Tag Archives: Basic Science

Apr20

Science Education – How I Would Do It.

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Science Education – How I Would Do It.


Of course, this is assuming that the world was a sensible place and I was in charge of all the important decision-making. Heh.

Over time, I’ve come to realize that a lot of the things I was taught in school didn’t stick because they weren’t interesting. They weren’t interesting because they were unrelated to my life, and I couldn’t see how they could possibly be important to me. I memorized things for tests, and I did a darn good job of it, good grades, good standardized test scores, but only because I had to, not because I wanted to.

As I got older some of it came back – and it stuck better because I had context to put it in. Before kids and before antidepressants, I read a lot of romance novels for escape (I know. . .I’m not proud, but I had an excuse.) Soon I discovered that there was a sub-genre of Historical Fiction – and some of these authors were real history buffs who included a lot of factual information. In the context of a story, with characters and plots that engaged me, I was finally learning something about history, which had bored me to tears in High School.

Later, I started reading some of the books and papers that had been assigned back then. . .suddenly they were interesting and made sense – because I now had a context for them. The context continued to expand, and more information became part of what I knew.

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For me, possibly moreso than for many people, context is essential. My ADHD mental filing system demands context and associations not only for learning, but for retrieving that learning. So when I teach people what I know, I teach it in context. I learn a lot by making mistakes, so I teach “do it this way because this other way doesn’t work,” and “we do it this way because otherwise we break this piece and the whole thing is ruined.” I teach “This part seems boring, but here are all the cool things we can do with it later.”

I also learned a lot from raising my own kids and volunteering in their schools, helping all kinds of other kids learn. You need to be able to express a single piece of information many different ways in order to get different kids to understand it. As a volunteer, I was able to sit with individual children and small groups. The kids who didn’t understand things when they were taught the same way to all 30-something students would get it if I spent some time with them and figured out what their individual contexts were.

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Fast forward to the mid 90s – I started antidepressants, and then I discovered that my ADHD had not actually gone away as the experts had told my parents it would, and as my parents told me it had. Now I had a reason to learn about the brain, starting with disorders and injuries, and what they taught us about the functions of various structures. That gave me a context to learn about brain development and genetics. This led to investigating epigenetics. Along the way, it also tied in to reading medical and science blogs and books, and any time a piece of knowledge stuck to something that was relevant to something I already knew, it also became relevant.

So why do you want to listen to someone who doesn’t have a degree in science or medicine when it comes to science or medicine? Because of the way I’m learning it. That whole “Translating Science into English” thing I mentioned a few posts back. Scientists have their own language, and it’s important that they do so they speak with clarity and precision. But if you don’t have the context that they do, it’s hard to understand – and easy to misinterpret. I didn’t learn this in the linear fashion that they did.

If you were to teach me vocabulary and facts and mechanisms, I’d remember it just as well as I did in high school. But give me a study of something that relates to something that interests me, and I will look up all those words and facts and mechanisms, and they’ll make sense because they’re part of something else. They have more meaning when they’re in context.

The other thing I learned came from watching scientists argue with one another. While they’re not always polite, they always present evidence. Most of them are critical thinkers, when someone says something that is questionable, they will (sometimes very methodically and in great detail) explain the flaws in the reasoning. Following along with this taught me the scientific method and why it’s important, how to evaluate how robust the data is by looking at the size of the study, the quality of the blinding, the strength of the variables and controls, how well it integrates existing evidence (and how strong that evidence is) and, most importantly, no matter how good a study may be, it’s never PROOF. It also doesn’t prove other things that weren’t part of the study. It’s also probably not a major breakthrough.

I learned about p-values, journal impact factors, the good and bad of peer review, the pros and cons of open access. I learned that not all “evidence” is actually evidence.

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The problem that many, many scientists have, though, is that they forget what it’s like to not know this. Sometimes they present what they know in a way that is off-putting to laypeople. Sometimes they present a press-release version of their findings, breathless with excitement and full of hyperbole, and that’s even worse. (That’s what we have The Daily Mail and Huffington Post for. Let them do their job.)

So if I were a science teacher, or I were designing a science education program, I’d throw out teaching the basics as freestanding facts. Get rid of the rote learning. Give the students just enough information to dive into a challenge and figure out the rest. Give the kindergarteners a bowl of cream and some food coloring and dish soap – let them play and then tell them how it works. Let the older kids listen to each others’ heartbeats, check each others’ blood pressure, draw pictures of hearts and veins and arteries, and use that to introduce the circulatory system. Make everything part of an experiment that related directly to them so that it was important. Let them figure out what’s correct and what’s incorrect as much as you can on their own by giving them questions as much as answers. Make the science interesting and integrate critical thinking into the lessons, and get them excited. This will be good for them, and good for society, because they’ll question everything – and come up with their answers based on what evidence is best supported.

