What is the Evidence for Evolution?

This is ostensibly a reply to my comment, and yet I am puzzled how to respond. Your comment assumes that my use of the phrase “scientists believe” indicates a lack of empirical evidence, and yet in the sentence immediately following the one you quoted, I discuss the evidence supporting this particular scientific belief. I see nothing in your response to indicate you processed anything beyond the first eight words of my reply, especially since you repeat the nonsensical claim that I and several others just explained to you did not carry water, and why.

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This paragraph is completely false. Readers should invert the assertions to get something resembling the truth.

There are some important things missing from this conversation about scientists irradiating their own gonads. Pictures, for example, but let’s hold off on that for a while. :smiley:

  1. The suggestion is that mutations must not be “good” or else everyone would want more of them. This is a strawman. In the context of evolution and genetics, mutations are like vitamin A. You have to have them, but too many of them is disaster. There is no innovation without variation, but runaway mutation is death.

  2. The snarky comment about gonads in an X-ray machine obscures the fact that biologists regularly subject experimental organisms to increased mutation rates, precisely so they can increase the amount of variation in order to do an experiment. The most common use of this approach is in a genetic screen. The basic idea is that the experimenter turns up the mutation rate, then introduces some form of selection that is intended to either a) reveal insights into the nuts and bolts of some biological process or, b) in some cases, is intended to obtain new versions of molecule or a process. Goal a) is almost always to break something. Goal b) is the opposite.

An example of a) is just about any genetic screen run by a developmental biologist over the past few decades. In the lab where I was a postdoc, half the scientists worked on the fruit fly and did genetic screens to find genes that controlled particular cellular processes. Instead of X-rays, they used a chemical mutagen that does pretty much the same thing. They intended to break genes, ideally just one or a few at a time. It is likely that over the years of doing screens like these, scientists turned up lots of new gene versions that weren’t merely broken. I know they frequently turned up variants with weird new “functions” and genes that were partially but not completely crippled. But since these weren’t the goal of the experiment, they weren’t studied further. There are probably exceptions, but I don’t know of any off the top of my head.

But then there’s b). In this type of experiment, the scientists are harnessing the power of evolution by turning up the mutation rate, typically while focusing on a single protein or RNA, then selecting for variants that have new or improved activities. I think X-rays are rarely if ever the mutation engine of choice, but that doesn’t matter. The point is that is common (and increasingly so) for scientists to deliberately increase the mutation rate in a system, for the specific purpose of creating variation and even innovation.

Gonads in an X-ray machine? Cute, but actually nothing even close to a counterargument in a discussion of evolutionary mechanisms.

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The first time I saw you post that argument—especially the genitals under the x-ray beam— I assumed you were being facetious. Does the fact that few physicians want to stick their hand into the rotating knives of a garbage disposal somehow prove that surgeons don’t really believe that a skillfully-applied knife can heal a diseased patient? Does that sound logical?

Yet, you seem to be doubling-down on that argument. Do you believe that that it is persuasive? I’m still wondering if there is some aspect of that type of absurdist argument that I’m missing. I will admit that I sometimes fail to catch some “obvious” aspect of an argument because I don’t recognize some pop culture reference, or some inside joke, or even some English idiom that is new to me. The expectation that if mutations were ever beneficial, then scientists would voluntarily subject their genitals to an x-ray beam sounds absolutely ridiculous to me. (By ridiculous, I don’t just mean the absurd x-ray experiment, although it is certainly ridiculous enough. I am mainly referring to the ridiculous “logic” of such an argument. That’s why I will feel relieved—while also feeling a bit foolish for my cluelessness—when someone explains to me the pop culture reference or whatever that makes all of the difference to the “colorful hyperbole” of your illustration.)

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Did you know that information = entropy? This means the 2nd law of thermodynamics guarantees that information content will increase with time, unless we do something to stop it.

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As has already been pointed out, the 2nd LOT says that increased entropy means expanding the information content. So you are wrong about that.

As to energy becoming available “for free”, I don’t understand what you mean by “for free” and why you think it is a problem. Yes, the universe is “running downhill” as Isaac Asimov used to say. Our sun is headed towards extinction, but, fortunately, we get several billion years of “free energy” in the meantime. That “free energy” gives us lots of food to eat, builds forests, and even stores energy in the form of coal and oil which we use in countless ways. If that is not a lot of “free energy”, then I guess I don’t know what you mean by the expression. Can you explain?

Solar energy builds trees and entire forests. It fuels reproduction. The sun’s free energy brings gestation, meiosis, and new human beings, generation after generation. That “free energy” produces all of those increasing-complexity kinds of things. So why are the evolutionary processes which are fueled by the sun somehow any different from any other biological process?

