What science is all about -- some thoughts

What is science all about? 
A. Let's start by defining terms. This is what the Free Dictionary says about science (1st meaning only):
1. a. The observation, identification, description, experimental investigation, and theoretical explanation of phenomena.

b. Such activities restricted to a class of natural phenomena.

c. Such activities applied to an object of inquiry or study.

I will restrict myself to meaning 1a, actually. How does science differ from three other honorable enterprises, namely the study of history, performing music, or working as a check-out person in a grocery store?
The study of history usually can't involve experimental investigation. You can't see what would have happened if George Washington hadn't crossed the Delaware, for example. You can guess, and your guess may be right, but you can't know. But you can experiment in science. You can find out what happens if someone takes their medicine every other day, rather than every day.
Music performance doesn't involve much identification (in that you are classifying something, such as rock types or species of grasses) and description, nor theoretical explanation. It may involve experimentation, though.
Grocery checkout persons don't do much identification, either, except what's already done for them in the bar codes on items. They may experiment, however, for example by smiling at some customers and not at others, but the amount of experimentation is limited. If they start only charging for every other container of milk to compare it with customer satisfaction, or giving more change that the customer is supposed to get, they'll get fired.

B. The controlled, replicable experiment, then, is one of the cornerstones of much science. Granted, even scientists can't experiment on everything. Historical geologists can't manipulate history any more than history professors can. Astronomers can't manipulate stars or galaxies. Where direct experiment isn't possible, most scientists may compare experiments, as it were, that nature has already provided. For example, how does the light from different stars, in different regions of the universe, compare?

A controlled experiment is one wherein, ideally, one property, and only one, is varied between groups, and everything else is the same. For example, you might test inbred fruit flies, all in the same environment, giving one a vitamin supplement, and one no such supplement, and compare their fertility. (It is usually impossible to make the environment absolutely identical for every organism, or for different attempts at the same experiment. Even inbred strains may have a little genetic variation.)

Replicable means that someone else can test what you have done, by trying the same experiment.

I understand that there is debate about how science really works, but I'm going to ignore it. See the Wikipedia article on "Science" for an introduction to this.

C. Science is clearly important. Think of social media, energy use, and ballistic missiles. The products of science, often called technology, are also important.

The previous sentence mentioned three important topics. None of them is a strictly scientific topic. All of them have legal, political, ethical, economic and even religious implications. That's true of most or all of the technological products of scientific work. If a scientist, for example, says that she is opposed to allowing illegal immigrants to get driver's licenses, or that human embryos can ethically be destroyed in the process of stem cell research, what she says on one of those subjects should carry no more weight than what a grocery clerk says, unless she is a legislator, in addition to being a scientist.

Sometimes scientists think that they are making scientific statements, but they aren't. They are merely scientists making statements, not making statements that are backed up by controlled, replicated, experiments. Watson and Crick, for example, claimed that they had discovered the secret of life, when they proposed the double helix. They had made an important contribution, but they hadn't discovered the secret of life. They hadn't explained how DNA came to be so central to living things in the first place. They hadn't given an explanation for how the information in DNA comes to be expressed (we now know a lot more about that, partly because of the work of Crick, himself.) Both of them, apparently, thought that they had ruled out any supernatural explanation for living things. But they hadn't. God could have created life with DNA as its main information carrier. I don't believe any experiment can rule that out (or prove it.) Hebrews 11:3 says "By faith, we understand that the universe has been framed by the word of God, so that what is seen has not been made out of things which are visible." God could have somehow written His signature in DNA, or in rock layers or clouds, or in astronomical objects, but He didn't. Or did He? The believer can and does see God's handiwork in all of these. The non-believer doesn't. We can choose to believe, or not to believe.

D. I don't want to leave the impression that science gets a better and better picture of how nature works only by doing experiments. As Thomas S. Kuhn pointed out, scientists get such a changed picture by new ways of looking at the world -- adopting a new paradigm. What experiments scientists do is determined by how they view the natural world. Galileo wouldn't have done any experiments on radio, because he didn't know there was such a thing. Newton didn't discover gravity. But he did (perhaps after watching an apple fall) realize that gravity could be explained as an attractive force. This wasn't because of any experiment that he did. The experiments came later.

