I wrote this paper 20 years ago!

Evolution Vs. Creationism

Brian Greene & Richard Dawkins discuss God.

Bike Lasers!

Emily Brooke has come up with a brilliant product that could save lives by making riding a bicycle more visible to the auto-aucracy. The idea: a front headlight combined with a LASER that projects an image of a bicycle street blaze a few meters in front of the rider. Combine this with inventions like the "invisible bike helmet" and we are on our way to widening the ranks of the urban-cyclist army. Ride on!

Morality without religion? Kenneth Miller fields my question

A little bird told me that Dr. Kenneth Miller would appear on the Huffington Post live this afternoon. I proceeded to create an account, log on, and record a video question for him. Lo and behold, Josh Zepp the HuffpostLive moderator aired my question. Skip to 21:25 in to see my question and subsequent answers. 

Miscreant Mimicry Among Creationists

For four long days my colleague Carl Zimmer has been wielding the battle axe for sound science education, fighting the good fight for evidence and evolution. In the aftermath of this battle I have noticed a disturbing trend among the current generation of evolution denialists - they are shape-shifting!

First, a brief history of the debate.

Since the publication of Charles Darwin's On the Origin of Species in 1859 a sub-group of stubborn Christians have been in a perpetual war with reality. Over the years the deniers of evolution have changed their name in order to re-frame their rhetorical attack on the mounting evidence supporting evolution. For the better part of the twentieth century they went by the title "creationists." They sincerely believe an imaginary sky-father "created" all living things six thousand years ago and just plopped them all down on earth in their present form before taking the next day off for a nap.

All was good from their perspective and they were allowed to tacitly poison science education in the United States for more than a century.

But alas, that pesky establishment clause in the US constitution caught up with them. In a 1987 Supreme Court decision six of the nine justices came down squarely on the side of science. Edwards v. Aguillard established that teaching creationism along with evolution in science classrooms is unconstitutional.

The stubborn creationists were undaunted. They knew what any good snake-oil salesmen knows. When your name gets smeared, just change your name. So began the rise of the "intelligent design" proponents. The idea being that the overtly Christian feel of the word "creation" would be remedied with a switch to the more scientific sounding "intelligent-design."  With this new name came new propaganda. Well, not really, as writing is tough work! So they just took an old creationist text-book and changed some words around a little bit so they could slip it into science classrooms without calling it creationism. The book was called "Of Pandas and People." 

The problem with this book was that the editors were lazy and left bits of the old "creationist" language behind in textual fossils. Where the text once read "creationist" it then read "cdesign proponentists."

In 2005 a group of nosy lawyers and science educators took issue with the use of this book in a science classroom in Dover, Pennsylvania. As a result the book and the faith-based science education it promoted was banned from science classrooms. It was deemed by a federal appeals court to violate the precedent set by the 1987 Supreme Court decision mentioned earlier.  

What's a creationists to do?

Here we are seven years later in a scary place where the intelligent design movement has dispensed with identifying themselves altogether and are now just publishing propoganda with scientific-sounding names.  

Enter the copy-cats.

In evolutionary biology some species copy the shape, color, smell, or sound of unrelated species. They do this to protect themselves in order to survive. This is called mimicry. Remember the scene in the Wizard of Oz when the scarecrow, tin man, and lion dress as the wicked witch's guards to enter her fortress unharmed? That is what I'm talking about.

Guess what? Evolution deniers are doing this like crazy! They are cloaking themselves in scientific sounding names so they can slip through the cracks and deliver their propaganda to students of biology caught unaware.

 Listen to these names.  Biologic Institute, Evolution News & Views, and Science and Human Origins.

These are a facebook page, a website, and a printed book respectively.