@williamdj, are you implying that you think that evolutionary processes are rendered impossible by The Laws of Thermodynamics because there is increased complexity? If yes, why isn’t the increased complexity of a seed growing into a tree or a fertilized egg into a human a violation?

Yes, decay is inevitable, but you surely can’t be saying that nothing ever grows/develops. Yet again, I must be missing some aspect of your argument. You said:

Sure they will. So what? In the meantime, those natural processes grow things: Solar radiation fuels the entire biosphere and feeds us. Lightning sends atmospheric nitrogen into the soil where bacteria feed nitrates to plant roots and become nitrogen-rich proteins. Rain waters lush growth and wind scatters seeds and brings waves of new growth. Does that sounds like ONLY decay?

What am I missing, @WilliamDJ? You appear to be making arguments in favor of the very things you deny!

Yes, eventually everything will decay. Eventually, if God does not bring the New Heaven and New Earth as promised, the universe will scatter its energy so that it becomes less and less able to do work. Meanwhile, there’s billions of years of growing complexity and not just decay.

Help me out here, William.

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Sure, evolution exists; no doubt! But the continuous beneficial adaptation of living nature (for instance the changes in the beaks of finches) is produced by recombination of gene variants and selection and by gene regulation, whereby the mutation repair mechanisms do not have to come in action. They are not produced by the accumulation of irreparable, inheritable, code expanding mutations.

Nylon eating bacteria, feature a beneficial recombination of gene variants from the gene pool of related tribes of bacteria.

Lactose digesting humans, feature a beneficial gene variant from the human gene pool.

I am one of the scientists that refuse to put their genitals under an X-ray machine to improve their sex cells. All my academic friends refuse it.

You seem unable to learn that the mechanism of recombination of gene variants and selection and gene regulation is beneficial, in contrast to the mechanism of accumulation of irreparable, inheritable, code expanding mutations. A population with dysfunctioning mutation repair suffers from cancers and Syndrome of Down like handicaps. According to Darwin, it loses the continual struggle for food, shelter and a partner with a population that possesses well functioning mutation repair.

Irreparable mutations require dysfunctional mutation repair, which is a severe selective disadvantage, leading to fast extinction of a population.

You are wrong. Putting organisms, organs or genes in family trees does not prove that they originated from each other by the accumulation of irreparable, code expanding, inheritable mutations. That mechanism only works in Wonderland, not in the real world. Your facts are beliefs.

Without the mutation repair mechanisms in every cell, the DNA would turn into complete chaos, within a life time.

Mutations are an enemy of the DNA, not a friend. They are antagonized by mutation repair mechanisms in every cell, and by numerous hurdle races for food, shelter and a partner.

Your are completely wrong. (I graduated in Thermodynamics in 1975 at the University of Technology of Delft). Order and information eventually turn into the maximal disorder (‘entropy’). All of this has been discussed lately on the Biologos forum at:
https://discourse…org/t/the-second-law-of-thermodynamics-also-holds-for-open-systems/26534

(1) The mechanism of recombination of gene variants and gene regulation, whereby the mutation repair mechanisms do not have to come in action, adapts the DNA to changing circumstances, and is comparable with the skillfully-applied knife of a surgeon. During the recombination (‘cross over’), the exchange of code expanding mutations appears impossible.

(2) Mutating your DNA by radiation, heat, chemical influences and natural decay, is comparable with sticking your hand into the blindly rotating knives of a garbage disposal.

Your comparison helps us to understand the difference between both mechanisms, and makes it crystal clear that the second mechanism cannot improve the DNA and expand it with new functionalities.

ILLUSTRATION 1
Video Script: Scene at the Radiotherapy Ward of a University Medical Centre.

PATIENT: “Doctor, you are going to radiate the lung cancer spots on my left lung for 30 days. Would it be possible to aim an additional mild dose on my genitals for a couple of days, to enhance the DNA in my sperm? If my lung cancer cannot be cured by you, my wife Alicia and I want to make a baby and bless it with improved DNA”.

DOCTOR: “Are you joking?”.

PATIENT: “Not at all!” < smiles>. Alicia and I strongly believe in the theory of evolution and in all the evolutionary scientists who have proved that mutations of the DNA are beneficial". < looks confidently>

DOCTOR: “Really?”

PATIENT: “Of course!” .“We have been raised by our parents and teachers in the power of evolution. We have read many books on it. We know exactly how evolution works and what it can do for us”. “All we need is a mild dose on my genitals that balances the positive effects of mutations with the negative effects, because - you know - life is a balance!” < Smiles confidently>. Mutations are like vitamin A. You have to have them, but too many of them is disaster. .

