Desperately Seeking Innovation

One of the biggest problems facing evolutionists is the explanation of how brand new information can be added to a genome. After all, if flagellates eventually evolved into philosophers, an enormous amount of truly original information had to be added to flagellates’ (and their descendents’) genomes. However, genomes are so well-designed and highly-structured, it is difficult to imagine a naturalistic process that could add information to them. Nevertheless, evolutionists have tried their best. One of the more popular notions is gene duplication followed by mutation. We know that genes can be duplicated. It happens quite frequently. The thought is that when a gene is duplicated, one of the copies can continue to produce the protein it is supposed to produce, while the other copy is free to mutate and find some completely new function.

While the thinking behind this idea is logical, experimental evidence to support it has been hard to find. As a result, evolutionists tend to jump on any experimental finding that might suggest the idea is accurate. This is well illustrated by an article that was linked by a commenter on a previous thread. The article claims that researchers have finally shown how a gene can pick up a brand new function, which can then be amplified and modified over time.

Unfortunately, the article’s claim is not accurate. I had already read the scientific paper on which the article was based1, so when I read the article, I understood how incorrect its claims are. However, I am sure the commenter and many other readers of Science Daily do not. As a result, I want to discuss the study’s actual findings. They are very interesting, and they tell us a lot about the genetics of bacterial adaptation. However, they don’t tell us anything about how genes acquire brand new functions or about how information can be added to a genome.

In the study, the authors examined populations of Salmonella enterica over many, many generations. Normal versions of these bacteria can produce (among other things) two amino acids, histidine and tryptophan, and they have many genes devoted to those processes. As is the case with most chemical reactions that go on in living systems, many of the steps in the production of these two amino acids need to be sped up, and the bacteria produce specific enzymes to do that. In this case, the researchers studied two different enzymes, one for speeding up a step in the production of histidine, and another for speeding up a step in the production of tryptophan. The genes that produce these enzymes are called HisA and TrpF, respectively.

The researchers chose a strain of Salmonella enterica that did not have the TrpF gene. As a result, bacteria in this strain cannot produce tryptophan and must instead acquire it from their environment. They found that after many generations of stressing these bacteria with low levels of tryptophan, a new strain was produced that could make its own tryptophan! The amount it could make was very low, but it was enough for them to survive without getting any tryptophan from their environment. They found that if they studied this strain for 3,000 generations in a tryptophan-free environment, the bacteria got better and better at making tryptophan.

So how did the bacteria develop the ability to make tryptophan, even though they didn’t have the necessary gene? The HisA gene that they use to produce histidine experienced two mutations. The first mutation stopped its ability to make histidine, but it produced an ability to make tryptophan slowly. The second mutation then restored its ability to make histidine and had no effect on its ability to make tryptophan. So the gene went from making one amino acid to making two amino acids. That sounds like the gene developed a brand new function, right? Actually, it didn’t, but more on that in a moment.

The main focus of the paper is what happened next. When they started following the new strain of bacteria, they found that its tryptophan-making abilities got better and better. This happened because the gene was duplicated, and the duplicates experienced more mutations. They found that in the end, three specific kinds of genes were produced from the duplication and subsequent mutation of the original, multipurpose gene. (1) Some lost their ability to make tryptophan and went back to making only histidine. (2) Others lost their ability to make histidine and devoted themselves solely to making tryptophan. (3) Still others kept making both amino acids, but they improved their ability to make tryptophan. So in the end, gene duplication and subsequent mutation did, indeed, lead to an improved ability to make tryptophan.

But what of the original two mutations that took a gene which could only make histidine and turned it into a gene which could make both histidine and tryptophan? Isn’t that a clear example of a gene acquiring a brand new function? No. What the Science Daily article leaves out, but the scientific paper includes, is the fact that the production methods for histidine and tryptophan are incredibly similar, at least when it comes to the steps in which these genes are involved. As a result, many bacteria (such as those from the genus Streptomyces and the genus Mycobacteria) do it with only one gene. So in the end, there are “specialist” genes and “generalist” genes involved in the production of these two amino acids. Some bacteria (like normal Salmonella enterica) use specialist versions of the genes, and as a result, they require both genes. Other bacteria (such as those from the genus Streptomyces and the genus Mycobacteria) use a generalist gene, and as a result, they don’t need two genes. The generalist gene has all the information necessary to produce both amino acids.