Coming to these titles cold one would assume they are legitimate organizations for teaching biology and evolution.  Not so. All three are propaganda outlets for the notorious "Discovery Institute."  (*)

You may know about this Seattle based outfit by their incessant call to "teach the controversy." Their goal being to have intelligent design taught along side Darwinian natural selection in biology classrooms around the country. This is total bullocks as there is no controversy. The physical evidence of evolution is overwhelming and grows with each new discovery in biology. This idea of being fair and balanced regarding every single topic discussed often confuses speculation and facts. Lawrence Krauss describes this dilemma well.

Too often in the media, speculative ideas are treated on the same footing as well-tested ones. As a result, it is sometimes hard to tell the difference between them. This is particularly unfortunate when firmly grounded ideas that are known to accurately describe the physical world (such as evolution and the big bang) are passed off as mere theoretical whims of a group of partisan scientists.

As a scientist, writer, and educator it is highly disturbing to see this kind of re-branding by the intelligent design community. By conflating scientific ideas with assumptions of faith and slapping a sciency-sounding name on their front page these groups further damage an already crippled science education program in the United States. Shame on them!

Back to Carl Zimmer.

Intelligent design proponents have been goading Carl with snarky ad hominem attacks on a combination of online forums including Facebook, his Discover Magazine blog - the Loom, and their own comment-free web space - "Evolution News & Views." He has been gracious with the amount of attention he has paid this group of pseudo-academics. Carl has responded at length to a series of games they have been playing with him over the past four days. Read all about it here. 

My advice to Carl is the same advice being given all over the web lately - Don't Feed the Trolls! That being said, I think he has done a great job of staving them off so far and keeping his talents where they belong, on HIS blog. As I walk away from these ceaseless trolls I keep in mind the perennial duty to play the role of a catcher in the rye. For as long as my words last I will attempt to catch those who have fallen into fuzzy-logic and irrational faith-based thought and bring them back to reason. I want to thank Carl for reaffirming my dedication to this goal and for exposing the harmful mimicry going on in the intelligent design community.  

(*) ~ in a previous version of this post I had incorrectly stated that the Discovery Institute and the Creation Museum in Petersburg, KY were of the same ilk. I was informed via a facebook friend that those organizations had cuts ties when the Dover descision came down in 2005. So as not to offend I have deleted mention of the creation museum. That batch of crazy is brought to you by Ken Ham. Apologies for the error and I hope this paragraph is sufficiently transparent.

The gang's all here: a killer thread

Steven Pinker, Richard Dawkins, Daniel Dennett, Jerry Coyne, Stewart Brand.
 
These are just a few of the intellectual heavy-hitters you will find in one of the best conversations I have ever witnessed on the web. While most blog comment threads quickly degenerate into ad hominem mudslinging and and worthless tangential banter, the comment thread I speak of is a well curated invite-only debate about one of the most perplexing ideas in natural philosophy - the evolution of altruism. 

Here are some rousing excerpts from the conversation - 

In which philosopher Dan Dennett proposes using intellectual judo against intelligent design proponents by co-opting the very word "design" to explain the intricate molecular machines produced by natural selection.

I recently overheard a conversation among some young people in a bar about the marvels of the nano-machinery discovered inside all cells. "When you see all those fantastic little robots working away, how can you possibly believe in evolution!" one exclaimed, and another nodded wisely. Somehow these folks had gotten the impression that evolutionary biologists thought that the intricacies and ingenuities of life's processes weren't all that wonderful. These evolution-doubters were not rednecks; they were Harvard Medical students!  They hugely underestimated the power of natural selection because they had been told by evolutionary biologists, again and again, that there is no actual design in nature, only the appearance of design. This episode strongly suggested to me that one of the themes that has been gaining ground in "common knowledge" is that evolutionary biologists are reluctant to "admit" or "acknowledge" the manifest design in nature. I recommend instead the expository policy of calling nature's marvels design, as real as any design in the universe, but just not the products of an intelligent designer. There could be a good use for "designoid," to refer to the truly only apparent design manifest, for example, in all the complicated chemical apparatus that cartoonists draw when they need to illustrate a laboratory—it looks impressive to the naïve eye, but is just a nonsensical hodgepodge of tubes, bunsen burners, retorts and the like. That is apparent design; the design in nature, in contrast, is typically as good as, or even much better than, the designs we "intelligent" artificers have yet devised. They work really well, which is as good a criterion of design as any, in my opinion.

