Tag Archives: Darwinian Evolution

Video, audio and summary of intelligent design discussion, with Ben Shapiro and Stephen C. Meyer

Stephen C. Meyer and Ben Shapiro discuss evolution and intelligent design
Stephen C. Meyer and Ben Shapiro discuss evolution and intelligent design

This is a must-see / must-hear conversation. Famous conservative Ben Shapiro discusses evolution and intelligent design with Dr. Stephen C. Meyer, author of “Signature in the Cell” (origin of life) and “Darwin’s Doubt” (fossil record). These are the two best books on intelligent design. Their conversation covers the most important issues in the origins debate.

So to start, here’s the full video:

And here is a link to the audio. You can download the MP3 there.

Someone actually put out an outline on Youtube, with a time-based index, so I’ll just steal that as a base, and add to it:

  • 1:34 What is your scientific background? Science undergraduate degree, professional geologist, later did a PhD in philosophy of science from Cambridge University.
  • 2:39 What is the difference between intelligent design and creationism? Creationism starts from the Bible and posits a shorter history of the universe. ID starts from the data of the natural world and is neutral about the age of the Earth / universe. Meyer accepts the old-Earth.
  • 3:36 How is Intelligent Design a scientific theory? The discovery of DNA reveals that code is central to living systems. Intelligent design uses the method of “inference to the best explanation” in order to argue that the best explanation for the code is an intelligent agent.
  • 6:10 What evidence would have to arise to make Intelligent Design Falsifiable? If a naturalistic mechanism was discovered that could produce biological information using the probabilistic resources of the universe, and the time available, then intelligent design would be falsified.
  • 7:26 Is religion separate from science or intertwined within it? There are three views: science is totally separate from religion, science is in total conflict with religion, science and religion agree on some issues, e.g. – the origin of the universe and Genesis 1:1. There are areas where science and religion overlap.
  • 9:55 Why are the most prominent Darwinians also militant atheists? Evolution is a theory that tries to explain nature using naturalistic mechanisms, so it is compatible with atheism.
  • 10:45 What does the theory of evolution say? The term evolution has multiple meanings, and should be defined before discussions. It can refer to change over time. It can refer to animals changing slightly to adapt to enviromental changes. It can refer to the idea that all animals evolved from simpler life forms, and that there is a tree of life showing how different types of organisms share common ancestors. And it can refer to the idea that purely undirected processes can explain the history of life using purely materialistic forces. It’s that final view that intelligent design challenges.
  • 13:15 Where is the discontinuity in naturalistic processes in the development of life? The first discontinuity is the origin of simple life from non-living components. The second discontinuity is the sudden appearance of different body plans in a very narrow window of time in the Cambrian era.
  • 15:42 Why does information theory suggest that code requires some sort of designer? DNA is a true information-bearing system identical to the software in computers, e.g. – operating system, applications.
  • 19:45 Can information be created by random mutation, and favorable mutations preserved by natural selection? Just as in software code, instructions must be added in order to develop new functionality. Random additions of characters will almost always degrade biological function. The number of possible sequences that do nothing useful is vastly higher than the number of sequences that perform biological functions. Doug Axe did research on this at Cambridge University, and he found that the number of functional sequences of amino acids is 1 in 10 to the 77th power. Given the probabilistic resources (replicating organisms)and the time available, it is extremely unlikely to find sequences that have functional information by chance.
  • 25:05 What about Stephen Jay Gould’s model of punctuated equilibrium – doesn’t it explain the sudden jumps in information? Gould’s mechanism is accurate according to the fossil record, which shows a lot of jumps. But he did not have a naturalistic explanation for sudden jumps in biological function. Darwinian mechanisms work slowly and would (in theory) produce different body plans gradually. But this is not what the fossil record shows.
  • 27:22 What is the mechanism for injecting information in the theory of intelligent design? The information comes in from an intelligence when new major body plans appear, and minor variations within types could be explained by evolution.
  • 29:25 Does the Miller-Urey experiment provide a naturalistic explanation for the building blocks necessary for the origin of life? The MU experiment only produced a few types of amino acids, it doesn’t say anything about how to sequence the amino acids in order to form protein folds that can perform biological functions. The MU experiment also pre-supposes conditions on the early Earth (reducing gases) that do not match what was there (oxidyzing or neutral gases).