So what does the experiment really show us? It shows us how generalist genes become specialist genes. Most likely, the original bacterial genome had a generalist gene involved in the production of both amino acids. However, over time, some species of bacteria experienced gene duplication and subsequent mutation that turned the generalist gene into two specialist genes, each devoted to making a separate amino acid. However, when the Salmonella enterica used in the experiment were deprived of their tryptophan-making gene, mutations were able to “revert” the histidine-making gene to a poor version of its original, generalist form. Gene duplication and subsequent mutation could then develop either two specialist genes again or one really good generalist gene.

So the experiment tells us something very valuable. It tells us that bacteria probably started out as generalists when it came to making these two amino acids, but over time, gene duplication and subsequent mutation produced several species that became specialists. When those bacteria are deprived of one specialist gene, the right mutations can revert the other specialist gene back to its generalist form, and the process can then start over again. Thus, while this study tells us nothing about new information being added to a genome, it does tell us something about how bacteria have changed over time.

It also shows how desperate evolutionists are to find a method that will produce real innovation in a genome. In the end, they call it an “innovation” when a bacterium reverts to old information! This reminds me of an event that happened a few years ago in Dr. Richard Lenski’s long-term bacterial evolution experiment. Even though that experiment confirms the creationist view of the genome, his team tried to spin it as an experiment that supports the evolutionary view of the genome. They said that bacteria which were unable to metabolize citrate in the presence of oxygen were eventually able to evolve the ability to do so.2 This, they claimed, was an example of a brand new trait emerging as a result of evolution.

However, Dr. Michael Behe pointed out that the bacteria in question always had the ability to metabolize citrate, but the ability was restricted to environments where there was no oxygen. As a result, Dr. Behe suggested that the most likely way this “new ability” evolved was by the destruction of a regulatory sequence that restricted the process to situations without oxygen. When that regulatory sequence was destroyed, the bacteria could suddenly metabolize citrate in all environments. Thus, this “new trait” was really the result of a loss of information in the genome.3 Subsequent genetic analysis of the bacteria involved demonstrated that Behe was correct.

So in the end, we see that mutation, gene duplication, and natural selection can “tinker” with information that is already in the genome, but so far, there is no evidence that they can produce brand new information.


1. Joakim Näsvall, Lei Sun, John R. Roth, and Dan I. Andersson, “Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence,” Science 338:384-387, 2012.
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2. Blount Z. D., Borland C. Z., and Lenski R., “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli,” Proceedings of the National Academy of Sciences USA 105:7899–7906, 2008.
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3. Michael J. Behe, “Experimental Evolution, Loss-Of-Function Mutations, and The ‘First Rule of Adaptive Evolution’,” The Quarterly Review of Biology, 85(4):419-445, 2010.
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19 thoughts on “Desperately Seeking Innovation”

    1. I did enjoy it, Shevrae. Thanks for posting it! I think the best phrase was, “He writes up a release, under the impression that he is Arthur C. Clarke.”

  1. That is pure speculation about what happened outside of the experiment. And not just outside the experiment, but in a different genus. For your guess to even be plausible, you’d have to either show an ancestor species of Salmonella that used one gene to produce both enzymes or show that a common ancestor of two geni (?) did so.

    But let’s assume you can show that. Can you show that the genes that “lost” the information retained it for later use? Where? How? Otherwise, then maybe some information was lost, but it was rediscovered anew again later.

    The experiment showed a population of bacteria that couldn’t do something at the beginning, and could do that thing at the end. The paper is remarkable because it shows exactly how it happened. The experiment preserved every generation within the experiment. And from this data, the paper proposes a model of how genes acquire new abilities.

    Are “specialist” and “generalist” genes established concepts or is it just a metaphor?