And in prophetic sweep Stewart Brand, founder of the Whole Earth Catalog, predicts horizontal gene transfer will be found to have broader influence on evolution than previously thought. If you are unfamiliar with the concept of horizontal gene transfer just think of updating your iPhone apps but on a genetic level.

My prediction is that new research in microbial ecology and evolution will change everything in how we think about genes and evolution. Because of the prevalence of "horizontal" gene transfer (by six different ways) in micro-organisms, they don't have Darwinian species, and their evolution looks Lamarckian—traits are acquired on the fly and passed on to offspring.
"Multi-level selection" is likely to extend downward below Darwinian species as well as upward into groups. Like everything in biology it will be messy and squishy. Simplistic Darwinian selection-by-mutation got pummeled by sexual recombination, chromosome doubling and tripling, kin selection, extended phenotype, endo-symbiosis (Margulis), regulatory genes, mitochondrial genomes, transgenic gene flow, and doubtless more to come.
The longer and closer you look, the gnarlier it gets, so far.

You can read the entire thread at The Edge where Steven Pinker started this particular conversation.

I have written about this debate here on Tom Paine's Ghost and for the World Science Festival.


One of the best summaries of the debate was written by my colleague Eric Michael Johnson for the Scientific American Blog Network. It is titled The Good Fight. Read it here. 

Reason Rally Highlights

BARP Goes the Weasel!

By Kristopher Hite

Looking back at discoveries of the past year the one that sticks out above all others to me was the identification of a single protein; a bacterial actin homologue dubbed BARP - Bacterial Actin Related Protein. The brilliance of this discovery comes from its directly contributing to our understanding of evolution, overturning decades of dogma, and providing a shiny new teaching tool.  The discovery was published in late 2009 as part of a massive sequencing project to fill in gaps of knowledge among bacterial and archael genomes.

With all the other sexy and more controversial stories about evolution - Ardi, Ida and so on, why do I pick this one? Aside from my biochemical inclination I thought this little piece of biological hardware deserved more exposure.  Though the paper was covered and lead author Jonathan Eisen interviewed for the nature podcast, it received relatively little coverage on the science blogs. Yes, the prolific science writer Carl Zimmer wrote a nice summary for the New York Times but the BARP bit is mentioned only briefly. I don't know if anyone realized what a great tool this discovery is to hammer even more nails in the coffin of the "irreducible complexity" argument for intelligent design. 

In January 2010 I had the pleasure to sit down and interview Eugenie Scott - executive director of the National Center for Science Education (NSCE).  As she explained the history of science education in the United States we came to an agreement on what one "take home" message should be for the average high school student - that all living things on earth share common ancestors, that all species have a common descent. This point may not seem earth-shattering to comprehend but I think many in America fail to realize the significance of this fact. The procession of science has uncovered an armory of teaching tools - fossilized trilobites, floating whale hip bones, and common DNA sequences. The more is known about the inner workings of the natural world the easier it should be for students to see and accept the facts. What then is the barrier to getting students to accept take-home messages like common descent? I would posit that fundamentalist opposition to evolution and the idea of the rapture have more than a little to do with it. Proponents of intelligent design often use a phrase coined by Lehigh University professor Michael Behe - irreducible complexity - in their defense of a necessary designer. This was a large part of Behe's arguments against teaching evolution as fact in the Kitzmiller vs. Dover, PA landmark court case.

Behe defines an irreducibly complex system as one "composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning." Brown University Biology Professor Ken Miller uses the analogy of a mouse trap to explain away irreducible complexity. Yes, all components of a mouse trap are necessary for overall function but each component can be have alternate uses.