  • 32:00 Is the RNA world hypothesis is a good explanation for the origin of life? Evolution requires that replication already be in place, because evolution assumes that mutations appear during the replication. The RNA world hypothesis suggests that sequences contain information, but also catalyze origin of life chemistry. The problem with RNA world is that it starts with self-replicating systems. And those replicating systems require the scientist to inject information into the system to get even the simplest replication started.
  • 34:56 How do scientists respond to the critiques of Darwinism proposed by intelligent design advocates? By and large, they accept them. They think that mutation and selection works once living systems are in place, but they realize it has no explanation for the origin of life or the sudden origin of body plans. (Tells about the  conference of the Royal Society, where problems with Darwinian mechanisms were discussed, and the 2003 MIT Press book by Muller and Newman).
  • 37:16 Why do people hold to Darwinian evolution in the face of these problems? Many scientists presuppose methodological naturalism, which requires that any explanation for the origin of life and the origin of major body plans involve materialist explanations only. No intelligent agents are allowed. The problems occur when assumption of naturalism causes scientists to propose incorrect explanations for what we observe in nature. It’s also not clear how naturalistic mechanisms could produce organisms who are capable of reason and free will.
  • 40:43 Does naturalistic evolution have an answer for conscious minds, reasoning, free will? No, consider the work of atheist scholar Thomas Nagel, who argues in his book “Mind and Cosmos” (Oxford University Press 2012) that the existence of mind is a disproof of the neo-Darwinian explanation for life. Darwinism stops us from accepting the reality of minds.
  • 42:06 So do naturalistic evolutionists have to explain away the mind as an illusion? First, we humans have immediate experience of consciousness, reason and free will. Second, our whole legal system is based on the idea free will, because you can’t hold someone guilty unless they chose to do something they knew was wrong. Third, we have an epidemic of suicide among young people. This is caused by a crisis of meaning. Intelligent design opens up the possibility of their being a mind behind the universe, who we could have a relationships with.
  • 44:53 Why aren’t schools allowed to be honest about the problems with neo-Darwinian evolution? The intellignt design view is to that teachers should be allowed to teach all the vidence for Darwinian evolution, and also discuss some of the problems with the theory. Students learning science should not be told that everything is solved. Students learn science better when they are presented with peer-reviewed evidence for and against a theory, rather than being indoctrinated.
  • 47:37 Is intelligent design theory connected to God? Intelligent design infers from the information content in nature that a mind with capabilities like ours injected information into living systems. Intelligent design is agnostic about the designer, because in principle, embodied or unembodied agents could inject information into living systems. Intelligent design is friendly to theism, because theists will immediately identify the mind as God. Furthermore, the fine-tuning in the initial conditions of the universe is another intelligent design argument. In that case, since the design occurs at the beginning of the universe, the intelligent agent acting prior to the creation of the universe would have to be supernatural, i.e. – God.
  • 50:53 Can naturalists say that the imposition of “function” on a sequence is arbitrary, in the same way that the English language is arbitrary? This won’t work, because biological function is not arbitrary in the same way as language. Biological function is not arbitrary, because sequences can be tested for function objectively by observing whether sequences can perform functions necessary for life, e.g. – replication.
  • 52:43 Doesn’t the multiverse explain away the improbabilities of the fine-tuning, the origin of life, and the development of life? No, because all models of the multiverse require fine-tuning in the mechanism that generates the different universes.
  • 55:42 What about cosmological models that eliminate the beginning of the universe? The standard Big Bang model and the inflationary model both posit a beginning of the universe. There is also the Borde-Guth-Vilenkin theory which proves that any universe that is expanding requires a beginning. The only chance for naturalists is quantum cosmologies, but this doesn’t work because 1) it requires an abstract reality of mathematics to actualize the physical universe, but this presupposes a mind. 2)  The model requires an earlier input of information, which can only have come from a mind.

If you listen to this lecture, or watch the video, and you enjoyed it, then please share. If you have questions, I can try to answer them for you – just leave your question in the comments, or shoot me an e-mail, or message me from the blog’s Facebook page, or direct message me on Twitter. I’ve invested a lot of time in this, and have been studying intelligent design since the late 1990s.

By the way, I listen to the Ben Shapiro podcast, (and the Andrew Klavan podcast), every day. I never miss an episode, and I think if you give them a try, you’ll enjoy them, too.

