Science & Nature Archive

Friday, June 16, 2017

Evolution in Action - Visualizing Bacteria Evolving Antibiotic Resistance

e. coliNot too long ago, I came across a question on Quora, Evolutionary biologists usually say that organisms adapt to their environment. Does this not contradict Darwinism?. It seemed like a good opportunity to explain how natural selection adapts organisms to their environments, and especially to use a recent experiment involving e. coli. Here's what I wrote, with some very minor edits.

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I'm going to assume that by 'Darwinism', you mean natural selection. Organisms adapting to their environments is pretty much textbook natural selection, but let's go through an example to see what this means.

There was a very interesting experiment/demonstration last year involving bacteria and antibiotics. A team of researchers from Harvard Medical School and Technion - Israel Institute of Technology made in effect a giant petri dish - a rectangle 2 ft x 4 ft. The unique aspect of this petri dish, besides its size, was that it was divided into regions with varying concentrations of an antibiotic. Either end of the rectangle was free of antibiotic. The next region in had the minimum concentration to kill the e. coli bacteria that were the subject of the experiment. Each subsequent region moving in increased the concentration ten fold, until the center region, which had a concentration 1000 times higher than what would normally kill e. coli.

e. coli experiment setup
Image Source: Screen Capture from Video Shown Below
(Click to embiggen)


So, the researchers seeded the antibiotic free ends with e. coli, and then let them grow, taking periodic photos of the petri dish, and combinging them all into a time lapse movie. I'd really recommend watching the whole thing. It's really very interesting, with more explanation than what I've provided here, and only 2 minutes long.


So, let's take a closer look at one instant to see what exactly is going on. At one point, the tray looked like this:

e. coli experiment screenshot 1
Image Source: Screen Capture from Video Shown Above
(Click to embiggen)


So, the antibiotic free ends are completely colonized by bacteria. The two regions with the lowest concentration of antibiotic have just begun to be colonized. There are several small resistant colonies, and you can see where each one of those colonies got their starts. What happened was that the original e. coli, with no antibiotic resistance spread across the agar until they hit the antibiotic. Since they weren't resistant, that was as far as they could go without dying. But those e. coli kept on living and reproducing, with mutations appearing throughout the population. In bacteria that just happened to be at the boundary of the antibiotic, who also happened to acquire just the right mutations to make them resistant to the antibiotic, they now had a whole new environment opened up to them and their descendants.

Notice that there's really no pattern to where those colonies got their starts. It was basically random, because mutations are random. No bacteria were trying to evolve. No bacteria were attempting to figure out a strategy to survive the antibiotic. Bacteria don't even have brains to try to do any of that. It was just whatever bacteria happened to be lucky enough to acquire the appropriate mutations by chance, an error at the chemical level when copying DNA.

Once those first resistant bacteria entered this new region, they spread. Then, once they hit the region with 10x the antibiotic concentration, they were contained again, until a few more bacteria happened to acquire the proper mutations by luck, and had a new environment opened up to them and their descendants. This repeated, until the bacteria were eventually colonizing the region with 1000x the concentration of antibiotic that would have killed the original e. coli that seeded the plate:

e. coli experiment screenshot 2
Image Source: Screen Capture from Video Shown Above
(Click to embiggen)


So, these e. coli were adapting to their environment. However, it wasn't any conscious intent, or Lamarckian type of use and disuse. It was random mutations creating variation in the e. coli populations. Whichever e. coli happened to be lucky enough to have mutations to survive the antibiotic were the ones that thrived. Any e. coli that weren't lucky enough to have those mutations were limited to their existing environments.

This experiment had a pretty strong selection pressure with the antibiotic, but the same principles are at work in nature with other selection pressures. Whatever individuals happen to be lucky enough to acquire by chance the mutations best suited to an environment will be the ones that have the most offspring, increasing the frequency of whatever mutation that benefited them. Multiply this over generations, with natural selection 'ratcheting' additional mutations, so that the population becomes better and better suited to the environment. That is what is meant by saying that organisms adapt to their environment.

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More info on the e. coli experiment:

Image source: Wikimedia Commons

Wednesday, April 5, 2017

How Bad are Unpronouncable Chemical Ingredients in Food?

