Robert Hazen: Origin of Life 101

Robert Hazen is a research scientist at the Carnegie Institution of Washington’s Geophysical Laboratory and Clarence Robinson Professor of Earth Science at George Mason University. Robert Hazen is also author of “Intelligent Design and the College Science Classroom: Should We “Teach the Controversy?”” Hazen, R. M. Intelligent design and the college classroom: Should we “teach the controversy”? Astrobiology 6, 106. (2006)

On the other hand, every student can benefit from an examination of the epistemological arguments that underlie this case. The fundamental distinction between science and religion as ways of knowing was central to the Dover case, and can serve to develop the critical thinking skills of all students. Of special relevance is the exploration of “gaps” in our scientific understanding. ID proponents point to these gaps (leaps of “irreducible complexity”) in their invocation of a designer. Scientists, on the other hand, see such gaps as opportunities for further research and exploration, especially in instances of “emergent complexity,” such as the origin of life.

05-14-2008: Note: During my final editing I switched from to an earlier version of the article and lost many edits. I have attempted to restore the article to its original state.

• “ID and the College Classroom: Should we ‘teach the controversy’?”. Presented several times during 2006-2007 as the Dover, Pennsylvania intelligent design trial evoked much debate. [PPT]
• Achieving Scientific Literacy: A Catechism for Science Education Reform”. This is my basic lecture on how to design science courses for undergraduates who are not science majors. [PPT]

On the Chemical Constitutuents of the Seeds of Datura Stramonium

Every now and then, while doing research, one runs into little gems of history. In the case of Datura Stramonium, I found a thesis by Isao Nishimura at the University of Wisconsin dated 1922. The thesis contains meticulous descriptions of experiments conducted to unravel the mysteries of Datura Stramonium.

The researcher prepared some microscopic drawings of the seeds, pointing out that earlier researchers had stated that the alkaloids were present in the outer layer, and that the endosperm and the embryo are free from alkaloids, although one researcher reported trace amounts of alkaloids.

To detect the presence of alkaloids a solution of iodine in potassium iodide was used to stain the alkaloids, even though it also reacts with starches.

Visual inspection showed that the endosperm and the embryo were wholly free of staining, showing the absence of alkaloids in these parts of the seeds.

The thesis also discusses the oils extracted from mature and immature seeds, observing that the former were yellowish in colour while the latter one was dark green.

Target Atmospheric CO2: Where Should Humanity Aim?

I have found that the same ignorance that surrounds evolutionary theory extends often to the issue of Global Warming.

James Hansen et al have released a report outlining the case for CO2

Paleoclimate data show that climate sensitivity is ~3°C for doubled CO2, including only fast feedback processes. Equilibrium sensitivity, including slower surface albedo feedbacks, is ~6°C for doubled CO2 for the range of climate states between glacial conditions and icefree Antarctica. Decreasing CO2 was the main cause of a cooling trend that began 50 million years ago, large scale glaciation occurring when CO2 fell to 425±75 ppm, a level that will be exceeded within decades, barring prompt policy changes. If humanity wishes to preserve a planet similar to that on which civilization developed and to which life on Earth is adapted, paleoclimate evidence and ongoing climate change suggest that CO2 will need to be reduced from its current 385 ppm to at most 350 ppm. The largest uncertainty in the target arises from possible changes of non-CO2 forcings. An initial 350 ppm CO2 target may be achievable by phasing out coal use except where CO2 is captured and adopting agricultural and forestry practices that sequester carbon. If the present overshoot of this target CO2 is not brief, there is a possibility of seeding irreversible catastrophic effects.

Read more at 350ppm or bust

Plants that defy evolution: Datura stramonium (Jimson Weed)

Some creationists consider the thorns on plants a problem for evolutionary theory. As I will show, this is based on a flawed understanding of evolutionary theory. But before I proceed, let me present the ‘argument‘ presented by Joseph Alden (uncle of  Gary McGuire)

Behe vs Lampreys: A modest proposal.

On Panda’s Thumb, Ian Musgrave shows how by doing hard work science has undermined further, the Irreducible Complexity argument about the blood clotting cascade as proposed by Michael Behe. In fact, the hard work supported a prediction made by Doolittle.

Ian challenges ID proponents to finally do some science

So I have a modest proposal. I would like to invite Dr. Behe, or any other ID advocate, to predict which coagulation factors are present in Amphioxus, search the Amphioxus genome database and report on whether the genes found match their predictions. The database is free, you can do it at home, and the only cost is your time.

Time for ID advocates to do some science. How about it?

Any Takers?

Kenneth R. Miller The Boston Globe “Trouble ahead for science”

Ken Miller in a May 8 OpEd the Boston Globe writes about “Expelled”:

Why is all this nonsense a threat to science? The reason is Stein’s libelous conclusion that science is simply evil. In an April 21 interview on the Trinity Broadcast Network, Stein called the Nazi murder of children “horrifying beyond words.” Indeed. But what led to such horrors? Stein explained: “that’s where science in my opinion, this is just an opinion, that’s where science leads you. Love of God and compassion and empathy leads you to a very glorious place. Science leads you to killing people.”

According to Stein, science leads you to “killing people.” Not to cures and vaccines, not to a deeper understanding of nature, not to wonders like computers and cellphones, and certainly not to a better life. Nope. Science is murder.