John C. Sanford’s genetic entropy hypothesis

Christianity and the progress of science
Christianity and the progress of science

JoeCoder sent me a recent peer-reviewed paper by John C. Sanford, so I’ve been trying to find something written by him at a layman’s level so I could understand what he is talking about.

Dr. Sanford’s CV is posted at the Cornell University web page.

I found this 20-minute video of an interview with him, in which he explains his thesis:

The most important part of that video is Sanford’s assertion that natural selection cannot remove deleterious mutations from a population faster than they arrive.

And I also found a review of a book that he wrote that explains his ideas at the layman level.

It says:

Dr. John Sanford is a plant geneticist and inventor who conducted research at Cornell University for more than 25 years. He is best known for significant contributions to the field of transgenic crops, including the invention of the biolistic process (“gene gun”).

[…]Sanford argues that, based upon modern scientific evidence and the calculations of population geneticists (who are almost exclusively evolutionists), mutations are occurring at an alarmingly high rate in our genome and that the vast majority of all mutations are either harmful or “nearly-neutral” (meaning a loss for the organism or having no discernible fitness gain). Importantly, Sanford also establishes the extreme rarity of any type of beneficial mutations in comparison with harmful or “nearly-neutral” mutations. Indeed, “beneficial” mutations are so exceedingly rare as to not contribute in any meaningful way. [NOTE: “Beneficial” mutations do not necessarily result from a gain in information, but instead, these changes predominantly involve a net loss of function to the organism, which is also not helpful to [Darwinism]; see Behe, 2010, pp. 419-445.] Sanford concludes that the frequency and generally harmful or neutral nature of mutations prevents them from being useful to any scheme of random evolution.

[…]In the next section of the book, Sanford examines natural selection and asks whether “nature” can “select” in favor of the exceedingly rare “beneficial” mutations and against the deleterious mutations. The concept of natural selection is generally that the organisms that are best adapted to their environment will survive and reproduce, while the less fit will not. Sanford points out that this may be the case with some organisms, but more commonly, selection involves chance and luck. But could this process select against harmful mutations and allow less harmful or even beneficial mutations to thrive? According to Sanford, there are significant challenges to this notion.

Stanford is a co-author of an academic book on these issues that has Dembski and Behe as co-authors.

Now, I do have to post something more complicated about this, which you can skip – it’s an abstract of a paper he co-authored from that book:

Most deleterious mutations have very slight effects on total fitness, and it has become clear that below a certain fitness effect threshold, such low-impact mutations fail to respond to natural selection. The existence of such a selection threshold suggests that many low-impact deleterious mutations should accumulate continuously, resulting in relentless erosion of genetic information. In this paper, we use numerical simulation to examine this problem of selection threshold.

The objective of this research was to investigate the effect of various biological factors individually and jointly on mutation accumulation in a model human population. For this purpose, we used a recently-developed, biologically-realistic numerical simulation program, Mendel’s Accountant. This program introduces new mutations into the population every generation and tracks each mutation through the processes of recombination, gamete formation, mating, and transmission to the new offspring. This method tracks which individuals survive to reproduce after selection, and records the transmission of each surviving mutation every generation. This allows a detailed mechanistic accounting of each mutation that enters and leaves the population over the course of many generations. We term this type of analysis genetic accounting.

Across all reasonable parameters settings, we observed that high impact mutations were selected away with very high efficiency, while very low impact mutations accumulated just as if there was no selection operating. There was always a large transitional zone, wherein mutations with intermediate fitness effects accumulated continuously, but at a lower rate than would occur in the absence of selection. To characterize the accumulation of mutations of different fitness effect we developed a new statistic, selection threshold (STd), which is an empirically determined value for a given population. A population’s selection threshold is defined as that fitness effect wherein deleterious mutations are accumulating at exactly half the rate expected in the absence of selection. This threshold is mid-way between entirely selectable, and entirely unselectable, mutation effects.