I ran across a new line of frozen lunches the other day, SmartMade by SmartOnes. One of the key selling points on the box is 'Made with real ingredients you can pronounce'. This seems to be a common attitude among people who don't understand chemistry as well as they could. But how bad for you are foods made up of all these strange sounding chemicals?

For example, here are the ingredients to a treat I eat nearly every weekend:

Ingredients for Weekend Treat


And here are the ingredients to an energy drink I drink nearly every day:

Ingredients for Energy Drink


Should I be worried about all those chemicals?

.
.
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Okay, it was a trick question. I cropped those images to hide what types of food they were. Here are the original, uncropped images, made by James Kennedy, showing what the foods were (click to go to source):

Egg Ingredients


Coffee Ingredients


Mr. Kennedy has a whole series of these types of images (as well as posters of them for download and for sale).

The whole point is that everything we eat is made up of chemicals. Living things, especially, are this whole complicated cocktail of chemicals. And most of those chemical names sound very foreign to those of us who don't study them on a regular basis. But that doesn't make them dangerous.

When certain chemicals are added to processed foods, it's done in a very controlled way. Instead of the cocktail of chemicals you get from natural foods, they're adding very specific ingredients, in tightly controlled quantities. There's nothing inherently dangerous about not being able to pronounce those chemicals, unless you think we should be avoiding eggs because they contain arginine and eicosatetraenoic acid.

Tuesday, March 28, 2017

Recommended Reading - Evolution

Tree of LifeI write quite a bit about evolution, but if you're new to this site or the subject of evolution, it might be a little overwhelming to just browse through the site and read the articles at random. So, this page offers some recommendations on entries to start off with, to give you a good foundation before moving on. I very strongly recommend reading the first four essays in the Foundation section. And if you happen to doubt evolution for religious reasons, and have seen presentations or read material from some of the more prominent creationists (e.g. Answers in Genesis, Kent Hovind, Discovery Institute, etc.), then I'd also recommended the entries from the 'Responses to Misunderstandings and Creationist Arguments' section.


The Foundation


Exploring Other Evolutionary Concepts


Responses to Misunderstandings and Creationist Arguments

The first two of these are probably the most informative. They're also rather long. I took the time to respond in decent detail to a myriad of misunderstandings and misconceptions about evolution. The third is offered as a kind of example of the bad arguments many creationists use.


Further Reading, This Site

I've written quite a bit more about evolution and creationism. You can find most of it in the following archives.

  • Science & Nature Archive
    Evolution will be mixed in here along with a variety of other science topics. These entries tend to be more straight science.
     
  • Skepticism, Religion Archive
    These tend to be focused on skepticism, so the evolution related articles mixed in here will be more in response to creationists.
     
  • My Quora Profile
    Okay, this isn't exactly this site, but I do write a bit about evolution on Quora, and only adapt some of those answers for this blog. Evolution related answers will be mixed in with all my other Quor answers.
     


Further Reading, Other Sources

I'm actually going to link to a Quora answer I wrote with those types of sources. You can also see what others suggested.

Image Source: DavidPratt.info

Monday, March 27, 2017

Understanding Evolution - The Basics

I discuss evolution enough on this blog that I figured I ought to do a post covering the basics. Just what is evolution, and how does it work? I'm going to try to focus mainly on describing what evolution is, but since there are so many misconceptions out there, a little bit of this post is going to be clarifying what evolution isn't. I'll admit up front that this explanation is a little animal-centric, even though evolution occurs in all types of life.


Defining Evolution and Understanding DNA

DNA MoleculeAt the most basic, evolution is change in a population over time. But to understand that change, first you need to understand where it comes from.

In a way, our cells and bodies are run by our DNA and genes. DNA is a long, chain-like chemical in almost all of our cells. Along the length of that chain are special sections called genes, that act like templates for making various chemicals that our cells will use. You can think of our DNA and genes somewhat like a set of instructions for how the cells will work. If A happens, do B. If C happens, do D. And on and on. It's all of these instructions interacting together that make our cells work the way they do, and then all of our cells interacting together to make our bodies work the way they do. This even affects the way we grow up and mature. There may be some genes that work together to tell certain cells to become muscles, and other cells to grow bones, and other cells to become nerves.