“Expelled” is a shoddy piece of propaganda that props up the failures of Intelligent Design by playing the victim card. It deceives its audiences, slanders the scientific community, and contributes mightily to a climate of hostility to science itself. Stein is doing nothing less than helping turn a generation of American youth away from science. If we actually come to believe that science leads to murder, then we deserve to lose world leadership in science. In that sense, the word “expelled” may have a different and more tragic connotation for our country than Stein intended.

NCSE: Eyeing ID

While legislatures focus on antievolution bills, a new video at Expelled Exposedhelps students see how evolution works.

Oakland, California, May 6, 2008 As attacks on evolution education remain in the news, with proposed antievolution legislation in Alabama, Florida, Louisiana, Michigan, and Missouri in the headlines,
a new video rebutting the basic premise of intelligent design creationism is now available on www.ExpelledExposed.com.

“Creationism Disproved?” is the third in a series of short videos commissioned by the National Center for Science Education, a non-profit organization that defends the teaching of evolution in the public schools. The video focuses on the evolution of the eye a favorite target of creationists.

“It’s common for creationists, especially ‘intelligent design’ creationists, to claim that complex structures like the eye or parts of the cell couldn’t have evolved step by step,” explains NCSE’s
executive director, Eugenie C. Scott. “It’s a tired objection indeed, Darwin himself anticipated, and refuted, the argument. But opponents of evolution continue to insist that such structures had to
be assembled all at once.”

Ken Dill, a researcher at the University of California, San Francisco featured in the video, adds: “In fact, complexity can evolve through small steps. We can infer the evolution of a very complex organ, like the eye, by looking at intermediate stages preserved in animals alive today. And just as a baby’s eye is built up step by step over nine months in the womb, the eye evolved in small steps over millions of years.”

Noting that the latest advances in science have only confirmed Darwin’s insights, Josh Rosenau, a biologist at NCSE, observed, “Scientists recently traced the evolution of a protein crucial to vision by comparing the genomes of many species, showing that the molecule, opsin, existed in the common ancestor of hydras, jellyfish, flies, fish, and people. Other researchers have traced the evolution
of genes critical to the growth and development of eyes in different branches of the tree of life. All those lines of evidence match the predictions of evolution.”

Louise S. Mead, a biologist and teacher who heads NCSE’s outreach to educators, hopes that students and teachers will use the video to dispel a common misconception about evolution. “Evolution can be
tough to learn and tough to explain, even independently of the prevalence of creationist misconceptions,” she explains. “Videos like this can help students see things in a new light.”

The National Center for Science Education is a non-profit organization dedicated to defending the teaching of evolution in the public schools. The NCSE maintains its archive of source material on
the history of creationism at its Oakland, California, headquarters.

On the web at www.ncseweb.org.

NCSEs other website, www.ExpelledExposed.com, is a resource for journalists, teachers, and curious moviegoers who want the full story behind the creationist movie Expelled: No Intelligence Allowed.

Contacts:
Eugenie C. Scott, scott@ncseweb.org, 800-290-6006
Josh Rosenau, rosenau@ncseweb.org, 800-290-6006
Louise S. Mead, mead@ncsewb.org, 800-290-6006

Office of Special Counsel raided

The Office of Special Counsel (OSC) has been raided

Bloch’s agency is a little known one that is charged with investigating whistleblower complaints, Hatch Act violations, and the like — but who is himself being investigated for retaliating against whistleblowers and politicizing his office. The Office of Personnel Management’s inspector general has been conducting that investigation since 2005. The feds are apparently investigating whether Bloch tried to obstruct that investigation by deleting his hard drive, among other things.

Remember that the OSC is the same agency which investigated the Richard von Sternberg affair. It would be interesting to see if emails can be recovered related to this incident as the conclusions by the OSC seemed to be at odds with what the emails from the Smithsonian people actually showed.

Gambler’s Ruin is Darwin’s Gain

Joe Felsenstein, Professor of Genome Sciences and of Biology and Adjunct Professor of Computer Science and of Statistics has a guest posting on Panda’s Thumb titled Gambler’s Ruin is Darwin’s Gain in which he exposes the vacuity of the Intelligent Design comments by Young Earth Creationist Salvador Cordova.

So yes, the mathematics of Gambler’s Ruin speaks to the issue of natural selection—but it confirms its effectiveness.

(The other issue raised by Cordova, that of interference between mutations at different loci, is the well-known Hill-Robertson effect. If the loci have more than a tiny amount of genetic recombination between them, the interference largely vanishes. Cordova and the other commenters there have forgotten this.)

PZ Myers at Pharyngula observes similarly in a posting titled ’squish’

That’s the sound you should hear when Joe Felsenstein takes on an idiotic claim by Sal Cordova. Would you believe that Cordova claims that Kimura and Ohta’s classic 1971 paper “shatters the modern synthesis”? That’s what he claims, on the basis of his poor understanding of the mathematics of population genetics, which is ridiculous on the face of it. So it’s very satisfying to see one of the big guns of population genetics take him down with one brief explanation: contrary to Cordova, the principle he’s describing confirms the effectiveness of natural selection.

Flunked, Not Expelled: Expelled Enjoined

Wesley Elsberry reports that Premise Media has been enjoined from further distribution of its Manufactroversy “Expelled”.

There was a hearing in the Yoko Ono copyright infringement case this past week, and Premise Media has been enjoined against further distribution of “Expelled” until the case is settled next hearing on May 19th.

That means that theaters that already have a copy may continue to show it, but no further prints may be sent out to other theaters, and no CD or DVD versions may be distributed, either.