Our investigations reveal that under a very wide range of parameter values, selection thresholds for deleterious mutations are surprisingly high. Our analyses of the selection threshold problem indicate that given even modest levels of noise affecting either the genotype-phenotype relationship or the genotypic fitness-survival-reproduction relationship, accumulation of low-impact mutations continually degrades fitness, and this degradation is far more serious than has been previously acknowledged. Simulations based on recently published values for mutation rate and effect-distribution in humans show a steady decline in fitness that is not even halted by extremely intense selection pressure (12 offspring per female, 10 selectively removed). Indeed, we find that under most realistic circumstances, the large majority of harmful mutations are essentially unaffected by natural selection and continue to accumulate unhindered. This finding has major theoretical implications and raises the question, “What mechanism can preserve the many low-impact nucleotide positions that constitute most of the information within a genome?”

Now I have been told by JoeCoder that there are many critical responses to his hypothesis, most of which have to do with whether natural selection can overcome the difficulty he is laying out. But since this is not my area of expertise, there is not much I can say to adjudicate here. Take it for what it is.

Positive arguments for Christian theism

John C. Sanford’s genetic entropy hypothesis

Christianity and the progress of science
Christianity and the progress of science

JoeCoder sent me a recent peer-reviewed paper by John C. Sanford, so I’ve been trying to find something written by him at a layman’s level so I could understand what he is talking about.

Dr. Sanford’s CV is posted at the Cornell University web page.

I found this 20-minute video of an interview with him, in which he explains his thesis:

The most important part of that video is Sanford’s assertion that natural selection cannot remove deleterious mutations from a population faster than they arrive.

And I also found a review of a book that he wrote that explains his ideas at the layman level.

It says:

Dr. John Sanford is a plant geneticist and inventor who conducted research at Cornell University for more than 25 years. He is best known for significant contributions to the field of transgenic crops, including the invention of the biolistic process (“gene gun”).

[…]Sanford argues that, based upon modern scientific evidence and the calculations of population geneticists (who are almost exclusively evolutionists), mutations are occurring at an alarmingly high rate in our genome and that the vast majority of all mutations are either harmful or “nearly-neutral” (meaning a loss for the organism or having no discernible fitness gain). Importantly, Sanford also establishes the extreme rarity of any type of beneficial mutations in comparison with harmful or “nearly-neutral” mutations. Indeed, “beneficial” mutations are so exceedingly rare as to not contribute in any meaningful way. [NOTE: “Beneficial” mutations do not necessarily result from a gain in information, but instead, these changes predominantly involve a net loss of function to the organism, which is also not helpful to [Darwinism]; see Behe, 2010, pp. 419-445.] Sanford concludes that the frequency and generally harmful or neutral nature of mutations prevents them from being useful to any scheme of random evolution.

[…]In the next section of the book, Sanford examines natural selection and asks whether “nature” can “select” in favor of the exceedingly rare “beneficial” mutations and against the deleterious mutations. The concept of natural selection is generally that the organisms that are best adapted to their environment will survive and reproduce, while the less fit will not. Sanford points out that this may be the case with some organisms, but more commonly, selection involves chance and luck. But could this process select against harmful mutations and allow less harmful or even beneficial mutations to thrive? According to Sanford, there are significant challenges to this notion.

Stanford is a co-author of an academic book on these issues that has Dembski and Behe as co-authors.

Now, I do have to post something more complicated about this, which you can skip – it’s an abstract of a paper he co-authored from that book:

Most deleterious mutations have very slight effects on total fitness, and it has become clear that below a certain fitness effect threshold, such low-impact mutations fail to respond to natural selection. The existence of such a selection threshold suggests that many low-impact deleterious mutations should accumulate continuously, resulting in relentless erosion of genetic information. In this paper, we use numerical simulation to examine this problem of selection threshold.

The objective of this research was to investigate the effect of various biological factors individually and jointly on mutation accumulation in a model human population. For this purpose, we used a recently-developed, biologically-realistic numerical simulation program, Mendel’s Accountant. This program introduces new mutations into the population every generation and tracks each mutation through the processes of recombination, gamete formation, mating, and transmission to the new offspring. This method tracks which individuals survive to reproduce after selection, and records the transmission of each surviving mutation every generation. This allows a detailed mechanistic accounting of each mutation that enters and leaves the population over the course of many generations. We term this type of analysis genetic accounting.