DOCTOR : “I think you need to speak with one of our psychologists” < looks worried>. I’ll make an appointment for you".

You edited what I actually wrote so that you could create a strawman. And understandable, since you are wrong about almost everything you write about.

To which we saw this reply:

Yet, I have to agree with Swamidass on this because I remember returning to grad school in midlife where I had to grasp some of the great classics of computer automation theory and information theory, including Shannon’s 1948 famous paper about INFORMATION = ENTROPY. (I remember the ACM Society putting it into a special “anniversary edition” of classic papers which changed computer science forever.) I had to remember for the final exam the famous information equals entropy equation shown here:

http://image.wikifoundry.com/image/1/o5EIZSLdYnuJIz70XX4iKw100131

I’ve usually found that those who oppose evolution theory like to quote Shannon, so this situation is a turnabout for me (that is, to see someone try to use Shannon against evolutionary processes.)

Thus, William, I’m baffled by your position. It defies everything I learned about biology, entropy, and information theory. So, where did Shannon go wrong? What do you know about entropy that Shannon didn’t? Can you explain the error in his famous equation?

Yes they do—after billions of years. In the meantime, what prevents pockets of greater order and complexity from forming? Why wouldn’t solar energy provide billions of years of order in the earth’s biosphere? Help me to understand this.

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You do not seem to be aware that regulatory genes do the regulating. And regulatory genes, like all other genes, are subject to mutation repair mechanisms.

What publications make you think otherwise?

Actually, nylonase is the result of an insertion mutation. Per Dennis Venema:

nylonase arose as a mutation in another protein coding gene—an insertion of a single DNA letter. This single insertion of one letter created a “stop codon”—three DNA letters that tell the ribosome to stop adding amino acids to the protein chain of the translated protein—as well as simultaneously creating a new “start codon”—three DNA letters that tell the ribosome to start making a protein chain from that point in the mRNA code. The new start codon, however, was not aligned with the old gene’s codons—the new gene was shifted over by one DNA letter. Thus, the resulting protein was brand new, and completely unlike the previous one.

Actually, lactase persistence is present in about 30% of the human population due to 6 different mutations that have arisen in the past 30,000 years or so.

You don’t seem to understand the rudiments of population genetics. The mutations with negative effects are subject to negative selection in the population. The mutations with positive effects (of which there are fewer) are subject to positive selection.

Sure, just as dropping a pencil from your hand does not prove the theory of gravity. In the mathematical or formal logic sense, science cannot prove anything.

However, arranging populations into pylogenies yields predictions that are far more accurate than arranging them onto a (simpler) axis of similarity. When you compare scientific models, the one that yields more accurate predictions wins. So common ancestry is the best scientific explanation for the features we see in the biosphere.

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William, I’ve truly tried but I can’t make sense of this illustration. To me it suggests a total misunderstanding of how mutations contribute to evolutionary advantages and disadvantages. Among other problems, it fails to reflect how such mutations can benefit populations yet NOT benefit the individual.

As I understand it, you could probably stage an experiment where all of the males of a population went through a procedure that induces mutations. That experiment might even kill off many individuals immediately and produce “negative” mutations which cause fatal birth defects in the next generation or major losses in fertility. But the experiment also might produce a male in the next generation that has a decided advantage—and that advantage might caught him to have many more offspring. Thus, a hundred generations later, we might find that virtually the entire population carried an advantageous gene from that one experiment, even though all of the other males who experienced that mutation-inducing procedure had very negative results. And that is why your “logic” here makes no sense to me. It suggests that you don’t understand how natural selection can sometimes vastly “multiply” an advantageous gene even while basically ignoring and “discarding” a disadvantageous gene.

Again, unless you recognize that what is “good” for the population may not be good for the individual (as in sickle-cell genes), you are going to misuse illustrations like “genitals in the x-ray machine.”

I can think of several other flaws in your analogy, but I thought the one I described above might be the easiest to explain. (I’ve found that a typical one paragraph argument against evolution can often require a half dozen paragraphs to debunk it. Why? Because one usually has to provide a start-from-nothing tutorial on various aspects of evolution in order to help readers to spot the errors in evidence and logic in just one misinformed claim. I remember this well in Duane Gish’s infamous lecturers—from which we get the term “The Gish Gallup”. He use to overwhelm his opponents with a machine gun barrage of erroneous claims.)

I’ll look to those better qualified professionals–because I’m not one—to decide whether I’ve explained my thoughts properly.