    1. Mia, I understand that you don’t like what a serious analysis of the paper reveals, but you can’t argue with it by dismissing it as “speculation.” The fact is that we know a single gene can catalyze both steps, and we also know that gene duplication leads to more genes. Thus, when you have two genes that each do what one gene can do, it is clear which gene came first…

      You don’t seem to understand the evolutionary process very well. Genes don’t “lose” information when they stop using it. There were two mutations that led to the HisA being able to make tryptophan poorly. The first mutation was a copy: three codons (codons 13-15 to be precise) from the gene were copied. Thus, the gene simply copied information that it already had, and when that duplicate information was added to the gene, it made the production of tryptophan possible. However, at that point, it lost the ability to make histidine. Did that mean the gene lost all histidine-related information? Of course not. A single amino acid substitution brought the ability back. Thus, the information to make histidine hadn’t been lost. It had simply been “covered up” by the addition of three codons, so it had to be “uncovered” by a second mutation.

      So the information wasn’t “lost” and then “rediscovered.” The original, generalist gene had the information of codons 13-15 in it twice. In addition, it had the proper amino acid to allow for histidine production. However, as one copy of the gene began to specialize, the the duplicated information was deleted. That stopped the production of tryptophan. Then, later on, the amino acid was shifted, probably because without the duplicated information, that made the enzyme better at making histidine. When the bacteria were stressed, duplicating the information in codons 13-15 allowed for tryptophan production again, and then the amino acid substitution allowed for histidine production. So this is clearly simply a reversion back to the more generalist state found in other bacteria.

      I agree that the paper showed a population of bacteria that couldn’t do something at the beginning and could do that thing at the end. However, it doesn’t show a gene acquiring a new ability. It shows a gene reverting to an old state in which the ability existed. That’s the importance of the paper.

      The terms “specialist” and “generalist” genes are not terms that I have read in the literature. However, the fact that mutations can lead to increased gene specificity is well understood in the literature. A gene that increases the specificity of the protein it produces is what I call a “specialist” gene. A gene that produces a protein with low specificity is what I call a “generalist” gene.

  2. Mia, for the sake of argument, lets postulate that new Information has been created from random processes.

    =—> The problem is that evolution has to have happened _everywhere,_ in _all_ instances of [C]reation, in _every_ form of Life throughout _all_ history. <—=

    Why is something _that_ "prevalent" this elusive in the laboratory?

  3. “It shows a gene reverting to an old state in which the ability existed.” Please cite the place in the paper where it says that. This is your MO, I’ve found. You give your interpretation of papers, thinking that it is valid science for you to look at the raw “data” and come to conclusions that the experimenters do not. It is not valid. Which is why I called the statement quoted above speculation. That is what it is. If you think the conclusion of the paper isn’t correct, why don’t you write a letter to the editor of the journal. I’m sure everyone involved would like to correct any errors that were made.

    1. Mia, I think you might be a bit confused about what scientists do. They look at data and then interpret the data to see what it means. So yes, it is my MO to give my interpretation of papers, because that’s what a scientist does.

      It seems your major concern is that my interpretation of the data is different from that of the authors. Once again, however, that’s how science is done. Often, a scientist (or a group of scientists) will collect data and write a paper on what they think it means. However, other scientists will look at the paper and see that the authors’ interpretation is wrong. That’s how science progresses.

      As I told you before, the data tell us exactly what happened: In many bacteria, there is one gene that can catalyze both reactions. In some bacteria, there are two genes, each of which catalyze a single reaction. Since the paper itself shows how gene duplication leads to specialization, it is clear that the one gene was duplicated in some bacteria, and through mutation and amplification, it became two genes, each of which specialized in a particular reaction. When one of those genes was removed, the other gene reverted to its original form so that both reactions could be catalyzed again. Indeed, we know exactly how that reversion took place, and no new information was generated.

      I think your major source of confusion lies in your idea that a new ability means new information in a genome. As both this study and the Lenski study I cited in my post indicate, that’s not a reasonable conclusion. As was the case in the Lenski experiment, a new trait came as the result of a loss of information. In this paper, a new trait came as a result of a reversion to a previous state. In both cases, no new information was generated. This has always been the sticking point for evolution. Try as they might, evolutionists simply cannot show new information being generated in a genome.

  4. W Nelson, the experiment lasted for 3,000 generations. The ecosystem was entirely controlled by the experimenters. They made a single small change to the enviroment and caused a single small genetic change in the bacteria, a very simple life form.

    Since bacteria, like more complex life such as humans, use genes for instructions on how to do things, to extrapolate to more complex life forms you just need more time. And if one genetic change can produce a new ability, many genetic changes can produce many different abilities.