By and large, whatever DNA we're born with is the DNA we'll have our whole lives. But, sometimes our cells make mistakes in copying the DNA. These mistakes are called mutations, and can change the instructions of our DNA. Mutations can be harmful, beneficial, or not even really do all that much and be neutral. Some of the most harmful mutations that can occur in our bodies lead to cancer. But most of those mutations don't affect evolution, because they only affect their owner's body, not their children. The only mutations that affect evolution are the ones that can be passed on to the next generation, the ones that occur in the specific cells that are going to come together to make a new baby - eggs and sperm. If mutations happen to either eggs or sperm, then the babies will have a slightly different set of instructions than their parents.

None of us pick and choose our DNA, or how we want it to change. We can't will ourselves to be taller, or for our children to be taller. And we can't change our DNA through actions. For example, when we go to the gym to work out, we'll get better cardiovascular health and bigger muscles, but we won't change any of our DNA having to do with muscles or health, and we certainly won't change any of the DNA in our eggs or sperm that way. So, no matter how much we work out, our children are going to get basically the same heart and muscle controlling DNA as we have. They'll start off with the same potential as we did, and if they want to be healthy and get big muscles, they'll have to go to the gym and do the work themselves.

When these changes to our DNA happen, they simply happen by chance. Like I already said, you can't pick the mutations. Your children can't pick the mutations. There's no invisible hand controlling the mutations. They're simply mistakes made at the chemical level, when cells don't quite make a perfect copy of the DNA. And we all have a handful of these mutations. Various studies (example) have found that people have anywhere from 60 to 200 of these mistakes. Thankfully, most of them are neutral and don't have much effect. And considering that we have around 20,000 genes, even 200 mistakes is a pretty small effect percentage-wise.

But, since there have been all these copying errors being made throughout all of history, it means that there are a lot of different versions of genes out there. I have a few genes different from yours. And you have a few genes different from your friends. Everybody has a slightly different set of all these different versions of genes. If you were to add up all the different variations of genes everybody has, you could figure out what percentage of the population had each variation. If you did that tally again in a hundred years, you might find that things had shifted a bit. If you kept on doing this tally, you could trace these shifts. You might even find some variations of genes disappearing completely, and some being so beneficial that they spread to everyone. That's evolution:

Evolution is the changes in the DNA of populations over time.

Here's how an actual evolutionary biologist, Douglas Futuyma, put it in the textbook he wrote on evolution:

Biological evolution ... is change in the properties of populations of organisms that transcend the lifetime of a single individual. The ontogeny of an individual is not considered evolution; individual organisms do not evolve. The changes in populations that are considered evolutionary are those that are inheritable via the genetic material from one generation to the next. Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportion of different alleles [variations of genes] within a population (such as those determining blood types) to the successive alterations that led from the earliest protoorganism to snails, bees, giraffes, and dandelions.


Natural Selection

One of the main drivers of evolution is natural selection (though not the only one). As discussed above, when organisms reproduce, they don't produce perfect clones of themselves. There are almost always slight differences. On top of that, for various reasons, not all of an organism's offspring are going to grow up to reproduce themselves. We're kind of insulated from this in modern society, but just think about the nature documentaries you watch where a sea turtle will go and lay 100 eggs in one nest. If all of those babies survived to go on and have their own babies, with all the new females laying 100 eggs per nest, and all their babies doing the same thing, it wouldn't take long before the world was overrun by sea turtles. But, many species of sea turtles are actually endangered, so we know that's not happening. The vast, vast majority of those baby sea turtles won't make it. They'll be eaten by predators, hit by speed boats, killed by disease, or somehow be felled by any of the multitude of dangers out there.

That's where these differences become important. Whatever slight differences happen to be beneficial will make their owners more likely to survive and reproduce. Any differences that happen to be harmful will make their owners less likely to reproduce, maybe even causing them to die before they get the chance. This is natural selection. It's not a conscious entity. Nobody is picking and choosing which mutations are going to become more common. It's just the way things work, the inevitable result of having variation among offspring, and producing more offspring than will reproduce themselves. So, the raw material comes from mutation, while natural selection acts like a filter, passing through beneficial mutations, and weeding out the harmful ones.