Apr15

Epigenetics Made Easy, Part 2

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Epigenetics Made Easy, Part 2

Let’s reiterate from the previous post, just in case you need a recap:

All cells are made from other cells; we start with a few that are the same, and as the number of cells increases, they begin to differentiate and become cells for specific body parts.

DNA is the blueprint for the final product (a sexually mature adult human being, for illustration purposes.) RNA is a segment of DNA that begins the process of cell differentiation, but the mechanism that actually creates the proteins that build cells is the epigenetic process, which depends upon histones interpreting the genetic instructions.

Once we are full grown, our bodies are almost always replacing cells rather than making new ones, and the new cells may not be exact duplicates of the cells that created them.

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histone modification

Yes, there is such a thing as histone modification. Yes, gene expression (in the form of cells that follow specific genetic instructions) can be changed during the epigenetic process. Yes, it’s possible for some of these changes to become heritable (passed on from parent to offspring.) But let me explain what’s reasonable and rational about these possibilities.

Histone Modification

You’ve heard of this, but usually in the form of “you can change your DNA by doing this thing or eating that thing” which is, essentially, not true. Histone modification takes place on a cellular level, and changes in different ways depending on what the chemicals that can modify histones are doing. I’ll save the technical terms and illustrations for another time. Baby steps.

What happens is that while a cell is preparing to replicate itself, a chemical can make the histones do something differently from the way they were instructed, and that makes the resulting copied cell different from the cell that created it. Right now, we have some very specific examples of changes that depend on specific chemical exposures (some from external environment, some from internal environment.) DNA is huge. We have a hundred trillion or so cells in our bodies. The genome is almost infinitely diverse. There are very few examples right now of direct cause and effect, and each one we discover in the future will be just as limited.

The number of possibilities alone makes it pure speculation to assume that a food given to a pregnant mouse that changes her babies’ fur color and body shape is going to do the same thing for a fully-grown adult, or even something similar!

Now the add another layer of complexity, these are the things that can happen when you modify the histones in a cell:

*a beneficial gene is suppressed
*a detrimental gene is suppressed
*a beneficial gene is activated
*a detrimental gene is activated

So if someone claims that a food or something “methylates” your genes (besides being wrong) it could easily be a bad thing!

Changing Gene Expression

I mentioned the prenatal modification above, and that’s because it’s an important thing to study. Why? Because in order for histone modification to have any observable and verifiable effect, it needs to happen early. Think about it. If you modify the histones of a four or eight celled creature, then a lot more cells are going to be made not according to plans. In an adult, modifying a single cell, or even a few cells, out of all the cells in our bodies, is going to have minimal impact. In order to change gene expression in an adult, exposure needs to be intense enough or prolonged enough to influence a large number of cells.

I like to use the example of skin, partly because it’s a cell type that’s replaced frequently, and partly because we can see a lot of the possible changes to it. It’s a good way to illustrate that an environmental factor can produce a change that does not alter gene expression, and how the level of exposure can make a difference in whether an epigenetic change is even possible.

If you go out into the sun, your skin changes color. It could get burned, it could get tanned. But when those darker skin cells make their replacements and die, the replacements are your original skin color. You have exposed yourself to an environmental factor that has an obvious effect on your body, but it doesn’t change your gene expression. Why? Because the exposure was not prolonged enough that the visible change was messing around with histones while the replacement cell was being created.

On the other hand, if you’re out in the sun all the time so that your skin is constantly in a damaged state, then those cells are more likely to be in that damaged state when they’re replicating themselves. This could still even be temporary, but it could change gene expression so that the replacement cells are cancerous, for example. (Cancer is epigenetic – but it could be caused by environment *or* part of the plan all along.) So you need to expose the same group of cells to the same environmental factor for long enough that most of the cells begin reproducing with the alteration in gene expression. . .and that is not guaranteed to be a good thing, so don’t buy into the hype.

Heritability of Epigenetic Changes

Yep, this has been studied, too, and it does sometimes happen. The most repeatable changes happen when the fathers’ bodies have changed. I credit that to the fact that sperm are constantly being made, and things like stress hormones or chemical exposures, or starvation, can change what genes go into what chromosomes in the sperm cells at that time. Give the dads some time to recover, you get a completely different result.