This is a re-post, slightly modified, from a post of mine on December 11, 2006. Thanks for reading.

Using light to control single brain cells (and thanks to a gene from algae)

Wired has posted an amazing report on how it is possible to control a single neuron in a mouse brain, by zapping it with light. The reason this works is because researchers have also inserted a gene for light sensitivity into the mouse, so the mouse is a mouse-algal hybrid. (Not really -- it's a mouse with one algal gene.) You've got to have a means of getting the light to trigger a single neuron, of course.

This is potentially of great importance, because drugs and electrical stimulation tend to be messy -- affect more than one neuron, or even lots of them. This is an invasive technique, but so are some others that we take for granted. It seems possible to do a great deal of good with this, perhaps curing, say, Parkinson's. In fact, the researchers are working on Parkinson-like mice. It's also possible, of course, that a great deal of harm might be done, but the same thing was, and is, true of techniques less high-tech, such as surgery.

Thanks for reading.

Did Pasteur disprove spontaneous generation?

Louis Pasteur is often celebrated as the scientist who disproved spontaneous generation. Did he?

First, it is necessary to determine what is meant by spontaneous generation.

The Free Dictionary says:
spontaneous generation

The supposed development of living organisms from nonliving matter, as maggots from rotting meat. The theory of spontaneous generation for larger organisms was easily shown to be false, but the theory was not fully discredited until the mid-19th century with the demonstration of the existence and reproduction of microorganisms, most notably by Louis Pasteur. Also called abiogenesis.

Merriam-Webster, however, does not give a definition for spontaneous generation, but links from a search for it to abiogenesis, which is defined as follows:
the supposed spontaneous origination of living organisms directly from lifeless matter . . .

There is some disagreement, then, about the very term, spontaneous generation. For the purposes of this post, spontaneous generation and abiogenesis are the same thing.

Spontaneous generation was studied by Pasteur, in the 19th century. If it actually happened, living things would just appear, as opposed to coming from pre-existing living things. Supposed examples of spontaneous generation included the appearance of thin worms, called horsehair worms, in horse drinking troughs. Some people believed that they spontaneously generated from horse hair, fallen into the water. Another supposed example was the appearance of mold and bacteria on food.

Pasteur's research, showing that, under some conditions, it was possible to prevent the invasion, by microorganisms, of environments that would have been conducive to their growth, led to the eventual rejection of spontaneous generation by scientists, and was important in establishing the germ theory of disease. An egg, or a small worm, must have gotten into the horse trough. A spore, or an airborne bacterium, must have gotten into the spoiled food. Infectious disease must have come from exposure.

The most important case of abiogenesis would have been the appearance of the first living things.

Did Pasteur disprove spontaneous generation? Not exactly. He did contribute to the downfall of the idea, but, in the sense that he ruled out all possible spontaneous generation by experiment, he didn't.

What do I mean? Suppose you asked me to prove that witches can't fly. I would try to find someone who is supposed to be a witch, and throw her off a high building. Surely, under such conditions, a witch would fly. (Let us not worry about petty details such as my murders of reputed witches.)

After, say, a hundred such experiments, in which flight was never observed, have I proved that witches can't fly? Well, no. In the first place, how can I be sure that my hundred women were, indeed, witches? Perhaps they were just people that someone else wanted to get rid of, so the someone else's contacted me, giving me false information.

Or, as is well known, witches need a broom to fly. If I threw my witches off a building with no broom, no wonder they didn't fly. Or, if I did, I wasn't giving them the right type of broom. Or, if I did give them the right type of broom, the buildings were somehow such that witches can't fly off of them, for example if the building was blessed during construction. Or, a skeptic could say, witches can only fly on certain days, and certain hours, and I didn't perform my experiments at the right time. Or certain rituals must be performed before flight is possible, and the rituals weren't performed, or were performed in the presence of a skeptic, which makes them invalid.

I have not, and can not, rule out the possibility that witches really can fly, if the moon is in the right phase, and all other conditions are correct. I have simply not tried the experiment under the proper conditions. However, I can still doubt that witches can fly, and my experiments may convince other people of the same thing.

