"Expelled, The Movie" Conversation Continues

The many Anonymice are still discussing world views on a post from last October.

(In case you wondered where I've been:

We've had our primary, with one hotly contested local Republican race ending in a cliff-hanger. The same seat was decided by 54 votes out of about 20,000 in 2006. This time, it looks like the winner may be decided by about 38 votes out of 30,000, before the mail in ballots are counted. We're expecting a recount.

It turns out that the consequences of politics and policy became personal this last 2 months. We've spent the last year - over 14 months, now - working out a plan to remodel our 65 year old house only to find out that the city adopted the new provisional FEMA flood plain map, and we can't remodel - we have to fill in the basement, tear down the old house, and build 2-3 feet higher. I'll admit that I haven't reacted very well. But, still, the City's bureaucrat literally lost the plan for 6 weeks before telling us that the concrete-poured-in-place house and basement that's still plumb, smooth and level after more than 60 years might float up and turn on its side.)

Texas Employees, Politics, and Science

(Just to be clear about where I'm coming from, I believe in a Creator and also believe that the evidence I've seen supports the evolution of species. When asked about evolution, I say, "It looks like that's how God did it." Now that I've alienated all but a few of my readers . . .)

The New York Times has an article today on the resignation of the Texas Education Agency (TEA) employee, Chris Comer. In my opinion, the NYT and the Austin American-Statesman focus on the wrong theme. The story is more about the politics of being a State employee than about the politics of science.

The blogosphere is full of comments relating her resignation to "creationists" and drawing an analogy to the movie, "Expelled."

However, there's a difference between speech and advocacy on scientific controversies while working in a academic position (even when paid by the State) and the same activity while working for a State Agency. While both should avoid frank political advocacy while on the State's time clock, the former is in the business of discussing and critiquing science. The Agency employee works directly for men and women who are themselves restrained by the voters of the State, who have their own politics.

The implication of the NYT piece is that Ms. Comer was under pressure due politics, the appointment of a new Chairman of the State Board of Education and the hiring of a woman who used to work for the Bush Administration. On further research, I found a possible connection between a statement that Ms. Comer made concerning the lack of "real" leadership at the TEA under an acting Commissioner and the appointment of the same man to the office of Commissioner.

In addition, it might help to know that the Texas Legislature recently mandated that each agency develop ethics policies.

Texas elects our State Board of Education, the Governor appoints (and the State Senate confirms) one of these elected officials to the Chair and he also appoints the Commissioner of the TEA. The TEA is the bureacracy that provides "leadership, guidance, and resources to help schools meet the educational needs of all students."

State employees are forbidden by policy to mix in politics while on the job and with State resources. At the very least, it's not wise to risk bringing pressure down on your appointed or elected bosses. The offense that led to Ms. Comer's resignation was sending an email from her TEA account that announced a talk entitled, "Creationism's Trojan Horse."

Ms. Comer and the author of the NYT article find something notable in the policy at TEA:

But several months ago, in response to an inquiry letter, Ms. Comer said she was instructed to strike her usual statement about the board’s support for teaching evolution and to quote instead the exact language of the high school biology standards as formulated for the Texas Essential Knowledge and Skills test.

“The student knows the theory of biological evolution,” the standards read, and is expected to “identify evidence of change in species using fossils, DNA sequences, anatomical similarities, physiological similarities and embryology,” as well as to “illustrate the results of natural selection in speciation, diversity, phylogeny, adaptation, behavior and extinction.”

I fail to see a problem in a policy requiring the quote. I would think that it would inform and educate any one with questions and protect State employees from political fallout.

Ms. Comer herself makes correlations between certain politically controversial subjects:

“I don’t see how I took a position by F.Y.I.-ing on a lecture like I F.Y.I. on global warming or stem-cell research,” Ms. Comer said.

And she did consider the email risky:

As for the e-mail, Comer said she did pause for a "half second" before sending it, but said she thought that because Forrest was a highly credentialed speaker, it would be OK.

For a step-by-step report about Ms. Comer's troubles at the TEA, see the Austin American-Statesman article and my earlier post.

Translation of Yamanaka, Yu "induced Pluripotent Stem Cells" (Revised)

Scientists who report their findings are expected to discuss the problems as well as the outcome of their research. This is usually found in the "Discussion," "Conclusions" or "Results" section of the paper. This is the best place to figure out what the researches intended, what they did and what the report means. (Then you go back and check to see if they proved what they "discussed." And then, you wait for other labs to confirm it.)