Across all reasonable parameters settings, we observed that high impact mutations were selected away with very high efficiency, while very low impact mutations accumulated just as if there was no selection operating. There was always a large transitional zone, wherein mutations with intermediate fitness effects accumulated continuously, but at a lower rate than would occur in the absence of selection. To characterize the accumulation of mutations of different fitness effect we developed a new statistic, selection threshold (STd), which is an empirically determined value for a given population. A population’s selection threshold is defined as that fitness effect wherein deleterious mutations are accumulating at exactly half the rate expected in the absence of selection. This threshold is mid-way between entirely selectable, and entirely unselectable, mutation effects.

Our investigations reveal that under a very wide range of parameter values, selection thresholds for deleterious mutations are surprisingly high. Our analyses of the selection threshold problem indicate that given even modest levels of noise affecting either the genotype-phenotype relationship or the genotypic fitness-survival-reproduction relationship, accumulation of low-impact mutations continually degrades fitness, and this degradation is far more serious than has been previously acknowledged. Simulations based on recently published values for mutation rate and effect-distribution in humans show a steady decline in fitness that is not even halted by extremely intense selection pressure (12 offspring per female, 10 selectively removed). Indeed, we find that under most realistic circumstances, the large majority of harmful mutations are essentially unaffected by natural selection and continue to accumulate unhindered. This finding has major theoretical implications and raises the question, “What mechanism can preserve the many low-impact nucleotide positions that constitute most of the information within a genome?”

Now I have been told by JoeCoder that there are many critical responses to his hypothesis, most of which have to do with whether natural selection can overcome the difficulty he is laying out. But since this is not my area of expertise, there is not much I can say to adjudicate here. Take it for what it is.

Positive arguments for Christian theism

John C. Sanford’s genetic entropy hypothesis

Apologetics and the progress of science
Apologetics and the progress of science

JoeCoder sent me a recent peer-reviewed paper by John C. Sanford, so I’ve been trying to find something written by him at a layman’s level so I could understand what he is talking about. (I am just a software engineer, not an expert in genetics). His CV is posted at the Cornell University web page.

I found this 20-minute video of an interview with him, in which he explains his thesis:

The most important part of that video is Sanford’s assertion that natural selection cannot remove deleterious mutations from a population faster than they arrive.

And I also found a review of a book that he wrote that explains his ideas at the layman level.

It says:

Dr. John Sanford is a plant geneticist and inventor who conducted research at Cornell University for more than 25 years. He is best known for significant contributions to the field of transgenic crops, including the invention of the biolistic process (“gene gun”).

[…]Sanford argues that, based upon modern scientific evidence and the calculations of population geneticists (who are almost exclusively evolutionists), mutations are occurring at an alarmingly high rate in our genome and that the vast majority of all mutations are either harmful or “nearly-neutral” (meaning a loss for the organism or having no discernible fitness gain). Importantly, Sanford also establishes the extreme rarity of any type of beneficial mutations in comparison with harmful or “nearly-neutral” mutations. Indeed, “beneficial” mutations are so exceedingly rare as to not contribute in any meaningful way. [NOTE: “Beneficial” mutations do not necessarily result from a gain in information, but instead, these changes predominantly involve a net loss of function to the organism, which is also not helpful to [Darwinism]; see Behe, 2010, pp. 419-445.] Sanford concludes that the frequency and generally harmful or neutral nature of mutations prevents them from being useful to any scheme of random evolution.

[…]In the next section of the book, Sanford examines natural selection and asks whether “nature” can “select” in favor of the exceedingly rare “beneficial” mutations and against the deleterious mutations. The concept of natural selection is generally that the organisms that are best adapted to their environment will survive and reproduce, while the less fit will not. Sanford points out that this may be the case with some organisms, but more commonly, selection involves chance and luck. But could this process select against harmful mutations and allow less harmful or even beneficial mutations to thrive? According to Sanford, there are significant challenges to this notion.

Stanford is a co-author of an academic book on these issues that has Dembski and Behe as co-authors.

Now, I do have to post something more complicated about this, which you can skip – it’s an abstract of a paper he co-authored from that book:

Most deleterious mutations have very slight effects on total fitness, and it has become clear that below a certain fitness effect threshold, such low-impact mutations fail to respond to natural selection. The existence of such a selection threshold suggests that many low-impact deleterious mutations should accumulate continuously, resulting in relentless erosion of genetic information. In this paper, we use numerical simulation to examine this problem of selection threshold.

