Wednesday, August 31, 2005

Public understanding of Science

In yesterday's NY Times Science section, there was an interesting article on Jon D Miller's findings on Science literacy in the US. From the article:

While scientific literacy has doubled over the past two decades, only 20 to
25 percent of Americans are "scientifically savvy and alert," he said in an
interview. Most of the rest "don't have a clue."

I then researched some of Dr Miller's research in PubMed and came across many interesting papers of his published in the journal Public Understanding of Science (this goes to show that there is a scientific peer reviewed Journal for almost anything). There he has an interesting article:
Miller, JD, Public understanding of, and attitudes toward,scientific research: what we know and what we need to know. Public Understand. Sci. 13 (2004) 273-294

There are many interesting facts in this article. In this article he defines "the level of understanding needed for scientific literacy to be sufficient to read and comprehend the Tuesday science section of The New York Times." Interesting! Maybe that's why they wrote an article about him.

Anyway ...

On understanding the meaning of scientific study (using experiments to test hypothesis):
Looking at the pattern over the last four decades, the percentage of US adults with a minimal level of understanding of the meaning of scientific study has increased from 12 percent in 1957 to 21 percent in 1999.

So then do Americans understand experimentation (have two experimental set ups where one variable is changed between the test experiment and the control experiment):
the percentage of US adults who understand the basic idea of an experiment has increased from approximately 22 percent in 1993 to 35 percent in 1999

Now facts:
-only 13% of Americans could describe what a molecule was
-on space "Fifty-five percent of adults responded correctly to the question 'Would you say that the Sun is a planet, a star, or something else?' Only 24 percent of adults knew that the size of the universe is expanding."
-only half knew that the earth rotates around the sun once a year (one fifth think that the SUN ROTATES AROUND THE EARTH, and 14% think that the earth rotates around the sun EACH DAY)
-only 11% understand the process of radioactive decay (the release of high energy particles during nuclear fission)
-on DNA "Studies of US adults over the last decade have found that about 40 percent have a minimally correct explanation of the meaning of DNA (NSB, 2000). In 1990, approximately 24 percent of US adults were able to provide an explanation of DNA that included its role in heredity."
-on genes "10 percent of US adults think that ordinary tomatoes do not contain genes and 45 percent do not know."

So if the average American doesn't know much, does that mean he does not support scientific research? No.
A substantial body of research from the end of World War II to the present indicates that an overwhelming majority of US adults are interested in science and technology, believe that it has contributed to our standard of living, and are willing to support it with government funding.


By the end of the twentieth century, only 14 percent of US adults thought that the government was spending too much on scientific research

So people ARE interested and supportive - so what is the problem?

The people who are Science literate (see definition above) are those people that took University level science courses.
Although some university science faculties view general education requirements with disdain, these analyses indicate that the courses promote civic scientific literacy among US adults despite the disappointing performance of US high school students in international testing.

So as I've commented on before American high schools are just not doing a good enough job. But here is the real surprise:
The US is the only major nation in the world that requires general education courses for its university graduates. University graduates in Europe or Japan can earn a degree in the humanities or social sciences without taking any science course at the university level. In cross-national studies, a slightly higher proportion of US adults qualify as scientifically literate than do adults in the European Union or Japan, and comparative structural equation analyses of those data show that this exposure to college-level science courses accounts for the US performance (Miller et al., 1997; Miller and Pardo, 2000).

So around the world - pre-university exposure to science is INADEQUATE. In addition outside the US, university exposure to science is also inadequate. This should be a wake-up call not only for the US, but everywhere!

The last paragraph of the article:
Finally, it is clear that the best long-term strategy for increasing civic scientific literacy is to improve pre-collegiate education so that all students who graduate from college are scientifically literate. The fact that college-level science courses are currently able to compensate in part for inadequate middle school and high school science should be of little consolation to the scientific community. A slightly higher proportion of US adults might qualify as more scientifically literate than European or Japanese adults, but the truth is that no major industrial nation in the world today has a sufficient number of scientifically literate adults. No pride can be taken in a finding that four out of five Americans cannot read and understand the science section of The New York Times.

Tuesday, August 30, 2005

Biology at Bob Jones University

Recently I bumped into this at the blog The Questionable Authority:

... a group of creationists are suing the University of California system in order to force UC to accept several of their classes that are currently not considered adequate. One of the courses in question is biology.

What do they want? To use textbooks published by Bob Jones University Press. The Questionable Authority then goes on to describe this Biology textbook and finds this passage:

The people who prepared this book have tried consistently to put the Word of God first and science any point God's Word is not put first, the authors apologize....

Now of course having stated this would end any discussion as to whether this textbook could be used in public schools. But now my interest is piqued. What do these guys really believe? So I went to their website and started to read the free chapter from the textbook.

So what is science (according to Bob Jones)?