In a similar way, it is impossible to prove, by experiment, that spontaneous generation can't occur. It is always possible to argue, for example, that it occurred, 8 kilometers under the surface of Iceland, on February 29, 2000, when the moon was in the right position. How can I show, by experiment, that it didn't? I can't. I wasn't there at the time. However, I can still doubt that it did. Pasteur's work helped to persuade scientists that spontaneous generation didn't occur. It didn't completely rule it out.

Whether Pasteur ever considered the implications for origins, I don't know. Perhaps he did. But, clearly, if abiogenesis of all types could be ruled out, living things could not have arisen from non-living material, but must have been supernaturally produced. Naturalistic theories of origins suppose that abiogenesis of this type did, in fact, occur, and, of course, rule out supernatural origins.

Some experiments have given support to the idea that life arose by abiogenesis, although we can't be completely sure what conditions were like on earth a few billion years ago. So abiogenesis may have occurred, and caused the appearance of the first living things. In fact, if you follow my argument above, you will see that it is impossible to experimentally rule out the possibility. I can doubt it, and, in fact, do doubt very much that that's how life began, but I can't scientifically prove that it didn't. I refer you to my earlier post on Hebrews 11:3, which speaks of the connection between faith and origins.

In sum, I don't think it is correct to say that Pasteur proved that spontaneous generation hadn't occurred. It is legitimate to doubt the possibility, in the present, or in the distant past, but it can't be disproved.

Thanks for reading.

What does a college biology professor say to a high school science class?

I was honored by a request, from a former student, now a high school teacher, that I speak to a high school science class this morning. She said "You can talk about science, your classroom experiences, academics, what professors expect from college students . . . that sort of thing. Sound interesting?"

In a word, yes. It's always interesting to distill experiences, in this case, 41 years of college teaching experiences. So here goes.

Science
A. Let's start by defining terms. This is what the Free Dictionary says about science (1st meaning only):

1. a. The observation, identification, description, experimental investigation, and theoretical explanation of phenomena.

b. Such activities restricted to a class of natural phenomena.

c. Such activities applied to an object of inquiry or study.

I will restrict myself to meaning 1a, actually. How does science differ from three other honorable enterprises, namely the study of history, performing music, or working as a clerk in a grocery store?
The study of history usually can't involve experimental investigation. You can't see what would have happened if George Washington hadn't crossed the Delaware, for example. You can guess, and your guess may be right, but you can't know. But you can experiment in science. You can find out what happens if someone takes their medicine every other day, rather than every day.
Music performance doesn't involve much identification (in that you are classifying something, such as rock types or species of grasses) and description, nor theoretical explanation. It may involve experimentation, though.
Grocery store clerks don't do much identification, either. They may experiment, however, for example by smiling at some customers and not at others, but the amount of experimentation is limited. If they start only charging for every other container of milk to compare it with customer satisfaction, or giving more change that the customer is supposed to get, they'll get fired.

B. The controlled, replicable experiment, then, is one of the cornerstones of much science. Granted, even scientists can't experiment on everything. Historical geologists can't manipulate history any more than history professors can. Astronomers can't manipulate stars or galaxies. Where direct experiment isn't possible, most scientists may compare experiments, as it were, that nature has already provided. For example, how does the light from different stars, in different regions of the universe, compare?

A controlled experiment is one wherein, ideally, one property, and only one, is varied between groups, and everything else is the same. For example, you might test inbred fruit flies, all in the same environment, giving one a vitamin supplement, and one no such supplement, and compare their fertility. (It is usually impossible to make the environment absolutely identical for every organism, or for different attempts at the same experiment. Even inbred strains may have a little genetic variation.)

Replicable means that someone else can test what you have done, by trying the same experiment.

I understand that there is debate about how science really works, but I'm going to ignore it. See the Wikipedia article on "Science" for an introduction to this.

C. Science is clearly important. Think of global warming, energy use, and stem cell research. The products of science, often called technology, are also important. For example, according to the latest mail from my congressman, he is proud that he was a principle [sic] sponsor of legislation to use high-technology means to detect illegal immigrants along the Mexican border.