  5. You are ignoring an important point about science. Peer review. First, you are not a peer. A nuclear chemist would never be asked to review this paper. Second, your rejection of the paper’s conclusions needs to be subject to review as well. So, please share your speculation with the editors of Science and see if they think your take has any merit.

    1. Mia, I think you are still confused on at least two points. Let me help clear up your confusion:

      (1) You seem to think that I am rejecting the paper’s conclusion. I am not. Nowhere in the paper is it even suggested that new information has been added to the genome of the bacterium. Indeed, the term “information” doesn’t appear anywhere in the paper. The authors are simply testing the innovation-amplification-divergence model. As they say:

      “We propose the innovation-amplification-divergence (IAD) model (Fig. 1A), which allows the evolution of new genes to be completed under continuous selection that favors maintenance of the functional duplicate copies and divergence of the extra copy from the parental allele (5).”

      They then conclude:

      “Thus, under suitable selective conditions, the IAD process rapidly generates genes with distinct enzymatic activities.”

      So all they are saying is that when a new generalist gene appears, duplication and amplification can turn it into two (perhaps more) specialist genes. I am not arguing against their conclusion at all. Indeed, I am using that conclusion to explain to you that no new information has been added to the genome.

      (2) You also seem confused about peer review and what its purpose is. In scientific journals, peer review is used to check the original research to make sure there are no overlooked errors in it. You are certainly correct that I would never be called on to peer review a paper like this. When I do peer review, it is in my area of speciality, as that’s where I can spot errors which might have been overlooked by the authors. Once the paper has passed peer review, it is then published in the scientific literature, and that’s when scientists who are not specialists can be at least somewhat confident of the results presented. If we nonspecialists then have a new or different interpretation of the results, it doesn’t go through peer review. Instead, we make our interpretation available to the general scientific community, and we see if it gains any traction. As a result, even if I were to write a letter to the editor, it would not undergo any kind of peer review. The editor might choose to publish the letter, or the editor might not. Of course, since I am not disputing any aspect of the paper, I don’t see why I would write such a letter. Even if I were disputing some aspect of the paper, I see little value in such letters, as their readership is rather low. Thus, while I have published a lot of original research in the scientific literature and have done peer review in my area of speciality, I have never written a single letter to the editor of a scientific journal.

      I hope I have helped clear up your confusion on these two issues.

  6. No it hasn’t. You are just introducing more confusions of your own. In this case, semantic confusion. While you claim that you aren’t arguing against their rightly narrow conclusion from their experiment, they would say that your further conclusion is not supported by their experiment. If they knew the way YECs use the term “information”, they would certainly say your conclusion is wrong. They would say “distinct enzymatic activities” satisfy what you call “new information.”

    2. “If we nonspecialists then have a new or different interpretation of the results, it doesn’t go through peer review. Instead, we make our interpretation available to the general scientific community, and we see if it gains any traction.” Non specialists with new or different interpretation of the results are not engaged in the scientific process. They are making unfounded speculations. You are not making your interpretation available to the general scientific community, you are publishing it on your YEC blog. And again, your interpretation is not valid. If it were, I would expect someone qualified to challenge the conclusion to either object in writing, reproduce the experiment themselves, or publish another experiment with evidence either against their conclusion or that supports a different one. Has that ever happened with any of the scores of blog posts where you offer your own interpretation beyond the conclusion of a paper?

    Bigger point, isn’t it amazing that ALL of the interpretations you offer on this blog all support YEC? I mean, there must be some papers that address Darwinian evolution or even contradict YEC that would not be amenable to your interpretations. Have you ever written about any of them? Can you tell me what you think the best evidence for evolution is? There must be some, right? Given that the overwhelming consensus of biologists is common descent with modification, you’d think there was a least some evidence for it.

    1. Mia, I am sorry that you are still confused. I think part of the problem is that you haven’t read the paper, so you don’t really know what its focus or conclusion really is. You now say that their conclusion is “rightly narrow.” I agree. The problem is that you originally said their conclusion was that new information was added to a genome. Clearly, that isn’t anything close to their “rightly narrow” conclusion. So which is it? Do they think that information was added to the genome, or is their conclusion “rightly narrow?” Also, given that you haven’t read the paper, I find it rather hard to believe that you can predict the authors’ reactions to the way young-earth creationists use the term “information” or their reaction to my analysis of their paper.

