet, and the endpoint will never be achieved.

I never said to remove "happenstance" from the applet, I said to remove it from evolution theory.

I said: Thus both this applet and the Schneider model are more supportive of Intelligent Design than Evolution by happenstance.

You replied: Nonsense. The fact that the applet itself is "designed" is no more an indication that the modeled process "requires" design than does the fact that Galileo purposely built ramps in order to study the effects of gravity upon rolling objects indicates that "intelligent design" must be involved for objects to roll down inclines.

I never even mentioned that the applet was designed. My point had to do with the logic in the source code vis-a-vis Schneider's evolution model. Both of them have a starting point and apply rules, i.e. an algorithm - and both of them use replacment scenarios.

That is not randomness, that is directed. Randomness has a strict meaning in mathematics.

Direction however would not necessary speak in favor of Intelligent Design were it not for the original formulation of "random mutations + natural selection > species". The issue is the freedom of movement - the boundaries. All mutations were not created equal, or conversely some genes are resistent to mutation.

Moreover, if you look at links provided elsewhere wrt to eyeness (Weiss, Gerhling) and the work of many others - naturally including the mathematicians (Rocha, etc.) - you will notice a strong shift away from "randomness" and towards other explanations - such as autonomous biological self-organizing complexity.

[shubi]

I couldn't find the exact page walsh copied from. Could you post the link?

I suspected this was probably bogus. I don't know any biologist who includes origin of life in teaching ToE. They might mention the abiogensis experiments, but not as a theory.

[shubi]

C14 is used more in archeology than paleontology. Other methods that measure millions of years are used more often for fossils. I don't know why creationists get hung up on C14, when it is past 6000 years anyway and thus in their fevered minds could not exist.

[Ichneumon]

I did post the link to the exact page. Those quotes are just *way* down the page, in the rightmost column.

I suspected this was probably bogus. I don't know any biologist who includes origin of life in teaching ToE. They might mention the abiogensis experiments, but not as a theory.

That's one possibility, another is that they actually appear in the textbooks, but with introductory material about how they are scenarios suggested by evidence, etc., which Spetner "forgot" to include as the relevant context.

For example, on amazon.com they show the table of contents of Miller & Levine's "Biology" textbook, which shows an entry for "1-3 Science: "Facts" and "Truth", pages 15-18". Want to bet that this introductory material puts all later claims in the book into perspect with regard to how statements of scientific "truth" are always prefaced by an implicit, "the known scenario which best fits the available evidence is..."?

[Ichneumon]

["No, he'd swear they did, because of the huge amount of evidence that they had."]

ROFLMAO. Yes you are right. That's exactly what he would claim.

Okay, I'll bite -- why do you find it hilarious that he would make a statement based on the evidence which supports it?

[Ichneumon]

But the debate needs to be constructive:

It is constructive -- I have already corrected several of your misconceptions. Unless you don't consider learning to be constructive.

I said: Remove the "happenstance" from evolution theory and either model could support either ID or Evolution.

You replied: False. Remove the "happenstance" (random variation) from the "Weasel" applet, and the endpoint will never be achieved.

I never said to remove "happenstance" from the applet,

We were discussing the applet as a model of evolution. Thus my interpretation of your comment.

I said to remove it from evolution theory.

My statement still stands: Remove the "happenstance" from evolution itself, and evolution will not occur (without direct and constant intervention).

I said: Thus both this applet and the Schneider model are more supportive of Intelligent Design than Evolution by happenstance.

You replied: Nonsense. The fact that the applet itself is "designed" is no more an indication that the modeled process "requires" design than does the fact that Galileo purposely built ramps in order to study the effects of gravity upon rolling objects indicates that "intelligent design" must be involved for objects to roll down inclines.

I never even mentioned that the applet was designed.

That is the most common objection leveled against such models in an attempt to deny the lessons they provide. Thus my interpretation of your remark. I'm glad to hear that's not your objection after all.

My point had to do with the logic in the source code vis-a-vis Schneider's evolution model. Both of them have a starting point and apply rules, i.e. an algorithm - and both of them use replacment scenarios.

And so does natural Darwinian evolution. Thus the value of the applet as a model.

That is not randomness, that is directed. Randomness has a strict meaning in mathematics.

By that hairsplitting, then so is natural Darwinian evolution "directed".

Direction however would not necessary speak in favor of Intelligent Design

Nor does it.

were it not for the original formulation of "random mutations + natural selection > species". The issue is the freedom of movement - the boundaries. All mutations were not created equal, or conversely some genes are resistent to mutation.

I fail to see any significance in this observation. Darwinian evolution does not require "pure" randomness in a "strict" mathematical sense. Nor does it require the complete absence of any "boundaries", nor equal mutation rates in all genes, or any of the other issues you raise. So what might your point be?

Moreover, if you look at links provided elsewhere wrt to eyeness (Weiss, Gerhling) and the work of many others - naturally including the mathematicians (Rocha, etc.) - you will notice a strong shift away from "randomness" and towards other explanations - such as autonomous biological self-organizing complexity.

i.e., selection. And if you think I've missed your point or am oversimplifying it by encompassing it in "selection", then I ask you to pause and reconsider for a while before responding.

[shubi]

"why do you find it hilarious that he would make a statement based on the evidence which supports it?"

I think they took off their aluminum hats again.

[shubi]

Thanks, I found the quotes. It looks like another quote mine project alright.

[DannyTN]

"why do you find it hilarious"

We are talking about "pigs with wings". He would claim as evolutionists always do, that he has tons of evidence, when in fact he has none.

No doubt he would line up pictures of pot bellied pigs next to large pigs, and winged pigs to support his case. He'd bring out the list of "29 evidences" in favor of evolution, most of which either refute evolution or are neutral.

He would go on and on about how wings evolved in birds and bats and how it's not surprising that wings evolved on pigs.

It's like watching the Iraqi Information Minister come out and with all confidence and seriousness say they are winning the war.

[stylin19a]

am i reading this right ? you are starting with an already defined answer. ("If you can look into the seeds of time, and say which grain will grow and which will not, speak then unto me.") and a preselected universe of elements.. and that's proof the evolutionary process is "intelligent" ? Nice Try.

Start with the letter "A" then throw all known letters\numbers\characters etc..into your applet and see if you can come up with that sentence.

Why didn't the "evolution process" find a less perfect match and accept it? like:

"If you can say, which grain will grow and which will not, speak then unto me and look into the seeds of time."