In the logical chronology of evolution complexity emerges incrementally by the acquisition of functional structures that appear by chance and remain due to conferred advantage. Behe has tried over and over to use the molecular structure of the bacterial flagellum as an example of an irreducibly complex system.  In response Ken Miller did an excellent job explaining how the components of bacterial flagella could emerge incrementally.

So what IS actin and how does its showing up in a bacterial specimen add to the arsenal of teaching tools against irreducible complexity?

actin filament

As you move your cursor around this page your muscles are contracting and relaxing, your brain is sending signals along tiny electrified strands called axons guiding these contractions. Among the myriad things that make this possible is the little protein called actin.  Deriving its name from the word "activating" actin enables muscular motion, provides train tracks inside each cell for directional transportation of other tools, and gives shape to most cells in your body.  Like oddly shaped legos these tiny building blocks bind to each other and form long filaments that grow and shrink.  A mesh-work of actin filaments push on the perimeter of each cell establishing shape.  Those long axons I mentioned before are extensions of brain cells (neurons). During development neurons send out these long extensions and it is the mesh-work of actin that leads the charge enabling all those millions of electronic connections between brain and body to form. 

The gene that codes for this little protein exists without much variation in all eukaryotic organisms. Eukaryote means simply "true nucleus." The distinction is made because the more ancient but still surviving bacteria do not have "true nuclei" they are therefore dubbed prokaryotes. The moment at which the first eukaryote appeared on earth marked the beginning of an explosion of diversity, and a fundamental branch point in the phylogenetic tree of life.

(Haliangium ochraceum)

 Unlike the carefully crafted nuts and bolts you can pick up at the hardware store cellular machinery is not designed for a purpose, it just appears by duplication, mutation, or other spontaneous variations of genetic material.  If it works it is retained, if its merely eating up metabolic resources it usually goes extinct.  This represents an important variation on pure chance that the process of evolution carries with it.  Richard Dawkins has illustrated the power of evolving systems to accumulate positive variation in his classic "Weseal" thought experiment. Self-replicating systems have the ability to retain random variation in their code by copying themselves. When a variation carries a positive effect for the code carrier (organism) then that carrier is more likely to make more copies of that advantageous variation.  New variation is possible because there are usually redundant bits of cellular machinery.  This is exactly what we see in the case of BARP.

If you asked any professor of cell biology any time prior to a year ago "Do bacteria contain a gene for actin?" they would, without hesitation, say "of course not." It was understood that the gene for actin was one that separated eukaryote from prokaryote. Bacteria have an unrelated gene  - MreB - that has a scaffolding function. They don't need actin.   Now it is shown that the gene for actin may have shown up in  marine bacteria (specifically the one named Haliangium ochraceum) prior to the evolutionary branch-point. If this is the case it means that actin was later recruited to its now prolific function giving shape and motion to eukaryote cells. Actin was not designed then implemented like machined parts in human created contraptions. According to this research it probably appeared by chance in marine bacteria, served some other unknown function, then just happened to work later on in evolution.  This, I think, is why many mechanical engineers have an aversion to studying the slimy, oozing, organic structures in nature. They are inherently messy and imperfect.  This is because they are not designed! They are the result of chance events captured inside self-replicating systems - us included.

This post has been submitted to the NESCent competition for a travel award for the ScienceOnline 2011 un-conference January 13-15 in North Carolina’s Research Triangle Park.




  




Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B., Hooper, S., Pati, A., Lykidis, A., Spring, S., Anderson, I., D’haeseleer, P., Zemla, A., Singer, M., Lapidus, A., Nolan, M., Copeland, A., Han, C., Chen, F., Cheng, J., Lucas, S., Kerfeld, C., Lang, E., Gronow, S., Chain, P., Bruce, D., Rubin, E., Kyrpides, N., Klenk, H., & Eisen, J. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Nature, 462 (7276), 1056-1060 DOI: 10.1038/nature08656