Let's look at a hypothetical example, and let's start off simple. Here's a hypothetical family tree, starting with two original parents up at the top, and going down through the generations. This is exaggerated compared to most traits in real life. Evolution is a gradual process, and you won't normally see things changing this rapidly, but this is just an example to illustrate concepts

Evolution Conceptual Family Tree - Single Lineage

So, let's just assume that for whatever reason, being darker is better in their environment. Our first two parents are light colored, but they somehow managed to survive and have children. Notice that their children have variation in their color. Some children are lighter, and some are darker. But remember that mutations are random, with no intentional change in any direction. So, because darker organisms do better in this hypothetical environment, the darker children are the ones that survive, find mates, and have children of their own, while the lighter children aren't so lucky, and don't have children to pass on their lighter coloration. Each generation is like this. Children are similar in color to the parents, with a little bit of variation, with some children being slightly lighter, and some slightly darker. It's the children who were lucky enough to have the beneficial traits that go on to have their own children.

And whether or not mutations are beneficial or harmful depends on the environment. There's a textbook example on this with the peppered moth. This is a type of moth from England. It's typical coloration was light with dark speckles - peppered. It was a very good camouflage on tree bark. Then, in the 1800s, the Industrial Revolution swept through England, and pollution became so bad that trees got a coating of soot making them black. So, the white and black speckles of the peppered moth were no longer good camouflage. Well, a mutation occurred that made some moths solid black - much better camouflage on the dirty trees. And that mutation swept through the population, until nearly all of the moths were solid black. Once people started paying more attention to pollution and putting scrubbers on smokestacks and other methods to reduce pollution, the soot started disappearing from the trees, and the black moths weren't as well camouflaged, anymore. And now, the speckled moths have become much more common. There's nothing inherently better about a moth being black or being speckled - it all depends on the environment the moth is in.

Peppered Moths
Black and Speckled Peppered Moths on a Tree (Image Source: Wikipedia)


It's All About Populations

Remember, evolution is all about populations. That's important, and one of the more common misconceptions, so let me repeat it a few times. Evolution is not about individuals. Individuals don't evolve. Evolution deals with populations. Populations evolve.

So, here's a more complicated family tree. It's not just one lineage, but a whole hypothetical population (albeit a very small one).

Evolution Conceptual Family Tree - Population

If you take the time to trace each lineage, you'll see a similar pattern to the simpler diagram up above. Each time two organisms mated and had children, their children were similar in shade to the parents, but with slight variation. And it was the individuals that were lucky enough to be born darker that were the ones that survived.

You also notice that the entire population is shifting together, gradually. The second generation doesn't look that much different than the first. And the third doesn't look that much different from the second. Each generation is similar to the previous generation, and similar to all the other organisms in its own generation, and similar to the following generation. There is never a sudden jump from light to dark. There is never a single organism that's completely new and different from it's parents. Yet, the final generation is substantially different from the first generation.

That's how evolution really works, but even more gradually. Organisms are always part of a population. They will have a few different variations of genes, but they'll always be similar to their parents, and the other members of their populations, and their offspring will also be similar. It's only over the course of generations that you'll notice the changes to the population.


Speciation

So, if evolution is always about populations, and populations change together, how did life branch out the way it has? Why are there separate species? How do species form?

Well, like most everything else in evolution, speciation isn't sudden, either. It's a gradual process. The first step is that somehow, a single population must be split into two isolated populations. This is often a geographic barrier, such as sea level rise forming a new sea, tectonic activity pushing up a new mountain range, a new canyon forming, grasslands giving way to forests or vice versa, or anything else that could split a population in two. Once this happens, there are now two independent populations. Let's take a look at another diagram.

Speciation Concept Diagram

If you were to 'zoom in' on that diagram, you'd see a whole bunch of individuals, mating with each other and having children, much like the diagram from the previous section. But that starts to get complicated and confusing, so just keep in mind that these are still populations of individuals interbreeding with each other.

Before the split, there was a single population. New mutations were popping up, but because the whole population was interbreeding together, all these new mutations were getting mixed throughout the population, and individuals in each generation were very similar to all the other organisms in their own generation. So, they had no problems finding mates and continuing that interbreeding.