Keep in mind that the normal set of instructions is the default. If you look at plants or other animals who’ve been genetically altered, a lot of times you’ll find that their offspring regress to the original, dominant form. In both human and animal studies, most of the epigenetic changes that were brought about by environmental exposure get passed down to the next generation, maybe the generation after that, and in a few cases, the third generation. Then things go back to normal.

I probably missed a few things, but I hope this is clear. Ask me stuff, tell me stuff. Thanks!

Apr15

Epigenetics Made Easy.

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Epigenetics Made Easy.

Tightly wrapped histones

No, not really. That’s a misleading title, but my hope here is that I can explain this in terms that are simple enough for people who aren’t scientists to understand. I’m hoping that because I’m not a professional scientist but am really, really into this stuff, the language and illustrations I use serve as a bridge for the gap in understanding.

So let’s start with the cell, and let’s use humans as an example. Even though epigenetics happens in every living thing, even plants, I want you to be able to identify personally with this so the information takes hold a little better. What do we know about genetics and conception and fetal development? Well, we start off with an assortment of genes and 46 chromosomes. We got all of them from our parents and grandparents and so on down the line, but it’s a mix between Mom’s side and Dad’s side, because her eggs start off with a random selection of 23 chromosomes (see my previous post about what random means) and his sperm also start off with a random selection of matching chromosomes.

Sperm meets egg, and there you go, 46 chromosomes in a single cell, and a complete, unique strand of DNA that has all the information needed to build a human body.

If you’ve watched videos of human development, you’ve seen how that one cell splits into two, two into four, four into eight, and then things really start to happen. In the beginning, each of those cells is exactly the same. Each time they split, they’re making another cell that’s just like they are. Remember this, because I’m going to mention it again later. . . Here’s how it looks, in case you haven’t actually seen it, in a video on in-vitro fertilization:

After this point, the cells begin to differentiate. Instead of simply reproducing copies of themselves, they start to become more specialized. They still contain all the DNA, but some of the instructions will be used, and some will be silenced. This starts with the transcription from DNA to RNA. What we used to believe (or at least what I was taught in school days in ancient times) was that the RNA was the sole messenger, containing only the information needed to make cells. That’s only kind of sort of true, and doesn’t explain a lot of confusing things that happen to human bodies. You see, it is part of the picture in cell differentiation, which is, to put it in simple terms, the process that makes one cell be a bone cell and another be a heart cell and another be a brain cell and so on. The RNA puts this in process by taking the pieces of the DNA that are needed to make a specific call and creating the proteins that manufacture that cell. With these instructions, cells continue to divide, but they’re not just making carbon copies of themselves.

We see this in fetal development because parts of the body from the brain, the eyes, the internal organs, to the fingers and toes, go from being kind of blobby and alien-looking, to functional and human-like. The manufacturing of differentiated cells continues throughout fetal development, and the differentiation is pretty much complete by the time a baby is born.

But there’s a piece missing – we know that RNA has instructions for making the proteins that manufacture differentiated cells, but it doesn’t make those proteins all by itself. This is where epigenetics comes in. The actual work of taking the orders from the RNA and making the proteins is done by histones. The DNA has the construction diagrams, the RNA is barking orders, the histones are doing the work.

This is still happening inside a cell. The cells are still dividing. It’s just that this epigenetic process is making two different cells out of one cell instead of two identical cells. The new cells aren’t coming out of nowhere, they’re coming from existing cells that are multiplying.

As we get older, we tend to go back to more of a model of cell replication. A cell duplicates itself, then dies after the new cell has been made. The epigenetic process takes place then, as well. Sometimes the cells won’t necessarily die, because we’re growing and need more cells. That’s done epigenetically, too, because the blueprint from the DNA says what the final adult product is supposed to be like, not just the infant version. As we get really older, the cells are trying to replace themselves, but they don’t do quite as good a job, and that’s an epigenetic process as well, because the instructions are getting messed up *after* the RNA. The histones just aren’t doing such a great job after a while.

The point here is that epigenetics is part of the process of cell development that is already written out in the DNA. The way it works without interference is genetic and heritable, and every single one of the many trillions of cells in your body was created the same way. The DNA has the plans, the RNA is the subcontractor, the histones are giving the orders to the proteins based on the instructions from the higher-ups.

Keep this in mind when you hear things about the amazing effects of environment on epigenetics. Yes, this is the part where things can get screwed up, because, yes, histones can be modified. But I’m going to save that for later, because this is a lot to absorb. I hope this makes sense, and if anyone has questions or corrections, please comment – I want to hear from you.