The Christian must evaluate the source of a statement. Scientific statements must be based on observation or else they are mere guesses. There is nothing wrong with a guess, as long as it is clearly labeled a guess or a belief. But Christians must disregard those guesses and beliefs that contradict the Bible.(from the introduction)

So Science is a collection of mere guesses?

Science can be defined as a body of facts that man has gathered by observing the physical universe. (p4)

Actually both of these passages are wrong. And if any textbook, dictionary has this idea, they are wrong too. Science is not guessing, not facts ... Science is a tool. It's a method. In fact later at the end of the fist chapter after another bad description of science "Science cannot explain things; it only describes." (p36) they do a good job of defining science:

Scientists devise models to explain the data they have obtained ... Putting together all the experimental information so that it "works" logically can produce a model. Further experimentation and testing of the model often reveal more information. If the results of these additional experiments agree with the model, they give greater validity to the explanation. If the results do not support the model, then either those data are in error, or the model must be greatly changed and retested or even discarded. (p36)

Wow, I'm impressed ... now if they could only remain consistent. Yes I am being nit-picky but little lapses of definition can muddle the whole debate. And to Bob Jones credit - it's not only them, it's all over the place. Science is a method that generates hypothesis or models.

So what else do they say? Some weird things like:

The Bible teaches that things are getting worse and that God is the source of all that is good. But some people claim that scientific efforts are improving man's existence and will continue to do so. (p3)

Go to The Questionable Authority for more of these statements. But otherwise ... not too bad. The intro deals with the importance of being critical in Science and of being critical about Science ... part of the Scientific Method is to be critical ... but since Bob Jones and Co think that Science is "facts" I guess generated by (secular) scientists, they have to be critical of those too.

There is then a discussion of spontaneous generation, and this is used to show the limitation of science. Basically the book describes some badly controlled experiments by Jan Baptist van Helmont and how this led to the belief that life could appear spontaneously. Experiments done later by Francesco Redi, with proper controls, disproved spontaneous generation. This purportedly shows the pit falls of Science. Actually this is a good lesson on how over time science gives better and better models through critical evaluation of previous work coupled with better and better experimental design. Science is inherently self critical and that is exactly why it advances from "not so good" models to "better" models.

Interestingly, the intro uses many concepts from post-modernism and relativism to argue that there is no such thing as (scientific) fact, only guesses - that is an interesting turn of events! I guess I agree, except that I would call them models instead of guesses. Science generates models, nothing else.

Next up is Inductive and Deductive reasoning. They pose the question of whether math (i.e. logical/deductive reasonning) to be trusted? They argue that a business may cook the books - so not always. Bottom line, any form of reasoning often works but sometimes fail ... so don't always trust them. They actually give a bad example of how logic is not always functional using (again) van Helmont and his plant experiment...
Statement 1: Plants, when growing in soil and water, gain weight.
Statement 2: Plants gain much more weight than is taken from soil.
Conclusion: Weight gain of plants comes almost entirely from water.
Of course the logic is not complete and an axiom is missing. But lets not think too much ... logic is faulty (I guess). So then is Science to be trusted? "A scientist employed by a tobacco company to research the effects of smoking might tend to emphasize results that would please his employer ..." (p15)

We get the picture ... although they do redeem themselves later on:
One wrong attitude towards science is to believe that science is anti-God.
Science is not evil because men have abused the use of scientific knowledge.
I guess it is a Biology text book, the scientific method can't be all that wrong (or else they would have nothing to teach).

I'll end this post with this funny passage from the accompanying teacher's manual. In it there is a nice (ironic?) quote about the belief of the extra-terrestrial origins of life:

Some scientists have recognized the improbability of abiogenesis [origin of life from the primordial soup] occurring on earth. For this reason, they theorize that life may have spontaneously arisen somewhere else in space and arrived here. This seems even more incredible and merely shifts the unproven process to another location where it cannot be tested. (p19 teacher's manual)

Monday, August 29, 2005

When will we learn that US schools need fixing

I'm not talking about teaching ID vs evolution (or is it the flying spaghetti monster vs evolution? ... I kid you not). No this is about the sorry state of public education in the US ... a favorite subject of mine.

Reading Bob Herbert's column in the NY Times I come across these stats:
First the bad news: Only about two-thirds of American teenagers (and just half of all black, Latino and Native American teens) graduate with a regular diploma four years after they enter high school.

Now the worse news: Of those who graduate, only about half read well enough to succeed in college.


The Program for International Assessment, which compiles reports on the reading and math skills of 15-year-olds, found that the U.S. ranked 24th out of 29 nations surveyed in math literacy. The same result for the U.S. - 24th out of 29 - was found when the problem-solving abilities of 15-year-olds were tested.


An education task force established by the center and the institute noted the following: "Young low-income and minority children are more likely to start school without having gained important school readiness skills, such as recognizing letters and counting. ... By the fourth grade, low-income students read about three grade levels behind nonpoor students. Across the nation, only 15 percent of low-income fourth graders achieved proficiency in reading in 2003, compared to 41 percent of nonpoor students."