      You claim that nonspecialists are making “unfounded speculations” when it comes to interpreting the results of experiments. I suspect that this misunderstanding comes from the fact that you are unfamiliar with the scientific process. Nonspecialists often make incredible contributions to the advancement of science specifically by offering new interpretations of studies produced by specialists. Let’s start with an example from history. Ernest Rutherford was a professor of physics. However, what did he win the Nobel prize in? He won the Nobel prize for chemistry. According to your judgement, any interpretations he made on chemistry experiments would be “unfounded speculations.” Yet he won the Nobel prize in that area

      Let’s look at another example from more modern times. Dr. Jerry Manning is an internationally-recognized expert in the field of microbiology. Until his recent retirement, he was a professor of biology at the University of California Irvine, and he had a vigorous research program in molecular biology and parasitology. What was his degree in? Physical chemistry. What was his initial research in? Physical chemistry. How did he become a recognized expert in microbiology? Because as a nonspecialist, he had some ideas about sequencing genes based on some papers he had read. Those “unfounded speculations,” as you call them, revolutionized the field of microbiology.

      Let’s end with an example that is more close to home. While I was cleaning platinum to be used in a nuclear chemistry experiment, I ran across an interesting effect: a heated strip of platinum would glow when put in a flame, but it would stop glowing the moment it was taken out of the flame. However, if the still-warm strip was quickly put over alcohol, it would start glowing again! As a Ph.D. chemist, I had my interpretation of why this happened. When I was lecturing to a group of high school students, I used this effect as a demonstration and then gave my interpretation. Afterwards, one of the students came up and told me that my interpretation was wrong. In the end, she convinced me that it was. So I hired her over the summer to figure out what the proper interpretation was. She was able to figure out the proper interpretation, and we ended up writing a paper about it, with her as first author. I am thrilled that this nonspecialist was willing to engage in “unfounded speculations,” because she ended up being right, and she ended up advancing our knowledge of a chemical process.

      You also claim that I am not making my conclusions available to the scientific community. Of course I am. My blog is available to everyone, and many of my readers are scientists. Thus, the scientific community does have access to my conclusions. Perhaps what bothers you is that I do make my conclusions available to everyone in an easy-to-understand, logical way. Somehow, this seems to threaten you.

      You ask whether or not any of my blog posts have shaped further research. I have no idea. I have only been blogging for a few years. However, I can say that I receive correspondences from scientists who are doing original research, and they often reference my blog positively. In addition, some of the commenters on this blog are scientists who are doing research, and their comments indicate that they find the blog helpful. Also, I receive correspondences from students in both university and graduate school who are studying various scientific fields, and they say they appreciate my blog. Thus, I think this blog will help to shape scientific research, at least in the years to come. I certainly hope that is the case.

      No, it’s not at all amazing that the interpretations I offer support the young-earth creationist view. One would expect most serious research to support the correct view of nature. You ask whether or not I have written about papers that address Darwinian evolution and do not support the young-earth creationist view. The answer is yes, of course. I write about science, and not all science supports the correct viewpoint, because science can be flawed. For example, not long ago, I wrote about feathered dinosaurs. Obviously, I think the conclusion of the paper is flawed, as do others. However, my conclusion was:

      Is this debate over? Certainly not. However, I think that at this point, there are two “take-home messages.” First, when you read about “feathered dinosaurs,” remember that their existence is very much an open question. There are many experts who claim that they existed. There are other equally-qualified experts who say there is no strong evidence for their existence. Based on my non-expert reading of the literature, it seems to me that those who say there is no strong evidence for feathered dinosaurs have the best arguments. Second, whenever you see a “reconstruction” of a fossil, take it with a grain of salt. Even when reconstructions (such as the one given above) are based on evidence, it is often later shown that the evidence used is incorrect.

      You ask about evidence for common descent with modification. Of course there is evidence for such an idea. I find that evidence to be very weak, however, and I find the evidence for the young-earth creationist view to be much more convincing. However, since this is my blog, I tend to write about what interests me.

      In your second comment, you ask for my interpretation of several papers on genomic adaptation. I have not read them yet, so I have no interpretation of them at this time. If I find any of them interesting, they will find their way to my blog. However, I find it odd that you ask for my interpretation. I thought that I was making “unfounded speculations” when I offered such interpretations. Why would you be interested in more “unfounded speculations?”