The previous sentence mentioned four important topics. I must say that none of them is a strictly scientific topic. All of them have legal, political, ethical, economic and even religious implications. If a scientist, for example, says that she is opposed to allowing illegal immigrants to get driver's licenses, or that human embryos can ethically be destroyed in the process of stem cell research, what she says on one of those subjects should carry no more weight than what a grocery clerk says, unless she is a legislator, in addition to being a scientist.

Sometimes scientists think that they are making scientific statements, but they aren't. They are merely scientists making statements, not making statements that are backed up by controlled, replicated, experiments. Watson and Crick, for example, thought that they had discovered the secret of life when they proposed the double helix. They had made an important contribution, but they hadn't discovered the secret of life. They hadn't explained how DNA came to be so central to living things in the first place. They hadn't given an explanation for how the information in DNA comes to be expressed (we now know a lot more about that, partly because of the work of Crick, himself.) Both of them, apparently, thought that they had ruled out any supernatural explanation for living things. But they hadn't. God could have created life with DNA as its main information carrier. I don't believe any experiment can rule that out (or prove it.)

D. Before leaving the subject of science, I don't want to leave the impression that science gets a better and better picture of how nature works only by doing experiments. As Thomas S. Kuhn pointed out, scientists get such a changed picture by new ways of looking at the world -- adopting a new paradigm. What experiments scientists do is determined by how they view the natural world. Galileo wouldn't have done any experiments on radio, because he didn't know there was such a thing. Newton didn't discover gravity. But he did (perhaps after watching an apple fall) realize that gravity could be explained as an attractive force. This wasn't because of any experiment that he did. The experiments came later.

Classroom Experiences
The best experiences I had in the classroom all involved (duh!) students. As a biologist, these were often on field trips, where we saw things that the textbooks (or I) could only describe. Sometimes they were in the lab, when something actually worked as they were supposed to(!). Once, an African-American student with sickle-cell anemia saw her own red blood cells sickle under the microscope (I got to see this, too) for the first, and, I suppose, the only time. (Red blood cells are normally circular. The cells of someone with sickle cell anemia assume an elongated shape when they become deprived of Oxygen.) I am sorry to say that this young lady didn't live long after this experience. She died from the complications of this terrible disease.

Often the most memorable experiences are one-time things, and happen when something goes wrong, or, at least not according to plan. I will relate two of mine. Once, a few students and I were injecting a rabbit. The rabbit died, for some reason. One of the students suggested that we dissect the rabbit, so we did. We had never seen the insides of a just-dead rabbit before, and seeing this was amazing. A rabbit's intestines include an (for a rabbit) enormous caecum, quite different from human anatomy.

Another such experience was when a student came in late for a bioethics class. I knew what had happened, because she had called and told me -- the class and I had been praying. Her father had just gotten a liver transplant. I had her sit on the table in front of the class and talk about it, and the rest of us asked her questions. Organ transplantation, of course, has some important ethical implications.

I have also had experiences where a student asked me a question that changed my way of thinking. One of my students asked me about human cloning, back in the middle 1970's. I hadn't thought much about it before, but decided that I should. Partly because of his question, the U. S. taxpayer supported my attendance at a six week conference on bioethics in 1979 at Indiana University. I was the only person in the group of a dozen or so who was trained as a biologist, and the only one from an evangelical Christian college/university. All of this resulted in a change in direction. I developed a new class at my school, and published a paper (the article is not available on-line, so far as I know -- the link is to a listing) on the subject.

Sometimes a student made a comment that changed my thinking. One once said "the Bible is inerrant, but our interpretation of it isn't."

I am glad to say that, sometimes, I could see students learn. Sometimes I could see that they had, when I graded their tests, quizzes, and papers.

Some of the greatest experiences came outside of class, when students came to talk to me about something unrelated to their class work, or I got to interact with, or observe them, in other settings.

I confess -- I married a student. (She came to college after being in the workplace for three years, so I didn't rob the cradle.)