The actual (Takahashi et al., "Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors," Cell (2007).) Cell article on reprogrammed adult fibroblast skin cells, the "induced Pluripotent Stem Cells) or "iPS," is available for free, here. The Science Magazine report about similar work by James Thomson from Wisconsin (the researcher who reported the production of human embryonic stem cells in the first place) is supposed to be published November 22, 2007. (Editorial note 11/30/07 – Science published the Thompson and Yu report the same day that Tamanaka's report was published, two days ahead of schedule. See my “translation,” here.)

To the best of my understanding, here's a translation into layman's terms about what the Takahashi/Yamaka report means:

While it took a lot of cells and more time than the researchers first expected because the human iPS grew much slower than the mouse iPS,

1. The cells that grew looked and functioned like human embryonic stem cells with a few minor differences,
2. They believe they proved that their technique is responsible for all the new pluripotent cells that were found in their cultures(there weren't any cells from another culture introduced accidentally or on purpose and which would make them look more successful than they were),
3. The cells could be directed to develop nerve cells and heart cells,
4. They were able to use several types of adult specialized cells to achieve iPS, and
5. The researchers suggest several possible ways to overcome the drawbacks of the process.

The authors believe that the inefficiency or the need to begin with lots of adult cells and wait a little longer for a substantial amount of human iPS should not be a "practical" problem because the adult cells are easy to obtain and labs all over the world should be able to reproduce their results. Since the technique should be well-funded (it qualifies for US Federal funding and is ethical, since no human beings have to die), the authors believe it will be possible for lots of researchers to work on them.

If I were to predict the future, I would anticipate banks of iPS - or even specialized or intermediate forms of cells that are produced from iPS - being stored for each of us, just in case. In the very long term, we will learn more about stimulating our on bodies' stem cells from research on these cells, so that we can repair or prevent damage without transplants or waiting for cultures to grow in the lab.

The major hurdle is that the cells were produced by the Recombinant DNA technique, using retroviruses in plasmids.

The retroviruses are a class of viruses that actually insert themselves into the DNA strands of animal or plant cells to become a part of that cell’s DNA and are copied when the cell reproduces. They are manufactured in the lab in the form of plasmids in order to carry genes into the experimental cells.

Plasmids are little bits of DNA, a mini-virus in a circle. Think of a chain with pairs of magnets or interlocking puzzle pieces that connect the ends and make a loop. When open, the plasmid becomes a strand of DNA which has ends that are "sticky.” When placed in a culture with mouse or human cells, the plasmids infect the cells and then move into the nuclei of the cells. The retroviral DNA is inserted or inserts itself into the DNA of the host cell because the sticky ends of the plasmid strand match or mate to certain areas of the host DNA.

Plasmids can be manufactured to carry copies of genes that researchers want to insert into the DNA of experimental cells. The technique is common in commercial and experimental labs for at least the last 30 years. In fact, "Recombinant DNA" is used to induce strains of bacteria and yeast cells in cultures to manufacture vaccines like the flu and Hepatitis B vaccine and the insulin used by diabetics these days. The particular retroviruses used by Tamanaka are said to be "strongly silenced in humans." In other words, they don't normally get reproduced as viruses when the cell divides. Once they are taken up in the cell DNA, the viruses used in research don't break out to become infectious viruses, again. However, some of them can induce the cells to form tumors or cancers if injected in an animal or human.


One of the possible problems that the article notes is that the new iPS cells each had several copies of the retrovirus included in their DNA. There is a concern that these bits may be responsible for the tumors that were seen in the mice used in the experiments. Before iPS can be used in humans, it will be necessary to learn to remove all the viral particles or to learn to make the cells without viruses that can cause tumors. Otherwise, there is a risk of causing cancer in patients.

The researchers note that another group of scientists have already reported that it is possible to insert one of the genes without using retroviruses and that the hope is to either find a way to insert the other three genes or to remove all traces of the virus.

There's also a suggestion that what they are actually inducing to grow is a sub-set of fibroblasts with the tendency to become embryonic-like stem cells.

Thomson framed: "iPS more relevant than embryonic"

Framing Science has a great quote from James Thomson, whose lab announced that they had proven a way to reprogram adult cells to become more primitive, embryonic-like stem cells, called "induced Pluripotent Cells."

I don't know how I missed this one yesterday:

". . . says Thomson, the scientist who in 1998 isolated stem cells from human embryos for the first time. "They are probably more clinically relevant than embryonic stem cells," he explains. "Immune rejection should not be a problem using these cells."

While you're over there, take a look at the articles from yesterday and today on what Dr. Nesbit believes is the significance of "The Discovery" and about the art of "framing science." If you're not familiar with the concept of framing, read some of the early and/or labeled posts to find out what it means to "frame" anything, science in particular.
(with a handy little list of words and meanings that you need to understand if you are at all interested in how science is reported and "framed" to influence the rest of us.)