Then, after whatever occurred to cause the split, new mutations kept appearing in each population, but the populations are now isolated. Mutations still get mixed throughout the smaller populations, but not between the two separate populations. These differences accumulate over time, and if the populations are isolated for long enough, they will build up enough different mutations that they're no longer similar enough to each other to breed. Even if the two populations came back in contact again, they'd be new species, and individuals from one population wouldn't be able to mate with individuals from the other population.

And if this repeats over, and over, and over, you'll eventually end up with a whole, complicated tree. Here's one more diagram, but with a slight twist. All the previous diagrams had the oldest generations at the top, and moved down through younger generations. That's the way it's normally shown in genealogy, but that's not the way it's normally shown in discussions on evolution. So, here's a diagram showing this type of family tree, with the oldest ancestors at the bottom, and the youngest descendants at the top.

Evolutionary Family Tree
Image Sources: David Peters Studios with some editing on my part

With all these different lineages, they can each 'experiment' in their own direction. And if their environments happen to be different, then different mutations will be favored in different lineages. For example, one lineage might favor a particular food source. One might live in a cold environment, while another might live in balmier conditions. Some might face different predators. Some might have less access to fresh water. Etc. Etc. All these differences will accumulate over the generations in all the different lineages, leading to a great variety of adaptations.


Summary

Evolution is all about populations. Specifically, it's the changes in the DNA of populations over time. Mutations are the raw material for evolution. They're random, with no conscious intent over what they'll be. And an organism's actions in life won't have any effect on the 'direction' of the mutations. Offspring will be imperfect copies of their parents, with the variation being random. Natural selection acts like a filter, passing through beneficial mutations, while weeding out the harmful ones, which over time can cause certain genes or variations of genes to become widespread. If a single population becomes split, the new populations will no longer be able to mix up any new mutations with each other, and after enough time, they will have accumulated enough different mutations that they'll no longer be able to interbreed - they will have become two different species.

Take all these phenomena, and multiply them over the millions and millions of years that life has existed on this planet, and they have produced the astonishing complexity and variety of life all around us.

DNA Image Source: Wikimedia Commons, with editing by me.
Note: All uncredited images are original artwork by me.

Wednesday, March 22, 2017

Understanding Evolution - Development of Eyes

Well, I just had an answer 'disappeared' on Quora. Since I kind of liked it, I'm going to repost it here, to make sure it's still easy to find. I made a few minor edits, plus added a whole brand new figure to help with the explanation. Here is my answer to the question of:

If evolution is true, why aren't there millions of creatures out there with partially developed features and organs?
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To give one concrete example, let's take a look at eyes:

Mollusc Eyes
(Image Source: StephenJayGould.org - futuyma_eye.gif)

None of those eyes are hypothetical. Every single one is a diagram of an eye from an existing, living organism, all of them snails, actually, and every single one of those eyes is beneficial to its owner. And each one of those organisms is the end result of all the evolution leading up to it.

So, let's look at that first eye. It's the simplest. It's basically a light sensitive cup. Even if it doesn't let its owner form an image, it still lets those snails detect light, and the direction the light is coming from. Many, many millions of years ago, an eye very much like that was the most advanced eye that any snail possessed. But, evolution is a branching pattern. Once a population splits into two species that can no longer interbreed, there's no more sharing of genetic mutations or adaptations between the species.

So, that ancient species of snail with that cup type eye split into two species, and those split into more, and those split into more. In at least one of those lineages, by chance, the mutations appeared that made the eye more closely resemble that second eye in the diagram above. But all of its cousins species still had the simpler cup type eye. And all those cousin species with the simpler cup type eyes were still doing a good enough job of surviving and reproducing in their own niches, so they still survived. The new species with the 'better' eye probably had advantages in certain niches, especially those that required being more active, and so probably did pretty well for itself, and proliferated into its own group of species with those 'better' eyes.

Well, a similar process repeated again. At least one lineage in that new group got the mutations to make an eye with even better imaging capabilities. Its cousins with the type 2 eye still had their own niches where they survived, as did its even more distant cousins with the type 1 eye. And this repeated over and over again, until you ended up with the existing variety of snails we have today, with eyes ranging from that very simple cup eye to 'camera' eyes with lenses.