How's that for a disturbing passage? Not only is the picture horribly bleak for low-income and minority kids, but we find that only 41 percent of nonpoor fourth graders can read proficiently.

So who is the The Program for International Assessment? From their website:
The Program for International Student Assessment (PISA) was developed by the OECD to assess the reading, mathematics and science literacy of 15-year-olds in participating countries. PISA assesses how well prepared students are for life beyond the classroom by focusing on the application of knowledge and skills to problems with a real-life context. PISA results reflect the influences of education systems and societies on young people up to the age of 15. PISA represents an international collaboration that provides information for policymakers and researchers throughout the world.

So who is the OECD? From their website:
The OECD grew out of the organization for European Economic Co-operation (OEEC), which was set up in 1947 with support from the United States and Canada to co-ordinate the Marshall Plan for the reconstruction of Europe after World War II.

This isn't some flyby lobbyist group. This is an international organization (partially set up by the US) studying how students and school systems from around the world are performing.

Lets look at the stats:

Look closely, Canada ranks 5th (and not too far off the top OECD country surveyed, Finland).

The solution to the American problem - learn from other countries' educational systems! (all you have to do is cross the 49th parallel!)

This includes:
-get higher qualified teachers (which will require higher wages for educators)
-fund all schools adequately (this means that school funding must not only equalized, as in California but also increased - something Californians have not done!)

I've gone through this whole education bit before, but this is the biggest threat to the future of this country. Just look at 15th century China - although it was by far the most technological country on the planet, the Chinese turned inward. They closed the borders, banned seafaring trade and could not learn from the other "barbarian nations" ... as a result the west eventually leapt ahead of China.

In 1834, the British (with a population an order of magnitude less than China but with far superior technology) could send a fleet of ships half way around the world and win wars against the mighty empire and force China to open it's borders to the Opium trade. With the lack of education and stupid ideas such as ID floating around, is this the fate of our mighty empire?

Saturday, August 27, 2005

Exactly What is a Gene?

Yesterday, I told you about my tinkering with one gene in an attempt to study it's mRNA product.

But what is a gene???

Simply put, a gene is a segment in your DNA that encodes for a protein (or at the very least a type of RNA product). The entire collection of genes in one organism is called a genome.

Remember the Central Dogma of Biology: DNA => RNA => Protein.

When a gene is "turned on" RNA polymerase is recruited to a stretch of DNA the preceeds the coding region and can then copy the DNA into RNA (i.e. transcription). This recruitment region, called the promoter, doesn't code for protein, it is simply there to start the transcription process. Other regions flanking the genes can recruit factors that influence whether the gene is turned on or off. These DNA regions afre usually called enhancer regions or enhancer elements.

So a gene is the whole thing. The coding regions of the DNA (which gets copied into pre-mRNA), the promoter, and the enhancer elements.

Friday, August 26, 2005

Playing Around with RNA

Instead of commenting on other's people's work ... (for that go to some other great science blogs) ... my new blog will try to have more original stuff.

First up, the synthetic gene. As you can tell by my URL and the title of my blog, my interest currently lies with mRNA. To figure out how mRNA gets localized, I've synthesized some in a test tube and microinjected it into nuclei of tissue culture cells (click here for some idea on what a tissue culture cell looks like). Above are two pics of the same field cells. Displayed in the second picture is what is called an injection marker, or a fluorescent substance to mark which cells are injected. Since this marker (FITC-70kD dextran) is too big to cross the nuclear membrane, it demonstrates that in all three cells, all the injection fluid entered the nucleus and not the rest of the cell (aka the cytoplasm).

But studying mRNA is a pain in the butt. RNA gets degraded quite easily. Also the way cells handle RNA remains unclear. One thing that I did to check that the injected cells are handling the RNA correctly, was to alter the mRNA so that it should have all the right signals to be translated into protein. To do this the mRNA must start with a Cap structure, then a leader sequence, followed by a Kozak sequence (named after Marilyn Kozak), a stop sequence and a polyA-tail (see here and here for more on mRNA). In addition the mRNA was modified so that it produces protein with a "FLAG tag" sequence that can be detected by fluorescent antibodies (see top picture) and a signal sequence, that targets the encoded protein to the endoplasmic reticulum (ER). Now if I try to probe the same cells for translated protein (encoded by my mRNA) voila, I see that the FLAG tag in a reticular type pattern reminiscent of the ER (top picture) in the same cells that I injected (see bottom pic).

Thursday, August 25, 2005

Haloscan commenting and trackback have been added to this blog.

The Big Move

Ok after talking about it for ever I've done it. I've made the jump.

Here is my old blog site:

Why did I do it?

Well the site was awful.

And then the adds ... for sites like this ... yeah I just couldn't take it anymore. So this is my new home, come back often, I'll post once a day (if I'm not busy).

And one further thing. Why am I calling it The Daily Transcript? Well let's just say that it's my little message.