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I’d like to see your citation for that because I’ve always heard that the nylonase in flavobacteria came from a frame-shift mutation.

Well, that’s fascinating, William DJ. Firstly, are you a scientist, and secondly, who asked you to volunteer for testicular radiation? As for the rest of your post, you don’t seem to present any evidence to support your opinions, apparently in the expectation that your authority alone will carry the argument. That’s no way to carry out a discussion on the internet. Your comments “You seem unable to learn…”, “You are wrong”, etc., mean nothing. If you have a contrary opinion to someone, you have to say what it is and then justify it, which I must say you haven’t yet. You seem to insist that beneficial alterations to DNA are only possible via gene shuffling, while any direct mutation, such as by cosmic radiation, must be deleterious, and is invariably “corrected”. I dispute this. Some mutations are not corrected, as you admit, and some lead to degenerative diseases. Others, in my opinion, lead to increased reproductive capacity in the organism, and are thus preferentially preserved. You do not explain why this is wrong, preferring merely to assert some kind of authority (a degree in Thermodynamics) as sufficient. I’m afraid it isn’t.

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Your assessment of his post is harsh but, admittedly, quite accurate. But I want to give William the benefit of the doubt and assume that he is collecting his citations and will be posting them soon. He is making a lot of very bold claims which totally defy well-established science, so I can only assume that he is carefully preparing a detailed defense. I for one am looking forward to it. This has been an interesting thread.

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@WilliamDJ

I would say there are two things almost anyone could say about the statements that I am quoting here in this posting:

  1. I don’t think you have enough information to make such a determination.

and

  1. It doesn’t really matter what you are calling it. You are playing fast and loose with semantics.

You admit there is evolution… BioLogos supporters believe God has His role in this Evolution. Presumably you do too.

So I’m not sure the point you think is so valuable to make - - amounts to anything.

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Oh, dear; I hope I wasn’t too harsh. I was trying to be helpful. I have on a few occasions been able to listen to “experts” who have been brought in to support one case or another, and have always been impressed by their humility. They never say that that know something (or that their opponents don’t know something) without explaining how they know it, (or where their opponents have gone wrong). They achieve eminence not by their innate authority, but by the strength of their support. Either they have seen or done something similar many times themselves, and speak from personal experience, or they have such an extensive knowledge of the literature that they can vicariously bring in other experts to help. After listening to real experts, one’s immediate reaction is not, “Gosh, what an expert” but “How obvious! Surely anybody could have seen that”. Which, of course, they could have, but didn’t.

However, I’d like people discussing different DNA here to give some opinions on what is meant by “improved” or “deteriorated” DNA, or how we know whether a mutation, or a gene shuffle, has produced “better” or “worse” DNA. Words like “beneficial”, “advantageous”, “disfunctioning” and “negative” all seem to me to be value judgements which cannot apply to a strand of DNA. A gene which causes an adverse reproductive effect on the organism which possesses it, but then “suffers” a mutation which disables its replication, may result in the greater reproductive success of the organism. So a “negative” change turns out to be “beneficial” after all!

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Oh, I think you were very helpful! And a little bit of harshness was a good thing when it happened in my life. I used to be an adamant anti-evolution Young Earth Creationist. (This was over a half-century ago) If not for some well placed harshness, I might have continued to repeat the bad arguments I had learned from my spiritual heroes much longer than I did.

I suppose it differs with the individual but I really needed some firm rebukes in those days. It got my attention.

Perhaps I should have used the word “direct” instead of “harsh”. In any case, Hugh, I thought your comments were helpful. I know that I appreciate directness. Otherwise, I might continue to repeat my mistakes.

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What a very generous comment. Thank you very much.

@Hugh_Farey

No doubt about it … the people who talk about “devolution” being different from “evolution” are almost always non-scientists.

If a snake is a reptile… a reptile without 4 legs… is that devolution?

Is a Whale a water-living Hippopotamus that has De-Volved into a legless water creature?

It’s impossible to make judgments like this … but because evolution usually tracks from the simple to the more complex, amateurs think “increased complexity” is a requirement of evolution - - even if you could define what “complexity” means.

There are some very small creatures that seem to have more than 2 genders… they are not just males or females… there are also other undefined states of existence. I would suggest that this is pretty complex reproductive strategy.

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I’ve been living in one of those for a long time.

And then there’s also West Virginia.

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In response to my request for evidentiary support of the claim, “hundreds of thousands of mutations occur in every cell every day,”

That lecture has no evidence to support your claim, William, but I suspect that you know that.

It’s easy to measure mutations. How about some actual evidence?

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