Expelled: movie to explore politics of science

Ben Stein on the movie, "Expelled,"

"Big Science in this area of biology has lost its way," says Stein. "Scientists are supposed to be allowed to follow the evidence wherever it may lead, no matter what the implications are. Freedom of inquiry has been greatly compromised, and this is not only anti-American, it's anti-science. It's anti-the whole concept of learning."

Don't be surprised if the same attacks and tactics are used against anyone involved with this movie. The point of the movie is not to prove or disprove evolution or intelligent design. The purpose is to report the personal attacks on anyone in academia who does not toe the line on evolution. Let me say that again: it's about the treatment of people, not the science.

For example, Stein meets Richard Sternberg, a double PhD biologist who allowed a peer-reviewed research paper describing the evidence for intelligence in the universe to be published in the scientific journal Proceedings. Not long after publication, officials from the National Center for Science Education and the Smithsonian Institution where Sternberg was a research fellow began a coordinated smear and intimidation campaign to get the promising young scientist expelled from his position. This attack on scientific freedom was so egregious that it prompted a congressional investigation.

On his journey, Stein meets other scientists such as astrobiologist Guillermo Gonzalez, who was denied tenure at Iowa State University in spite of his extraordinary record of achievement. Gonzalez made the mistake of documenting the design he has observed in the universe. There are others, such as Caroline Crocker, a brilliant biology teacher at George Mason University who was forced out of the university for briefly discussing problems with Darwinian theory and for telling the students that some scientists believe there is evidence of design in the universe. The list goes on and on.

Unlike some other documentary films, Expelled doesn't just talk to people representing one side of the story. The film confronts scientists such as Richard Dawkins, author of The God Delusion, influential biologist and atheist blogger PZ Myers and Eugenie Scott, head of the National Center for Science Education. The creators of Expelled crossed the globe over a two-year period, interviewing scores of scientists, doctors, philosophers and public leaders. The result is a startling revelation that freedom of thought and freedom of inquiry have been expelled from publicly-funded high schools, universities and research institutions.

Sam Harris at the Aspen Ideas Festival

Sam Harris, author of the books, The End of Faith: Religion, Terror, and the Future of Reason and Letter to a Christian Nation, was given a forum at the Aspen Ideas Festival. I'm not sure how I ended up finding the video, "Believing the Unbelievable: The Clash Between Faith and Reason in the Modern World," but I believe I was referred by one of the Science Blog forums. I can't remember which one, and, as far as I can tell, only one of these blogs is owned by a believer.

Which is probably how I got lost. There's a bit of a row, right now, concerning the derision of believers by "Pharyngula." (Which is surprising, since that seems to be his purpose in blogging.) I was once again struck by the idea that science and religion are incompatible, chased some links, and ended up watching a video from the Festival.

Mr. Harris spent his time at the Festival blurring the edges between “Christianity, Judaism, and Islam,” with a little Hinduism and Buddha thrown in to strengthen his point. There doesn’t seem to be any difference in his viewpoint, although he does grudgingly admit to a questioner that “moderate” Christians and Jews have been influenced by the belief in human rights and equality by secular, outside influences, while Muslims have remained isolated and so have not “evolved.”

Beyond the fallacy of treating all religions as one, Mr. Harris denies that atheism is a religion, using his second favorite technique, mockery and one liners designed to encourage his listeners to laugh with him. He mocks the Second Commandment: “Is this as good as it gets? . . . How about, ‘don’t deep fry all of your food?’” and mocks the idea that agnostics are a separate from believers and atheists by saying, “I haven’t met too many agnostics about Zeus.”

The biggest logical fallacy in which Harris engages is his statement that religions change from without, due to secular ideas about human rights. In fact, the Judeo-Christian tradition teaches that we are all created in the image of God.

While Christians have cited the fact that very young children naturally display concern for others and seem to understand the concepts of justice and beauty as proof of God, Mr. Harris believes that this actually disproves the “usefulness” of religion. While he admits that 70% of (I presume, U.S.) college graduates believe in the Biblical God, he strongly commends “peer review” in science.

His major point seems to be that “much of the Bible and Koran is life-destroying gibberish.” He dismisses the rest. While he insists that believers who promote their religions or teach their children to follow them are enabling religious fanatics who kill in the name of religion, shouldn’t Harris, who has been called an "Atheist Evangelist" take responsibility for enabling those who kill and enslave to suppress religion, as in China? Or the Western academic powers that be that harass, deny recommendations, employment and funding to those who fall out of favor, such as Richard Sternberg (see the review at Sternberg's site and at National Public Radio)?