Here's a hypothetical, and overly simple, family tree of how this might have happened (you can do searches for snail phylogenetic trees to find some real ones). Imagine that the colors represent snails with a certain type of eye. Black is the original cup type eye. Blue is the type 2 eye. Red is the type 3 eye. And on through green, magenta, and cyan. Note how once a lineage evolves an eye, it's the only lineage with that eye*. For example, once the type 2 eye evolved in a single species of snail, only descendants of that species had type 2 eyes, because they were the only ones that could inherit it. It couldn't share that trait with its cousins. Also, snails with the original type 1 cup type eyes didn't all of a sudden all go extinct, and continued to evolve in their own lineages.

Hypothetical Snail Family Tree
Hypothetical Overly-Simple Snail Family Tree
Image Sources: David Peters Studios and StephenJayGould.org, with some editing on my part

And keep in mind, eyes are only one feature of snails. The living snails with the cup type eyes have still been evolving since that ancient ancestor, and have changed in other ways. They just haven't acquired the mutations that would have changed their eyes. Or more precisely, they just haven't acquired mutations to make their eyes better at resolving images. They may still have had other mutations affecting their eyes, such as light sensitivity.

So, do the existing snails with cup type eyes have a 'partially developed' organ? Well, I guess in one sense they do, because we know that an ancient animal with a similar type of eye eventually gave rise to descendants with a more complex camera type eye. But it's not 'partially developed' in the same sense as a half built bridge that can't ferry traffic. It's a perfectly functional eye that serves a purpose and is beneficial to the snail. And there's no guarantee that any of its future descendants will necessarily develop any of the more advanced eyes.

That's how it is with every organism and every feature on the organism. As long as we manage to escape extinction, we will all evolve in the future, from us humans to ants to dandelions (as populations - individuals don't evolve). Some of our existing features and organs will change. So, with the benefit of hindsight, those future organisms (at least the ones smart enough to be thinking about evolution) will be able to look back to how we are now, and recognize which of our now existing organs were only 'partially developed'.

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*Saying that common traits never appear in separate lineages is actually a little bit of an oversimplification. For traits that are more likely to evolve, they may evolve more than once in more than one lineage, in a process known as convergent evolution. However, the traits will have evolved independently, since separate lineages can't share DNA**. Additionally, the genetic basis will almost always be different, since it was separate mutations in the separate lineages that led to a similar structure. And the traits themselves may only be superficially similar. As a good example relevant to this essay, us vertebrates have also evolved camera type eyes. But, as you would expect given that we evolved them independently, the similarities are only superficial, and there are some very fundamental differences between our eyes and mollusc eyes.

**Okay, that's a little bit of an oversimplification, as well, but horizontal gene transfer is exceedingly rare in multicellular organisms.

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For a slightly different perspective, to quote my summary from another answer, "evolution doesn't have foresight or a plan. For that matter, it's not a conscious entity at all, even if anthropomorphizing sometimes helps to explain it. Evolution only works through small incremental changes, and each of the changes has to be beneficial if the organisms are going to survive and pass those changes on to future generations. Every organism alive, past and present, is in a sense the end result of all the evolutionary history leading up to it. But in another sense, as long as they don't go extinct, evolution never stops, so every organism is also a transitional form to whatever its descendants might be."

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For the full story of what happened to my Quora answer, it wasn't anything malicious - it was the result of Quora's policy of merging similar questions. I had already answered one question, If theory of evolution is true, why aren't there more semi-evolved species with hands coming out of their skulls or other half-baked monstrosities?, and even adapted it to an entry on this site, Understanding Evolution - Origin of Limbs. Well, someone went and asked a similar question, If evolution is true, why aren't there millions of creatures out there with partially developed features and organs?. I wrote up an answer, looking at it a little differently than I had the first time. When someone noticed that both questions were similar, they merged the questions. Since Quora's policy is to only have one answer per user per question, when the questions were merged, they took my most popular answer and kept that. So, my newer answer more or less disappeared, and is basically only available by direct link or through my profile.

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