Academics, and what professors expect from their students
Every professor is different. Different classes under the same professor may be different, and different universities, or different departments at the same university, may have different expectations.

Nonetheless, a few hints. They're just commonsense, mostly.
Go to class. That's pretty elementary, but it's good advice. Some classes aren't worth going to, or some sessions of a class may be a waste of time, but you should make it your goal to go to all your classes. Most universities don't monitor class attendance as rigidly as most high schools, nor do they usually contact your parents if you don't go, and the temptation to skip classes will be there. Don't do it. I have known some cases where students who could have had a promising academic career have messed it up, just by not going.
Be prompt, if at all possible, and if you can't be, let the professor know why, even if she doesn't seem to care (or even know who you are).
Sit where you won't be distracted, preferably in the front.
Stay awake.

Get enough sleep. You and I can do many things with little or no sleep, such as many types of work, or carrying on a social life, but serious learning often becomes a casualty when you don't get enough sleep.
There is a school of student thought that believes that the best way to study for a big test is to stay up all night before it is scheduled. Wrong! Sleeping on what we have learned helps us to remember it longer. "Cramming" for a test is probably better than no study at all, but it isn't very efficient, and it may mean that we don't function very well in actually taking a test, or in the other things we need to do on the day after a night with little sleep. We tend to forget material learned in a cram session rapidly. Often, we'll need to retain that material for a long time. In college classes, there are often two or three tests during a semester, then a comprehensive final, covering the entire course material. Or, in preparing for some professions, there may be a comprehensive qualifying exam, covering much of everything you are supposed to have learned in college. You will need to retain facts and principles for a long time.

Study. The best way to study for a big test is to study as you go along. Read your book. Review what went on in the previous class session before the next one. Ideally, you should know what the class will be about before you go, and be prepared with questions or comments. Study with someone else sometimes. Study should be about what's important. That is, what the professor may ask you, but also, what is important about this chapter, this diagram, this term, this lab experiment. Getting another perspective on this often helps. Even if another student knows a lot less than you, it will often help you to explain the material to someone else.

Look over terms and diagrams, chapter summaries, and questions at the end of a section or chapter, in your textbook. (Some texts won't have some, maybe any, of these things, especially in upper-level courses.)

P. S. Obtain your textbooks. Textbooks are expensive, and, let's face it, in a few classes, you don't really need them. But, in most classes, not having a text is a serious handicap. It's silly to spend good money for tuition, travel, lodging, and whatever other expenses you may have going to college, and not get textbooks. (You may be able to buy used copies, or borrow a text from someone who had the course in a previous semester.)

Most people learn through more than one sense. (Some learn mostly by hearing, some by seeing, some from other senses. In some classes, handling things may be important.) Hear your subject (In class, by recording the class, if that helps, or if you can't be present -- most professors will allow you to tape a class, or have someone else tape it for you -- they'll be thrilled that you care!) and read about it, so you've got two ways of getting it into your brain.

Turn your assignments in on time. Maybe even early. Give your professor cardiac arrest!
This means planning ahead. Start those papers, book reports, lab reports, and projects before the night before they are due.

Get noticed, for good reasons. Sit near the front, ask good questions, stay awake, occasionally talk to the professor after class, or in her office, or in other settings. Don't be a pest, but act like an adult who is interested in the subject matter.

Be interested in the subject matter.
Sometimes that's difficult. Try, anyway. Never ask "What good is this going to do us?" about a class as a whole. Your professor may not have a good answer (she should) but generally you are stuck with the class, anyway. The university, or your chosen profession, require it. Make the best of it. Sometimes you may get noticed in a good way by asking about the relevance of a particular topic, or by suggesting a relevant topic that the class doesn't seem to be going to cover.
Often, you will be helped by finding material other than the text that deals with the subject matter. The Wikipedia, although not totally inerrant, is a good source on almost any academic subject.

Pray a lot.
Pray for your professor, any teaching assistants she has, your classmates, and, of course, yourself. Ask for God's help in studying, in understanding the material, in getting to class, in staying awake, in taking a test. And, of course, do your part -- you can pray yourself into a failure, if you don't do what you are supposed to.

Thanks for reading.