The objective of this research was to investigate the effect of various biological factors individually and jointly on mutation accumulation in a model human population. For this purpose, we used a recently-developed, biologically-realistic numerical simulation program, Mendel’s Accountant. This program introduces new mutations into the population every generation and tracks each mutation through the processes of recombination, gamete formation, mating, and transmission to the new offspring. This method tracks which individuals survive to reproduce after selection, and records the transmission of each surviving mutation every generation. This allows a detailed mechanistic accounting of each mutation that enters and leaves the population over the course of many generations. We term this type of analysis genetic accounting.

Across all reasonable parameters settings, we observed that high impact mutations were selected away with very high efficiency, while very low impact mutations accumulated just as if there was no selection operating. There was always a large transitional zone, wherein mutations with intermediate fitness effects accumulated continuously, but at a lower rate than would occur in the absence of selection. To characterize the accumulation of mutations of different fitness effect we developed a new statistic, selection threshold (STd), which is an empirically determined value for a given population. A population’s selection threshold is defined as that fitness effect wherein deleterious mutations are accumulating at exactly half the rate expected in the absence of selection. This threshold is mid-way between entirely selectable, and entirely unselectable, mutation effects.

Our investigations reveal that under a very wide range of parameter values, selection thresholds for deleterious mutations are surprisingly high. Our analyses of the selection threshold problem indicate that given even modest levels of noise affecting either the genotype-phenotype relationship or the genotypic fitness-survival-reproduction relationship, accumulation of low-impact mutations continually degrades fitness, and this degradation is far more serious than has been previously acknowledged. Simulations based on recently published values for mutation rate and effect-distribution in humans show a steady decline in fitness that is not even halted by extremely intense selection pressure (12 offspring per female, 10 selectively removed). Indeed, we find that under most realistic circumstances, the large majority of harmful mutations are essentially unaffected by natural selection and continue to accumulate unhindered. This finding has major theoretical implications and raises the question, “What mechanism can preserve the many low-impact nucleotide positions that constitute most of the information within a genome?”

If you think all this is interesting, there is a much longer lecture here, which I have not watched. JoeCoder has watched it and he endorses it.

Now I have been told by JoeCoder that there are many critical responses to his hypothesis, most of which have to do with whether natural selection can overcome the difficulty he is laying out. But since this is not my area of expertise, there is not much I can say to adjudicate here, I won’t be able to respond to these. I hope that I will have time to come back to this and read about it at some point. I do have an e-book of the that collection of papers book I linked to above.

Positive arguments for Christian theism

Is there a smooth pathway from micro-evolution to macro-evolution?

From Luke Nix who blogs at Faithful Thinkers.

Excerpt:

Macroevolutionary changes are a lot of microevolutionary changes, but they are in a specific series that follow a specific pathway. The missing premise in this argument is that the pathway from ancestor to claimed offspring (many generations down the road) is clear of obstacles.

In his book, “The Edge of Evolution” Michael Behe shows that scientists have observed such an obstacle in the lab. The obstacle was not time, it is in the genetic pathway that must be traversed if macroevolutionary changes are to take place in reality. Since an obstacle has been observed, we now have a false premise in the argument. Since there is a false premise, the argument fails. There is a difference between micro- and macro-evolutionary changes. A lot of microevolutionary changes are necessary for macroevolution, but they are not sufficient. The other sufficient condition (a clear genetic pathway) still has yet to be met. Since both sufficient conditions for macroevolution have not been met, it has not been demonstrated. And since changes over time has been demonstrated, there is a need to distinguish between the two. To prevent confusion about what we know to be true and what we don’t, this distinction must be made.

There is only one way that this can be overcome by the naturalist: find a pathway that would be clear by default in nature. Notice that I have added one more piece to the missing premise above: “…clear by default in nature“. I have to add that last qualification because as scientists are looking for a way to overcome this obstacle, they are introducing their own intelligence- fine-tuning the process, then “allowing nature to take its course”. Their conclusion of naturalistic macroevolution will depend on a premise that is founded on intelligence. That would undermine the whole argument for naturalistic (macro)evolution.

This is one of the ways to show that evolution is true – by showing a pathway to macro-evolutionary change in the lab. If people expect me to believe in the grandiose claims of fully naturalistic evolution through a stepwise process, then why can’t I see the pathway myself? If you make the claim that it happened, then I want to see the evidence for the claim.

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