  7. Dr. Wile,

    I admire your patience in answering Mia! You’re so skilled at finding and pointing out errors clearly, and considerately. I hope to be able to this in future! I’ve already found myself getting sidetracked when I converse, and missing errors in logic…I guess this improves with experience?

    I wonder that Mia continued to post repeatedly, and even that she would read the blog in the first place with her (blinded?) attitude. However, it made for an informative read!

    Thanks again for the great article and patience comments!

    1. I am glad that the exchange has benefited you, Inazuma. Yes, the ability to converse productively with those who disagree with you does improve with experience. It also improves the more knowledgeable you are in the area being discussed. This is why I read the works of many people with whom I disagree. I am more interested in learning about a subject than pushing a specific agenda.

  8. Politeness is great, but it doesn’t make anything said politely right.

    “One would expect most serious research to support the correct view of nature.” Most serious research supports common descent with modification. Actually, all serious research supports it, but there is no way you can claim “most serious research” supports YEC. That’s laughable. Again, you are assuming that your interpretations are the correct view of nature. Who made you the arbiter? Can you site anyone that has agreed with your interpretations? There are scientists who read this blog I’m told, maybe one of them wrote a concurring comment at some point.

    You surely claim that YEC can accommodate both feathered and non feathered dinosaurs. It’s not like Noah said whether the dinosaurs on the ark had feathers or not.

    What is the best evidence for common descent with modification? If you are intellectually honest, you should be able to present the opposing case without mangling it.

    1. Mia, I agree that being polite doesn’t mean your views are correct. However, I have noticed that those who cannot defend their position with evidence are much more likely to hurl insults than are those who can defend their position with evidence.

      You claim, “Most serious research supports common descent with modification. Actually, all serious research supports it…” As this blog (and many, many other scientific resources) indicates, that is simply not true. In fact, most serious scientific research supports young-earth creationism. You might call this position “laughable,” but it is heavily supported by the evidence. You might consider evidence to be “laughable,” but I don’t. Also, if my statement is so “laughable,” why does it bother you so much? I know of all sorts of laughable positions out there, and they don’t bother me at all.

      You ask, “Who made you the arbiter?” No one did, but then again, I never claimed to be “the arbiter.” I just make science accessible to a lot of people. That doesn’t make me an “arbiter.” It makes me a science educator.

      You ask, “Can you site [sic] anyone that has agreed with your interpretations?” Of course. For example, the scientists at agree with me enough that they carry my books. In addition, Dr. Alan Gillen wrote a book called The Genesis of Germs. He references me in the book, and lists me in the acknowledgements because he thinks I helped him so much with it. However, it is important to note that even those who do not agree with me appreciate what I write. For example, geologist Kevin Nelstead doesn’t agree with my YEC views, but he appreciates this blog and often comments on it – sometimes positively, sometimes negatively. In addition, evolutionary biologist Dr. Douglas Hayworth has commented on this blog positively. In the end, people who are serious about science are interested in reading various views of the data.

      I think you need to look into the feathered dinosaurs issue a bit more, because you seem rather confused on that point as well. If you read the article I linked, you will see that the current view of feathered dinosaurs is not consistent with the YEC view. According to the article, the “fuzz” found on certain dinosaur fossils is supposed to be “protofeathers,” and they are supposed to show how dinosaurs evolved feathers so that they eventually became birds. This is, of course, completely inconsistent with the YEC viewpoint.

      I was hoping that the link to my discussion of feathered dinosaurs would make you take a serious look at this blog. I am sorry that it didn’t. I have already discussed what I consider the best evidence for common descent with modification on this blog. It’s the “shared mistakes” in pseudogenes argument. As my discussion indicates, I don’t find the argument persuasive.

  9. I for one read the many scientific perspectives from evolutionary, creation science and intelligent design sources in order to weigh up the evidence(s) to arrive at my own conclusions.

    Dr Wile’s I am very grateful for the time and effort you put into your work. Your blog is a wonderful resource.

    1. Jason, I think that’s the best way to arrive at reasonable conclusions. I am glad that my blog is a help to you in your endeavor!

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